{ "generated_at_local": "2026-08-13 14:13:17", "generated_at_utc": "2026-08-13 14:13:32", "days": 14, "window_utc": { "mindate": "2026/07/30", "maxdate": "2026/08/13" }, "ranking": "research_relevance_score(topic_priority + research_signal + source_metadata + recency + cross_domain)", "signal_ontology": { "selection": { "label": "Selection", "weight": 3.0, "patterns": [ "\\bdN/dS\\b", "positive selection", "purifying selection", "diversifying selection", "episodic selection", "selective sweep", "codon model", "\\bHyPhy\\b|\\bBUSTED\\b|\\bFEL\\b|\\bMEME\\b|\\bFUBAR\\b" ] }, "viral_evolution": { "label": "Viral evolution", "weight": 2.6, "patterns": [ "immune escape", "antigenic drift", "antigenic mapping", "host jump|host shift|spillover", "recombination|reassortment", "variant|lineage replacement" ] }, "metagenomics_surveillance": { "label": "Metagenomics / surveillance", "weight": 2.4, "patterns": [ "metagenomic surveillance", "genomic surveillance", "wastewater|WBE|sewage", "virome|viromics|viral metagenomics", "strain tracking|functional profiling|MAGs?\\b|AMR\\b", "built environment|urban microbiome|MetaSUB" ] }, "cancer_evolution": { "label": "Cancer evolution", "weight": 2.4, "patterns": [ "clonal evolution|clonal selection|clonal expansion", "subclonal|tumou?r phylogen|tumou?r evolution", "mutational signature", "driver mutation", "single-cell" ] }, "methods": { "label": "Methods", "weight": 1.7, "patterns": [ "phylogenetic|phylogenomic|phylodynamic", "Bayesian inference|BEAST|coalescent", "benchmark|evaluation|best practices", "Snakemake|Nextflow|CWL|WDL|reproducible|container|Docker|Singularity|Apptainer", "machine learning|deep learning|transformer|foundation model|protein language model|ESM|AlphaFold" ] }, "emerging_threat": { "label": "Emerging threat", "weight": 2.2, "patterns": [ "zoonosis|zoonotic|spillover", "outbreak|pandemic potential|pandemic preparedness", "early warning|sentinel surveillance|biosurveillance", "emerging pathogen|emergence" ] } }, "themes": { "Selection & codon models": { "priority": 1.35 }, "Cancer evolution & somatic selection": { "priority": 1.2 }, "Recombination & mosaicism": { "priority": 1.2 }, "Phylodynamics & transmission": { "priority": 1.2 }, "Urban / built environment virome": { "priority": 1.3 }, "Wastewater / WBE viral surveillance": { "priority": 1.25 }, "Pandemic preparedness & biosurveillance": { "priority": 1.15 }, "Atlases, compendia, reference resources": { "priority": 1.1 }, "Metagenomics benchmarking & pipelines": { "priority": 1.05 }, "ML for evolution & pathogens": { "priority": 1.0 } }, "sections": [ { "label": "Selection & codon models", "query": "(((\"dN/dS\" OR \"codon model\" OR HyPhy OR FEL OR MEME OR FUBAR OR BUSTED OR \"branch-site\") AND (selection OR evolution OR adaptive OR constraint)) OR ((\"episodic selection\" OR \"positive selection\" OR \"diversifying selection\") AND (virus OR pathogen))) AND (\"computational evolutionary biology\" OR \"molecular evolution\" OR phylogenomics OR phylodynamics OR HyPhy OR \"codon model\") NOT (case report OR randomized OR psychology)", "count": 8, "items": [ { "pmid": "42390272", "title": "Genetic variation, recombinant characteristics, and seroprevalence analysis of echovirus 3 causing severe and mild cases of hand, foot, and mouth disease in Guizhou Province.", "authors": "Fajin Li, Fei Su, Dan Wang, Fumin Zhang, Jun Guo, Guanghai Yao", "journal": "Microbiology spectrum", "pubdate": "2026-07-02", "pubdate_utc": "2026-07-02T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42390272/", "abstract_snippet": "Echovirus 3 (E-3) has recently been identified as an emerging pathogen associated with both severe and mild cases of hand, foot, and mouth disease (HFMD) in Guizhou Province, China. Although these strains exhibit distinct clinical phenotypes, their underlying …", "score": 16.123, "score_components": { "theme_priority": 1.35, "research_signal": 12.1, "venue": 0.0, "recency": 1.173, "cross_domain": 1.5 }, "signal_components": { "selection": 3.0, "viral_evolution": 5.2, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Selection", "Viral evolution", "Methods", "Emerging threat" ], "theme": "Selection & codon models" }, { "pmid": "42560611", "title": "Complete Mitochondrial Genome of Turrum coeruleopinnatum Provides Phylogenetic Context and Candidate Selection Signals Within Carangidae.", "authors": "Yang Chen, Xuehui Diao, Yixuan Lin, Jinghua Wu, Ruling Wei", "journal": "Biochemical genetics", "pubdate": "2026-08-06", "pubdate_utc": "2026-08-06T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42560611/", "abstract_snippet": "The complete mitochondrial genome of Turrum coeruleopinnatum was sequenced and characterized to expand mitogenomic resources for Carangidae and to evaluate its phylogenetic placement and candidate selection signals. The circular mitogenome was 16,553 bp in len…", "score": 14.986, "score_components": { "theme_priority": 1.35, "research_signal": 10.7, "venue": 0.0, "recency": 1.436, "cross_domain": 1.5 }, "signal_components": { "selection": 9.0, "methods": 1.7 }, "signal_classes": [ "Selection", "Methods" ], "theme": "Selection & codon models" }, { "pmid": "42555057", "title": "Genome evolution and long-term demographic history in true crocodiles.", "authors": "Ana M Saldarriaga-Gómez, Agusto Luzuriaga-Neira, Mario Vargas-Ramírez, George Amato, Evon Hekkala", "journal": "G3 (Bethesda, Md.)", "pubdate": "2026-08-05", "pubdate_utc": "2026-08-05T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42555057/", "abstract_snippet": "Reference-quality genomes remain scarce for true crocodiles (Crocodylus), limiting comparative analyses of genome evolution and demographic history. Here, we generated and analyzed 2 long-read genomes, 1 for Crocodylus intermedius and 1 for C. niloticus, to in…", "score": 13.732, "score_components": { "theme_priority": 1.35, "research_signal": 9.455, "venue": 0.0, "recency": 1.427, "cross_domain": 1.5 }, "signal_components": { "selection": 7.755, "methods": 1.7 }, "signal_classes": [ "Selection", "Methods" ], "theme": "Selection & codon models" }, { "pmid": "42546033", "title": "Development of a rapid comQ-targeted quantitative polymerase chain reaction assay for specific identification and quantification of Bacillus subtilis subsp. natto.", "authors": "Mayu Takizawa, Daisuke Kyoui, Rika Horiguchi, Ayano Sakurai, Taketo Kawarai, Naoki Narisawa", "journal": "PloS one", "pubdate": "2026-08-03", "pubdate_utc": "2026-08-03T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42546033/", "abstract_snippet": "Bacillus subtilis subsp. natto is a specialized functional group essential for fermented soybean production. Despite its industrial importance, genetic differentiation of this lineage remains challenging because of its high genomic similarity within the B. sub…", "score": 11.961, "score_components": { "theme_priority": 1.35, "research_signal": 7.7, "venue": 0.0, "recency": 1.411, "cross_domain": 1.5 }, "signal_components": { "selection": 6.0, "methods": 1.7 }, "signal_classes": [ "Selection", "Methods" ], "theme": "Selection & codon models" }, { "pmid": "42566464", "title": "Novel insights into tomato leaf curl New Delhi virus introduction and evolution in Southeastern France using an advanced long-read sequencing workflow.", "authors": "Atiwich Patthamapornsirikul, Victor Golyaev, Eric Verdin, Claire Goillon, Hindi Boolell, Sam Dierickx", "journal": "PLoS pathogens", "pubdate": "2026-08-07", "pubdate_utc": "2026-08-07T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42566464/", "abstract_snippet": "The Mediterranean population of tomato leaf curl New Delhi virus (ToLCNDV-ES) is characterized by a high genetic uniformity, distinguishing it from its Asian counterparts. ToLCNDV-ES is thought to have a monophyletic origin, likely resulting from a single reco…", "score": 11.594, "score_components": { "theme_priority": 1.35, "research_signal": 7.3, "venue": 0.0, "recency": 1.444, "cross_domain": 1.5 }, "signal_components": { "selection": 3.0, "viral_evolution": 2.6, "methods": 1.7 }, "signal_classes": [ "Selection", "Viral evolution", "Methods" ], "theme": "Selection & codon models" }, { "pmid": "42463133", "title": "CAPHEINE, or Everything and the Kitchen Sink: A Workflow for Automating Selection Analyses Using HyPhy.", "authors": "Hannah Verdonk, Danielle Callan, Sergei Pond", "journal": "Genome biology and evolution", "pubdate": "2026-08-01", "pubdate_utc": "2026-08-01T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42463133/", "abstract_snippet": "Here, we present CAPHEINE, a computational workflow that starts with a set of unaligned pathogen sequences and a reference genome and performs a comprehensive exploratory evolutionary analysis of the input data. CAPHEINE pairs nicely with studies of site-level…", "score": 10.345, "score_components": { "theme_priority": 1.35, "research_signal": 6.0, "venue": 1.6, "recency": 1.395, "cross_domain": 0.0 }, "signal_components": { "selection": 6.0 }, "signal_classes": [ "Selection" ], "theme": "Selection & codon models" }, { "pmid": "42320408", "title": "Genomic epidemiology of two travel-associated pediatric measles viruses within the B3 Lineage.", "authors": "Sydney Stanley, Rose C Patrick, Michael Elkan, Jeffrey Fink, Bonnie Oh, Yan Sun", "journal": "Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology", "pubdate": "2026-06-18", "pubdate_utc": "2026-06-18T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42320408/", "abstract_snippet": "Children's Hospital of Philadelphia (CHOP) identified a MeV case in late 2023 and also early 2025, both of which were associated with international travel. Of the 24 MeV genotypes, the B3 and D8 lineages have been the most prevalent globally since 2021. Initia…", "score": 8.632, "score_components": { "theme_priority": 1.35, "research_signal": 4.7, "venue": 0.0, "recency": 1.082, "cross_domain": 1.5 }, "signal_components": { "selection": 3.0, "methods": 1.7 }, "signal_classes": [ "Selection", "Methods" ], "theme": "Selection & codon models" }, { "pmid": "42270014", "title": "Endogenous viral elements and PIWI gene evolution in Spodoptera: diversity, conservation, and piRNA production.", "authors": "Salvador Herrero, Lino Ometto, Javier López-Rius, Adriá Mengual-Martí, Annamaria Mattia, Patricia Hernández-Martínez", "journal": "Insect biochemistry and molecular biology", "pubdate": "2026-06-10", "pubdate_utc": "2026-06-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42270014/", "abstract_snippet": "Endogenous viral elements (EVEs) are viral sequences that have integrated into host genomes. While these elements can be considered molecular fossils of past infections, in some cases, they are co-opted and contribute to host fitness. For instance, in arthropo…", "score": 5.383, "score_components": { "theme_priority": 1.35, "research_signal": 3.0, "venue": 0.0, "recency": 1.033, "cross_domain": 0.0 }, "signal_components": { "selection": 3.0 }, "signal_classes": [ "Selection" ], "theme": "Selection & codon models" } ] }, { "label": "Cancer evolution & somatic selection", "query": "(((\"cancer evolution\" OR \"tumor evolution\" OR \"somatic evolution\" OR \"clonal evolution\") AND (genomics OR sequencing OR phylogen* OR \"single-cell\")) OR ((cancer OR tumor OR lymphoma OR leukemia) AND (\"positive selection\" OR \"clonal selection\" OR \"driver mutation\" OR \"dN/dS\" OR \"selection inference\")) OR ((\"mutational signature\" OR \"mutational signatures\") AND (cancer OR tumor) AND (evolution OR selection OR phylogeny))) AND (\"computational evolutionary biology\" OR \"molecular evolution\" OR phylogenomics OR phylodynamics OR HyPhy OR \"codon model\") NOT (case report OR randomized OR psychology)", "count": 1, "items": [ { "pmid": "41997582", "title": "Viral Mimicry by Repeats Mediates Evolutionary Trade-Offs in Cancer-Immune Coevolution.", "authors": "Siyu Sun, Benjamin D Greenbaum", "journal": "Cancer discovery", "pubdate": "2026-08-03", "pubdate_utc": "2026-08-03T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/41997582/", "abstract_snippet": "During cancer evolution, derepressed repetitive elements (REs) can trigger innate immune responses via \"viral mimicry,\" imposing selective immune pressure on emerging tumor cells. We propose that RE mimics mediate transitions from initial antitumorigenic immun…", "score": 2.611, "score_components": { "theme_priority": 1.2, "research_signal": 0.0, "venue": 0.0, "recency": 1.411, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Cancer evolution & somatic selection" } ] }, { "label": "Recombination & mosaicism", "query": "(((recombination OR \"mosaic genome\" OR breakpoint OR \"gene conversion\") AND (virus OR virome OR pathogen)) OR ((RDP OR GARD OR \"recombination detection\") AND (sequence OR alignment))) AND (\"computational evolutionary biology\" OR \"molecular evolution\" OR phylogenomics OR phylodynamics OR HyPhy OR \"codon model\") NOT (case report OR randomized OR psychology)", "count": 25, "items": [ { "pmid": "42390272", "title": "Genetic variation, recombinant characteristics, and seroprevalence analysis of echovirus 3 causing severe and mild cases of hand, foot, and mouth disease in Guizhou Province.", "authors": "Fajin Li, Fei Su, Dan Wang, Fumin Zhang, Jun Guo, Guanghai Yao", "journal": "Microbiology spectrum", "pubdate": "2026-07-02", "pubdate_utc": "2026-07-02T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42390272/", "abstract_snippet": "Echovirus 3 (E-3) has recently been identified as an emerging pathogen associated with both severe and mild cases of hand, foot, and mouth disease (HFMD) in Guizhou Province, China. Although these strains exhibit distinct clinical phenotypes, their underlying …", "score": 15.973, "score_components": { "theme_priority": 1.2, "research_signal": 12.1, "venue": 0.0, "recency": 1.173, "cross_domain": 1.5 }, "signal_components": { "selection": 3.0, "viral_evolution": 5.2, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Selection", "Viral evolution", "Methods", "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42439533", "title": "Phylogenetic and biological features of severe fever with thrombocytopenia syndrome virus from multi-species infections in eastern China.", "authors": "Hao Wang, Dali Xu, Chengyunxiao Li, Xueying Tian, Bo Pang, Ti Liu", "journal": "Microbiology spectrum", "pubdate": "2026-07-13", "pubdate_utc": "2026-07-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42439533/", "abstract_snippet": "Severe fever with thrombocytopenia syndrome (SFTS), caused by SFTS virus (SFTSV), is an emerging tick-borne disease with high mortality and complex transmission dynamics. Since its first identification in China, SFTS has become an endemic infectious disease wi…", "score": 15.45, "score_components": { "theme_priority": 1.2, "research_signal": 11.5, "venue": 0.0, "recency": 1.25, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "metagenomics_surveillance": 2.4, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Methods", "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42390251", "title": "Tracking the shifting landscape of SARS-CoV-2 variants in Lebanon among healthcare workers and hospitalized patients.", "authors": "Habib Alkalamouni, Mirna Bou Hamdan, Farouk Abou Hassan, Fatima Dakroub, Lama Hamadeh, Alissar Rady", "journal": "Microbiology spectrum", "pubdate": "2026-07-02", "pubdate_utc": "2026-07-02T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42390251/", "abstract_snippet": "Genomic surveillance of SARS-CoV-2 is critical for tracking viral evolution and informing public health responses. This study characterized variants circulating among healthcare workers (HCWs) and hospitalized patients in Lebanon between January 2022 and