Recombination & mosaicism
15 result(s)Show 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)
Min Chen, Huichao Chen, Yanling Ma, Manhong Jia, Wenfei Ding · AIDS research and human retroviruses · 2026-02-06
Yunnan Province has historically been a major gateway for the introduction of HIV-1 into China. The border region with northern Myanmar has become a significant hotspot for HIV-1 recombination. This study identified and characterized a novel circulating recomb…
Yu Leng, Han-Zheng Mu, Ning Cui, Le-Tian Fang, Rong Wang, Xin-Yu Ni · Nature communications · 2026-03-27
Severe fever with thrombocytopenia syndrome virus (SFTSV), an emerging pathogen from the family Phenuiviridae, poses severe threats to public health in East Asia. In this study, we elucidate SFTSV's epidemiological dynamics, transmission patterns, and molecula…
János Ágoston, Asztéria Almási, Katalin Salánki, László Palkovics · PloS one · 2026-03-23
Snowdrops are economically important early-spring flowering geophytes. They are protected both in Hungary and across the European Union, and their international trade is regulated under the Washington Convention. Despite their importance, virological research …
Lili Sheng, Yi Li, Jianqun Deng, Yalin Cao, Yijing Chen, Yimin Cai · International journal of biological macromolecules · 2026-03-18
Bacteriophages and bacteria engage in an ancient evolutionary arms race that drives molecular innovation and genetic diversification. Bacteria evolve resistance mechanisms while phages counter with escape mutations, generating diverse defense and counter-defen…
Xianchen Meng, Na Li, Jingjing Xu, Yushan Wei, Jianjun Zhang, Zhimin Wan · Virology · 2026-02-04
Recently, chicken infectious bronchitis (IB), caused by the infectious bronchitis virus (IBV), has emerged as one of the top diseases in the poultry industry in China. Site mutations and recombination events contribute to the high genetic diversity of IBV. In …
Rory P Mulloy, Danyel Evseev, Noga Sharlin, Maxwell P Bui-Marinos, Émile Lacasse, Isabelle Dubuc · PLoS biology · 2026-04-01
Viruses face selective pressure to evade cellular antiviral responses to control the outcome of an infection. However, due to their limited genome size, viruses must adopt unique strategies to confront cellular sensors. Since its emergence in humans, SARS-CoV-…
Wenjian Luo, Weimin Guo, Yiqiang Li, Cheng Zhao, Zhijun Weng, Biyan Duan · Emerging microbes & infections · 2026-04-01
Human adenovirus type 55 (HAdV-55), formerly designated as HAdV-11a, is a notable recombinant pathogen linked to severe respiratory infections. Since its reclassification as HAdV-55 in 2010, numerous outbreaks of pneumonia associated with it have been document…
Ziyue Pan, Yan Zhao, Siqi Shan, Tianjun Xu, Yuena Sun · Fish & shellfish immunology · 2026-03-20
Lysozyme is a key antimicrobial molecule in the innate immune system of fish, playing a central role in defending against pathogen invasion. In this study, a novel c-type lysozyme (mmi-LyzC) was identified and functionally characterized from Miichthys miiuy. T…
Siqi Shan, Wenxin Li, Ziyue Pan, Tianjun Xu, Yuena Sun · Developmental and comparative immunology · 2026-03-03
Galectin-2, a member of the galectin family, functions as an immunoregulatory molecule and plays significant roles in inflammatory responses, apoptosis, and the maintenance of immune homeostasis. In this study, we identified and characterized a galectin from a…
Hazim O Khalifa, Temesgen Mohammed, Hazem Ramadan, Afra Abdalla, Akela Ghazawi, Farah Al-Marzooq · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2026-02-17
Extended-spectrum β-lactamase-producing Escherichia coli are globally disseminated pathogens whose success is driven by clonal expansion and horizontal gene transfer. However, the population structure and evolutionary relationships of these organisms in the Un…
Thanh-Tan Nguyen, Hieu Tran-Van · Fish & shellfish immunology · 2026-02-09
