# Daily PubMed Watch (evo • virome • metagenomics)

**Updated:** 2026-04-03 13:54:55  
**Window:** last 14 day(s)  
**Ranking:** Score (theme priority + keyword signals + venue + recency)


## Selection & codon models — 3 result(s)

- **[Positive and relaxed selection on mitochondrial DNA in parasitic versus predatory mites.](https://pubmed.ncbi.nlm.nih.gov/41923602/)**  
  Justin Havird, Endong Wang, Kendra Zwonitzer, Georgina Aitolo, Xuenong Xu, Bo Zhang · Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026-04-02  
  _PI score:_ `12.336`  
  _Mitochondrial genomes (mtDNA) have distinct evolutionary trajectories owing to their inheritance, ploidy and underlying mutation rates, making them prone to accumulate slightly deleterious mutations. Positive selection on mtDNA has been suggested to be importa…_
- **[The influence of size, longevity and environmental temperature on mitochondrial DNA evolution in fishes.](https://pubmed.ncbi.nlm.nih.gov/41923603/)**  
  Sabrina Le Cam, Mathieu Mortz, Alexis Gagnier-Michel, France Dufresne, Pierre U Blier · Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026-04-02  
  _PI score:_ `6.836`  
  _The link between longevity and mitochondrial function has been documented; therefore, we suspect that the evolution of mitochondrial DNA (mtDNA) is linked to the evolution of longevity. We selected 128 fish species with a wide range of longevity and inhabiting…_
- **[Detailed molecular investigation of Marek's disease virus circulating in organised poultry farms in India revealed emergence of highly virulent MDV causing varied tissue tropism.](https://pubmed.ncbi.nlm.nih.gov/40960479/)**  
  A K Mariappan, R Ramalingam, M V Srinivas, M Sharma, R Singh, K Dhama · British poultry science · 2025-09-17  
  _PI score:_ `1.826`  
  _1. The current study analysed Marek's Disease virus (MDV) strains, genome characteristics and associated pathology, with reference to the central nervous system, in naturally occurring field cases across India.2. A total of 179 birds, aged less than 18 weeks, …_

## Cancer evolution & somatic selection — 2 result(s)

- **[Evolution of multiple myeloma from a genomic perspective.](https://pubmed.ncbi.nlm.nih.gov/41359792/)**  
  Francesco Maura, Mehmet Samur, Nikhil Munshi · Blood · 2026-03-26  
  _PI score:_ `5.627`  
  _In this review, we explore the role of complex interactions between genomic evolution, environmental and genetic predispositions, and immune surveillance in disease progression from precursor conditions smoldering multiple myeloma and monoclonal gammopathy of …_
- **[Detailed molecular investigation of Marek's disease virus circulating in organised poultry farms in India revealed emergence of highly virulent MDV causing varied tissue tropism.](https://pubmed.ncbi.nlm.nih.gov/40960479/)**  
  A K Mariappan, R Ramalingam, M V Srinivas, M Sharma, R Singh, K Dhama · British poultry science · 2025-09-17  
  _PI score:_ `1.676`  
  _1. The current study analysed Marek's Disease virus (MDV) strains, genome characteristics and associated pathology, with reference to the central nervous system, in naturally occurring field cases across India.2. A total of 179 birds, aged less than 18 weeks, …_