Septe…", "score": 13.673, "score_components": { "theme_priority": 1.2, "research_signal": 9.8, "venue": 0.0, "recency": 1.173, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "metagenomics_surveillance": 2.4, "emerging_threat": 2.2 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42462268", "title": "Genomic mining of Bacillus safensis and Enterococcus lactis from food sources.", "authors": "Daniel Jesuwenu Ajose, Ifeoma Irene Adetoyinbo, Christ-Donald Kaptchouang Tchatchouang", "journal": "Letters in applied microbiology", "pubdate": "2026-08-03", "pubdate_utc": "2026-08-03T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42462268/", "abstract_snippet": "The growing complexity of food-safety systems and the increasing emergence of multidrug-resistant (MDR) foodborne pathogens demonstrate the importance of enhanced genomic surveillance. This study employed whole genome sequencing (WGS) to characterise the genom…", "score": 12.811, "score_components": { "theme_priority": 1.2, "research_signal": 8.7, "venue": 0.0, "recency": 1.411, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 4.8, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Metagenomics / surveillance", "Methods", "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42589152", "title": "Detection and Genotyping of Human Adenoviruses in Wastewater from Bulgaria by Targeted Surveillance, In Vitro Cultivation, and Whole-Genome Sequencing.", "authors": "Sergei Ivanov, Zoltan Urshev, Anton Hinkov, Petya Angelova, Kalina Shishkova, Stoyan Shishkov", "journal": "Biology", "pubdate": "2026-08-04", "pubdate_utc": "2026-08-04T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42589152/", "abstract_snippet": "Adenoviruses are detected in wastewater at significantly higher frequencies than most other enteric viruses. The aim of this study was to determine the abundance of human adenoviruses in samples collected from wastewater treatment plants in Sofia, Plovdiv, Bur…", "score": 11.719, "score_components": { "theme_priority": 1.2, "research_signal": 7.6, "venue": 0.0, "recency": 1.419, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance" ], "theme": "Recombination & mosaicism" }, { "pmid": "42566464", "title": "Novel insights into tomato leaf curl New Delhi virus introduction and evolution in Southeastern France using an advanced long-read sequencing workflow.", "authors": "Atiwich Patthamapornsirikul, Victor Golyaev, Eric Verdin, Claire Goillon, Hindi Boolell, Sam Dierickx", "journal": "PLoS pathogens", "pubdate": "2026-08-07", "pubdate_utc": "2026-08-07T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42566464/", "abstract_snippet": "The Mediterranean population of tomato leaf curl New Delhi virus (ToLCNDV-ES) is characterized by a high genetic uniformity, distinguishing it from its Asian counterparts. ToLCNDV-ES is thought to have a monophyletic origin, likely resulting from a single reco…", "score": 11.444, "score_components": { "theme_priority": 1.2, "research_signal": 7.3, "venue": 0.0, "recency": 1.444, "cross_domain": 1.5 }, "signal_components": { "selection": 3.0, "viral_evolution": 2.6, "methods": 1.7 }, "signal_classes": [ "Selection", "Viral evolution", "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42135467", "title": "Concepts of RNA virus evolution for the design of better antiviral countermeasures.", "authors": "Quang-Dinh Tran, Marco Vignuzzi", "journal": "Nature reviews. Microbiology", "pubdate": "2026-05-14", "pubdate_utc": "2026-05-14T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42135467/", "abstract_snippet": "This century, global human health has been marked by a seemingly increasing list of outbreaks and epidemics caused by RNA viruses - masters of rapid evolution, host switching and immune escape. With a propensity for mutation, coupled with recombination, reasso…", "score": 10.984, "score_components": { "theme_priority": 1.2, "research_signal": 7.4, "venue": 0.0, "recency": 0.884, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "emerging_threat": 2.2 }, "signal_classes": [ "Viral evolution", "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42525736", "title": "Genome-wide analyses of an avian herpesvirus identify 10 loci associated with tumorigenicity and vaccine escape.", "authors": "Alejandro Ortigas-Vasquez, Utsav Pandey, Andrew S Bell, Daniel W Renner, Matthew J Jones, Hans H Cheng", "journal": "Science advances", "pubdate": "2026-07-29", "pubdate_utc": "2026-07-29T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42525736/", "abstract_snippet": "Comparative genomic studies of Marek's disease virus (MDV) conducted in the past two decades have proven powerful for identifying genomic loci driving historical shifts in virulence. However, past efforts were limited to comparing a few strains at a time, lack…", "score": 10.971, "score_components": { "theme_priority": 1.2, "research_signal": 6.9, "venue": 0.0, "recency": 1.371, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42409079", "title": "Landscape and ecological correlates of tick-associated viruses in Inner Mongolia, China.", "authors": "Chunfu Li, Jian Li, Rui Ma, Yanli Zhang, Yurun Miao, Mengyun Liu", "journal": "The Journal of infection", "pubdate": "2026-07-06", "pubdate_utc": "2026-07-06T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42409079/", "abstract_snippet": "Ticks harbour complex RNA viromes containing both confirmed pathogens and numerous viruses with unknown transmission routes. Defining the diversity and ecological correlates of these viral communities is critical for assessing potential risks to human and anim…", "score": 10.6, "score_components": { "theme_priority": 1.2, "research_signal": 6.7, "venue": 0.0, "recency": 1.2, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "metagenomics_surveillance": 2.4, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42349632", "title": "Feline bocaparvovirus in domestic cats with gastrointestinal disease.", "authors": "Anna Salvaggiulo, Francesco Pellegrini, Michele Camero, Gardenia Gatta, Nicandro Rodi, Alessio Lorusso", "journal": "Veterinary journal (London, England : 1997)", "pubdate": "2026-06-25", "pubdate_utc": "2026-06-25T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42349632/", "abstract_snippet": "Feline bocaparvoviruses (FeBoVs) have been detected in association with gastrointestinal disease in domestic cats. This study investigated the prevalence and genetic characteristics of FeBoVs in Italy by screening 126 rectal swabs from cats with acute gastroen…", "score": 10.526, "score_components": { "theme_priority": 1.2, "research_signal": 6.7, "venue": 0.0, "recency": 1.126, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "metagenomics_surveillance": 2.4, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42127850", "title": "Pathogen identification and analysis of broiler bronchial obstruction syndrome using high-throughput sequencing technology.", "authors": "Yingli Mu, Xuejing Wang, Jianing Xu, Yuqing Yang, Jue Wang, Juxiang Liu", "journal": "Poultry science", "pubdate": "2026-05-01", "pubdate_utc": "2026-05-01T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42127850/", "abstract_snippet": "To identify the genetic characteristics of dominant pathogens in broilers suffered from bronchial obstruction syndrome in Hebei Province, high-throughput sequencing technology was employed for pathogen detection after pathological examinations. Pathological ex…", "score": 10.42, "score_components": { "theme_priority": 1.2, "research_signal": 6.9, "venue": 0.0, "recency": 0.82, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42466896", "title": "Unraveling the complexity of PRRSV-2 recombination: recombination frequency, replication efficiency, and backbone fitness define highly recombinogenic backbone and evolutionary bottlenecks.", "authors": "Weixin Wu, Xinyu Fang, Xiang Gao, Junnan Zhang, Qiongqiong Zhou, Peng Gao", "journal": "Microbiology spectrum", "pubdate": "2026-07-17", "pubdate_utc": "2026-07-17T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42466896/", "abstract_snippet": "Recombination is a primary driver of porcine reproductive and respiratory syndrome virus (PRRSV) evolution. Currently, lineage 1 NADC30-like virus (L1C) and lineage 8 HP-PRRSV (L8E) recombinants dominate in China, whereas recombinants harboring the lineage fiv…", "score": 8.779, "score_components": { "theme_priority": 1.2, "research_signal": 4.8, "venue": 0.0, "recency": 1.279, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "emerging_threat": 2.2 }, "signal_classes": [ "Viral evolution", "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42249518", "title": "Accessory regions and horizontal gene transfer shape the evolution of clonal Colletotrichum nymphaeae infecting strawberry.", "authors": "Joris A Alkemade, Alan G Buddie, Anthony Kermode, Timothy G Barraclough", "journal": "The New phytologist", "pubdate": "2026-06-05", "pubdate_utc": "2026-06-05T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42249518/", "abstract_snippet": "Rapid adaptation in fungal plant pathogens is often attributed to sexual recombination, yet many important pathogens are largely clonal. We investigated how genetic and phenotypic diversity arises in the predominantly asexual fungus Colletotrichum nymphaeae, t…", "score": 8.703, "score_components": { "theme_priority": 1.2, "research_signal": 5.0, "venue": 0.0, "recency": 1.003, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance" ], "theme": "Recombination & mosaicism" }, { "pmid": "42394128", "title": "Identification of a Complex HIV-1 Circulating Recombinant Form (CRF203_cpx) Originating from Three Main Circulating Recombinant Forms in China.", "authors": "Min Chen, Huichao Chen, Yanling Ma, Wenfei Ding, Manhong Jia", "journal": "AIDS research and human retroviruses", "pubdate": "2026-07-02", "pubdate_utc": "2026-07-02T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42394128/", "abstract_snippet": "Yunnan Province is recognized as a hotspot for the emergence of HIV-1 recombinant forms due to its complex epidemiological history. This study identified a novel circulating recombinant form (CRF) of HIV-1 in the region, designated as CRF203_cpx. Near-full-len…", "score": 8.673, "score_components": { "theme_priority": 1.2, "research_signal": 4.8, "venue": 0.0, "recency": 1.173, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "emerging_threat": 2.2 }, "signal_classes": [ "Viral evolution", "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42413860", "title": "Phylogenetic characterization of partial spike gene sequences of canine coronavirus from shelter dogs in the Republic of Korea.", "authors": "Yeeun Kim, Sung-Geun Lee, Dongseob Tark", "journal": "Veterinary journal (London, England : 1997)", "pubdate": "2026-07-10", "pubdate_utc": "2026-07-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42413860/", "abstract_snippet": "This study investigated the molecular characteristics of canine coronavirus (CCoV) circulating in animal shelters in Korea, focusing on phylogenetic characterization of the partial spike (S) gene. A total of 339 rectal swabs were analyzed to assess the prevale…", "score": 8.228, "score_components": { "theme_priority": 1.2, "research_signal": 4.3, "venue": 0.0, "recency": 1.228, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42103022", "title": "Genotypic diversity and zoonotic potential of Salmonella enterica from multiple hosts: implications for One Health.", "authors": "Maria Eduarda de Souza Teixeira Campos, Dircéia Aparecida da Costa Custódio, Carine Rodrigues Pereira, Jéssica Luana Felix Moreira, Bruno Borges Silva, Vasco Ariston de Carvalho Azevedo", "journal": "Microbial pathogenesis", "pubdate": "2026-05-06", "pubdate_utc": "2026-05-06T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42103022/", "abstract_snippet": "Salmonella enterica is a major zoonotic pathogen with significant impact on human and animal health. In this study, 28 isolates obtained from 20 domestic and wild animals in Brazil were characterized using phenotypic antimicrobial susceptibility testing, epide…", "score": 8.144, "score_components": { "theme_priority": 1.2, "research_signal": 4.6, "venue": 0.0, "recency": 0.844, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 2.4, "emerging_threat": 2.2 }, "signal_classes": [ "Metagenomics / surveillance", "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42579153", "title": "Clade-specific evolution and genome plasticity underlying antimicrobial resistance in Enterococcus faecium.", "authors": "Krishna Patel, Monica Chavan, Jigna Shah, Shruti Chatterjee", "journal": "Archives of microbiology", "pubdate": "2026-08-11", "pubdate_utc": "2026-08-11T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42579153/", "abstract_snippet": "A commensal organism has transformed into the leading multidrug resistant (MDR) hospital acquired pathogen, with serious implication on global public health. The ability of Enterococcus faecium to rapidly adapt through its great genomic plasticity, horizontal …", "score": 5.078, "score_components": { "theme_priority": 1.2, "research_signal": 2.4, "venue": 0.0, "recency": 1.478, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Recombination & mosaicism" }, { "pmid": "42525515", "title": "A generative model for bipartite gene-sharing networks.", "authors": "Jaime Iranzo, Pedro Jódar, Eugene V Koonin, Susanna Manrubia, José A Cuesta", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "pubdate": "2026-07-29", "pubdate_utc": "2026-07-29T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42525515/", "abstract_snippet": "Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a scale-free distributio…", "score": 4.771, "score_components": { "theme_priority": 1.2, "research_signal": 2.2, "venue": 0.0, "recency": 1.371, "cross_domain": 0.0 }, "signal_components": { "emerging_threat": 2.2 }, "signal_classes": [ "Emerging threat" ], "theme": "Recombination & mosaicism" }, { "pmid": "42557571", "title": "Comprehensive genomic characterization of extraintestinal pathogenic Escherichia coli isolated from neonates: multiple center insights into virulence, resistance, and transmission dynamics.", "authors": "Dongmiao Zhang, Yijun Ding, Wenqing Kang, Xueping Zhu, Zheng Cao, Yangfang Li", "journal": "Genome medicine", "pubdate": "2026-08-05", "pubdate_utc": "2026-08-05T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42557571/", "abstract_snippet": "Neonatal extraintestinal pathogenic Escherichia coli (ExPEC), which can cause severe long-term sequelae by systemic infections, is gradually becoming the primary pathogen threatening neonatal health. The lack of large-scale genomic epidemiological investigatio…", "score": 4.327, "score_components": { "theme_priority": 1.2, "research_signal": 1.7, "venue": 0.0, "recency": 1.427, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42413229", "title": "Molecular cloning, characterization and pathogen-induced expression analysis of the Chinese soft-shelled turtle (Pelodiscus sinensis) interleukin-18.", "authors": "Zhihui Xiao, Jiehao Xu, Yingjuan Xie, Zhi Dong, Chaonan Zhang, Yiwei Hu", "journal": "Developmental and comparative immunology", "pubdate": "2026-07-07", "pubdate_utc": "2026-07-07T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42413229/", "abstract_snippet": "The Chinese soft-shelled turtle (Pelodiscus sinensis) is an economically valuable aquaculture species whose production is often constrained by bacterial and viral diseases. Interleukin-18 (IL18) plays a pivotal role in regulating innate and adaptive immune res…", "score": 4.107, "score_components": { "theme_priority": 1.2, "research_signal": 1.7, "venue": 0.0, "recency": 1.207, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42271057", "title": "Gene ancestries reveal diverse microbial associations during eukaryogenesis.", "authors": "Moisès Bernabeu, Saioa Manzano-Morales, Marina Marcet-Houben, Toni Gabaldón", "journal": "Nature", "pubdate": "2026-06-10", "pubdate_utc": "2026-06-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42271057/", "abstract_snippet": "The origin of eukaryotes remains a central enigma in biology1. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon2,3. However, the nature, timing and contributions of other potential bacterial par…", "score": 3.933, "score_components": { "theme_priority": 1.2, "research_signal": 1.7, "venue": 0.0, "recency": 1.033, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Recombination & mosaicism" }, { "pmid": "42528383", "title": "The mycobacterial selenocysteine machinery: presence and expression.", "authors": "Phani Rama Krishna Behra, Malavika Ramesh, B M Fredrik Pettersson, Leif A Kirsebom", "journal": "RNA biology", "pubdate": "2026-08-05", "pubdate_utc": "2026-08-05T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42528383/", "abstract_snippet": "The Mycobacterium genus includes more than 190 species that occupies diverse ecological niches. Some are non-pathogenic and environmental, whereas others cause severe diseases both in humans and animals, e.g. tuberculosis (TB) and leprosy. Selenocysteine (Sec)…", "score": 2.627, "score_components": { "theme_priority": 1.2, "research_signal": 0.0, "venue": 0.0, "recency": 1.427, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Recombination & mosaicism" }, { "pmid": "42208876", "title": "Molecular characterization, expression analysis, and functional identification of Lccystatin M from Large Yellow Croaker (Larimichthys crocea) in immune defense against Pseudomonas plecoglossicida infection.", "authors": "Chenpeng Lu, Yadong Xue, Ping Han, Xiumei Liu, Jianming Chen, Xubo Wang", "journal": "Fish & shellfish immunology", "pubdate": "2026-05-27", "pubdate_utc": "2026-05-27T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42208876/", "abstract_snippet": "Cystatins are key molecules widely involved in the regulation of cellular proteases and innate immune responses. In recent years, research on this family in the innate immunity of teleosts has deepened, gradually revealing their crucial roles in immune defense…", "score": 2.153, "score_components": { "theme_priority": 1.2, "research_signal": 0.0, "venue": 0.0, "recency": 0.953, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Recombination & mosaicism" }, { "pmid": "42167559", "title": "CgHb-like modulates the energy metabolism, histone acetylation and inflammatory responses in oysters during Vibrio splendidus stimulation.", "authors": "Jie Wang, Muchun He, Jinyuan Leng, Jinyong Zhang, Renle Chang, Weishuai Shan", "journal": "Fish & shellfish immunology", "pubdate": "2026-05-20", "pubdate_utc": "2026-05-20T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42167559/", "abstract_snippet": "Hemoglobin (Hb) is the iron-containing oxygen-transport metalloprotein in red blood cells of vertebrates and some invertebrates. In the present study, a Hb homolog was identified from oyster Crassostrea gigas (defined as CgHb-like). CgHb-like transcripts were …", "score": 2.115, "score_components": { "theme_priority": 1.2, "research_signal": 0.0, "venue": 0.0, "recency": 0.915, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Recombination & mosaicism" }, { "pmid": "42107613", "title": "Characterization of a C-type lectin (OnCLEC10A) in Oreochromis niloticus functioning as a pattern recognition receptor with antibacterial properties.", "authors": "Miao Cui, Gaojun Zheng, Shixu Wang, Jingwen Liang, Xianji Xu, Jinhui Wu", "journal": "Fish & shellfish immunology", "pubdate": "2026-05-08", "pubdate_utc": "2026-05-08T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42107613/", "abstract_snippet": "C-type lectins (CTLs) constitute a superfamily of Ca2+-dependent carbohydrate-recognition proteins involved in pathogen recognition and elimination. In the present study, a C-type lectin family 10 member from Oreochromis niloticus (tentatively named OnCLEC10A)…", "score": 2.054, "score_components": { "theme_priority": 1.2, "research_signal": 0.0, "venue": 0.0, "recency": 0.854, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Recombination & mosaicism" } ] }, { "label": "Phylodynamics & transmission", "query": "(((phylodynamic* OR \"time-resolved phylogeny\" OR BEAST OR \"birth-death\" OR coalescent) AND (virus OR pathogen)) OR ((\"genomic epidemiology\" OR \"phylodynamic inference\") AND (outbreak OR transmission))) AND (\"computational evolutionary biology\" OR \"molecular evolution\" OR phylogenomics OR phylodynamics OR HyPhy OR \"codon model\") NOT (case report OR randomized OR psychology)", "count": 15, "items": [ { "pmid": "42578762", "title": "Emergence and local dissemination of NDM-14-producing Klebsiella pneumoniae ST147: a phylodynamic and epidemiological investigation.", "authors": "Gabriele Arcari, Mattia Carbotti, Riccardo Pavesi, Paolo Gigante, Riccardo Capuano, Domenico Caleca", "journal": "Antimicrobial agents and chemotherapy", "pubdate": "2026-08-11", "pubdate_utc": "2026-08-11T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42578762/", "abstract_snippet": "NDM-14-producing Klebsiella pneumoniae ST147 has recently emerged as a high-risk clone in Europe, but its local dissemination dynamics remain poorly defined. We investigated a 6-month outbreak across three hospitals within a regional healthcare network in Lomb…", "score": 15.278, "score_components": { "theme_priority": 1.2, "research_signal": 11.1, "venue": 0.0, "recency": 1.478, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "metagenomics_surveillance": 2.4, "methods": 1.7, "emerging_threat": 4.4 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Methods", "Emerging threat" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42378013", "title": "Global genomic surveillance of Salmonella in the environment: assessing virulence and antimicrobial resistance at scale.", "authors": "Viraj Bandsode, Shamsul Qumar, Anuradha Singh, Debaleena Das, Humera Quadriya, Mahanga Nyambero", "journal": "mBio", "pubdate": "2026-06-22", "pubdate_utc": "2026-06-22T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42378013/", "abstract_snippet": "Salmonella is a globally distributed zoonotic pathogen with widespread environmental persistence; however, genomic characterization of environmental isolates from underrepresented regions remains limited. Current global data sets are predominantly populated wi…", "score": 12.507, "score_components": { "theme_priority": 1.2, "research_signal": 8.7, "venue": 0.0, "recency": 1.107, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 4.8, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Metagenomics / surveillance", "Methods", "Emerging threat" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42495449", "title": "Genomic epidemiology of carbapenem resistance in Acinetobacter baumannii in Chile.", "authors": "Pablo Araya-Vega, Maximiliano Matus-Köhler, Victoria Mardones-Verdugo, Sofía Gómez-Inostroza, Paulina González-Muñoz, Esteban Paredes-Osses", "journal": "JAC-antimicrobial resistance", "pubdate": "2026-07-23", "pubdate_utc": "2026-07-23T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42495449/", "abstract_snippet": "Carbapenem-resistant Acinetobacter baumannii (CRAb) is a World Health Organization (WHO) critical priority pathogen, yet genomic data from Chile are scarce. Here, we investigated the genetic diversity of Chilean isolates, focusing on molecular epidemiology, ca…", "score": 10.724, "score_components": { "theme_priority": 1.2, "research_signal": 6.7, "venue": 0.0, "recency": 1.324, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "metagenomics_surveillance": 2.4, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Methods" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42429792", "title": "A genomic framework for tracking antibiotic resistance genes: global dissemination of cfr-family genes.", "authors": "Hao Liu, Xianyang Huang, Xiaoqian Li, Yue Li, Zerui Shang, Huimin Zhou", "journal": "Antimicrobial agents and chemotherapy", "pubdate": "2026-07-10", "pubdate_utc": "2026-07-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42429792/", "abstract_snippet": "The global spread of antimicrobial resistance (AMR) calls for advanced surveillance frameworks capable of tracking high-risk resistance genes across genomic, temporal, and ecological environments. To address this, we designed an integrated genomic epidemiology…", "score": 10.628, "score_components": { "theme_priority": 1.2, "research_signal": 6.7, "venue": 0.0, "recency": 1.228, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "metagenomics_surveillance": 2.4, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Methods" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42442739", "title": "Rapid Expansion of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Genotype D1.1 Virus across Flyway Regions, North America, Fall 2024.", "authors": "Matthew Scotch, Temitope O C Faleye, Angelica Urquidez-Negrete, Arvind Varsani, Ann Fan, Anne Justice-Allen", "journal": "Emerging infectious diseases", "pubdate": "2026-07-13", "pubdate_utc": "2026-07-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42442739/", "abstract_snippet": "Highly pathogenic avian influenza clade 2.3.4.4b virus continues to circulate in North America and has caused severe human disease. That clade includes genotype D1.1, which became dominant in birds in late 2024. Recent phylodynamic reconstructions place D1.1 e…", "score": 10.25, "score_components": { "theme_priority": 1.2, "research_signal": 6.3, "venue": 0.0, "recency": 1.25, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 2.4, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Metagenomics / surveillance", "Methods", "Emerging threat" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42320408", "title": "Genomic epidemiology of two travel-associated pediatric measles viruses within the B3 Lineage.", "authors": "Sydney Stanley, Rose C Patrick, Michael Elkan, Jeffrey Fink, Bonnie Oh, Yan Sun", "journal": "Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology", "pubdate": "2026-06-18", "pubdate_utc": "2026-06-18T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42320408/", "abstract_snippet": "Children's Hospital of Philadelphia (CHOP) identified a MeV case in late 2023 and also early 2025, both of which were associated with international travel. Of the 24 MeV genotypes, the B3 and D8 lineages have been the most prevalent globally since 2021. Initia…", "score": 8.482, "score_components": { "theme_priority": 1.2, "research_signal": 4.7, "venue": 0.0, "recency": 1.082, "cross_domain": 1.5 }, "signal_components": { "selection": 3.0, "methods": 1.7 }, "signal_classes": [ "Selection", "Methods" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42579695", "title": "Genomic epidemiology of multidrug-resistant and ESBL-producing Proteus mirabilis in a military referral hospital in Ethiopia.", "authors": "Yacob Mohammed Yusuf, Adey Feleke Desta, Desta Ayana, Helen Nigussie Aychegrew, Rajiha Abubeker, Biruk Samson", "journal": "PloS one", "pubdate": "2026-08-11", "pubdate_utc": "2026-08-11T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42579695/", "abstract_snippet": "Multidrug-resistant Proteus mirabilis has emerged as an important healthcare-associated pathogen; however, genomic epidemiological data from sub-Saharan Africa remain limited, particularly in military hospital settings. This study aimed to characterize the phe…", "score": 8.278, "score_components": { "theme_priority": 1.2, "research_signal": 4.1, "venue": 0.0, "recency": 1.478, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 2.4, "methods": 1.7 }, "signal_classes": [ "Metagenomics / surveillance", "Methods" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42545215", "title": "Genetic evolution, phylodynamics, geographic spread of H9N2 avian influenza viruses in China from 2014 to 2025: an increasing potential zoonotic risk.", "authors": "Zifeng Pang, Peiting Zhong, Cuishan Mai, Junkun Fan, Yejia Wu, Yao Zhang", "journal": "Emerging microbes & infections", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42545215/", "abstract_snippet": "Subtype H9N2 of the avian influenza virus (AIV) poses a growing threat to the poultry industry and public health. However, since 2014, there has been no systematic study of its genetic evolution, genotype, spatial dynamics, and pathogenicity in China. Therefor…", "score": 8.086, "score_components": { "theme_priority": 1.2, "research_signal": 3.9, "venue": 0.0, "recency": 1.486, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42116424", "title": "Retail pork markets as underrecognized hubs of tigecycline resistance: Genomic epidemiology of tet(X4)-harboring Escherichia coli and global ST195 dissemination.", "authors": "Jinger Chen, Junhao Peng, Yudi Wu, Kaifeng Chen, Qiqi Hong, Zixin Xu", "journal": "Food research international (Ottawa, Ont.)", "pubdate": "2026-04-16", "pubdate_utc": "2026-04-16T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42116424/", "abstract_snippet": "Antimicrobial resistance in the food chain threatens public health, yet the tigecycline resistance gene tet(X4) remains under-characterized in retail pork markets. Here, we investigated the presence, genetic features, and dissemination of tet(X4)-harboring bac…", "score": 7.552, "score_components": { "theme_priority": 1.2, "research_signal": 4.1, "venue": 0.0, "recency": 0.752, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 2.4, "methods": 1.7 }, "signal_classes": [ "Metagenomics / surveillance", "Methods" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42276095", "title": "Wastewater-based sequencing of respiratory syncytial virus to investigate lineage dynamics and antigenic site mutations: a retrospective genomic epidemiology study.", "authors": "Jolinda de Korne-Elenbaas, Auguste Rimaite, Ivan Topolsky, David Dreifuss, Charlyne Bürki, Lara Fuhrmann", "journal": "The Lancet. Microbe", "pubdate": "2026-06-11", "pubdate_utc": "2026-06-11T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42276095/", "abstract_snippet": "Respiratory syncytial virus (RSV) infections pose a substantial health burden, particularly for clinically vulnerable populations such as infants and older adults. Although novel immunoprophylactic interventions show promise in providing protection, many count…", "score": 7.039, "score_components": { "theme_priority": 1.2, "research_signal": 4.8, "venue": 0.0, "recency": 1.039, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 4.8 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42567280", "title": "Exact phylodynamic likelihood via structured Markov genealogy processes.", "authors": "Aaron A King, Qianying Lin, Edward L Ionides", "journal": "Theoretical population biology", "pubdate": "2026-08-07", "pubdate_utc": "2026-08-07T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42567280/", "abstract_snippet": "We show that each member of a broad class of Markovian population models induces a unique stochastic process on the space of genealogies. We construct this genealogy process and derive exact expressions for the likelihood of an observed genealogy in terms of a…", "score": 6.044, "score_components": { "theme_priority": 1.2, "research_signal": 3.4, "venue": 0.0, "recency": 1.444, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "Phylodynamics & transmission" }, { "pmid": "41533667", "title": "A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum.", "authors": "Kin Onn Chan, Dario N Neokleous, Shahrul