Toll-like receptor 22 (TLR22) in Pangasianodon hypophthalmus is a key component of the fish innate immune system, responsible for recognizing pathogen-associated molecular patterns (PAMPs). However, its bacterial recognition mechanisms remain largely unexplore…
Shengwen Niu, Ning Fu, Yuyu Wang, Mengxin Xing, Meiling An, Hongli Xu · Fish & shellfish immunology · 2026-01-29
C-type lectins (CTLs) are members of pattern recognition receptors (PRRs), which can bind to carbohydrates on the surface of pathogens and take part in the immune response of shrimp. In this study, we identified and characterized a novel stomach-predominant C-…
Mizanur Rahman Washim, Natsuki Morimoto, Takechiyo Sumiyoshi, Aki Nishihara, Siva Nallaperumal, Tomoya Kono · Fish & shellfish immunology · 2026-01-26
Interleukin-1β is a pro-inflammatory cytokine with pluripotent roles in mediating immune response. In fish, IL-1β plays a major role in inflammatory responses to pathogenic infections, though its immunological functions through direct stimulation have not been…
Li-Qun Wang, Guang-Xue Liu, Pan-Hong Liang, Li Li, Tao-Shan Li, Ai-Ming Guo · Veterinary parasitology · 2026-01-13
Cysticercosis, caused by the larval stage of T. solium, remains a major neglected tropical disease with severe clinical and socioeconomic consequences in endemic regions. Although cyclic AMP-dependent protein kinase (PKA) signaling is fundamental to parasite d…
Kenichi Komabayashi, Shuji Chikaoka, Hiroki Awano, Akiko Abe, Dai Sendo, Masayuki Furuyama · Japanese journal of infectious diseases · 2025-07-31
Since we reported the first parechovirus A3-associated myalgia (PeVA3-M) outbreak in Yamagata in 2008 as an emerging disease, we have investigated PeVA3 infections as part of the National Epidemiological Surveillance of Infectious Diseases, Japan, in sentinel …
Phylodynamics & transmission
6 result(s)Show 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)
Andrea Sánchez-Serrano, Carlos Francés-Cuesta, Nuria Jiménez-Hernández, Lidia Ruiz-Roldán, Javier Colomina-Rodríguez, Devi Carolina Salas-Olortegui · Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases · 2026-01-07
Gonorrhoea, caused by Neisseria gonorrhoeae, is a significant public health challenge due to the rising incidence of antimicrobial resistant (AMR) strains. The Valencian Region, one of the top tourist destinations in Eastern Spain, has witnessed an increase of…
Kimberly R Andrews, Jennifer Chang, Cornelius Roemer, James Hadfield, Victor Lin, Anderson F Brito · bioRxiv : the preprint server for biology · 2026-03-26
Genome sequencing provides an exceptional window into the evolutionary and epidemiological dynamics of endemic and emerging pathogens, and thus allows for better, more targeted, public health interventions. Online genomic surveillance platforms can provide nea…
Ighor Arantes, Fernanda de Bruycker-Nogueira, Carla de Oliveira, Patrícia Carvalho Sequeira, Otília Lupi, Michele Borges · Memorias do Instituto Oswaldo Cruz · 2026-03-30
Oropouche virus (OROV), an arbovirus endemic to the Amazon region, has recently expanded into non-endemic areas including Rio de Janeiro State, Brazil. To characterise the spatio-temporal dynamics and ecological factors associated with OROV transmission in Rio…
Uwem Okon Edet, Meseko Clement, Mkpuma Nnabuike Nicodemus, Odianosen Ehiakhamen, Yushau Umar, Ismail Shittu · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2026-03-27
The exact role played by Nigeria in the global monkeypox virus (MPXV) outbreak of 2022 remains unclear, despite exported cases to Singapore, the United Kingdom (UK), the United States of America (USA), and Israel from 2018 to 2022. We sought to resolve the ori…
Shuangshuang Li, Guoli Li, Xueqian He, Yawen Yu, Yingying Zhang, Huiqiong Jia · International journal of antimicrobial agents · 2026-01-24
Klebsiella pneumoniae is an opportunistic pathogen responsible for both hospital and community-acquired infections. It is broadly classified into classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp), with the latter being linked to increased mo…