## Recombination & mosaicism — 15 result(s)

- **[Identification of a Novel HIV-1 Circulating Recombinant Form (CRF181_BC) with a Unique Subtype B Backbone from the China-Myanmar Border Region.](https://pubmed.ncbi.nlm.nih.gov/41652843/)**  
  Min Chen, Huichao Chen, Yanling Ma, Manhong Jia, Wenfei Ding · AIDS research and human retroviruses · 2026-02-06  
  _PI score:_ `7.582`  
  _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…_
- **[Molecular evolution and spatial transmission of severe fever with thrombocytopenia syndrome virus.](https://pubmed.ncbi.nlm.nih.gov/41896574/)**  
  Yu Leng, Han-Zheng Mu, Ning Cui, Le-Tian Fang, Rong Wang, Xin-Yu Ni · Nature communications · 2026-03-27  
  _PI score:_ `5.436`  
  _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…_
- **[Recombinant Potyvirus lilimaculae in asymptomatic Galanthus nivalis: Ecological and evolutionary implications.](https://pubmed.ncbi.nlm.nih.gov/41871069/)**  
  János Ágoston, Asztéria Almási, Katalin Salánki, László Palkovics · PloS one · 2026-03-23  
  _PI score:_ `5.403`  
  _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 …_
- **[Evolutionary and functional characterization of the chimeric enzyme eliminase (ElmA) in Escherichia coli K5.](https://pubmed.ncbi.nlm.nih.gov/41861875/)**  
  Lili Sheng, Yi Li, Jianqun Deng, Yalin Cao, Yijing Chen, Yimin Cai · International journal of biological macromolecules · 2026-03-18  
  _PI score:_ `5.363`  
  _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…_
- **[The molecular, antigenic, and pathogenic characterization of novel IBV of GI-22 lineage endemic in China.](https://pubmed.ncbi.nlm.nih.gov/41666590/)**  
  Xianchen Meng, Na Li, Jingjing Xu, Yushan Wei, Jianjun Zhang, Zhimin Wan · Virology · 2026-02-04  
  _PI score:_ `5.069`  
  _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 …_
- **[Evolution of a truncated nucleocapsid protein enhances SARS-CoV-2 fitness by suppressing antiviral responses.](https://pubmed.ncbi.nlm.nih.gov/41920932/)**  
  Rory P Mulloy, Danyel Evseev, Noga Sharlin, Maxwell P Bui-Marinos, Émile Lacasse, Isabelle Dubuc · PLoS biology · 2026-04-01  
  _PI score:_ `2.678`  
  _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-…_
- **[High pathogenicity of human adenovirus type 55 in adult males: a meta-analysis and phylogenetic study of HAdV-55 epidemics worldwide over the past six decades.](https://pubmed.ncbi.nlm.nih.gov/41854194/)**  
  Wenjian Luo, Weimin Guo, Yiqiang Li, Cheng Zhao, Zhijun Weng, Biyan Duan · Emerging microbes & infections · 2026-04-01  
  _PI score:_ `2.678`  
  _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…_
- **[The C-type lysozyme of Miichthys miiuy exhibits specific antibacterial activity against Gram-negative bacteria.](https://pubmed.ncbi.nlm.nih.gov/41866098/)**  
  Ziyue Pan, Yan Zhao, Siqi Shan, Tianjun Xu, Yuena Sun · Fish & shellfish immunology · 2026-03-20  
  _PI score:_ `2.579`  
  _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…_
- **[Identification and Antimicrobial Characterization of Galectin-2 in Miichthysmiiuy.](https://pubmed.ncbi.nlm.nih.gov/41786259/)**  
  Siqi Shan, Wenxin Li, Ziyue Pan, Tianjun Xu, Yuena Sun · Developmental and comparative immunology · 2026-03-03  
  _PI score:_ `2.45`  
  _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…_
- **[Phylogenomic and population genomic insights into the dissemination of ESBL-producing Escherichia coli causing bloodstream infections in the United Arab Emirates.](https://pubmed.ncbi.nlm.nih.gov/41713669/)**  
  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  
  _PI score:_ `2.353`  
  _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…_
- **[Characterization of Toll-like receptor 22 in striped catfish (Pangasianodon hypophthalmus): Recognition of Gram-positive and Gram-negative bacteria.](https://pubmed.ncbi.nlm.nih.gov/41672286/)**  
  Thanh-Tan Nguyen, Hieu Tran-Van · Fish & shellfish immunology · 2026-02-09  
  _PI score:_ `2.301`  
  _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…_
- **[Novel stomach-predominant C-type lectin (LvnCTL) triggers immune response against Vibrio parahaemolyticus and WSSV in shrimp Litopenaeus vannamei.](https://pubmed.ncbi.nlm.nih.gov/41619827/)**  
  Shengwen Niu, Ning Fu, Yuyu Wang, Mengxin Xing, Meiling An, Hongli Xu · Fish & shellfish immunology · 2026-01-29  
  _PI score:_ `2.233`  
  _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-…_
- **[Two interleukin-1β types reinforce innate immune response modulation in Japanese medaka, Oryzias latipes.](https://pubmed.ncbi.nlm.nih.gov/41605265/)**  
  Mizanur Rahman Washim, Natsuki Morimoto, Takechiyo Sumiyoshi, Aki Nishihara, Siva Nallaperumal, Tomoya Kono · Fish & shellfish immunology · 2026-01-26  
  _PI score:_ `2.215`  
  _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…_
- **[The catalytic subunit of cAMP-dependent protein kinase in Taenia solium cysticerci (TsPKA-c): A promising molecular target for the development of novel anti-cysticercosis therapeutics.](https://pubmed.ncbi.nlm.nih.gov/41547087/)**  
  Li-Qun Wang, Guang-Xue Liu, Pan-Hong Liang, Li Li, Tao-Shan Li, Ai-Ming Guo · Veterinary parasitology · 2026-01-13  
  _PI score:_ `2.142`  
  _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…_
- **[Parechovirus A3 Infections, Including Myalgia, in Yamagata, Japan, Between 2022 and 2023 and Their Next-Generation Sequencing Analyses.](https://pubmed.ncbi.nlm.nih.gov/40738664/)**  
  Kenichi Komabayashi, Shuji Chikaoka, Hiroki Awano, Akiko Abe, Dai Sendo, Masayuki Furuyama · Japanese journal of infectious diseases · 2025-07-31  
  _PI score:_ `1.561`  
  _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)