Anuar, Rafe M Brown, Carl R Hutter, Indraneil Das", "journal": "Systematic biology", "pubdate": "2026-08-06", "pubdate_utc": "2026-08-06T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/41533667/", "abstract_snippet": "The evolutionary dynamics of cryptic species remain poorly understood, and their detection relies primarily on methods that quantify divergence, assuming that gene flow is absent. Here, we examine how gene flow shapes the evolutionary trajectories and species …", "score": 6.036, "score_components": { "theme_priority": 1.2, "research_signal": 3.4, "venue": 0.0, "recency": 1.436, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42379474", "title": "Genomic characterization of a large-scale chikungunya outbreak in China.", "authors": "Lirong Cao, Dongfeng Kong, Jingzhi Lou, Xiran Wang, Fang Yang, Ying Ye", "journal": "The Journal of infection", "pubdate": "2026-06-30", "pubdate_utc": "2026-06-30T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42379474/", "abstract_snippet": "In July 2025, a large chikungunya outbreak occurred in southern China, with more than 5000 cases reported within a single month. However, the genomic basis of this urban outbreak remains poorly characterized. A total of 804 CHIKV-positive clinical specimens we…", "score": 4.559, "score_components": { "theme_priority": 1.2, "research_signal": 2.2, "venue": 0.0, "recency": 1.159, "cross_domain": 0.0 }, "signal_components": { "emerging_threat": 2.2 }, "signal_classes": [ "Emerging threat" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42276094", "title": "Comparison of phylogenetic metrics of transmission between symptomatic and asymptomatic tuberculosis in individuals who were incarcerated in Brazil in 2008-24: a retrospective genomic epidemiology study.", "authors": "Kesia Esther da Silva, Paulo César Pereira Dos Santos, Daniel Henrique Tsuha, Katharine S Walter, Eunice Atsuko Totumi Cunha, Caroline Colijn", "journal": "The Lancet. Microbe", "pubdate": "2026-06-12", "pubdate_utc": "2026-06-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42276094/", "abstract_snippet": "Tuberculosis control efforts have traditionally targeted symptomatic individuals; however, the role of asymptomatic cases in sustaining transmission is increasingly recognised. We aimed to quantify the contribution of asymptomatic tuberculosis to recent transm…", "score": 3.945, "score_components": { "theme_priority": 1.2, "research_signal": 1.7, "venue": 0.0, "recency": 1.045, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Phylodynamics & transmission" }, { "pmid": "42177155", "title": "Corrigendum to \"Phylogenetic and phylodynamic analysis of respiratory syncytial virus strains circulating in children less than five years of age in Karachi-Pakistan\" [Infection, Genetics and Evolution, 2024, volume 126, article 105694].", "authors": "Fatima Aziz, Nida Farooqui, Tanveer Abbas, Mahnoor Javaid, Wardah Rafaqat, Alnara Zhamalbekova", "journal": "Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases", "pubdate": "2026-05-23", "pubdate_utc": "2026-05-23T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42177155/", "abstract_snippet": "", "score": 3.831, "score_components": { "theme_priority": 1.2, "research_signal": 1.7, "venue": 0.0, "recency": 0.931, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Phylodynamics & transmission" } ] }, { "label": "Urban / built environment virome", "query": "(((virome OR \"viral metagenomics\" OR viromics) AND (\"built environment\" OR urban OR subway OR transit OR surface)) OR ((\"urban microbiome\" OR MetaSUB) AND (virus OR virome OR phage))) AND (\"computational evolutionary biology\" OR \"molecular evolution\" OR phylogenomics OR phylodynamics OR HyPhy OR \"codon model\") NOT (case report OR randomized OR psychology)", "count": 0, "items": [] }, { "label": "Wastewater / WBE viral surveillance", "query": "(((\"wastewater surveillance\" OR WBE OR sewage) AND (virus OR virome OR pathogen OR SARS-CoV-2)) OR ((wastewater OR sewage) AND (\"viral metagenomics\" OR viromics) AND (variant OR lineage OR evolution))) AND (\"computational evolutionary biology\" OR \"molecular evolution\" OR phylogenomics OR phylodynamics OR HyPhy OR \"codon model\") NOT (case report OR randomized OR psychology)", "count": 5, "items": [ { "pmid": "42589152", "title": "Detection and Genotyping of Human Adenoviruses in Wastewater from Bulgaria by Targeted Surveillance, In Vitro Cultivation, and Whole-Genome Sequencing.", "authors": "Sergei Ivanov, Zoltan Urshev, Anton Hinkov, Petya Angelova, Kalina Shishkova, Stoyan Shishkov", "journal": "Biology", "pubdate": "2026-08-04", "pubdate_utc": "2026-08-04T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42589152/", "abstract_snippet": "Adenoviruses are detected in wastewater at significantly higher frequencies than most other enteric viruses. The aim of this study was to determine the abundance of human adenoviruses in samples collected from wastewater treatment plants in Sofia, Plovdiv, Bur…", "score": 11.769, "score_components": { "theme_priority": 1.25, "research_signal": 7.6, "venue": 0.0, "recency": 1.419, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance" ], "theme": "Wastewater / WBE viral surveillance" }, { "pmid": "42177889", "title": "Characterization, lytic activity, and therapeutic efficacy of a novel phage, BUCT789, lysing drug-resistant Escherichia coli in Galleria mellonella larvae.", "authors": "Rashid Ahmad, Zakirullah, Mengzhe Li, Yigang Tong", "journal": "Virology", "pubdate": "2026-05-23", "pubdate_utc": "2026-05-23T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42177889/", "abstract_snippet": "Severe infections caused by multidrug-resistant Escherichia coli (E. coli) highlight the necessity for new therapeutics. Phage therapy is an alternative treatment approach for multidrug-resistant E. coli infections. Here, we report the isolation and characteri…", "score": 7.781, "score_components": { "theme_priority": 1.25, "research_signal": 4.1, "venue": 0.0, "recency": 0.931, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 2.4, "methods": 1.7 }, "signal_classes": [ "Metagenomics / surveillance", "Methods" ], "theme": "Wastewater / WBE viral surveillance" }, { "pmid": "42552315", "title": "Multidrug-resistant and virulence traits in genetically distinct vesicular Leptospira inhabiting farmland and sewage in Southern India.", "authors": "Amin Sonam, Asif Hameed, Paul Stothard, Jason R Grant, Rouchelle Charmaine Tellis, Ananthapadmanabha Bhagwath Arun", "journal": "Scientific reports", "pubdate": "2026-08-04", "pubdate_utc": "2026-08-04T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42552315/", "abstract_snippet": "The occurrence, taxonomic identity, drug resistance pattern and virulence traits of cultivable environmental Leptospira inhabiting the Indian subcontinent remain largely unexplored. Here, we describe the isolation and characterization of six novel strains of L…", "score": 5.069, "score_components": { "theme_priority": 1.25, "research_signal": 2.4, "venue": 0.0, "recency": 1.419, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Wastewater / WBE viral surveillance" }, { "pmid": "42378761", "title": "Dairy farm waste as a source of novel and globally disseminated multidrug-resistant Escherichia coli clones: A genomic and phylogeographic study.", "authors": "Muhammad Shoaib, Minjia Tang, Asim Munir, Muhammad Shafiq, Mashkoor Mohsin, Xuejing Zhang", "journal": "Journal of hazardous materials", "pubdate": "2026-06-27", "pubdate_utc": "2026-06-27T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42378761/", "abstract_snippet": "Dairy farm waste may serve as a reservoir for multidrug-resistant (MDR) Escherichia coli clones, but the genomic characteristics and dissemination potential of such clones remain incompletely understood. Here, we performed whole-genome sequencing and comprehen…", "score": 4.789, "score_components": { "theme_priority": 1.25, "research_signal": 2.4, "venue": 0.0, "recency": 1.139, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Wastewater / WBE viral surveillance" }, { "pmid": "42390091", "title": "Extensive library of Ruminococcus gnavus phages revealing genomic and phenotypic diversity with novel clusters.", "authors": "Arata Sakiyama, Ayaka Washizaki, Keiko Inaba-Hasegawa, Most Hushna Ara Naznin, Keigo Ide, Masayuki Takase", "journal": "Microbiology spectrum", "pubdate": "2026-06-22", "pubdate_utc": "2026-06-22T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42390091/", "abstract_snippet": "Ruminococcus gnavus is a prevalent member of human gut microbiota and is associated with inflammatory bowel disease. Phage-based microbiota engineering represents a promising approach for alleviating dysbiosis; however, knowledge regarding R. gnavus phages rem…", "score": 4.757, "score_components": { "theme_priority": 1.25, "research_signal": 2.4, "venue": 0.0, "recency": 1.107, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Wastewater / WBE viral surveillance" } ] }, { "label": "Pandemic preparedness & biosurveillance", "query": "(((\"pandemic preparedness\" OR biosurveillance OR \"pathogen surveillance\") AND (genomics OR sequencing)) OR ((\"early warning\" OR \"sentinel surveillance\") AND (metagenomics OR sequencing))) AND (\"computational evolutionary biology\" OR \"molecular evolution\" OR phylogenomics OR phylodynamics OR HyPhy OR \"codon model\") NOT (case report OR randomized OR psychology)", "count": 5, "items": [ { "pmid": "42439533", "title": "Phylogenetic and biological features of severe fever with thrombocytopenia syndrome virus from multi-species infections in eastern China.", "authors": "Hao Wang, Dali Xu, Chengyunxiao Li, Xueying Tian, Bo Pang, Ti Liu", "journal": "Microbiology spectrum", "pubdate": "2026-07-13", "pubdate_utc": "2026-07-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42439533/", "abstract_snippet": "Severe fever with thrombocytopenia syndrome (SFTS), caused by SFTS virus (SFTSV), is an emerging tick-borne disease with high mortality and complex transmission dynamics. Since its first identification in China, SFTS has become an endemic infectious disease wi…", "score": 15.4, "score_components": { "theme_priority": 1.15, "research_signal": 11.5, "venue": 0.0, "recency": 1.25, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "metagenomics_surveillance": 2.4, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Methods", "Emerging threat" ], "theme": "Pandemic preparedness & biosurveillance" }, { "pmid": "42390251", "title": "Tracking the shifting landscape of SARS-CoV-2 variants in Lebanon among healthcare workers and hospitalized patients.", "authors": "Habib Alkalamouni, Mirna Bou Hamdan, Farouk Abou Hassan, Fatima Dakroub, Lama Hamadeh, Alissar Rady", "journal": "Microbiology spectrum", "pubdate": "2026-07-02", "pubdate_utc": "2026-07-02T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42390251/", "abstract_snippet": "Genomic surveillance of SARS-CoV-2 is critical for tracking viral evolution and informing public health responses. This study characterized variants circulating among healthcare workers (HCWs) and hospitalized patients in Lebanon between January 2022 and Septe…", "score": 13.623, "score_components": { "theme_priority": 1.15, "research_signal": 9.8, "venue": 0.0, "recency": 1.173, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 5.2, "metagenomics_surveillance": 2.4, "emerging_threat": 2.2 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Emerging threat" ], "theme": "Pandemic preparedness & biosurveillance" }, { "pmid": "42378013", "title": "Global genomic surveillance of Salmonella in the environment: assessing virulence and antimicrobial resistance at scale.", "authors": "Viraj Bandsode, Shamsul Qumar, Anuradha Singh, Debaleena Das, Humera Quadriya, Mahanga Nyambero", "journal": "mBio", "pubdate": "2026-06-22", "pubdate_utc": "2026-06-22T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42378013/", "abstract_snippet": "Salmonella is a globally distributed zoonotic pathogen with widespread environmental persistence; however, genomic characterization of environmental isolates from underrepresented regions remains limited. Current global data sets are predominantly populated wi…", "score": 12.457, "score_components": { "theme_priority": 1.15, "research_signal": 8.7, "venue": 0.0, "recency": 1.107, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 4.8, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Metagenomics / surveillance", "Methods", "Emerging threat" ], "theme": "Pandemic preparedness & biosurveillance" }, { "pmid": "42506928", "title": "Alignment-free k-mer-guided design of a pan-Orthoflavivirus RT-qPCR assay.", "authors": "Khanate Sayasit, Chutikarn Chaimayo, Warinya Nuwong, Tharathip Boondouylan, Nattaya Tanlieng, Kamol Suwannakarn", "journal": "Journal of clinical microbiology", "pubdate": "2026-07-27", "pubdate_utc": "2026-07-27T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42506928/", "abstract_snippet": "The co-circulation and rapid expansion of the genus Orthoflavivirus, including dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), Yellow fever virus (YFV), and Japanese encephalitis virus (JEV), pose significant global health challenges. Developing…", "score": 9.605, "score_components": { "theme_priority": 1.15, "research_signal": 5.6, "venue": 0.0, "recency": 1.355, "cross_domain": 1.5 }, "signal_components": { "methods": 3.4, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "Pandemic preparedness & biosurveillance" }, { "pmid": "42258901", "title": "DNA barcoding reveals novel biodiversity in ticks (Acari: Ixodida: Ixodidae) of Ethiopia.", "authors": "Electra F Chadd, Bersissa Kumsa, Laura Caicedo-Quiroga, Yvonne-Marie Linton", "journal": "Veterinary parasitology", "pubdate": "2026-06-04", "pubdate_utc": "2026-06-04T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42258901/", "abstract_snippet": "Identification of hard ticks (Acari: Ixodida: Ixodidae) is problematic due to inconsistent diagnostic characters, sexual dimorphism, individual variation, and vast morphological differences among life stages, as well as distortion through blood feeding. DNA ba…", "score": 4.348, "score_components": { "theme_priority": 1.15, "research_signal": 2.2, "venue": 0.0, "recency": 0.998, "cross_domain": 0.0 }, "signal_components": { "emerging_threat": 2.2 }, "signal_classes": [ "Emerging threat" ], "theme": "Pandemic preparedness & biosurveillance" } ] }, { "label": "Atlases, compendia, reference resources", "query": "(((atlas OR database OR compendium OR \"reference catalog\" OR resource) AND (virome OR microbiome OR pathogen)) OR ((\"large-scale\" OR global) AND (virome OR microbiome) AND (metadata OR harmonization))) AND (\"computational evolutionary biology\" OR \"molecular evolution\" OR phylogenomics OR phylodynamics OR HyPhy OR \"codon model\") NOT (case report OR randomized OR psychology)", "count": 25, "items": [ { "pmid": "42390272", "title": "Genetic variation, recombinant characteristics, and seroprevalence analysis of echovirus 3 causing severe and mild cases of hand, foot, and mouth disease in Guizhou Province.", "authors": "Fajin Li, Fei Su, Dan Wang, Fumin Zhang, Jun Guo, Guanghai Yao", "journal": "Microbiology spectrum", "pubdate": "2026-07-02", "pubdate_utc": "2026-07-02T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42390272/", "abstract_snippet": "Echovirus 3 (E-3) has recently been identified as an emerging pathogen associated with both severe and mild cases of hand, foot, and mouth disease (HFMD) in Guizhou Province, China. Although these strains exhibit distinct clinical phenotypes, their underlying …", "score": 15.873, "score_components": { "theme_priority": 1.1, "research_signal": 