Jianguang Cai, Yanwei Zhang, Shuang Wu, Peihui Liu, Shuxiang Qiu, Qiongcheng Chen · International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2026-01-22
This study aimed to elucidate the global origins, evolutionary trajectory, and adaptive strategies of the MT28-ptxP3 macrolide-resistant Bordetella pertussis lineage driving the recent resurgence. We integrated long-term epidemiologic surveillance data from Sh…
Atlases, compendia, reference resources
17 result(s)Show 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)
Pedro Serra, Javier Forment, Michela Chiumenti, Alberto Fereres, José Alberto Pereira, Hans J Maree · Virus research · 2026-03-06
The citrus industry is threatened by a devastating bacterial disease known as Huanglongbing (HLB) or citrus greening. Current control measures largely rely on chemical suppression of insect vectors, primarily Diaphorina citri and Trioza erytreae. A promising a…
Ayixon Sánchez-Reyes, Itzayana Chavarría-Quintanilla, Martín Vargas-Suárez, Miguel A Cevallos, Itzel Gaytán, Herminia Loza-Tavera · G3 (Bethesda, Md.) · 2026-04-01
Notwithstanding the ecological significance of the Cladosporium genus, which includes several cosmopolitan fungi reported as saprobes, plant pathogens, and causes of allergic and cutaneous diseases in humans, only 41 genomes have been reported. Here, we report…
Bora Kim, Ah-In Yang, Sung-Hong Joe, Hae-In Joe, Na-Ri Shin · Antonie van Leeuwenhoek · 2026-03-28
A novel Gram-stain-negative, aerobic, motile, and rod-shaped bacterium, designated strain 20L07
Jonald Low, Haohong Tu, Mohamed Elbadawey, Ali Wayes, Nicholas Jakubovics, Siew Woh Choo · PeerJ · 2026-03-24
Chronic otitis media with effusion (COME) is a prevalent pediatric condition characterized by persistent middle ear effusion, potentially leading to hearing loss and developmental delays. We investigated the diversity, antibiotic resistance, and virulence pote…
César X García-Laviña, Pablo Smircich, Susana Castro-Sowinski · Applied and environmental microbiology · 2026-03-24
Antarctica harbors diverse
Samira Pakbaz, Ehsan Hasanvand, Assunta Bertaccini, Sara Gharouni-Kardani · Pathogens (Basel, Switzerland) · 2026-03-23
Sesame is an oilseed crop threatened by a phyllody disease associated with the presence of phytoplasmas, which can reduce yields by up to 80%. The molecular identification of these bacteria in crops located in Western Iran was achieved from samples showing sym…
Thitima Suwannasaeng, Pratsanee Hiengrach, Waewta Kuwatjanakul, Kittipan Samerpitak, Kiatichai Faksri, Sunchai Payungporn · PeerJ · 2026-03-20
Although fungal eye infections are a major cause of visual impairment worldwide, standard clinical laboratory methods remain slow, insensitive, and limited in their taxonomic resolution. Sequencing of the full ribosomal RNA (rRNA) operon provides a comprehensi…
Ziyue Pan, Yan Zhao, Siqi Shan, Tianjun Xu, Yuena Sun · Fish & shellfish immunology · 2026-03-20
Lysozyme is a key antimicrobial molecule in the innate immune system of fish, playing a central role in defending against pathogen invasion. In this study, a novel c-type lysozyme (mmi-LyzC) was identified and functionally characterized from Miichthys miiuy. T…
Siqi Shan, Wenxin Li, Ziyue Pan, Tianjun Xu, Yuena Sun · Developmental and comparative immunology · 2026-03-03
Galectin-2, a member of the galectin family, functions as an immunoregulatory molecule and plays significant roles in inflammatory responses, apoptosis, and the maintenance of immune homeostasis. In this study, we identified and characterized a galectin from a…
Haoyu Li, Wenjun Zhao, Xiaoxiao Li, Xiaoyue Wang, Hanqi Wei, Wanlian Zhang · Microbial pathogenesis · 2026-02-12
Acinetobacter baumannii is a typical extensively drug-resistant Gram-negative opportunistic pathogen. Bacteriophages and their encoded lytic proteins, such as endolysins and holins, represent a promising novel therapeutic approach. A broad-host-range lytic pha…
Aneta Kovarova, Kate Ryan, Anna Tumeo, Francesca McDonagh, Christina Clarke, Martin Cormican · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2026-02-10
