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APOBEC3 mutagenesis drives therapy resistance in breast cancer Nat. Genet. (IF 31.7) Pub Date : 2025-05-16 Avantika Gupta, Andrea Gazzo, Pier Selenica, Anton Safonov, Fresia Pareja, Edaise M. da Silva, David N. Brown, Hong Shao, Yingjie Zhu, Juber Patel, Juan Blanco-Heredia, Bojana Stefanovska, Michael A. Carpenter, Yanjun Chen, Isabella Vegas, Xin Pei, Denise Frosina, Achim A. Jungbluth, Marc Ladanyi, Giuseppe Curigliano, Britta Weigelt, Nadeem Riaz, Simon N. Powell, Pedram Razavi, Reuben S. Harris, Jorge
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Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption Nat. Genet. (IF 31.7) Pub Date : 2025-05-16 Caroline Nava, Benjamin Cogne, Amandine Santini, Elsa Leitão, François Lecoquierre, Yuyang Chen, Sarah L. Stenton, Thomas Besnard, Solveig Heide, Sarah Baer, Abhilasha Jakhar, Sonja Neuser, Boris Keren, Anne Faudet, Sylvie Forlani, Marie Faoucher, Kevin Uguen, Konrad Platzer, Alexandra Afenjar, Jean-Luc Alessandri, Stephanie Andres, Chloé Angelini, Bernard Aral, Benoit Arveiler, Tania Attie-Bitach
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A new compression strategy to reduce the size of nanopore sequencing data Genome Res. (IF 6.2) Pub Date : 2025-05-15 Kavindu Jayasooriya, Sasha P Jenner, Pasindu Marasinghe, Udith Senanayake, Hassaan Saadat, David Taubman, Roshan Ragel, Hasindu Gamaarachchi, Ira W Deveson
Nanopore sequencing is an increasingly central tool for genomics. Despite rapid advances in the field, large data volumes and computational bottlenecks continue to pose major challenges. Here we introduce ex-zd, a new data compression strategy that helps address the large size of raw signal data generated during nanopore experiments. Ex-zd encompasses both a lossless compression method, which modestly
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Transcription factors form a ternary complex with NIPBL/MAU2 to localize cohesin at enhancers Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Gregory Fettweis, Kaustubh Wagh, Diana A Stavreva, Alba Jiménez-Panizo, Sohyoung Kim, Michelle Lion, Andrea Alegre-Martí, Lorenzo Rinaldi, Thomas A Johnson, Elise Gilson, Manan Krishnamurthy, Li Wang, David A Ball, Tatiana S Karpova, Arpita Upadhyaya, Didier Vertommen, Juan Fernández Recio, Eva Estébanez-Perpiñá, Franck Dequiedt, Gordon L Hager
While the cohesin complex is a key player in genome architecture, how it localizes to specific chromatin sites is not understood. Recently, we and others have proposed that direct interactions with transcription factors lead to the localization of the cohesin-loader complex (NIPBL/MAU2) within enhancers. Here, we identify two clusters of LxxLL motifs within the NIPBL sequence that regulate NIPBL dynamics
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A specialized TFIIB is required for transcription of transposon-targeting noncoding RNAs Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Xia Cai, Zhihao Zhai, Tomoko Noto, Gang Dong, Xue Wang, Mingmei Liucong, Yujie Liu, Christiane Agreiter, Josef Loidl, Kazufumi Mochizuki, Miao Tian
Transposable elements (TEs) pose threats to genome stability. Therefore, small RNA-mediated heterochromatinization suppresses the transcription and hence the mobility of TEs. Paradoxically, transcription of noncoding RNA (ncRNA) from TEs is needed for the production of TE-targeting small RNAs and/or recruiting the silencing machinery to TEs. Hence, specialized RNA polymerase II (Pol II) regulators
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Analysis of quadruplex propensity of aptamer sequences Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Anne Cucchiarini, Michaela Dobrovolná, Václav Brázda, Jean-Louis Mergny
Aptamers are short DNA or RNA sequences that can fold into unique three-dimensional structures, enabling them to bind specifically to target molecules with high affinity, similar to antibodies. A distinctive feature of many aptamers is their ability to adopt a G-quadruplex (G4) fold, a four-stranded structure formed by guanine-rich sequences. While G4 formation has been proposed or demonstrated for
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During recombinase-mediated homology recognition RecQ helicases inhibit formation of toxic long-lived D-loops that could promote genomic instability Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Claudia Danilowicz, Athalia Meron, Mara Prentiss