12.1, "venue": 0.0, "recency": 1.173, "cross_domain": 1.5 }, "signal_components": { "selection": 3.0, "viral_evolution": 5.2, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Selection", "Viral evolution", "Methods", "Emerging threat" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42429792", "title": "A genomic framework for tracking antibiotic resistance genes: global dissemination of cfr-family genes.", "authors": "Hao Liu, Xianyang Huang, Xiaoqian Li, Yue Li, Zerui Shang, Huimin Zhou", "journal": "Antimicrobial agents and chemotherapy", "pubdate": "2026-07-10", "pubdate_utc": "2026-07-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42429792/", "abstract_snippet": "The global spread of antimicrobial resistance (AMR) calls for advanced surveillance frameworks capable of tracking high-risk resistance genes across genomic, temporal, and ecological environments. To address this, we designed an integrated genomic epidemiology…", "score": 10.528, "score_components": { "theme_priority": 1.1, "research_signal": 6.7, "venue": 0.0, "recency": 1.228, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "metagenomics_surveillance": 2.4, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Metagenomics / surveillance", "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42407323", "title": "Genome-wide identification and characterization of β-defensin genes across sixteen Eulipotyphla species: Insights into gene diversification and evolutionary dynamics.", "authors": "Wenhao Huang, Xinyu Tang, Huiyu Jiang, Yawen Deng, Ting Lu, Jiayue Peng", "journal": "Developmental and comparative immunology", "pubdate": "2026-07-06", "pubdate_utc": "2026-07-06T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42407323/", "abstract_snippet": "β-defensins, a class of cationic antimicrobial peptides (AMPs), play a crucial role in innate host defense. While these peptides have been extensively studied in vertebrates, their evolutionary history and functional characteristics in Eulipotyphla remain larg…", "score": 9.0, "score_components": { "theme_priority": 1.1, "research_signal": 5.2, "venue": 0.0, "recency": 1.2, "cross_domain": 1.5 }, "signal_components": { "selection": 3.0, "emerging_threat": 2.2 }, "signal_classes": [ "Selection", "Emerging threat" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42545215", "title": "Genetic evolution, phylodynamics, geographic spread of H9N2 avian influenza viruses in China from 2014 to 2025: an increasing potential zoonotic risk.", "authors": "Zifeng Pang, Peiting Zhong, Cuishan Mai, Junkun Fan, Yejia Wu, Yao Zhang", "journal": "Emerging microbes & infections", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42545215/", "abstract_snippet": "Subtype H9N2 of the avian influenza virus (AIV) poses a growing threat to the poultry industry and public health. However, since 2014, there has been no systematic study of its genetic evolution, genotype, spatial dynamics, and pathogenicity in China. Therefor…", "score": 7.986, "score_components": { "theme_priority": 1.1, "research_signal": 3.9, "venue": 0.0, "recency": 1.486, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42589030", "title": "Isolation, Genomic Evolution, and Pathogenicity of Clostridium perfringens Type A Causing Hemorrhagic Enteritis in Adult Yaks in Southwest China.", "authors": "Long Zhao, Yongqiang Miao, Zhen Yang, Kefei Shen, Dengfeng Xu, Suhui Zhang", "journal": "Animals : an open access journal from MDPI", "pubdate": "2026-08-03", "pubdate_utc": "2026-08-03T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42589030/", "abstract_snippet": "Clostridium perfringens type A causes neonatal clostridial enteritis, hemorrhagic enteritis, and sudden death syndrome in cattle. This study examined a fatal outbreak at a fattening farm housing 58 adult yaks in Southwest China, with an incidence of 22.41% (13…", "score": 7.911, "score_components": { "theme_priority": 1.1, "research_signal": 3.9, "venue": 0.0, "recency": 1.411, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42532458", "title": "Genomic analysis of a clinical Enterobacter hormaechei isolate from a postoperative left atrial myxoma patient.", "authors": "Jinzhen Zhao, Miaoxian Fang, Liming Lei, Guiyan Zhang", "journal": "Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases", "pubdate": "2026-07-30", "pubdate_utc": "2026-07-30T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42532458/", "abstract_snippet": "Enterobacter hormaechei is an opportunistic pathogen increasingly implicated in healthcare-associated infections, including bloodstream infections. However, the genomic and pathogenic features of clinical isolates from specific surgical settings remain incompl…", "score": 7.879, "score_components": { "theme_priority": 1.1, "research_signal": 3.9, "venue": 0.0, "recency": 1.379, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42531256", "title": "First report of Corynespora cassiicola causing leaf spot on Begonia fimbristipula in China.", "authors": "Xiaobo Zhang, Xiaoyi Zuo, Jianhua Lu, Ya Xiao, Yuanshun Wang, Huan Chen", "journal": "PloS one", "pubdate": "2026-07-30", "pubdate_utc": "2026-07-30T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42531256/", "abstract_snippet": "Begonia fimbristipula, an economically important medicinal plant in southern China, has recently suffered severe yield losses from leaf spot disease in Guizhou and Hunan Provinces; the causal pathogen remains unknown. Field surveys were conducted across multip…", "score": 7.879, "score_components": { "theme_priority": 1.1, "research_signal": 3.9, "venue": 0.0, "recency": 1.379, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42379819", "title": "Epidemiological and molecular characterization of multidrug-resistant Corynebacterium striatum in a tertiary hospital in China.", "authors": "Xia Li, Hong Li, Chunyan Gao, Ziyang Li, Lili Ding, Yu Wang", "journal": "Microbiology spectrum", "pubdate": "2026-06-30", "pubdate_utc": "2026-06-30T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42379819/", "abstract_snippet": "Corynebacterium striatum has emerged as an important opportunistic nosocomial infection; however, epidemiological and antimicrobial resistance data from China remain limited. This study explored the epidemiological distribution, antimicrobial susceptibility pr…", "score": 7.659, "score_components": { "theme_priority": 1.1, "research_signal": 3.9, "venue": 0.0, "recency": 1.159, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42269619", "title": "The genetic repertoire of deep-sea microbiome: From sequence to structure and function.", "authors": "Yang Guo, Zongan Wang, Denghui Li, Lele Wang, Hongxia Lan, Fei Guo", "journal": "Cell host & microbe", "pubdate": "2026-06-10", "pubdate_utc": "2026-06-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42269619/", "abstract_snippet": "The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated de…", "score": 7.333, "score_components": { "theme_priority": 1.1, "research_signal": 5.2, "venue": 0.0, "recency": 1.033, "cross_domain": 0.0 }, "signal_components": { "viral_evolution": 5.2 }, "signal_classes": [ "Viral evolution" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42554767", "title": "Whole genome sequencing and annotation of a non-pathogenic Fusarium brachygibbosum TZ1MST22 strain isolated from Medicago sativa in Southern Tunisian oases.", "authors": "Amani Ben Alaya, Abdelmalek Lekired, Manel Chaouachi, Bilel Khiari, Imen Ben Slimene, Naceur Djébali", "journal": "Functional & integrative genomics", "pubdate": "2026-08-05", "pubdate_utc": "2026-08-05T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42554767/", "abstract_snippet": "Fusarium sambucinum species complex (FSAMSC) includes not only major mycotoxin-producing pathogens but also non-pathogenic endophytic species that can promote plant growth and stress tolerance. However, the molecular mechanisms underlying these contrasting lif…", "score": 5.927, "score_components": { "theme_priority": 1.1, "research_signal": 3.4, "venue": 0.0, "recency": 1.427, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42557545", "title": "Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.", "authors": "Álvaro Rodríguez Del Río, Yongxing Cui, India Mansour, Matthias C Rillig", "journal": "BMC genomics", "pubdate": "2026-08-04", "pubdate_utc": "2026-08-04T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42557545/", "abstract_snippet": "Most soil prokaryotic species remain uncultivated, limiting our understanding of the terrestrial microbiome. Metagenomic sequencing, and particularly the study of metagenome-assembled genomes (MAGs), represents an unprecedented opportunity to characterize the …", "score": 4.919, "score_components": { "theme_priority": 1.1, "research_signal": 2.4, "venue": 0.0, "recency": 1.419, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42390091", "title": "Extensive library of Ruminococcus gnavus phages revealing genomic and phenotypic diversity with novel clusters.", "authors": "Arata Sakiyama, Ayaka Washizaki, Keiko Inaba-Hasegawa, Most Hushna Ara Naznin, Keigo Ide, Masayuki Takase", "journal": "Microbiology spectrum", "pubdate": "2026-06-22", "pubdate_utc": "2026-06-22T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42390091/", "abstract_snippet": "Ruminococcus gnavus is a prevalent member of human gut microbiota and is associated with inflammatory bowel disease. Phage-based microbiota engineering represents a promising approach for alleviating dysbiosis; however, knowledge regarding R. gnavus phages rem…", "score": 4.607, "score_components": { "theme_priority": 1.1, "research_signal": 2.4, "venue": 0.0, "recency": 1.107, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42329047", "title": "Application of antibiotics for the selective isolation of previously uncultured species from activated sludge.", "authors": "Stefania Andrea Rosso Villanelo, Sofie Zacho Vestergaard, Lei Liu, Yu Yang, Inge Søkilde Pedersen, Per Halkjær Nielsen", "journal": "Microbiology spectrum", "pubdate": "2026-06-22", "pubdate_utc": "2026-06-22T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42329047/", "abstract_snippet": "The microbial communities in activated sludge (AS) drive pollutant degradation and nutrient transformation into biomass and gaseous products, while also enabling resource recovery processes. In these systems, microorganisms grow as flocs, whose aggregation pro…", "score": 4.607, "score_components": { "theme_priority": 1.1, "research_signal": 2.4, "venue": 0.0, "recency": 1.107, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42573622", "title": "Borborobacter xinjiangensis sp. nov., a moderately halophilic bacterium isolated from grapevine rootstock in Xinjiang, China.", "authors": "Xue Li, Yu Tao, Ming Li, Qingzhuang Zhang, Guohong Wu, Jinge Hu", "journal": "Archives of microbiology", "pubdate": "2026-08-10", "pubdate_utc": "2026-08-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42573622/", "abstract_snippet": "A Gram-negative, facultatively anaerobic, non-motile, and non-spore-forming rod-shaped bacterium, designated strain NGMCC 1.201702T, was isolated from grapevine rootstock in a vineyard in the Xinjiang Uygur Autonomous Region, China. This isolate represents the…", "score": 4.269, "score_components": { "theme_priority": 1.1, "research_signal": 1.7, "venue": 0.0, "recency": 1.469, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42579340", "title": "Allolecanicillium elzae gen. et sp. nov. (Cordycipitaceae): revised taxonomy with new combinations, its entomopathogenicity and mass production.", "authors": "Ana Carla da Silva Santos, Athaline Gonçalves Diniz, Sheila Karine Belo Pedroso, Renan do Nascimento Barbosa, Roger Fagner Ribeiro Melo, Neiva Tinti de Oliveira", "journal": "International journal of systematic and evolutionary microbiology", "pubdate": "2026-08", "pubdate_utc": "2026-08-01T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42579340/", "abstract_snippet": "In a previous study, an isolate identified as Akanthomyces sensu lato, obtained from the citrus blackfly Aleurocanthus woglumi in Brazil, was shown to be pathogenic towards its host. Phylogenetic evidence indicated that this isolate belongs to a new taxon. Thi…", "score": 4.195, "score_components": { "theme_priority": 1.1, "research_signal": 1.7, "venue": 0.0, "recency": 1.395, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42578965", "title": "Taphrina neopruni sp. nov., a novel species associated with plum pockets on Prunus salicina.", "authors": "Kyoung-Mo Koo, Jin-Woo Park, Min-Jun Ko, Gyo-Seon Shin, Ji-Hyun Park, Hyeon-Dong Shin", "journal": "International journal of systematic and evolutionary microbiology", "pubdate": "2026-08", "pubdate_utc": "2026-08-01T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42578965/", "abstract_snippet": "The ascomycete genus Taphrina comprises dimorphic plant-parasitic pathogens, several species of which cause plum pockets. Plum pocket pathogens on Japanese plum (Prunus salicina) were collected from seven localities in Korea, including Gimcheon (KCTC 37381T/KA…", "score": 4.195, "score_components": { "theme_priority": 1.1, "research_signal": 1.7, "venue": 0.0, "recency": 1.395, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42554727", "title": "The genome, transcriptome and metabolome of Aspergillus welwitschiae Ocstreb1 from wild halophytic rice, Oryza coarctata, indicates its distinctiveness.", "authors": "Nishat Tamanna, Md Nafis Ul Alam, Arifa Akhter Airin, Habibul Bari Shozib, Md Rakibul Islam, Zeba I Seraj", "journal": "Microbial genomics", "pubdate": "2026-08", "pubdate_utc": "2026-08-01T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42554727/", "abstract_snippet": "Aspergillus welwitschiae is a widespread fungus with diverse roles as a plant mutualist, opportunistic human pathogen and industrial enzyme producer. The endophytic strain AwOcstreb1, isolated from halophytic rice (Oryza coarctata), promotes growth in commerci…", "score": 4.195, "score_components": { "theme_priority": 1.1, "research_signal": 1.7, "venue": 0.0, "recency": 1.395, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42549087", "title": "Data of annotated draft genome assemblies of three bacterial isolates from the 'Panchabrihi' rice, soybean, and bean-associated niches in Bangladesh.", "authors": "Nusrat Sultana, Abed Chaudhury, Saria Farheen", "journal": "Data in brief", "pubdate": "2026-07-16", "pubdate_utc": "2026-07-16T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42549087/", "abstract_snippet": "We have collected the bacterial communities inhabiting the rhizosphere and seed-surface of selected crop plants ('Panchabrihi' rice, soybean, and bean) in Bangladesh and created a draft genome assembly database of the isolated bacterial strains. Three bacteria…", "score": 4.072, "score_components": { "theme_priority": 1.1, "research_signal": 1.7, "venue": 0.0, "recency": 1.272, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42462719", "title": "Evolutionary radiation of Polaromonas from mountain glaciers downstream.", "authors": "Grégoire Michoud, Aileen Geers, Hannes Peter, Amy C Thorpe, Zhi-Ping Zhong, Virginia Rich", "journal": "Current biology : CB", "pubdate": "2026-07-16", "pubdate_utc": "2026-07-16T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42462719/", "abstract_snippet": "Habitat transitions are central to microbial ecology and evolution and have been extensively studied across vastly different environments, such as between saline and non-saline environments. However, microbial habitat transitions along other large-scale enviro…", "score": 4.072, "score_components": { "theme_priority": 1.1, "research_signal": 1.7, "venue": 0.0, "recency": 