Enterobacter vonholyi isolate E323169 represents a rare case of co-carriage of the antimicrobial resistance genes (ARGs) bla Species identification for E323169 was initially assigned by MALDI-TOF and subsequently confirmed using a multifactorial genomic workfl…
Henrik Christensen, Egle Kudirkiene, John Elmerdahl Olsen · Veterinary microbiology · 2026-02-09
Trueperella pyogenes is an important pathogen of ruminants and occasionally other animals. In the current study, we isolated bacteria from uterus of Danish healthy dairy cows (n = 56) and cows judged by veterinarians to suffer from post partum uterine disease …
Shuangshuang Li, Guoli Li, Xueqian He, Yawen Yu, Yingying Zhang, Huiqiong Jia · International journal of antimicrobial agents · 2026-01-24
Klebsiella pneumoniae is an opportunistic pathogen responsible for both hospital and community-acquired infections. It is broadly classified into classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp), with the latter being linked to increased mo…
Mariana J Shayo, Davis Kuchaka, Melkiory Beti, Patrick Kimu, Boaz Wadugu, Emilie E B Jensen · Virology · 2026-01-23
Human adenoviruses (HAdVs) are important pathogens that are associated with a wide array of clinical diseases, particularly in the pediatric population. Despite numerous reports of HAdV infections in Tanzania, there are currently no whole genome sequences from…
Mana Esaki, Kosuke Okuya, Manabu Onuma, Makoto Ozawa · Virology · 2026-01-22
We report the first confirmed case of high pathogenicity avian influenza virus (HPAIV) infection in a peregrine falcon (Falco peregrinus) on Amami-Oshima Island, a region known for its unique biodiversity. The isolate, A/peregrine falcon/Kagoshima/5704A001/202…
Ying Xu, Ning Ling, Cendrine Mony, Philippe Vandenkoornhuyse · The New phytologist · 2026-01-22
The plant and its associated microbiota constitute a holobiont. Within this framework, the seed endophyte reservoir, shaped through multigenerational selection, exhibits pronounced host specificity, mutualistic potential, and signatures of co-evolution. We hyp…
Jiacan Xu, Junnan Fang, Ruigang Wu, Yichen Wang, Chun Zhang, Xuming Wang · Microbiological research · 2026-01-04
Maize yields rely heavily on chemical fertilizers, yet over half of the applied nitrogen remains unutilized, and excessive use harms soil, highlighting the need for sustainable alternatives. Plant growth-promoting rhizobacteria (PGPR) enhance plant growth and …
Metagenomics benchmarking & pipelines
25 result(s)Show 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)
Mariem Ayed, Vasco Cadavez, Ursula Gonzales-Barron · Italian journal of food safety · 2026-03-25
Protozoan parasites such as Cryptosporidium spp., Giardia duodenalis, Toxoplasma gondii and Cyclospora cayetanensis remain difficult-to-control hazards in food due to environmental persistence, low infectious doses, and the interpretability gap between nucleic…
Arianna Ceruti, Marina Bisia, Georgios Balatsos, Rea Maja Kobialka, Md Fahad Zamil, Anamul Hasan · Acta tropica · 2026-03-25
Mosquitoes transmit numerous infectious diseases, with climate change expanding their global distribution through warmer environments. Next-generation sequencing offers significant advantages for mosquito genomic surveillance and potential early warning system…
Brian Merritt, Jeremy D Ratcliff, Stanley Ta, Gunars Osis, Matthew R Mauldin, Peter M Thielen · Bioinformatics (Oxford, England) · 2026-04-01
TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comp…
Haley Anne Hallowell, Justin Malogan, Jotham Suez · mSystems · 2026-02-04
The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other …
Luis L Marques, Armando J Pinho, Diogo Pratas · Bioinformatics (Oxford, England) · 2026-03-30
Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100 bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matchin…
Holly N Kersey, Dominic J Acri, Luke C Dabin, Kelly A Hartigan, Richard Mustaklem, Jung Hyun Park · Cell reports methods · 2026-03-23