- **[The recent introduction of mosaic mtr-carrying Neisseria gonorrhoeae lineages boosts local transmission.](https://pubmed.ncbi.nlm.nih.gov/41513037/)**  
  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  
  _PI score:_ `7.71`  
  _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…_
- **[Nextstrain automates real-time phylodynamic analysis of open data for endemic and emerging pathogens.](https://pubmed.ncbi.nlm.nih.gov/41929033/)**  
  Kimberly R Andrews, Jennifer Chang, Cornelius Roemer, James Hadfield, Victor Lin, Anderson F Brito · bioRxiv : the preprint server for biology · 2026-03-26  
  _PI score:_ `6.427`  
  _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…_
- **[Sustained Oropouche virus transmission in Rio de Janeiro's Atlantic Forest: genomic evidence over a two-year period.](https://pubmed.ncbi.nlm.nih.gov/41919903/)**  
  Ighor Arantes, Fernanda de Bruycker-Nogueira, Carla de Oliveira, Patrícia Carvalho Sequeira, Otília Lupi, Michele Borges · Memorias do Instituto Oswaldo Cruz · 2026-03-30  
  _PI score:_ `5.461`  
  _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…_
- **[Emergence and diversity of monkeypox virus Clade IIb sub-lineages in Nigeria (1971-2023) and its role in the 2022 global outbreak.](https://pubmed.ncbi.nlm.nih.gov/41905479/)**  
  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  
  _PI score:_ `5.436`  
  _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…_
- **[Global epidemiological trend of Klebsiella pneumoniae ST23: Emergence of KL57 lineage carrying dual carbapenemases.](https://pubmed.ncbi.nlm.nih.gov/41587624/)**  
  Shuangshuang Li, Guoli Li, Xueqian He, Yawen Yu, Yingying Zhang, Huiqiong Jia · International journal of antimicrobial agents · 2026-01-24  
  _PI score:_ `2.204`  
  _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…_
- **[Genomic epidemiology and evolutionary dynamics of Bordetella pertussis: A comparative study between China and Global Strains (2018-2024).](https://pubmed.ncbi.nlm.nih.gov/41579932/)**  
  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  
  _PI score:_ `2.192`  
  _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…_

## Urban / built environment virome — 0 result(s)

_No new items in this window._

## Wastewater / WBE viral surveillance — 2 result(s)

- **[Isolation, Screening, and Characterization of Gordonia paraffinivorans DGM-81 Exhibiting Antimicrobial Activity Against Methicillin-Resistant Staphylococcus aureus (MRSA).](https://pubmed.ncbi.nlm.nih.gov/41876906/)**  
  Mumtaz, Simran Kaur, Simran Gagneja, Vinod D Chaudhari, Ravi P N Mishra · Current microbiology · 2026-03-24  
  _PI score:_ `4.861`  
  _The increasing prevalence of antibiotic-resistant infections necessitates the development of novel antimicrobial medications. Actinomycetes are recognized for producing a diverse array of naturally occurring biologically active compounds. Natural environments …_
- **[Comparative morphological, genomic, and functional characterization of two newly isolated lytic caudoviricetes phages targeting Escherichia coli and Salmonella.](https://pubmed.ncbi.nlm.nih.gov/41882051/)**  
  Mohamed T Shaaban, Ohood Sallam, Soumya K Manikandan, Amany A M Ahmed, Tareq M Osaili, Mohamed Hamad · Scientific reports · 2026-03-26  
  _PI score:_ `2.677`  
  _Foodborne_

## Pandemic preparedness & biosurveillance — 1 result(s)

- **[Emergence of dual β-lactam and colistin resistance via bla](https://pubmed.ncbi.nlm.nih.gov/41679575/)**  
  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  
  _PI score:_ `2.257`  
  _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…_