1.272, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42439565", "title": "Non-destructive label-free automated identification of bacterial colonies at the species level directly on agar media using digital holography and convolutional neural network algorithms.", "authors": "Prisca Perlemoine, Jordan Belissard, Bruno Burtschell, Nassim Halli, Luc Martin, Camille Brunet", "journal": "Microbiology spectrum", "pubdate": "2026-07-13", "pubdate_utc": "2026-07-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42439565/", "abstract_snippet": "This study aimed to establish a thorough proof of concept for an innovative, fully automated, non-destructive, and label-free approach for the identification of bacterial colonies directly on agar plates, integrating digital holography with artificial intellig…", "score": 4.05, "score_components": { "theme_priority": 1.1, "research_signal": 1.7, "venue": 0.0, "recency": 1.25, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42379812", "title": "The Deep Darkness microbiome: functional and taxonomic diversity in an oligotrophic temperate cave.", "authors": "Philips O Akinwole, Nina G Shaffer, Emma E C Jacobs, Zoe Green, Thi Doan, Crimson Hickman", "journal": "Microbiology spectrum", "pubdate": "2026-06-30", "pubdate_utc": "2026-06-30T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42379812/", "abstract_snippet": "Many subterranean ecosystems are chronically energy limited, yet the mechanisms governing microbial community assembly and metabolic function under extreme carbon scarcity remain poorly resolved. We combined 16S rRNA gene sequencing with community-level physio…", "score": 3.959, "score_components": { "theme_priority": 1.1, "research_signal": 1.7, "venue": 0.0, "recency": 1.159, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42584709", "title": "Complete Genome Sequence of Atractylodes virus A, a Novel Carlavirus Infecting Atractylodes lancea.", "authors": "Tingting Li, Hailing Zuo, Yuyu Liu, Yuezhen Liu, Lei Chen, Meng Wang", "journal": "Archives of virology", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42584709/", "abstract_snippet": "Atractylodes lancea is an important medicinal crop, but viral diseases have become increasingly severe in recent years. Viruses in the genus Carlavirus are common plant pathogens that are primarily transmitted by aphids and can cause stunted growth and reduced…", "score": 2.586, "score_components": { "theme_priority": 1.1, "research_signal": 0.0, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42579675", "title": "Rapid and consistent genetic clustering of environmental Legionella pneumophila isolates using accessible single-step WGS analysis tools.", "authors": "Hanno Schmidt, Sven-Ernö Bikár, Bettina Lieb, Daniela Lotz, Tobias Brand, Moritz Brandstetter", "journal": "PloS one", "pubdate": "2026-08-11", "pubdate_utc": "2026-08-11T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42579675/", "abstract_snippet": "Genetic characterization of pathogen isolates is increasingly important in healthcare settings, yet the bioinformatic workflows required can be complex and resource-intensive. Here we analyzed 19 environmental Legionella pneumophila isolates using whole genome…", "score": 2.578, "score_components": { "theme_priority": 1.1, "research_signal": 0.0, "venue": 0.0, "recency": 1.478, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42574651", "title": "A chromosome-level genome assembly of Thecaphora frezzii, cause of peanut smut, reveals the largest genome of the true smut fungi.", "authors": "Nicholas Greatens, M Brian Couger, Mariano Maestro, Guillermo Cabrera Walsh, Sergio Morichetti, Luke J Tallon", "journal": "G3 (Bethesda, Md.)", "pubdate": "2026-08-10", "pubdate_utc": "2026-08-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42574651/", "abstract_snippet": "Peanut smut, caused by the fungus Thecaphora frezzii, is a significant disease of peanuts in Argentina. Infected plants have seeds replaced by a mass of dark teliospores, reducing yield and seed quality. Following successful in vitro culture of the fungus in i…", "score": 2.569, "score_components": { "theme_priority": 1.1, "research_signal": 0.0, "venue": 0.0, "recency": 1.469, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Atlases, compendia, reference resources" }, { "pmid": "42405784", "title": "Bacterial diversity and community assembly mechanisms in alpine wetland soils under the influence of grazing.", "authors": "Xu Ai, Cao Yu, Ji Yangyue, Zou Shuzhen, Kang Di", "journal": "Microbiology spectrum", "pubdate": "2026-07-06", "pubdate_utc": "2026-07-06T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42405784/", "abstract_snippet": "Wetlands are among the world's most significant ecosystems. Studying how different grazing intensities affect soil bacterial diversity and community assembly in alpine wetlands is crucial for their sustainable management. Based on 16S sequencing technology, th…", "score": 2.3, "score_components": { "theme_priority": 1.1, "research_signal": 0.0, "venue": 0.0, "recency": 1.2, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Atlases, compendia, reference resources" } ] }, { "label": "Metagenomics benchmarking & pipelines", "query": "((metagenomics AND (benchmark* OR pipeline OR \"best practices\" OR reproducible OR workflow)) OR ((Kraken2 OR MetaPhlAn OR Bracken OR Centrifuge OR Kaiju) AND (benchmark* OR evaluation))) AND (benchmark* OR workflow OR pipeline OR Snakemake OR Nextflow OR WDL) NOT (case report OR randomized OR psychology)", "count": 25, "items": [ { "pmid": "42460892", "title": "Freeze-Drying as a Novel Concentrating Method for Wastewater Detection of SARS-CoV-2.", "authors": "Rui Dong, Elizabeth Noriega Landa, Hugues Ouellet, Wen-Yee Lee, Chuan Xiao", "journal": "Environmental science & technology", "pubdate": "2026-08-04", "pubdate_utc": "2026-08-04T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42460892/", "abstract_snippet": "Detecting viral RNA from wastewater has emerged as a cost-effective approach for community-level surveillance during the recent SARS-CoV-2 pandemic. Although various concentrating methods have been developed, none are optimal across all key requirements for wa…", "score": 10.269, "score_components": { "theme_priority": 1.05, "research_signal": 6.3, "venue": 0.0, "recency": 1.419, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 2.4, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Metagenomics / surveillance", "Methods", "Emerging threat" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42379825", "title": "ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.", "authors": "Saidi Wang, Mintong Chen, Di Jiao", "journal": "Microbiology spectrum", "pubdate": "2026-06-30", "pubdate_utc": "2026-06-30T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42379825/", "abstract_snippet": "Resolving bacterial strain diversity from shotgun metagenomic data is fundamental to understanding intra-host evolution, transmission dynamics, and phenotypic heterogeneity. However, current probabilistic approaches face a severe \"identifiability limit\" when d…", "score": 10.209, "score_components": { "theme_priority": 1.05, "research_signal": 6.5, "venue": 0.0, "recency": 1.159, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Viral evolution", "Methods", "Emerging threat" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42289215", "title": "Artificial intelligence in clinical metagenomic pathogen detection: A critical review of pipeline integrations, challenges, and future directions.", "authors": "Jiayue Dai, Xinru Tan, Jun Ma", "journal": "Journal of microbiological methods", "pubdate": "2026-06-14", "pubdate_utc": "2026-06-14T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42289215/", "abstract_snippet": "Metagenomic next-generation sequencing (mNGS) has expanded the scope of clinical diagnostics by enabling culture-independent detection of microorganisms in patient samples. However, mNGS clinical utility remains constrained by substantial computational demands…", "score": 9.407, "score_components": { "theme_priority": 1.05, "research_signal": 5.8, "venue": 0.0, "recency": 1.057, "cross_domain": 1.5 }, "signal_components": { "metagenomics_surveillance": 2.4, "methods": 3.4 }, "signal_classes": [ "Metagenomics / surveillance", "Methods" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42568342", "title": "Benchmarking Full-Length ITS Metabarcoding Across Illumina 2 × 500, PacBio, and Oxford Nanopore Sequencing Using Mock and Soil Communities.", "authors": "Leho Tedersoo, Marko Prous, Meirong Chen, Sten Anslan, Irja Saar, Benjamin Dubois", "journal": "Molecular ecology resources", "pubdate": "2026-08", "pubdate_utc": "2026-08-01T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42568342/", "abstract_snippet": "Metabarcoding is a powerful tool for biodiversity comparisons, where standard-size DNA barcodes (> 500 bases) offer better taxonomic resolution than shorter ones. Still, the choice of sequencing platforms and bioinformatics pipelines may strongly affect inferr…", "score": 8.245, "score_components": { "theme_priority": 1.05, "research_signal": 4.3, "venue": 0.0, "recency": 1.395, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Methods" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42454932", "title": "Construction and validation of a phenotypic prediction model for bacterial gentamicin resistance using deep learning with gene sequences.", "authors": "Jun Li, Siyan Xue, Lingxuan Hou, Zhixuan Zhang, Kaixuan Yuan, Xiaozhong Chen", "journal": "Microbiology spectrum", "pubdate": "2026-07-15", "pubdate_utc": "2026-07-15T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42454932/", "abstract_snippet": "The emergence of bacterial resistance to antibiotics poses a significant threat to human health; thus, there is an urgent need for new strategies in understanding the mechanisms of resistance and further fast prediction of it. Deep learning models offer promis…", "score": 7.714, "score_components": { "theme_priority": 1.05, "research_signal": 3.9, "venue": 0.0, "recency": 1.264, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42585229", "title": "De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.", "authors": "James A Fellows Yates, Alexander Hübner, Maxime Borry, Christina Warinner", "journal": "PLoS computational biology", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42585229/", "abstract_snippet": "Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both sequencing methods and de novo assembly techniques have not only resulted in a flood …", "score": 4.936, "score_components": { "theme_priority": 1.05, "research_signal": 2.4, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42545024", "title": "DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.", "authors": "Jessica A P Carlson-Jones, Thomas R Goddard, Bhavya Papudeshi, Vijini Mallawaarachchi, Katrine L Whiteson, Morgyn S Warner", "journal": "Clinical microbiology reviews", "pubdate": "2026-08-03", "pubdate_utc": "2026-08-03T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42545024/", "abstract_snippet": "SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using molecular-based approaches. Techniques such as 16S rRNA gene …", "score": 4.861, "score_components": { "theme_priority": 1.05, "research_signal": 2.4, "venue": 0.0, "recency": 1.411, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42454926", "title": "Exploratory analysis of livestock waste treatment impacts on microbial diversity and antimicrobial resistance gene abundance.", "authors": "Jade Davies, Jessica Ireland-Hughes, Silvia Stronati, Richard P Smith, Claire Oastler, Javier Nunez-Garcia", "journal": "Microbiology spectrum", "pubdate": "2026-07-15", "pubdate_utc": "2026-07-15T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42454926/", "abstract_snippet": "The potential spread of antimicrobial resistance (AMR) through agricultural waste is underexplored and may contribute to the dissemination of AMR genes into the environment. This pilot study used metagenomic sequencing to investigate how anaerobic digestion (A…", "score": 4.714, "score_components": { "theme_priority": 1.05, "research_signal": 2.4, "venue": 0.0, "recency": 1.264, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42541893", "title": "Portable metagenomics for preventive surveillance and outbreak control in livestock and poultry: Pathogen detection, resistome profiling, and antimicrobial stewardship.", "authors": "Muhammad Saeed Akhtar, Wajid Zaman", "journal": "Research in veterinary science", "pubdate": "2026-07-31", "pubdate_utc": "2026-07-31T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42541893/", "abstract_snippet": "Conventional diagnostics for livestock and poultry outbreaks commonly rely on culture or targeted PCR panels, which may be too slow or too narrow to guide early control decisions. Portable metagenomics, particularly real-time nanopore sequencing, offers a rout…", "score": 4.637, "score_components": { "theme_priority": 1.05, "research_signal": 2.2, "venue": 0.0, "recency": 1.387, "cross_domain": 0.0 }, "signal_components": { "emerging_threat": 2.2 }, "signal_classes": [ "Emerging threat" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42389176", "title": "Long-read whole-genome sequencing dataset of microbial communities from industrially and municipally impacted freshwater wetlands in South Africa.", "authors": "Onyedikachi Ubani, Veronica M Ngole-Jeme", "journal": "Data in brief", "pubdate": "2026-06-19", "pubdate_utc": "2026-06-19T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42389176/", "abstract_snippet": "This article describes a long-read whole-genome shotgun sequencing dataset generated from microbial communities inhabiting industrially and municipally impacted freshwater wetlands in South Africa. Surface water samples were collected from five strategically s…", "score": 4.538, "score_components": { "theme_priority": 1.05, "research_signal": 2.4, "venue": 0.0, "recency": 1.088, "cross_domain": 0.0 }, "signal_components": { "metagenomics_surveillance": 2.4 }, "signal_classes": [ "Metagenomics / surveillance" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42570679", "title": "A Multidimensional Optimization Strategy for High-Purity Primary Rat Microglia Isolation with Preserved Functional Responsiveness.", "authors": "Xiaoxian Sun, Danqing Yan, Yuxi Zhang, Dipeng Li, Mengmin Liu, Wenhan Wang", "journal": "Journal of neuroscience methods", "pubdate": "2026-08-08", "pubdate_utc": "2026-08-08T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42570679/", "abstract_snippet": "Primary microglia are essential for studying neuroinflammation and microglia-mediated neuropathology. However, conventional shaking-based isolation methods often yield unstable purity, astrocytic contamination, and heterogeneous activation states. We developed…", "score": 4.202, "score_components": { "theme_priority": 1.05, "research_signal": 1.7, "venue": 0.0, "recency": 1.452, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42587714", "title": "Artificial Intelligence for Integrated Analysis of Non-Blood Biological Fluids: From Biomarker Discovery to Clinical Decision-Support Systems.", "authors": "Valentina Becherucci, Francesca Romano, Edda Russo", "journal": "Diagnostics (Basel, Switzerland)", "pubdate": "2026-08-06", "pubdate_utc": "2026-08-06T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42587714/", "abstract_snippet": "The analysis of non-blood biological fluids, including cerebrospinal fluid (CSF), serous effusions, and synovial fluid, plays a central role in laboratory medicine by providing essential diagnostic and prognostic information for neurological, infectious, infla…", "score": 