Single-nucleus RNA sequencing (snRNA-seq) enables resolving cellular heterogeneity in complex tissues by using nuclei instead of cells, overcoming limitations of single-cell RNA sequencing and enabling analysis of frozen and hard-to-isolate tissues. Despite ad…
Kingsley King-Gee Tam, Carl J E Suster, Winkie Fong, Tanya Golubchik, Varsha Sivalingam, Neisha Jeoffreys · The Journal of infectious diseases · 2026-03-21
The resurgence of Mycoplasma pneumoniae (MP), first reported in China in 2023 was attributed to waning post-pandemic immunity with notable increases in macrolide-resistant MP (MRMP) (>80%). In Australia, infections peaked in early 2024, particularly among chil…
Ahmet Arıhan Erözden, Nalan Tavşanlı, Gamze Demirel, Nazmiye Ozlem Sanli, Mahmut Çalışkan, Muzaffer Arıkan · PeerJ · 2026-03-27
Anticancer peptides (ACPs) are increasingly recognized as promising therapeutic candidates due to their ability to selectively target cancer cells. However, the systematic discovery of novel ACPs, particularly from high-throughput sequencing datasets, remains …
Feilong Deng, Yanhua Han, Yunjuan Peng, Zhijian Xu, Jianbo Yang, Jinling He · The ISME journal · 2026-04-02
Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and li…
Weihao Li, Manman Lv, Mengqing Cheng, Yemin Han, Haotian Yu, Yan Huang · Journal of breath research · 2026-04-01
Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-cha…
Jesse Erens, Christopher Heine, Stefan Lötters, Henrik Krehenwinkel, Andrew J Crawford, Luis Alberto Rueda-Solano · Molecular ecology resources · 2026-04
Field-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recomb…
Pranav Dawar, Lye Meng Markillie, Sarah M Williams, Hugh D Mitchell, Johannes W Bagnoli, Joshua Cantlon-Bruce · Lab on a chip · 2026-03-31
Single-cell multiomic platforms provide a comprehensive snapshot of cellular states and cell types by offering critical insights into the spatiotemporal regulation of biomolecular networks at a systems level, thereby defining the basis of multicellularity. Her…
Gregory A Sprenger, Jay E Gee, Mindy G Elrod, Zachary P Weiner, Christopher A Gulvik · Microbiology spectrum · 2026-03-30
Shotgun metagenomics, when sufficient read depth exists for each taxon, enables capturing metagenome-assembled genomes (MAGs) directly from a microbial community. In 2021, an aromatherapy spray contaminated with
Hatoon A Niyazi, Hanouf A Niyazi, Hind AbdulMajed, Noha Juma, Noof Helmi, Mona Alqarni · Future microbiology · 2026-03-27
This study aimed to investigate the global genetic diversity, evolutionary relationships, and antimicrobial resistance (AMR) profiles of A total of 72,057 The pan-genome revealed a large accessory component, reflecting extensive genomic plasticity and adaptabi…
Arief Muammar, Endah Retnaningrum, Budi Setiadi Daryono, Irfan Dwidya Prijambada, Yuki Yashima, Clemens Peterbauer · Applied microbiology and biotechnology · 2026-03-25
Functional metagenomics has emerged as an effective tool for discovering novel enzymes directly from environmental samples, overcoming the limitations of traditional culture-based methods. In this study, we used a functional metagenomic approach on stool sampl…
Genevieve A Mortensen, Haley Schmidt, Predrag Radivojac, Yuzhen Ye, David M Haas · Microbiology spectrum · 2026-03-25
The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and gestational diabetes mellitus (GDM) remains poorly understood. This study explores how the gut microbiome diffe…
Kimberley S M Benschop, Florian Zwagemaker, Lili Andersson-Li, Cristina Andrés, Andrés Antón, Carla Berengua · Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2026-03-24
Enteroviruses (EVs) are a common cause of a wide spectrum of infectious diseases, ranging from mild respiratory illnesses to severe neurological conditions, particularly affecting children. Current molecular methods, such as 5'UTR-based PCR for detection and (…