## Atlases, compendia, reference resources — 17 result(s)

- **[New viral sequences and endogenous viral elements (EVE) in world-wide populations of Trioza erytreae, the African citrus psyllid.](https://pubmed.ncbi.nlm.nih.gov/41796646/)**  
  Pedro Serra, Javier Forment, Michela Chiumenti, Alberto Fereres, José Alberto Pereira, Hans J Maree · Virus research · 2026-03-06  
  _PI score:_ `4.872`  
  _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…_
- **[Chromosome-level assembly and phylophenetic insights of Cladosporium oxysporum A3.I.1, a fungus with the ability to degrade polyurethane polymers.](https://pubmed.ncbi.nlm.nih.gov/41742723/)**  
  Ayixon Sánchez-Reyes, Itzayana Chavarría-Quintanilla, Martín Vargas-Suárez, Miguel A Cevallos, Itzel Gaytán, Herminia Loza-Tavera · G3 (Bethesda, Md.) · 2026-04-01  
  _PI score:_ `2.578`  
  _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…_
- **[Dyella stictolepturae sp. nov., isolated from the larva gut of red-brown longhorn beetle (Stictoleptura succedanea).](https://pubmed.ncbi.nlm.nih.gov/41902982/)**  
  Bora Kim, Ah-In Yang, Sung-Hong Joe, Hae-In Joe, Na-Ri Shin · Antonie van Leeuwenhoek · 2026-03-28  
  _PI score:_ `2.544`  
  _A novel Gram-stain-negative, aerobic, motile, and rod-shaped bacterium, designated strain 20L07_
- **[Genomic insights into the diversity, antibiotic resistance, and virulence potential of staphylococci isolated from pediatric patients with chronic otitis media with effusion (COME).](https://pubmed.ncbi.nlm.nih.gov/41907467/)**  
  Jonald Low, Haohong Tu, Mohamed Elbadawey, Ali Wayes, Nicholas Jakubovics, Siew Woh Choo · PeerJ · 2026-03-24  
  _PI score:_ `2.511`  
  _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…_
- **[From genome to lifestyle: adaptive strategies of](https://pubmed.ncbi.nlm.nih.gov/41873973/)**  
  César X García-Laviña, Pablo Smircich, Susana Castro-Sowinski · Applied and environmental microbiology · 2026-03-24  
  _PI score:_ `2.511`  
  _Antarctica harbors diverse_
- **[Identification and Biological Features of Sesame Phyllody-Associated Phytoplasmas in Western Iran.](https://pubmed.ncbi.nlm.nih.gov/41901792/)**  
  Samira Pakbaz, Ehsan Hasanvand, Assunta Bertaccini, Sara Gharouni-Kardani · Pathogens (Basel, Switzerland) · 2026-03-23  
  _PI score:_ `2.503`  
  _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…_
- **[Identification of pathogenic fungi causing ocular infections using full rRNA operon sequencing with Oxford Nanopore Technologies.](https://pubmed.ncbi.nlm.nih.gov/41877864/)**  
  Thitima Suwannasaeng, Pratsanee Hiengrach, Waewta Kuwatjanakul, Kittipan Samerpitak, Kiatichai Faksri, Sunchai Payungporn · PeerJ · 2026-03-20  
  _PI score:_ `2.479`  
  _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…_
- **[The C-type lysozyme of Miichthys miiuy exhibits specific antibacterial activity against Gram-negative bacteria.](https://pubmed.ncbi.nlm.nih.gov/41866098/)**  
  Ziyue Pan, Yan Zhao, Siqi Shan, Tianjun Xu, Yuena Sun · Fish & shellfish immunology · 2026-03-20  
  _PI score:_ `2.479`  
  _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…_
- **[Identification and Antimicrobial Characterization of Galectin-2 in Miichthysmiiuy.](https://pubmed.ncbi.nlm.nih.gov/41786259/)**  
  Siqi Shan, Wenxin Li, Ziyue Pan, Tianjun Xu, Yuena Sun · Developmental and comparative immunology · 2026-03-03  
  _PI score:_ `2.35`  
  _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…_
- **[A novel Queuovirinae subfamily phage targeting Acinetobacter baumannii: Isolation, characterization, and synergistic lysis system.](https://pubmed.ncbi.nlm.nih.gov/41690646/)**  
  Haoyu Li, Wenjun Zhao, Xiaoxiao Li, Xiaoyue Wang, Hanqi Wei, Wanlian Zhang · Microbial pathogenesis · 2026-02-12  
  _PI score:_ `2.22`  
  _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…_
- **[Emergence of dual β-lactam and colistin resistance via bla](https://pubmed.ncbi.nlm.nih.gov/41679575/)**  
  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  
  _PI score:_ `2.207`  
  _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…_
- **[Characterization of Trueperella pyogenes strains from uterus of cow and an analysis of their phylogenic association with strains from other anatomic locations and hosts.](https://pubmed.ncbi.nlm.nih.gov/41687473/)**  
  Henrik Christensen, Egle Kudirkiene, John Elmerdahl Olsen · Veterinary microbiology · 2026-02-09  
  _PI score:_ `2.201`  
  _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 …_
- **[Global epidemiological trend of Klebsiella pneumoniae ST23: Emergence of KL57 lineage carrying dual carbapenemases.](https://pubmed.ncbi.nlm.nih.gov/41587624/)**  
  Shuangshuang Li, Guoli Li, Xueqian He, Yawen Yu, Yingying Zhang, Huiqiong Jia · International journal of antimicrobial agents · 2026-01-24  
  _PI score:_ `2.104`  
  _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…_
- **[Genomic diversity of human adenoviruses in Tanzanian children under five: Insights into F40, F41, B, and rare A18 genotypes.](https://pubmed.ncbi.nlm.nih.gov/41619541/)**  
  Mariana J Shayo, Davis Kuchaka, Melkiory Beti, Patrick Kimu, Boaz Wadugu, Emilie E B Jensen · Virology · 2026-01-23  
  _PI score:_ `2.098`  
  _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…_
- **[Genetically distinct H5N2 high pathogenicity avian influenza virus isolated from a peregrine falcon on Amami-Oshima Island, Japan, harboring enhanced pathogenicity-associated amino acids in the PA protein.](https://pubmed.ncbi.nlm.nih.gov/41604901/)**  
  Mana Esaki, Kosuke Okuya, Manabu Onuma, Makoto Ozawa · Virology · 2026-01-22  
  _PI score:_ `2.092`  
  _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…_
- **[Differential 'resuscitation' from the seed microbiota: a plant-holobiont ecological strategy for buffering stresses.](https://pubmed.ncbi.nlm.nih.gov/41568587/)**  
  Ying Xu, Ning Ling, Cendrine Mony, Philippe Vandenkoornhuyse · The New phytologist · 2026-01-22  
  _PI score:_ `2.092`  
  _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…_
- **[Exploring the genomic features and plant growth-promoting properties of Enterobacter vonholyi Y16 isolated from maize rhizosphere.](https://pubmed.ncbi.nlm.nih.gov/41512536/)**  
  Jiacan Xu, Junnan Fang, Ruigang Wu, Yichen Wang, Chun Zhang, Xuming Wang · Microbiological research · 2026-01-04  
  _PI score:_ `1.994`  
  _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)