Mutations in RecQ family helicases underlie human genetic disorders associated with genomic instability and cancer predisposition, but questions remain about how properly functioning RecQ reduces these deleterious effects. Importantly, some of the deleterious effects may result from incorrect repair of DNA double-strand breaks (DSBs) by recombinase proteins. Displacement loops (D-loops) are three-strand
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CRISPR-BEasy: a free web-based service for designing sgRNA tiling libraries for CRISPR-dependent base editing screens Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Vincent Chapdelaine-Trépanier, Shamika Shenoy, Wardah Masud, Amisha Minju-OP, Marie-Anne Bérubé, Sebastian Schönherr, Lukas Forer, Amélie Fradet-Turcotte, Daniel Taliun, Raquel Cuella-Martin
CRISPR-dependent base editing (BE) enables the modeling and correction of genetic mutations at single-base resolution. Base editing screens, where point mutations are queried en masse, are powerful tools to systematically draw genotype–phenotype associations and characterise the function of genes and other genomic elements. However, the lack of user-friendly web-based tools for designing base editing
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Onkopus: precise interpretation and prioritization of sequence variants for biomedical research and precision medicine Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Nadine S Kurz, Kevin Kornrumpf, Tim Tucholski, Klara Drofenik, Alexander König, Tim Beißbarth, Jürgen Dönitz
One of the major challenges in precision oncology is the identification of pathogenic, actionable variants and the selection of personalized treatments. We present Onkopus, a variant interpretation framework based on a modular architecture, for interpreting and prioritizing genetic alterations in cancer patients. A multitude of tools and databases are integrated into Onkopus to provide a comprehensive
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ASOptimizer: optimizing chemical diversity of antisense oligonucleotides through deep learning Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Seokjun Kang, Daehwan Lee, Gyeongjo Hwang, Kiwon Lee, Mingeun Kang
Antisense oligonucleotides (ASOs) are a promising class of gene therapies that can modulate the gene expression. However, designing ASOs manually is resource-intensive and time-consuming. To address this, we introduce a user-friendly web server for ASOptimizer, a deep learning-based computational framework for optimizing ASO sequences and chemical modifications. Given a user-provided ASO sequence,
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LitSense 2.0: AI-powered biomedical information retrieval with sentence and passage level knowledge discovery. Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Lana Yeganova,Won Kim,Shubo Tian,Donald C Comeau,W John Wilbur,Zhiyong Lu
LitSense 2.0 (https://www.ncbi.nlm.nih.gov/research/litsense2/) is an advanced biomedical search system enhanced with dense vector semantic retrieval, designed for accessing literature on sentence and paragraph levels. It provides unified access to 38 million PubMed abstracts and 6.6 million full-length articles in the PubMed Central (PMC) Open Access subset, encompassing 1.4 billion sentences and
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LIGYSIS-web: a resource for the analysis of protein-ligand binding sites Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Javier S Utgés, Stuart A MacGowan, Geoffrey J Barton
LIGYSIS-web is a free website accessible to all users without any login requirement for the analysis of protein-ligand binding sites. LIGYSIS-web hosts a database of 65,000 protein-ligand binding sites across 25,000 proteins. LIGYSIS sites are defined by aggregating unique relevant protein–ligand interfaces across different biological assemblies of the same protein deposited on the PDBe. Additionally
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CapBuild: a cloud-native tool for adeno-associated virus capsid engineering. Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Anne H Klein,Michael J Kuiper,Mark Burgess,Anuradha Wickramarachchi,Yatish Jain,Denis C Bauer,Laurence Wilson
Adeno-associated virus (AAV) capsid engineering is essential for advancing gene therapy but remains limited by structural complexity and computational constraints. To address these challenges, we developed CapBuild, a cloud-native web server that streamlines AAV capsid prediction, assembly and engineering. CapBuild provides two distinct workflows: a PDB-based pipeline for assembling complete capsids