4.186, "score_components": { "theme_priority": 1.05, "research_signal": 1.7, "venue": 0.0, "recency": 1.436, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42474352", "title": "Masking recurrent contaminants in reference sequences improves specificity of clinical metagenomic sequencing.", "authors": "Judith Bergada-Pijuan, Ian Pichler, Maryam Zaheri, Verena Kufner, Michael Huber", "journal": "Journal of clinical microbiology", "pubdate": "2026-07-20", "pubdate_utc": "2026-07-20T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42474352/", "abstract_snippet": "Viral metagenomic next-generation sequencing (mNGS) is a powerful approach for pathogen detection in clinical diagnostics; however, accurate virus identification depends critically on the quality of reference databases. Diagnostic specificity is frequently com…", "score": 4.051, "score_components": { "theme_priority": 1.05, "research_signal": 1.7, "venue": 0.0, "recency": 1.301, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42502630", "title": "Whole genome dataset of bacterial strains isolated from urine analysed by Oxford Nanopore sequencing technologies in Ouagadougou, Burkina Faso.", "authors": "Pamane Djagbaré, Ezechiel Bionimian Tibiri, Wendyam Marie Christelle Nadembèga, Pakyendou Estel Name, Lassina Traoré, Emmanuel Sampo", "journal": "Data in brief", "pubdate": "2026-07-04", "pubdate_utc": "2026-07-04T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42502630/", "abstract_snippet": "A collection of 21 bacterial isolates recovered from urine specimens collected between September 2018 and February 2019 at Saint-Camille and SCHIPHRA hospitals in Ouagadougou, Burkina Faso, is presented. Isolates were identified using the API 20E system and te…", "score": 3.936, "score_components": { "theme_priority": 1.05, "research_signal": 1.7, "venue": 0.0, "recency": 1.186, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42390758", "title": "A two-step centrifugal microfluidic platform for semi-automated IGRA detection of tuberculosis based on chemiluminescence.", "authors": "Tianwei Li, Lei Wang, Shenghua Dong, Zhen Tan, Lingxuan Liu, Xiaolei Zhang", "journal": "The Analyst", "pubdate": "2026-08-10", "pubdate_utc": "2026-08-10T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42390758/", "abstract_snippet": "Tuberculosis (TB) is one of the leading fatal infectious diseases globally. As recommended by the WHO, interferon-γ release assay (IGRA) is an important method for accurate and efficient TB diagnosis; however, it is limited to the central labs due to multiple …", "score": 2.519, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.469, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42476558", "title": "Comparative Metabolomics Reveals the Production of Sulfated Metabolites by Human Gut Bacteria.", "authors": "Gabriel D D'Agostino, Cecilia H Kim, Jinseok Park, Yancong Zhang, Bashar Amer, Eric A Franzosa", "journal": "Journal of the American Chemical Society", "pubdate": "2026-08-05", "pubdate_utc": "2026-08-05T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42476558/", "abstract_snippet": "The sulfated metabolome─the collection of sulfate-containing metabolites─is an emerging source of structurally unique bioactive compounds that influence metabolism, immune responses, and neurological function. Recent studies have shown that, in addition to hos…", "score": 2.477, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.427, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42535896", "title": "Intra-amniotic infection: diagnosis, nomenclature, clinical significance, management, and microbiologic tools used for the diagnosis.", "authors": "Pisut Pongchaikul, Puntabut Warintaksa, Piroon Jenjaroenpun, Anunya Opasawatchai, Rapeewan Settacomkul, Pornpun Vivithanaporn", "journal": "Clinical microbiology reviews", "pubdate": "2026-07-31", "pubdate_utc": "2026-07-31T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42535896/", "abstract_snippet": "SUMMARYIntra-amniotic infection is the main cause of spontaneous preterm birth and adverse maternal-fetal outcomes; therefore, rapid, robust, and accurate diagnosis remains a clinical priority. Conventional microbiological techniques, especially culture-based …", "score": 2.437, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.387, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42439573", "title": "Clinical impact of 16S rRNA RC-PCR NGS on infectious disease management.", "authors": "Merlijn H I van Haren, Lieke Ten Have, Pieter D Koopman, Jochem B Buil, Ianthe Maat, Janette C Rahamat-Langendoen", "journal": "Microbiology spectrum", "pubdate": "2026-07-13", "pubdate_utc": "2026-07-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42439573/", "abstract_snippet": "16S rRNA metagenomics provides a culture-independent method for diagnosing infections with fastidious or uncultivable organisms, guiding targeted therapy, and detecting polymicrobial communities. This study utilizes reverse complement (RC)-PCR next-generation …", "score": 2.3, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.25, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42439510", "title": "Effects of elexacaftor/tezacaftor/ivacaftor on the nasal microbial metagenome in cystic fibrosis.", "authors": "Tom L Hertramph, Marie Dorda, Sophia T Pallenberg, Annette Sauer-Heilborn, Felix C Ringshausen, Matthias Steglich", "journal": "Microbiology spectrum", "pubdate": "2026-07-13", "pubdate_utc": "2026-07-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42439510/", "abstract_snippet": "Mutation-specific cystic fibrosis (CF) transmembrane conductance regulator (CFTR) modulator therapy with elexacaftor/tezacaftor/ivacaftor (ETI) has dramatically improved clinical outcomes for people with CF (pwCF), yet its impact on the nasal microbial metagen…", "score": 2.3, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.25, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42370707", "title": "Validation of an integrated metagenomic pipeline combining optimized wet-lab processing and tiered reporting for CSF pathogen detection.", "authors": "Alec Victorsen, Todd P Knutson, Lucas Bolender, Sabrina Jung, Patricia Ferrieri, Bharat Thyagarajan", "journal": "Microbiology spectrum", "pubdate": "2026-06-29", "pubdate_utc": "2026-06-29T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42370707/", "abstract_snippet": "Metagenomic next-generation sequencing (mNGS) in the infectious disease diagnostic space has been gaining traction and is popular for aiding in the diagnosis of central nervous system infections. However, many challenges and obstacles remain in making this tec…", "score": 2.203, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.153, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42315032", "title": "Comparative methodological study of ultracentrifugation and a commercial kit for the isolation and characterization of outer membrane vesicles from Burkholderia thailandensis.", "authors": "Maria Luiza Francisconi Lubanco Thomé, Natália Yukari Kashiwaqui, Mariane Ansoni Ferreira, Angelica Maria Mazuera Zapata, Camila Fernanda Rodero, Valtencir Zucolotto", "journal": "Journal of microbiological methods", "pubdate": "2026-06-18", "pubdate_utc": "2026-06-18T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42315032/", "abstract_snippet": "Outer Membrane Vesicles (OMVs) are nanostructures naturally produced by Gram-negative bacteria, playing a relevant role in processes such as horizontal gene transfer, quorum sensing modulation, antibacterial and antibiofilm activity, and presenting potential a…", "score": 2.132, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.082, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42306954", "title": "Harnessing next-generation microbial diagnostics to optimize infection management in immunocompromised hosts.", "authors": "Danielle Lee, Nicholas J Norton, Adam P Dale", "journal": "Current opinion in infectious diseases", "pubdate": "2026-06-17", "pubdate_utc": "2026-06-17T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42306954/", "abstract_snippet": "Conventional microbiological tests have limitations in the microbial diagnosis of immunocompromised patients. Next-generation sequencing (NGS) technologies have the potential to overcome some of these challenges by enabling rapid, comprehensive, and hypothesis…", "score": 2.126, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.076, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42376246", "title": "Magnetic nanoparticles enable clinically relevant in vitro diagnosis of β-lactam allergy.", "authors": "Jose A Céspedes, Maria I Montañez, Isabel M Jiménez, Violeta Gil-Ocaña, Esther Matamoros, María Salas", "journal": "Materials today. Bio", "pubdate": "2026-06-15", "pubdate_utc": "2026-06-15T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42376246/", "abstract_snippet": "β-lactam antibiotics are the leading cause of drug-induced hypersensitivity reactions. Yet available in vitro diagnostics still show limited sensitivity, specificity and reproducibility. In this work, we report the use of magnetic silica-coated nanoparticles f…", "score": 2.113, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.063, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42376290", "title": "PacBio HiFi sequencing datasets of culture-enriched airborne microbial cave communities from dolomitic Sudwala Caves, South Africa.", "authors": "Victoria Onumanyi, Henry Joseph Oduor Ogola, Grace Nkechinyere Ijoma, Khomotso Semenya", "journal": "Data in brief", "pubdate": "2026-06-13", "pubdate_utc": "2026-06-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42376290/", "abstract_snippet": "We present a dataset integrating physico-chemical air quality measurements with long-read PacBio HiFi shotgun metagenomic sequences from culture-enriched airborne samples collected in Sudwala Caves, one of the oldest known cave systems in South Africa. This re…", "score": 2.101, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.051, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" }, { "pmid": "42286360", "title": "A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA.", "authors": "Stefania Morelli, Sara Romano, Giulia Cosenza, Sergio Abate, Livia Lombardi, Elena Pilli", "journal": "Analytical and bioanalytical chemistry", "pubdate": "2026-06-13", "pubdate_utc": "2026-06-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42286360/", "abstract_snippet": "Species identification from highly degraded DNA remains a major challenge across ecology, conservation genetics, wildlife forensics, and museum science, where samples are often scarce, contaminated, and embedded in complex matrices. Under these conditions, sta…", "score": 2.101, "score_components": { "theme_priority": 1.05, "research_signal": 0.0, "venue": 0.0, "recency": 1.051, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "Metagenomics benchmarking & pipelines" } ] }, { "label": "ML for evolution & pathogens", "query": "(((\"machine learning\" OR \"deep learning\" OR transformer) AND (virus OR pathogen OR evolution OR phylogeny)) OR ((\"protein language model\" OR ESM) AND (mutation OR evolution OR fitness))) AND (\"machine learning\" OR \"deep learning\" OR transformer OR \"foundation model\" OR \"protein language model\" OR ESM) NOT (case report OR randomized OR psychology)", "count": 25, "items": [ { "pmid": "42581815", "title": "Additional sectioning and AI-assisted diagnosis reveal underdiagnosis of serous (pre)malignancies in fallopian tube specimen from BRCA1/2 carriers.", "authors": "Anouk B Bouwmeester, Tamar A Gootzen, Marielle Nobbenhuis, Vilius Rudaitis, Caroline B van den Berg, Heleen J van Beekhuizen", "journal": "Histopathology", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42581815/", "abstract_snippet": "Germline BRCA1/2 pathogenic variant carriers are at increased risk for high-grade serous carcinoma (HGSC) and are therefore advised to have a risk-reducing salpingo-oophorectomy (RRSO) around the age of 40. A risk of 0.9% to develop peritoneal HGSC (pHGSC) rem…", "score": 8.286, "score_components": { "theme_priority": 1.0, "research_signal": 4.3, "venue": 0.0, "recency": 1.486, "cross_domain": 1.5 }, "signal_components": { "viral_evolution": 2.6, "methods": 1.7 }, "signal_classes": [ "Viral evolution", "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42584105", "title": "AI for Accelerated Materials Discovery: From Generative Design to Autonomous Realization.", "authors": "Jaehwan Choi, Seongmin Kim, Junkil Park, Junyoung Choi, Sunggi An, Yousung Jung", "journal": "Chemical reviews", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42584105/", "abstract_snippet": "Artificial intelligence (AI) is fundamentally transforming materials discovery, shifting the paradigm from labor-intensive trial-and-error approaches to data-driven, automated workflows. This review examines emerging AI methodologies for accelerated materials …", "score": 7.886, "score_components": { "theme_priority": 1.0, "research_signal": 3.9, "venue": 0.0, "recency": 1.486, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42584103", "title": "Surface-Enhanced Raman Spectroscopy for Viral Diagnostics: Principles, Strategies, Clinical Challenges, and Future Directions.", "authors": "Yanjun Yang, Yiping Zhao", "journal": "Chemical reviews", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42584103/", "abstract_snippet": "Viral outbreaks such as SARS-CoV, MERS-CoV, and COVID-19 underscore the urgent need for rapid, sensitive, and scalable diagnostic technologies. Current standard methods, including nucleic acid amplification tests and immunoassays, offer complementary strengths…", "score": 7.886, "score_components": { "theme_priority": 1.0, "research_signal": 3.9, "venue": 0.0, "recency": 1.486, "cross_domain": 1.5 }, "signal_components": { "methods": 1.7, "emerging_threat": 2.2 }, "signal_classes": [ "Methods", "Emerging threat" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42586769", "title": "The Physicochemical Basis of Protein Evolution: Property-Informed Evolutionary Models (PRIME).", "authors": "Hannah Kim, Konrad Scheffler, Anton Nekrutenko, Darren P Martin, Steven Weaver, Ben Murrell", "journal": "Molecular biology and evolution", "pubdate": "2026-08-13", "pubdate_utc": "2026-08-13T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42586769/", "abstract_snippet": "Standard probabilistic models of coding sequence evolution effectively identify where and when selection acts but remain agnostic to the mechanistic realization of these forces. We introduce PRIME (PRoperty Informed Models of Evolution), a framework of codon-l…", "score": 7.695, "score_components": { "theme_priority": 1.0, "research_signal": 3.4, "venue": 1.8, "recency": 1.495, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42585243", "title": "Twelve quick tips for applying deep learning to animal sounds.", "authors": "Burooj Ghani, Anne Leonie Baier, Vincent J Kalkman, Dan Stowell", "journal": "PLoS computational biology", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42585243/", "abstract_snippet": "Deep learning is transforming the study of animal sound, enabling the automated identification of species, individuals, behaviors, and ecological patterns from large collections of recordings. While bioacoustic machine-learning models are growing more powerful…", "score": 6.881, "score_components": { "theme_priority": 1.0, "research_signal": 4.394, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 4.394 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42585906", "title": "Machine-learning-assisted process interpretation of composting time across composting systems