- **[Current research trends towards the control of protozoans in foods.](https://pubmed.ncbi.nlm.nih.gov/41885787/)**  
  Mariem Ayed, Vasco Cadavez, Ursula Gonzales-Barron · Italian journal of food safety · 2026-03-25  
  _PI score:_ `8.069`  
  _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…_
- **[MosquitoID: Rapid metagenomic sequencing for offline mosquito surveillance.](https://pubmed.ncbi.nlm.nih.gov/41895431/)**  
  Arianna Ceruti, Marina Bisia, Georgios Balatsos, Rea Maja Kobialka, Md Fahad Zamil, Anamul Hasan · Acta tropica · 2026-03-25  
  _PI score:_ `6.269`  
  _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…_
- **[TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection.](https://pubmed.ncbi.nlm.nih.gov/41923365/)**  
  Brian Merritt, Jeremy D Ratcliff, Stanley Ta, Gunars Osis, Matthew R Mauldin, Peter M Thielen · Bioinformatics (Oxford, England) · 2026-04-01  
  _PI score:_ `5.928`  
  _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…_
- **[Tools and approaches to study the human gut virome: from the bench to bioinformatics.](https://pubmed.ncbi.nlm.nih.gov/41636510/)**  
  Haley Anne Hallowell, Justin Malogan, Jotham Suez · mSystems · 2026-02-04  
  _PI score:_ `4.619`  
  _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 …_
- **[FALCON2: compression-based metagenomic classification of ancient viruses.](https://pubmed.ncbi.nlm.nih.gov/41913056/)**  
  Luis L Marques, Armando J Pinho, Diogo Pratas · Bioinformatics (Oxford, England) · 2026-03-30  
  _PI score:_ `4.311`  
  _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…_
- **[Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing.](https://pubmed.ncbi.nlm.nih.gov/41875869/)**  
  Holly N Kersey, Dominic J Acri, Luke C Dabin, Kelly A Hartigan, Richard Mustaklem, Jung Hyun Park · Cell reports methods · 2026-03-23  
  _PI score:_ `4.253`  
  _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…_
- **[Genomic Surveillance Reveals Emergence and Spread of Macrolide-Resistant Mycoplasma pneumoniae in Australia During the 2023-2024 Epidemic.](https://pubmed.ncbi.nlm.nih.gov/41861844/)**  
  Kingsley King-Gee Tam, Carl J E Suster, Winkie Fong, Tanya Golubchik, Varsha Sivalingam, Neisha Jeoffreys · The Journal of infectious diseases · 2026-03-21  
  _PI score:_ `4.237`  
  _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…_
- **[MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.](https://pubmed.ncbi.nlm.nih.gov/41918857/)**  
  Ahmet Arıhan Erözden, Nalan Tavşanlı, Gamze Demirel, Nazmiye Ozlem Sanli, Mahmut Çalışkan, Muzaffer Arıkan · PeerJ · 2026-03-27  
  _PI score:_ `4.086`  
  _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 …_
- **[Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.](https://pubmed.ncbi.nlm.nih.gov/41925227/)**  
  Feilong Deng, Yanhua Han, Yunjuan Peng, Zhijian Xu, Jianbo Yang, Jinling He · The ISME journal · 2026-04-02  
  _PI score:_ `2.536`  
  _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…_
- **[Feasibility of Low-Biomass Exhaled Breath Microbiome Sequencing Using a PDC-Sampler in Febrile and Healthy Individuals.](https://pubmed.ncbi.nlm.nih.gov/41921531/)**  
  Weihao Li, Manman Lv, Mengqing Cheng, Yemin Han, Haotian Yu, Yan Huang · Journal of breath research · 2026-04-01  
  _PI score:_ `2.528`  
  _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…_
- **[A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.](https://pubmed.ncbi.nlm.nih.gov/41913691/)**  
  Jesse Erens, Christopher Heine, Stefan Lötters, Henrik Krehenwinkel, Andrew J Crawford, Luis Alberto Rueda-Solano · Molecular ecology resources · 2026-04  
  _PI score:_ `2.528`  
  _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…_
- **[High-throughput single-cell proteomics and transcriptomics from same cells with a nanoliter-scale, spin-transfer approach.](https://pubmed.ncbi.nlm.nih.gov/41789571/)**  
  Pranav Dawar, Lye Meng Markillie, Sarah M Williams, Hugh D Mitchell, Johannes W Bagnoli, Joshua Cantlon-Bruce · Lab on a chip · 2026-03-31  
  _PI score:_ `2.519`  
  _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…_
- **[Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agent](https://pubmed.ncbi.nlm.nih.gov/41910375/)**  
  Gregory A Sprenger, Jay E Gee, Mindy G Elrod, Zachary P Weiner, Christopher A Gulvik · Microbiology spectrum · 2026-03-30  
  _PI score:_ `2.511`  