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CellHit: a web server to predict and analyze cancer patients’ drug responsiveness Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Francesco Carli, Natalia De Oliveira Rosa, Simon Blotas, Pierluigi Di Chiaro, Luisa Bisceglia, Mariangela Morelli, Francesca Lessi, Anna Luisa Di Stefano, Chiara Maria Mazzanti, Gioacchino Natoli, Francesco Raimondi
We present the CellHit web server (https://cellhit.bioinfolab.sns.it/), a web-based platform designed to predict and analyze cancer patients’ responsiveness to drugs using transcriptomic data. By leveraging extensive pharmacogenomics datasets from the Genomics of Drug Sensitivity in Cancer v1 and v2 (GDSC) and Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) and transcriptomic data
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ClusterONE Web: a tool for discovering and analyzing overlapping protein complexes Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-16 Marcelo Baez, Ruben Jimenez, Luca Cernuzzi, Alberto Paccanaro
Protein–protein interactions (PPIs) are central to many cellular processes, and the assembly of proteins into complexes is essential for biological function. Clustering with overlapping neighborhood expansion (ClusterONE) has been successfully used to detect overlapping protein complexes in both weighted and unweighted PPI networks. Here, we present ClusterONE Web, a freely available, web-based tool
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Methodological opportunities in genomic data analysis to advance health equity Nat. Rev. Genet. (IF 39.1) Pub Date : 2025-05-15 Brieuc Lehmann, Leandra Bräuninger, Yoonsu Cho, Fabian Falck, Smera Jayadeva, Michael Katell, Thuy Nguyen, Antonella Perini, Sam Tallman, Maxine Mackintosh, Matt Silver, Karoline Kuchenbäcker, David Leslie, Nilanjan Chatterjee, Chris Holmes
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Cell-type deconvolution methods for spatial transcriptomics Nat. Rev. Genet. (IF 39.1) Pub Date : 2025-05-14 Lucie C. Gaspard-Boulinc, Luca Gortana, Thomas Walter, Emmanuel Barillot, Florence M. G. Cavalli
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Preventing polyglutamine assembly Nat. Genet. (IF 31.7) Pub Date : 2025-05-14 Kyle Vogan
Huntington’s disease belongs to a class of repeat expansion disorders whose pathology is marked by the expression of toxic polyglutamine-containing proteins that assemble into insoluble protein aggregates. To study factors that influence the solubility of native polyglutamine-containing proteins, Saad et al. focused on FOXP2, a transcription factor harboring a stretch of 40 consecutive glutamines.
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Nanoscale-folding of mitotic chromosomes Nat. Genet. (IF 31.7) Pub Date : 2025-05-14 Petra Gross
The mechanisms underlying the extreme folding and contraction of genomic DNA into mitotic chromosomes remain incompletely understood. To address this, Jan Ellenberg and colleagues applied a DNA-tracing approach previously established for interphase cells that is based on fitting of sequentially resolved DNA fluorescence in situ hybridization (FISH) signals, using a FISH probe library they designed
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A systematic assessment of transcription factor function Nat. Genet. (IF 31.7) Pub Date : 2025-05-14 Chiara Anania
In eukaryotes, transcription factors (TFs) are known to regulate transcription by binding to the enhancers and promoters of target genes. Despite extensive research on this topic, numerous questions about TF specificity, cooperativity and function remain unanswered. To address some of these in a systematic way, Mahendrawada et al. used yeast as a model organism, owing to its relatively small number
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Complete genomes of six ape species Nat. Genet. (IF 31.7) Pub Date : 2025-05-14 Wei Li
Living ape species are close evolutionary relatives of humans and their genomes are essential for human genomic and evolutionary studies. Yoo et al. generated complete genome assemblies of six ape species: chimpanzee (Pan troglodytes), bonobo (Pan paniscus), gorilla (Gorilla gorilla), Bornean orangutan (Pongo pygmaeus), Sumatran orangutan (Pongo abelii) and siamang (Symphalangus syndactylus). For diploid
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New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis Genome Biol. (IF 10.1) Pub Date : 2025-05-14 Bingchao Wu, Dan Luo, Yuesen Yue, Haidong Yan, Min He, Xixi Ma, Bingyu Zhao, Bin Xu, Jie Zhu, Jing Wang, Jiyuan Jia, Min Sun, Zheni Xie, Xiaoshan Wang, Linkai Huang
Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear. Here, we present a high-quality haplotype-resolved genome of the upland ecotype “Jingji31.” We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative
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Charting the regulatory landscape of TP53 on transposable elements in cancer Genome Res. (IF 6.2) Pub Date : 2025-05-13 Xuan Qu, Yonghao Liang, Colin McCornack, Xiaoyun Xing, Heather Schmidt, Chad Tomlinson, Catrina Fronick, Edward A. Belter, Jr., Juan F. Macias-Velasco, Ting Wang
The relationship between TP53 and transposable elements (TEs) has been obscure. Given the important role of TEs in oncogenesis, a comprehensive profiling of TE expression dynamics under the regulation of TP53 provides valuable resources for more clarity in TP53's roles in cancer. In this study, we characterized the TE transcriptomic landscape using long-read RNA-seq and short-read RNA-seq in three
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Tissular chromatin states cartography based on double-barcoded DNA arrays capturing unloaded PA-Tn5 Transposase Genome Res. (IF 6.2) Pub Date : 2025-05-13 Maria Grazia Mendoza-Ferri, Gwendoline Lozachmeur, Maximilien Duvina, Laetitia Perret, Didier Merciris, Anne Gigout, Marco Antonio Mendoza-Parra
Recent developments in spatial omics are revoluzionating our understanding of tissue structures organization and their deregulation in disease. Here, we present a strategy for capturing chromatin histone modification signatures across tissue sections by taking advantage of a double-barcoded DNA arrays design compatible with in situ protein A-Transposase Tn5 tagmentation. This approach has been validated
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Ribosome association inhibits stress-induced gene mRNA localization to stress granules Genes Dev. (IF 7.5) Pub Date : 2025-05-13 Noah S. Helton, Benjamin Dodd, Stephanie L. Moon
The integrated stress response (ISR) is critical for resilience to stress and is implicated in numerous diseases. During the ISR, translation is repressed, stress-induced genes are expressed, and mRNAs condense into stress granules. The relationship between stress granules and stress-induced gene expression is unclear. We measured endogenous stress-induced gene mRNA localization at the single-molecule
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Cell type- and factor-specific nonsense-mediated RNA decay Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-14 Kun Tan, Jonathan Sebat, Miles F Wilkinson
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that influences several biological processes. Specific features in messenger RNAs (mRNAs) have been found to trigger decay by NMD, leading to the assumption that NMD sensitivity is an intrinsic quality of a given transcript. Here, we provide evidence that, instead, an overriding factor dictating NMD sensitivity is the cell
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MOBHunter: a data integration platform for identification and classification of mobile genetic elements in microbial genomes Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-14 Camila Rojas-Villalobos, Francisco J Ossandon, Camila Castillo-Vilcahuaman, Pedro Sepúlveda-Rebolledo, David Castro-Salinas, Abraham Zapata-Araya, Dilanaz Arisan, Tomás Perez-Acle, Francisco Issotta, Raquel Quatrini, Ana Moya-Beltrán
Horizontal gene transfer plays a critical role in microbial genome evolution and adaptation. Integrated foreign DNA fragments encompass various types of mobile genetic elements (MGEs), ranging from small transposons to conspicuous integrative and conjugative elements. These regions often confer advantageous traits, including antibiotic resistance or novel metabolic capabilities, and contain foreign
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M1CR0B1AL1Z3R 2.0: an enhanced web server for comparative analysis of bacterial genomes at scale Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-14 Yair Shimony, Edo Dotan, Elya Wygoda, Naama Wagner, Iris Lyubman, Noa Ecker, Gianna Durante, Gal Mishan, Jeff H Chang, Oren Avram, Tal Pupko
Large-scale analyses of bacterial genomic datasets contribute to the comprehensive characterization of complex microbial dynamics among different strains and species. Such analyses often include open reading frame extraction, orthogroup inference, phylogeny reconstruction, and functional annotation of proteins. We have previously developed the M1CR0B1AL1Z3R web server, a “one-stop shop” for conducting