Amol Dattatraya Mahajan, Pramod Maruti Jadhav, Avinash Rohidas Memane, Gautam Kumar Jha, Swapan Kumar Jana, Prasad Deepak Dandekar · Biotechnology and applied biochemistry · 2026-03-23
Pneumococcal pneumonia, caused by Streptococcus pneumoniae, has emerged as a global health threat, especially in children below 5 years of age and elderly population. S. pneumoniae remains a major global health threat which necessitates scalable and high-yield…
Josipa Lipovac, Mile Šikić, Riccardo Vicedomini, Krešimir Križanović · GigaScience · 2026-03-23
Strain-level metagenomic classification is essential for understanding microbial diversity and functional potential, yet remains challenging, particularly when sample composition is unknown and reference databases are large and redundant. Here we present MADRe…
Arpit Mehta, Vitalii Stebliankin, Kalai Mathee, Giri Narasimhan · Journal of computational biology : a journal of computational molecular cell biology · 2026-03-23
RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study …
McKenna Loop Yao, Yitao Dai, Wenjun Zhang · Annual review of biochemistry · 2026-03-20
The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbe…
Madjid Morsli, Chloé Magnan, Florian Salipante, Adeline Dubois, Sophie Schuldiner, Nicolas Cellier · Diabetic medicine : a journal of the British Diabetic Association · 2026-02-15
Diabetic foot osteomyelitis (DFOM) is a serious medical condition that necessitates robust diagnostic tools for effective clinical management. Conventional diagnostic methods for DFOM rely heavily on bacterial culture, which is time-consuming and may fail to c…
Yue Wu, Xinyu Yu, Jiameng Qi, Ying Chen, Rongrong Wang, Junfang Liu · International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2026-01-22
Mucormycosis is a rapidly progressive and highly lethal fungal infection in liver transplant recipients, with early diagnosis remaining a major challenge. This study aimed to evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for ea…
Brontë R Shelton, Joana Larrere, Diego Yusta Belsham, Marina Omacini, Andrés Argüelles-Moyao, Erika Buscardo · The New phytologist · 2026-01-11
The advancement of technology in recent decades has given us an unprecedented ability to observe the natural world. With modern sequencing and bioinformatics technologies, we can obtain more information about the microscopic world, and its interactions with th…
Rodrigo Campos-Silva, Fahimeh Rahimi, Jaya Joshi, Cătălin Voiniciuc, Juannan Zhou, Andrew D Hanson · Analytical biochemistry · 2026-01-03
Enzyme biochemistry can now draw on hundreds of thousands of prokaryotic genomes and metagenomes to identify orthologous genes for research, biocatalysis, and metabolic engineering. In many applications, adaptation to O
ML for evolution & pathogens
25 result(s)Show 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)
Samuel Sledzieski, Sonya M Hanson · Current opinion in structural biology · 2026-03-31
The conformational ensemble of a protein and its corresponding probabilities and dynamics are crucial determinants of its function, but are difficult to access with traditional experimental and computational technologies. This review examines the landscape of …
Haokai Hong, Liang Feng, Min Jiang, Kay Chen Tan · Evolutionary computation · 2026-03-27
Multi-objective optimization problems (MOPs) require the simultaneous optimization of conflicting objectives. Real-world MOPs often exhibit complex characteristics, including high-dimensional decision spaces, many objectives, or computationally expensive evalu…
Markus Plass, Andreas Holzinger, Robert Reihs, Heimo Müller · Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society · 2026-03-28
Today, the integration of next-generation sequencing (NGS) into clinical genomics is increasingly AI-driven, with artificial intelligence (AI) underpinning every stage from data processing to decision support. While NGS enables rapid and scalable analysis of c…
Chun-Xi Shan, Yan-He Wang, Qiang Xu, Guo-Lin Wang, Chen-Long Lv, Li-Qun Fang · BMC infectious diseases · 2026-04-02