  _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_
- **[Pan-genome analysis and phylogenetic characterization of](https://pubmed.ncbi.nlm.nih.gov/41889316/)**  
  Hatoon A Niyazi, Hanouf A Niyazi, Hind AbdulMajed, Noha Juma, Noof Helmi, Mona Alqarni · Future microbiology · 2026-03-27  
  _PI score:_ `2.486`  
  _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…_
- **[A fast workflow to explore active enzymes from environmental samples through functional metagenomics.](https://pubmed.ncbi.nlm.nih.gov/41882344/)**  
  Arief Muammar, Endah Retnaningrum, Budi Setiadi Daryono, Irfan Dwidya Prijambada, Yuki Yashima, Clemens Peterbauer · Applied microbiology and biotechnology · 2026-03-25  
  _PI score:_ `2.469`  
  _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…_
- **[Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.](https://pubmed.ncbi.nlm.nih.gov/41879323/)**  
  Genevieve A Mortensen, Haley Schmidt, Predrag Radivojac, Yuzhen Ye, David M Haas · Microbiology spectrum · 2026-03-25  
  _PI score:_ `2.469`  
  _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…_
- **[Next generation sequencing approaches for the detection and characterization of enteroviruses in clinical, public health, and research settings: Expert view of the European non-polio enterovirus network (ENPEN).](https://pubmed.ncbi.nlm.nih.gov/41905022/)**  
  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  
  _PI score:_ `2.461`  
  _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 (…_
- **[Optimization of Fermentation Conditions Using Design of Experiment (DoE) to Enhance the Production of Antigenic Capsular Polysaccharides From Streptococcus pneumoniae Serotype 18C for Pneumococcal Vaccine Development.](https://pubmed.ncbi.nlm.nih.gov/41873143/)**  
  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  
  _PI score:_ `2.453`  
  _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…_
- **[MADRe: Strain-level Metagenomic Classification Through Assembly-Driven Database Reduction.](https://pubmed.ncbi.nlm.nih.gov/41871361/)**  
  Josipa Lipovac, Mile Šikić, Riccardo Vicedomini, Krešimir Križanović · GigaScience · 2026-03-23  
  _PI score:_ `2.453`  
  _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…_
- **[MEditome: Computational Detection of RNA Edit Sites Using](https://pubmed.ncbi.nlm.nih.gov/41869825/)**  
  Arpit Mehta, Vitalii Stebliankin, Kalai Mathee, Giri Narasimhan · Journal of computational biology : a journal of computational molecular cell biology · 2026-03-23  
  _PI score:_ `2.453`  
  _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 …_
- **[Natural Products from the Oral Microbiome.](https://pubmed.ncbi.nlm.nih.gov/41861238/)**  
  McKenna Loop Yao, Yitao Dai, Wenjun Zhang · Annual review of biochemistry · 2026-03-20  
  _PI score:_ `2.429`  
  _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…_
- **[Enhancing diabetic foot osteomyelitis diagnosis with metagenomics next-generation sequencing, proof of concept.](https://pubmed.ncbi.nlm.nih.gov/41693232/)**  
  Madjid Morsli, Chloé Magnan, Florian Salipante, Adeline Dubois, Sophie Schuldiner, Nicolas Cellier · Diabetic medicine : a journal of the British Diabetic Association · 2026-02-15  
  _PI score:_ `2.19`  
  _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…_
- **[Metagenomic next-generation sequencing enables early detection and outcome improvement in perioperative mucormycosis after liver transplantation: A single-center experience.](https://pubmed.ncbi.nlm.nih.gov/41579937/)**  
  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  
  _PI score:_ `2.042`  
  _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…_
- **[Fungal ecology in the age of 'omics.](https://pubmed.ncbi.nlm.nih.gov/41521629/)**  
  Brontë R Shelton, Joana Larrere, Diego Yusta Belsham, Marina Omacini, Andrés Argüelles-Moyao, Erika Buscardo · The New phytologist · 2026-01-11  
  _PI score:_ `1.981`  
  _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…_
- **[Mining bacterial (meta)genomes for enzymes active in aerobic, mesophilic conditions.](https://pubmed.ncbi.nlm.nih.gov/41490614/)**  
  Rodrigo Campos-Silva, Fahimeh Rahimi, Jaya Joshi, Cătălin Voiniciuc, Juannan Zhou, Andrew D Hanson · Analytical biochemistry · 2026-01-03  
  _PI score:_ `1.939`  
  _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)