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DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-14 Ziying Zhang, Liang Xu, Shuai Zhang, Chunxiang Peng, Guijun Zhang, Xiaogen Zhou
Atomic structure modeling is a crucial step in determining the structures of protein complexes using cryo-electron microscopy (cryo-EM). This work introduces DEMO-EMol, an improved server that integrates deep learning-based map segmentation and chain fitting to accurately assemble protein–nucleic acid (NA) complex structures from cryo-EM density maps. Starting from a density map and independently modeled
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CausalCCC: a web server to explore intracellular causal pathways enabling cell–cell communication Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-14 Louise Dupuis, Orianne Debeaupuis, Franck Simon, Hervé Isambert
Understanding cell–cell communication (CCC) pathways from single-cell or spatial transcriptomic data is key to unraveling biological processes. Recently, multiple CCC methods have been developed but primarily focus on refining ligand–receptor (L-R) interaction scores. A critical gap for a more comprehensive picture of cellular crosstalks lies in the integration of upstream and downstream intracellular
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CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-14 Karol Wróblewski, Mateusz Zalewski, Aleksander Kuriata, Sebastian Kmiecik
Simulating protein structure flexibility using classical methods is computationally demanding, especially for large proteins. To address this challenge, we have been developing the CABS-flex method, which enables fast simulations of protein structural flexibility by combining a coarse-grained simulation approach with all-atom detail. Previously available as the CABS-flex 2.0 web server, the method
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MAGNETIC: a web server to fetch gene network based on motif distribution in promoters Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-14 Atreyi Chakraborty, Saksham Srimali, Rohan Topno, Ajinkya Ranshur, Mallur Srivatsan Madhusudhan
Our web server MAGNETIC (Motif Associated Gene NETworks in Chromosomes) allows users to search the human genome for correlations between promoter regions of genes. The correlations take into consideration the similarity of the abundance of 5/6-mer motifs in gene promoters. The promoters could be 1, 2, or 6 kb upstream of the gene start site. Genes with similar motif abundances are linked to form a
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Predicting gene expression from DNA sequence using deep learning models Nat. Rev. Genet. (IF 39.1) Pub Date : 2025-05-13 Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel, Jeroen de Ridder
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Genome-wide analyses identify 30 loci associated with obsessive–compulsive disorder Nat. Genet. (IF 31.7) Pub Date : 2025-05-13 Nora I. Strom, Zachary F. Gerring, Marco Galimberti, Dongmei Yu, Matthew W. Halvorsen, Abdel Abdellaoui, Cristina Rodriguez-Fontenla, Julia M. Sealock, Tim Bigdeli, Jonathan R. Coleman, Behrang Mahjani, Jackson G. Thorp, Katharina Bey, Christie L. Burton, Jurjen J. Luykx, Gwyneth Zai, Silvia Alemany, Christine Andre, Kathleen D. Askland, Julia Bäckman, Nerisa Banaj, Cristina Barlassina, Judith Becker
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STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data Genome Res. (IF 6.2) Pub Date : 2025-05-12 Congcong Hu, Nana Wei, Jiyuan Yang, Hua-Jun Wu, Xiaoqi Zheng
The rapid advance of spatially resolved transcriptomics technologies has yielded substantial spatial transcriptomics data. Deriving biological insights from these data poses nontrivial computational and analysis challenges, of which the most fundamental step is spatial domain detection (or spatial clustering). Although a number of tools for spatial domain detection have been proposed in recent years
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AutoMLST2: a web server for phylogeny and microbial taxonomy. Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-13 Bita Pourmohsenin,Arthur Wiese,Nadine Ziemert
Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology, ecology, and drug discovery, yet it remains a challenging task. AutoMLST2 (https://automlst2.ziemertlab.com) is a web server designed to facilitate automated phylogenetic reconstruction and microbial taxonomy analysis for bacterial and archaeal genomes.