Accurate and timely early warning of seasonal influenza epidemics continues to pose a critical public health challenge. Innovative methodologies leveraging network data sources, such as internet search queries, serve as a valuable complement to traditional lab…
Michael Levin, Aizhan Surumbayeva, Max Li, Igor Astsaturov, Yunyun Zhou · Computational biology and chemistry · 2026-03-27
Disruption of transcription termination (DoTT) occurs when RNA polymerase II reads past a gene's normal 3' end, generating downstream "readthrough" RNA. DoTT has been reported under stresses such as viral infection and metabolic perturbation. But, many existin…
Peter C DeWeirdt, Emily M Mahoney, Michael T Laub · Science (New York, N.Y.) · 2026-04-02
Antiphage defense systems protect bacteria from viral infection and have inspired important biotechnologies such as CRISPR-Cas9 while also revealing the evolutionary roots of eukaryotic innate immunity. Many systems have been discovered by genomic colocalizati…
Zhijun Ding, Haoyun Yang, Yingchen Zhou, Chiyu Wang, Liyan Ma, Kana Ren · BMJ public health · 2026-03-26
The low coverage of human papillomavirus (HPV) vaccination hinders the elimination of cervical cancer in China. This study aimed to investigate barriers to HPV vaccination using social media data to promote vaccine uptake. Social media posts related to HPV vac…
Mingzhe Shen, Guy W Dayhoff, Daniel Kortzak, Jana Shen · bioRxiv : the preprint server for biology · 2026-03-29
Ionization states play crucial roles in protein functions. Yet despite decades of research, predicting protein p
Fatema Bhinderwala, Aishwarya Korgaonkar, Kota Gopalakrishna, Thomas C Mathers, Shuji Shigenobu, J Fernando Bazan · bioRxiv : the preprint server for biology · 2026-03-28
Many insects manipulate plants by injecting effector proteins. In one extreme example of this molecular "hijacking", Parasites introduce specialized "effector" proteins into hosts, both to suppress host immunity and to release nutrients. The molecular function…
Tatiana M Shamorkina, Sofia Kalaidopoulou Nteak, Sokchea Lay, Ashwin Adrian Kallor, Sowath Ly, Veasna Duong · medRxiv : the preprint server for health sciences · 2026-03-23
Dengue virus (DENV) is a major burden to global public health, affecting hundreds of millions annually. Children represent the major proportion of global dengue cases, ranging from asymptomatic or subclinical presentation to dengue fever (DF) and severe dengue…
Janna Hastings, Marie Wosny, Jaycee Kennett, Ava Homiar, Gin S Malhi, Toshi A Furukawa · BMJ mental health · 2026-04-02
More effective and better tolerated treatments are urgently needed for people with mental health disorders, such as anxiety, depression and psychosis. However, the rate of translation of positive results from early phase studies into clinically validated treat…
Ernest Mordret, Alexandre Hervé, Florian Tesson, Hugo Vaysset, Tyler Clabby, Arthur Loubat · Science (New York, N.Y.) · 2026-04-02
The bacterial pangenome contains a vast diversity of antiphage systems, whose overall extent is still unknown. In this study, we developed complementary machine learning approaches to systematically predict antiphage function from genomic context, protein sequ…
Quoc Toan Phan, Huy Ngoc Nguyen, Khuong V Dinh · npj biodiversity · 2026-04-01
Vietnam is a global hotspot, hosting 493 Odonata species, with ~95% evaluated by the IUCN. Odonata species play vital ecological roles in aquatic and terrestrial ecosystems; yet, they face escalating threats from climate change, habitat loss, and pollution. Ad…
Yuanyuan Chen, Tianbiao Yang, Tianlu Chen, Huanming Xiao, Kejun Zhou, Keke Ding · Cell reports. Medicine · 2026-03-31
Accurate, non-invasive liver fibrosis detection is essential for chronic liver disease management, particularly with rising metabolic dysfunction-associated liver disease (MASLD) and chronic hepatitis B (CHB). While the Fibrosis-4 (FIB-4) index is widely used,…
Bufan Jin, Langjian Zhu, Huizhong Chang, Yanrong Wei, Yuanchun Tang, Yue Gao · Cell reports · 2026-03-31