- **[The landscape of machine learning approaches for modeling protein conformational ensembles.](https://pubmed.ncbi.nlm.nih.gov/41924827/)**  
  Samuel Sledzieski, Sonya M Hanson · Current opinion in structural biology · 2026-03-31  
  _PI score:_ `5.469`  
  _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 …_
- **[Enhancing Generalization and Scalability for Multi-Objective Optimization with Population Pre-Training.](https://pubmed.ncbi.nlm.nih.gov/41926713/)**  
  Haokai Hong, Liang Feng, Min Jiang, Kay Chen Tan · Evolutionary computation · 2026-03-27  
  _PI score:_ `5.436`  
  _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…_
- **[Integrating AI into clinical practice: Human-centered design requirements for next-generation sequencing workflows.](https://pubmed.ncbi.nlm.nih.gov/41921369/)**  
  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  
  _PI score:_ `4.944`  
  _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…_
- **[Forecasting influenza activity based on internet retrieval behavior and meteorological data in four megacities of China.](https://pubmed.ncbi.nlm.nih.gov/41928100/)**  
  Chun-Xi Shan, Yan-He Wang, Qiang Xu, Guo-Lin Wang, Chen-Long Lv, Li-Qun Fang · BMC infectious diseases · 2026-04-02  
  _PI score:_ `4.486`  
  _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…_
- **[DoTT-ML: Condition-aware detection of transcriptional readthrough from RNA-seq with optional ML-based prioritization.](https://pubmed.ncbi.nlm.nih.gov/41930502/)**  
  Michael Levin, Aizhan Surumbayeva, Max Li, Igor Astsaturov, Yunyun Zhou · Computational biology and chemistry · 2026-03-27  
  _PI score:_ `4.236`  
  _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…_
- **[DefensePredictor: A machine learning model to discover prokaryotic immune systems.](https://pubmed.ncbi.nlm.nih.gov/41926577/)**  
  Peter C DeWeirdt, Emily M Mahoney, Michael T Laub · Science (New York, N.Y.) · 2026-04-02  
  _PI score:_ `3.686`  
  _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…_
- **[Identifying barriers to human papillomavirus vaccination in China: a topic modelling analysis of social media (2018-2024).](https://pubmed.ncbi.nlm.nih.gov/41919197/)**  
  Zhijun Ding, Haoyun Yang, Yingchen Zhou, Chiyu Wang, Liyan Ma, Kana Ren · BMJ public health · 2026-03-26  
  _PI score:_ `3.627`  
  _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…_
- **[Protein Electrostatic Properties are Finetuned Through Evolution.](https://pubmed.ncbi.nlm.nih.gov/41928971/)**  
  Mingzhe Shen, Guy W Dayhoff, Daniel Kortzak, Jana Shen · bioRxiv : the preprint server for biology · 2026-03-29  
  _PI score:_ `3.452`  
  _Ionization states play crucial roles in protein functions. Yet despite decades of research, predicting protein p_
- **[Rapidly evolving aphid gall effector proteins exhibit saposin-like folds.](https://pubmed.ncbi.nlm.nih.gov/41928989/)**  
  Fatema Bhinderwala, Aishwarya Korgaonkar, Kota Gopalakrishna, Thomas C Mathers, Shuji Shigenobu, J Fernando Bazan · bioRxiv : the preprint server for biology · 2026-03-28  
  _PI score:_ `3.444`  
  _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…_
- **[Plasma proteomics identifies early markers of endothelial and inflammatory activation associated with dengue disease severity in children.](https://pubmed.ncbi.nlm.nih.gov/41929307/)**  
  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  
  _PI score:_ `3.403`  
  _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…_
- **[Automatically detecting trends and open questions from mental health publications: a Wellcome-funded GALENOS project.](https://pubmed.ncbi.nlm.nih.gov/41927103/)**  
  Janna Hastings, Marie Wosny, Jaycee Kennett, Ava Homiar, Gin S Malhi, Toshi A Furukawa · BMJ mental health · 2026-04-02  
  _PI score:_ `2.486`  
  _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…_
- **[Protein and genomic language models uncover the unexplored diversity of bacterial immunity.](https://pubmed.ncbi.nlm.nih.gov/41926572/)**  
  Ernest Mordret, Alexandre Hervé, Florian Tesson, Hugo Vaysset, Tyler Clabby, Arthur Loubat · Science (New York, N.Y.) · 2026-04-02  
  _PI score:_ `2.486`  
  _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…_
- **[Vietnamese Odonata: bridging global biodiversity, ecological, and conservation gaps in a changing world.](https://pubmed.ncbi.nlm.nih.gov/41922718/)**  
  Quoc Toan Phan, Huy Ngoc Nguyen, Khuong V Dinh · npj biodiversity · 2026-04-01  