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DIGITtally—a new tool for streamlining and simplifying Drosophila melanogaster meta-analysis Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-13 Andrew Gillen, Shannon Keenan, Maiken Skov, Mehwish Akram, Shireen A Davies, Julian A T Dow
Drosophila melanogaster has one of the deepest research bases within the life sciences, with a wealth of high-quality tissue- and cell type-specific transcriptomic data available. However, integrating large datasets derived from disparate sources is not trivial. We have designed a broadly applicable solution to this problem in the form of the Drosophila Interesting Genes in Individual Tissues-tally
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BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-13 Jennifer Vendetti, Nomi L Harris, Michael V Dorf, Alex Skrenchuk, J Harry Caufield, Rafael S Gonçalves, John B Graybeal, Harshad Hegde, Timothy Redmond, Christopher J Mungall, Mark A Musen
BioPortal (https://bioportal.bioontology.org) is the world’s most comprehensive repository of biomedical ontologies. It provides infrastructure for finding, sharing, searching, and utilizing biomedical ontologies. Launched in 2005, BioPortal now includes 1549 ontologies (1182 of them public). Its open, freely accessible website enables anyone (i) to browse the ontology library, (ii) to search for terms
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Simultaneous single-cell sequencing of RNA and DNA at scale with DEFND-seq Nat. Rev. Genet. (IF 39.1) Pub Date : 2025-05-12 Timothy R. Olsen
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X-linked competition — implications for human development and disease Nat. Rev. Genet. (IF 39.1) Pub Date : 2025-05-12 Philip M. Boone, Teresa Buenaventura, James W. D. King, Matthias Merkenschlager
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Genomics of schizophrenia, bipolar disorder and major depressive disorder Nat. Rev. Genet. (IF 39.1) Pub Date : 2025-05-12 Michael J. Owen, Nicholas J. Bray, James T. R. Walters, Michael C. O’Donovan
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An integrated transcriptomic cell atlas of human endoderm-derived organoids Nat. Genet. (IF 31.7) Pub Date : 2025-05-12 Quan Xu, Lennard Halle, Soroor Hediyeh-zadeh, Merel Kuijs, Rya Riedweg, Umut Kilik, Timothy Recaldin, Qianhui Yu, Isabell Rall, Tristan Frum, Lukas Adam, Shrey Parikh, Raphael Kfuri-Rubens, Manuel Gander, Dominik Klein, Fabiola Curion, Zhisong He, Jonas Simon Fleck, Koen Oost, Maurice Kahnwald, Silvia Barbiero, Olga Mitrofanova, Grzegorz Jerzy Maciag, Kim B. Jensen, Matthias Lutolf, Prisca Liberali
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Three-dimensional genome landscape of primary human cancers Nat. Genet. (IF 31.7) Pub Date : 2025-05-12 Kathryn E. Yost, Yanding Zhao, King L. Hung, Kaiyuan Zhu, Duo Xu, M. Ryan Corces, Shadi Shams, Bryan H. Louie, Shahab Sarmashghi, Laksshman Sundaram, Jens Luebeck, Stanley Clarke, Ashley S. Doane, Jeffrey M. Granja, Hani Choudhry, Marcin Imieliński, Andrew D. Cherniack, Ekta Khurana, Vineet Bafna, Ina Felau, Jean C. Zenklusen, Peter W. Laird, Christina Curtis, William J. Greenleaf, Howard Y. Chang
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Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells Genome Biol. (IF 10.1) Pub Date : 2025-05-12 Judith Hyle, Wenjie Qi, Mohamed Nadhir Djekidel, Wojciech Rosikiewicz, Beisi Xu, Chunliang Li
CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies report that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq. Here, we investigate RNA’s
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One but not the same — the many genomes of the brain Nat. Rev. Genet. (IF 39.1) Pub Date : 2025-05-09 Tracy A. Bedrosian
In this Journal Club, Tracy Bedrosian describes a 2001 paper by Rehen et al. that provided early evidence of pervasive somatic variation throughout the human brain.