Understanding how human-specific cis-regulatory elements (CREs) drive gene expression in the adult brain remains elusive. Here, we profile the prefrontal cortex (PFC) of adult human, macaque, and mouse using single-nucleus transcriptomic (106,266 cells) and ge…
Jianing Yan, Jingzhi Wang, Haotian Dong, Guoliang Ye, Yongfu Shao · NPJ precision oncology · 2026-03-31
VDAC2's known role in cancer and immune regulation via enhancing the CD8
Symeon V Savvopoulos, Irina Scheffner, Andreas Reppas, Wilfried Gwinner, Haralampos Hatzikirou · Communications medicine · 2026-03-31
Many factors cause kidney transplant graft failure. To identify at-risk patients and tailor treatment, failure risks must be accurately predicted. We are trying to predict the temporal progression of graft function (as treated with estimated glomerular filtrat…
Meng Liu, Ke Liang, Miaomiao Li, Xueling Zhu, Xinwang Liu · IEEE transactions on pattern analysis and machine intelligence · 2026-03-31
Temporal graph learning focuses on graph deep learning in real-world dynamic scenarios, which uses interaction sequence instead of adjacency matrix to observe the graph dynamic changes more microscopically from the perspective of time evolution. However, curre…
Mubarak A Alamri, Abdullah S Alawam · Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2026-03-31
The dynamic mutational landscape of SARS-CoV-2, especially within the spike glycoprotein's RBD, continues to undermine the effectiveness of available therapeutics. Although ACE2-derived peptides have previously been explored as spike inhibitors, their rational…
Samantha Franklin, Pranoti Sahasrabhojane, Tomo Hayase, Eiko Hayase, Chia-Chi Chang, Jayastu Senapati · mSystems · 2026-03-31
Neutropenic fever (NF) is often the first sign of infection in patients with hematologic malignancies, but its cause is frequently unknown, leading to broad-spectrum antibiotic use without confirmed infections. Although research links gut microbiome disruption…
Jie Wang, Miao Zhu, Zongzhe Jiang, Guohui Liao, Caimin Xu, Nan Jiang · International journal of biological macromolecules · 2026-03-30
Diabetic foot ulcer (DFU) is a complication of diabetes, characterized by impaired healing and chronic wounds that compromise quality of life. Migrasomes are newly discovered organelles involved in processes such as morphogenesis and angiogenesis, but their ro…
Qamar Abuhassan, Hamzeh J Al-Ameer, Pareshkumar N Patel, S Renuka Jyothi, Gunjan Singh, Laxmidhar Maharana · Clinica chimica acta; international journal of clinical chemistry · 2026-03-30
Glioblastoma (GBM) is one of the most lethal primary brain tumors and is characterized by profound molecular heterogeneity, rapid progression, and limited therapeutic responsiveness. Traditional diagnostic and treatment paradigms have struggled to capture the …
Shuo Dai, Qihuang Wang, Shuyou Zhang, Lei Huang, Songhe Zhang, Yijun Yao · Journal of environmental management · 2026-03-30
China faces widespread soil contamination by polycyclic aromatic hydrocarbons (PAHs) due to rapid industrialization. However, the continuous spatiotemporal evolution of this contamination under shifting energy structures remains poorly quantified. To bridge th…
Shaochu Zheng, Jinling Tang, Xiaopu Wu, Cao Qing, Yun Jiang, Wei Lu · Biochimica et biophysica acta. Molecular basis of disease · 2026-03-30
Bronchiectasis is a chronic neutrophilic respiratory disease frequently complicated by Pseudomonas aeruginosa (P. aeruginosa) infection. Neutrophil extracellular traps (NETs) exert dual effects in host defense and airway injury, while the roles of CYBB and the…
Zhenhua Du, Xiaomei Liu, Zhi Lv, Bengang Wang, Yu Xia, Wala Abduljabbar Mohammed Al-Duais · MedComm · 2026-03-24
Cancer is a highly complex and heterogeneous disease involving multiple pathophysiological events. Despite significant advances in modern medicine, the molecular mechanisms of cancer are still largely unknown. Omics methods have opened new avenues for identify…