involving multiple organic wastes: Key explanatory contributions of temperature evolution during the cooling-maturation phase.", "authors": "Xia Yao, Weilin Fu, Chun Song, Xueyan Zhang, Shiyu Lv, Yongzhen Ding", "journal": "Journal of environmental management", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42585906/", "abstract_snippet": "Composting time across organic waste systems is associated with feedstock composition, operating conditions, and stage-specific temperature evolution. Conventional approaches have difficulty characterizing nonlinear variation among multiple process variables. …", "score": 5.886, "score_components": { "theme_priority": 1.0, "research_signal": 3.4, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42580645", "title": "From Andes to the dry diagonal: phylogenomics and trait evolution elucidate the radiation of cacti in South American drylands.", "authors": "Monique Romeiro-Brito, Flávia M Lanna, Milena C Telhe, Bryan C Carstens, Luciano A Digiampietri, Daniela C Zappi", "journal": "Molecular phylogenetics and evolution", "pubdate": "2026-08-11", "pubdate_utc": "2026-08-11T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42580645/", "abstract_snippet": "The expansion of arid and dry ecosystems during the Miocene played a key role in the diversification of succulent plants; however, the relative contributions of biotic traits and environmental factors linked to aridity remain unclear. We investigate diversific…", "score": 5.878, "score_components": { "theme_priority": 1.0, "research_signal": 3.4, "venue": 0.0, "recency": 1.478, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42580373", "title": "Artificial Intelligence in Cardiovascular Imaging and Risk Stratification: From Algorithmic Discovery to Meaningful Clinical Implication.", "authors": "Xu Xia, Wasim Ullah Khan, Qaisar Khan, Chen Zhong, Muhammad Shehzad Khan", "journal": "Trends in cardiovascular medicine", "pubdate": "2026-08-11", "pubdate_utc": "2026-08-11T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42580373/", "abstract_snippet": "Cardiovascular disease (CVD) remains the leading global cause of mortality, with timely diagnosis and precise risk stratification serving as cornerstones of effective management. Traditional cardiovascular imaging and risk assessment have long been constrained…", "score": 5.878, "score_components": { "theme_priority": 1.0, "research_signal": 3.4, "venue": 0.0, "recency": 1.478, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42590339", "title": "Multiscale Numerical Modelling and Structural Design of Bulk Heterojunction Nanocomposites for Organic Photovoltaics: From Molecular Interfaces to Device Optimization.", "authors": "Jie Dong, Ziyan Guo, Wei Hao, Hanying Li", "journal": "Materials (Basel, Switzerland)", "pubdate": "2026-08-01", "pubdate_utc": "2026-08-01T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42590339/", "abstract_snippet": "Bulk heterojunction (BHJ) active layers in organic photovoltaics (OPVs) are nanostructured composites in which electron-donating and electron-accepting semiconductors form interpenetrating phases for exciton dissociation and charge transport. The power convers…", "score": 5.795, "score_components": { "theme_priority": 1.0, "research_signal": 3.4, "venue": 0.0, "recency": 1.395, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42587642", "title": "Autopsy Pathology's Paradigm Shift: Artificial Intelligence and Emerging Technologies in the Era of Digitally Integrated Death Investigation.", "authors": "Ivan Dieb Miziara, Carmen Silvia Molleis Galego Miziara", "journal": "Diagnostics (Basel, Switzerland)", "pubdate": "2026-07-30", "pubdate_utc": "2026-07-30T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42587642/", "abstract_snippet": "Background: Autopsy pathology remains the reference standard for determining the cause of death, reconstructing disease and injury mechanisms, ensuring diagnostic quality, and supporting medical education and forensic investigations. However, declining autopsy…", "score": 5.779, "score_components": { "theme_priority": 1.0, "research_signal": 3.4, "venue": 0.0, "recency": 1.379, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42583406", "title": "Quantitative CT analysis in lung cancer research: a bibliometric analysis based on Web of Science [2005-2025].", "authors": "Jinde Wang, Jinhu Miao, Han Yang, Chulin Wang, Shijia Cao, Weishan Shi", "journal": "Journal of thoracic disease", "pubdate": "2026-06-23", "pubdate_utc": "2026-06-23T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42583406/", "abstract_snippet": "Quantitative computed tomography (CT) analysis plays an increasingly critical role in the diagnosis, treatment response assessment, and prognostic stratification of lung cancer. However, existing narrative and systematic reviews have not systematically delinea…", "score": 5.513, "score_components": { "theme_priority": 1.0, "research_signal": 3.4, "venue": 0.0, "recency": 1.113, "cross_domain": 0.0 }, "signal_components": { "methods": 3.4 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42590647", "title": "MEMS Data-Driven Intelligent Identification of Rotation-Angle Response and Shear Band Position in Gravelly Soil Slopes.", "authors": "Di Wu, Yongzhe Feng, Gurong Yao, Hualin Song, Zhiwen Lu, Ming Wu", "journal": "Sensors (Basel, Switzerland)", "pubdate": "2026-08-02", "pubdate_utc": "2026-08-02T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42590647/", "abstract_snippet": "Identifying shear band locations is essential for precursor recognition and early warning of progressive failure in gravelly soil slopes. However, conventional displacement monitoring methods mainly capture macroscopic slope deformation and remain limited in d…", "score": 4.603, "score_components": { "theme_priority": 1.0, "research_signal": 2.2, "venue": 0.0, "recency": 1.403, "cross_domain": 0.0 }, "signal_components": { "emerging_threat": 2.2 }, "signal_classes": [ "Emerging threat" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42587136", "title": "Mechanistic machine learning for prediction of prime editing outcomes.", "authors": "Alvin Hsu, Peter J Chen, Angus H Li, Colin F Hemez, Xin D Gao, Markus Terrey", "journal": "Nature biotechnology", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42587136/", "abstract_snippet": "Prime editing (PE) can make specific local changes to genomic DNA in living systems but its efficient application currently requires extensive optimization of PE guide RNA (pegRNA) sequences. Here we present OptiPrime, a machine learning model of PE efficiency…", "score": 4.186, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42584630", "title": "Stabilizing Anion-Derived Interphase by Machine-Learning-Accelerated Screening of Out-of-Shell Co-Solvents for Aqueous Zinc Batteries.", "authors": "Yaxin Ru, Feng Wang, Xiaoyu Yu, Yiming Chen, Zeheng Lv, Yuan Tian", "journal": "Journal of the American Chemical Society", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42584630/", "abstract_snippet": "Aqueous zinc batteries (AZBs) lack a stable anion-derived solid electrolyte interphase (SEI) on the Zn anode, resulting in severe competition between Zn deposition and the hydrogen evolution reaction (HER). A conventional in-shell co-solvent coordinates strong…", "score": 4.186, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42584531", "title": "Erjingwan Alleviates Parkinson's Disease via Activation of PPARA-Mediated Autophagy.", "authors": "Shaopeng Cao, Yongmei Wu, Han Yang, Xiaotian Qi, Zhaoyang Qiu", "journal": "Applied biochemistry and biotechnology", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42584531/", "abstract_snippet": "Parkinson's disease (PD) is characterized by progressive dopaminergic neuronal degeneration and neuroinflammation. Traditional Chinese medicine (TCM) formulas exhibit potential neuroprotective effects, yet the active components and underlying mechanisms of Erj…", "score": 4.186, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42583916", "title": "Global research trends in perioperative pressure injury prevention: A bibliometric analysis from repositioning to technology-assisted strategies.", "authors": "Nova Maryani, Cahyo Budiyantoro, Bowo Adiyanto, Ardi Pramono", "journal": "Journal of perioperative practice", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42583916/", "abstract_snippet": "Perioperative pressure injuries remain a major patient safety challenge, particularly among critically ill and immobilised patients. Although repositioning remains a cornerstone of prevention, recent advances indicate a transition towards interdisciplinary and…", "score": 4.186, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42583692", "title": "Trainable Hydrogels: Mechanistic Principles, Training Strategies, and Frontier Applications.", "authors": "Shiyue Liu, Fengli Zhang, Mingqiong Tong, Lili Wu, Yanyan Zhao, Hongyan Cao", "journal": "Small (Weinheim an der Bergstrasse, Germany)", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42583692/", "abstract_snippet": "Hydrogels represent a versatile family of soft materials, yet their adaptive behavior and programmable functionality face substantial limitations under complex operational environments. Drawing upon the biological principle whereby skeletal muscles undergo str…", "score": 4.186, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42581812", "title": "Machine learning force field development and basic physical property studies for molten salt reactor fuel salt LiF-BeF2-UF4.", "authors": "Xinyu Li, Yu-Han Lv, Lei Zhang, Tao Bo", "journal": "Physical chemistry chemical physics : PCCP", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42581812/", "abstract_snippet": "As one of the most promising technological pathways for Generation IV advanced reactors, molten salt reactors (MSRs) rely on the fuel salt LiF-BeF2-UF4 (FLiBeU), whose microstructural characteristics and fundamental physical properties determine the reactor's …", "score": 4.186, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42581251", "title": "Research hotspots, knowledge structure, and emerging trends in healthcare robotics for older adults: a bibliometric analysis (2015-2026).", "authors": "Xi Ling, Ruiqin Yan", "journal": "Journal of robotic surgery", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42581251/", "abstract_snippet": "Although applications in the field of Robotic Technologies for Older Adults' Healthcare are becoming increasingly widespread, existing research has largely focused on specific application scenarios, and a comprehensive understanding of the global research land…", "score": 4.186, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42580128", "title": "Toxicity-guided assessment of disinfection by-products via machine learning and network toxicology.", "authors": "Jie Wang, Zhujun Liu, Ruipeng Lai, Xianyu Song, Yukun Zhang, Shuangliang Zhao", "journal": "Water research", "pubdate": "2026-08-08", "pubdate_utc": "2026-08-08T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42580128/", "abstract_snippet": "Disinfection by-products (DBPs) in drinking water pose significant health risks due to their cytotoxicity, bioaccumulation potential, and interactions with biological targets. Here, we develop a toxicity-guided and interpretable framework integrating molecular…", "score": 4.152, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.452, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42590676", "title": "Asynchronous Cross-Modal Dynamic Graph Learning for Intelligent Sensing of AI Computing Infrastructure Expansion.", "authors": "Zhe Xiang, Shangshan Chen, Xinrui Hu, Xu Xu, Yang Yang, Jingyi Yang", "journal": "Sensors (Basel, Switzerland)", "pubdate": "2026-08-03", "pubdate_utc": "2026-08-03T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42590676/", "abstract_snippet": "The rapid expansion of artificial intelligence computing infrastructure and the semiconductor industry has made the dynamic sensing of policy planning, technological innovation, capital investment, and physical construction essential for industrial monitoring …", "score": 4.111, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.411, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42583306", "title": "Research trends in cytokine regulation of immunotherapy in non-small cell lung cancer: a bibliometric and BERTopic analysis from 2015 to 2025.", "authors": "Xiangnv Meng, Yongsheng Li, Fu Mi, Xi Yang, Sha Sha, Xiaoliu Shi", "journal": "Journal of thoracic disease", "pubdate": "2026-06-29", "pubdate_utc": "2026-06-29T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42583306/", "abstract_snippet": "Cytokines are key regulators of antitumor immunity in non-small cell lung cancer (NSCLC), particularly in the context of immunotherapy. However, the global knowledge structure and thematic evolution of cytokine-regulated immunotherapy in NSCLC have not been sy…", "score": 3.853, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.153, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42583211", "title": "Evolution, hotspots, and future directions of artificial intelligence in asthma research: a Web of Science-based bibliometric analysis [2016-2026].", "authors": "Huangjun You, Tian Zhu, Chongchong Liu, Shilin Li, Weiming Sun", "journal": "Journal of thoracic disease", "pubdate": "2026-06-29", "pubdate_utc": "2026-06-29T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42583211/", "abstract_snippet": "While artificial intelligence (AI) offers unprecedented capabilities for predictive modeling and precision asthma management, there is an urgent clinical necessity to successfully translate these rapid algorithmic innovations into real-world respiratory care. …", "score": 3.853, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.153, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42583290", "title": "A bibliometric analysis of artificial intelligence applications in heart failure.", "authors": "Ziyang Zhang, Yunxia Li, Tie Li, Hongfeng Wang, Yanxin Wang", "journal": "Journal of thoracic disease", "pubdate": "2026-06-22", "pubdate_utc": "2026-06-22T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42583290/", "abstract_snippet": "Heart failure (HF) remains a leading cause of mortality and morbidity worldwide, posing substantial challenges for early and accurate diagnosis as well as personalized therapeutic management. With the rapid evolution of artificial intelligence (AI), substantia…", "score": 3.807, "score_components": { "theme_priority": 1.0, "research_signal": 1.7, "venue": 0.0, "recency": 1.107, "cross_domain": 0.0 }, "signal_components": { "methods": 1.7 }, "signal_classes": [ "Methods" ], "theme": "ML for evolution & pathogens" }, { "pmid": "42584623", "title": "Cooperative Multimetal Chemistry Enables Precision Synthesis of High-Entropy Oxide Nanocrystal Catalysts.", "authors": "Baixu Zhu, Liping Liu, Alex N Butrum-Griffith, Zhengxing Peng, Feipeng Yang, Chenyu Yan", "journal": "Journal of the American Chemical Society", "pubdate": "2026-08-12", "pubdate_utc": "2026-08-12T00:00:00+00:00", "link": "https://pubmed.ncbi.nlm.nih.gov/42584623/", "abstract_snippet": "High-entropy oxides (HEOs) offer vast compositional design space for discovering emergent functionalities, yet their controlled nanoscale synthesis remains challenging. Here, we develop a generalizable colloidal strategy that enables precision synthesis of HEO…", "score": 2.486, "score_components": { "theme_priority": 1.0, "research_signal": 0.0, "venue": 0.0, "recency": 1.486, "cross_domain": 0.0 }, "signal_components": {}, "signal_classes": [], "theme": "ML for evolution & pathogens" } ] } ] }