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Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay Genome Res. (IF 6.2) Pub Date : 2025-05-09 Marcus J. Viscardi, Enisha Sehgal, Joshua A. Arribere
Premature stop codon–containing mRNAs can produce truncated and dominantly acting proteins that harm cells. Eukaryotic cells protect themselves by degrading such mRNAs via the nonsense-mediated mRNA decay (NMD) pathway. The precise reactions by which cells attack NMD-target mRNAs remain obscure, precluding a biochemical understanding of NMD and hampering therapeutic efforts to control NMD. Here, we
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Drosha: a new tumor suppressor in pineoblastoma Genes Dev. (IF 7.5) Pub Date : 2025-05-09 Zhixuan Huang, Xueli Ren, Jian Hu
To investigate the pathogenesis and target the vulnerability of human pineoblastoma, researchers have developed multiple genetically engineered mouse models that represent distinct molecular subtypes of the disease. In this issue of Genes & Development, Fraire and colleagues (doi:10.1101/gad.352485.124) examined the roles of key microRNA (miRNA) processing components Drosha and Dicer1. Loss of either
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Cohesin in 3D: development, differentiation, and disease Genes Dev. (IF 7.5) Pub Date : 2025-05-09 Maria Solé-Ferran, Ana Losada
Cohesin contributes to genome spatial organization and sister chromatid cohesion. In this way, it not only supports accurate chromosome segregation and efficient DNA repair but also regulates gene expression. These functions are essential during embryonic development, the process that converts the fertilized egg into a complex organism with billions of specialized cells organized into tissues and organs
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Specific branches of the proteostasis network regulate the toxicity associated with mistranslation. Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 Donovan W McDonald,Rebecca N Dib,Christopher De Luca,Ashmi Shah,Martin L Duennwald
All cellular functions rely on accurate protein biosynthesis. Yet, many variants of transfer RNA (tRNA) genes that induce amino acid misincorporation are found in human genomes. Mistranslation induces pleiotropic effects on proteostasis, ranging from protein misfolding to impaired protein biosynthesis and degradation. We employ Saccharomyces cerevisiae (budding yeast), a genetically and biochemically
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CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 David Farré-Gil, Genis Bayarri, Charles A Laughton, Adam Hospital, Modesto Orozco
We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the user to obtain a dynamic representation of long segments of linear, circular, or protein–DNA segments thanks to a Langevin dynamics coarse-grained (CG) model working with a machine-learning (ML) fitted C1′-resolution Hamiltonian. The CG trajectories can
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Unveiling the multifaceted domain polymorphism of the Menshen antiphage system Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 Huan Li, Yongjun Tan, Dwaipayan Basu, Kevin D Corbett, Dapeng Zhang
Recent advances have significantly enriched our understanding of complex bacteria–phage interactions. To date, over one hundred bacterial antiphage systems have been identified, yet the mechanisms of many, including the recently discovered Menshen system, remain elusive. We employed comparative genomics and protein bioinformatics for a systematic investigation of the Menshen system, focusing on its
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Emergence of CpG-cluster blanket methylation in aged tissues: a novel signature of epigenomic aging Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 Yong-Kook Kang, Byungkuk Min, Jaemin Eom, Jung Sun Park, Jaewoong Jang, Sangkyun Jeong
Aging is accompanied by widespread DNA methylation changes across the genome. While age-related methylation studies typically focus on individual CpGs, cluster analysis provides more robust data and improved interpretation. We characterized age-associated CpG-cluster methylation changes in mouse spleens, peripheral blood mononuclear cells, and livers. We identified a novel signature termed blanket
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Laboratory evolution of the bacterial genome structure through insertion sequence activation Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 Yuki Kanai, Atsushi Shibai, Naomi Yokoi, Saburo Tsuru, Chikara Furusawa