  _PI score:_ `2.478`  
  _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…_
- **[A metabolite-augmented FIB-4 machine learning panel achieves superior liver fibrosis staging in chronic liver disease.](https://pubmed.ncbi.nlm.nih.gov/41923623/)**  
  Yuanyuan Chen, Tianbiao Yang, Tianlu Chen, Huanming Xiao, Kejun Zhou, Keke Ding · Cell reports. Medicine · 2026-03-31  
  _PI score:_ `2.469`  
  _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,…_
- **[Characterization of functional human-specific regulatory elements in prefrontal cortical cells.](https://pubmed.ncbi.nlm.nih.gov/41920741/)**  
  Bufan Jin, Langjian Zhu, Huizhong Chang, Yanrong Wei, Yuanchun Tang, Yue Gao · Cell reports · 2026-03-31  
  _PI score:_ `2.469`  
  _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…_
- **[Perspectives from machine learning and multi-omics to decoding the effects of VDAC2 malignant subsets on tumor evolution.](https://pubmed.ncbi.nlm.nih.gov/41917254/)**  
  Jianing Yan, Jingzhi Wang, Haotian Dong, Guoliang Ye, Yongfu Shao · NPJ precision oncology · 2026-03-31  
  _PI score:_ `2.469`  
  _VDAC2's known role in cancer and immune regulation via enhancing the CD8_
- **[Identification of a personalized eGFR threshold improves the prediction of kidney failure risk after transplantation.](https://pubmed.ncbi.nlm.nih.gov/41917186/)**  
  Symeon V Savvopoulos, Irina Scheffner, Andreas Reppas, Wilfried Gwinner, Haralampos Hatzikirou · Communications medicine · 2026-03-31  
  _PI score:_ `2.469`  
  _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…_
- **[Dictionary Multi-Modal Temporal Graph Learning.](https://pubmed.ncbi.nlm.nih.gov/41915508/)**  
  Meng Liu, Ke Liang, Miaomiao Li, Xueling Zhu, Xinwang Liu · IEEE transactions on pattern analysis and machine intelligence · 2026-03-31  
  _PI score:_ `2.469`  
  _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…_
- **[Machine learning-guided rational engineering of ACE2-derived peptides for broad-spectrum neutralization of SARS-CoV-2 variants.](https://pubmed.ncbi.nlm.nih.gov/41915253/)**  
  Mubarak A Alamri, Abdullah S Alawam · Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2026-03-31  
  _PI score:_ `2.469`  
  _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…_
- **[Short-chain fatty acid-producing microbes differentiate non-infectious and infectious neutropenic fever in leukemia.](https://pubmed.ncbi.nlm.nih.gov/41914747/)**  
  Samantha Franklin, Pranoti Sahasrabhojane, Tomo Hayase, Eiko Hayase, Chia-Chi Chang, Jayastu Senapati · mSystems · 2026-03-31  
  _PI score:_ `2.469`  
  _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…_
- **[Tetraspanin 7-mediated endothelial migrasomes unveil a novel mechanism of angiogenesis through the PI3K/AKT pathway in diabetic wound healing.](https://pubmed.ncbi.nlm.nih.gov/41921800/)**  
  Jie Wang, Miao Zhu, Zongzhe Jiang, Guohui Liao, Caimin Xu, Nan Jiang · International journal of biological macromolecules · 2026-03-30  
  _PI score:_ `2.461`  
  _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…_
- **[Integrating multi-omics data and artificial intelligence for personalized medicine in glioblastoma.](https://pubmed.ncbi.nlm.nih.gov/41921727/)**  
  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  
  _PI score:_ `2.461`  
  _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 …_
- **[Model-based assessment of historical and future soil PAHs trends in China under divergent energy scenarios.](https://pubmed.ncbi.nlm.nih.gov/41916242/)**  
  Shuo Dai, Qihuang Wang, Shuyou Zhang, Lei Huang, Songhe Zhang, Yijun Yao · Journal of environmental management · 2026-03-30  
  _PI score:_ `2.461`  
  _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…_
- **[Revisiting the NETs-CYBB-p38 MAPK axis in bronchiectasis: The underlying oxidative injury mechanism.](https://pubmed.ncbi.nlm.nih.gov/41916025/)**  
  Shaochu Zheng, Jinling Tang, Xiaopu Wu, Cao Qing, Yun Jiang, Wei Lu · Biochimica et biophysica acta. Molecular basis of disease · 2026-03-30  
  _PI score:_ `2.461`  
  _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…_
- **[Multiomics Research Strategies in Cancer: A Growing and Innovative Field.](https://pubmed.ncbi.nlm.nih.gov/41930321/)**  
  Zhenhua Du, Xiaomei Liu, Zhi Lv, Bengang Wang, Yu Xia, Wala Abduljabbar Mohammed Al-Duais · MedComm · 2026-03-24  
  _PI score:_ `2.411`  
  _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…_