The genome structure fundamentally shapes bacterial physiology, ecology, and evolution. Though insertion sequences (IS) are known drivers of drastic evolutionary changes in the genome structure, the process is typically slow and challenging to observe in the laboratory. Here, we developed a system to accelerate IS-mediated genome structure evolution by introducing multiple copies of a high-activity
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AmrProfiler: a comprehensive tool for identifying antimicrobial resistance genes and mutations across species Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 Anargyros Skoulakis, Vasiliki Kostoula, Konstantinos Daniilidis, Christos-Georgios Gkountinoudis, Efthymia Petinaki, Artemis G Hatzigeorgiou
Antimicrobial resistance (AMR) remains a critical challenge in public health and research. AmrProfiler is a comprehensive tool with three specialized modules: identifying acquired AMR genes, resistance-associated mutations, and ribosomal RNA (rRNA) gene mutations across nearly 18 000 bacterial species. By integrating and refining data from established databases, it provides a robust framework for AMR
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PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 Ondřej Schindler, Tomáš Svoboda, Adrián Rošinec, Tomáš Raček, Gabriela Bučeková, Dominik Tichý, Karel Berka, Radka Svobodová
The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230 000 experimentally determined structures. The chemical reactivity of proteins is based on the electron density distribution, which is usually approximated by partial atomic charges. However, because of the size and high variability, there is not yet a universal and accurate
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ReQuant: improved base modification calling by k-mer value imputation Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 Roy Straver, Carlo Vermeulen, Joe R Verity-Legg, Marc Pagès-Gallego, Dieter G G Stoker, Alexander van Oudenaarden, Jeroen de Ridder
Nanopore sequencing allows identification of base modifications, such as methylation, directly from raw current data. Prevailing approaches, including deep learning (DL) methods, require training data covering all possible sequence contexts. These data can be prohibitively expensive or impossible to obtain for some modifications. Hence, research into DNA modifications focuses on the most prevalent
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PLIP 2025: introducing protein–protein interactions to the protein–ligand interaction profiler Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-10 Philipp Schake, Sarah Naomi Bolz, Katja Linnemann, Michael Schroeder
PLIP, the protein–ligand interaction profiler, analyses molecular interactions in protein structures. PLIP detects eight types of non-covalent interactions. Initially focused on small-molecule, DNA, and RNA interactions to a protein, the current release incorporates protein–protein interactions. We document the usefulness of this feature by comparing PLIP interactions of the cancer drug venetoclax
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Parent-of-origin regulation by maternal auts2 shapes neurodevelopment and behavior in fish Genome Biol. (IF 10.1) Pub Date : 2025-05-09 Antoine Emile Clément, Constance Merdrignac, Sergi Roig Puiggros, Dorine Sévère, Aurélien Brionne, Thomas Lafond, Thaovi Nguyen, Jérôme Montfort, Cervin Guyomar, Alexandra Dauvé, Amaury Herpin, Denis Jabaudon, Violaine Colson, Florent Murat, Julien Bobe
Parental experience can influence progeny behavior through gamete-mediated non-genetic inheritance, that is, mechanisms that do not involve changes in inherited DNA sequence. However, underlying mechanisms remain poorly understood in vertebrates, especially for maternal effects. Here, we use the medaka, a model fish species, to investigate the role of auts2a, the ortholog of human AUTS2, a gene repressed
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Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations Genome Biol. (IF 10.1) Pub Date : 2025-05-09 Sebastian Gregoricchio, Aleksandar Kojic, Marlous Hoogstraat, Karianne Schuurman, Suzan Stelloo, Tesa M. Severson, Tracy A. O’Mara, Marjolein Droog, Abhishek A. Singh, Dylan M. Glubb, Lodewyk F. A. Wessels, Michiel Vermeulen, Flora E. van Leeuwen, Wilbert Zwart
The incidence and mortality of endometrial cancer (EC) is on the rise. Eighty-five percent of ECs depend on estrogen receptor alpha (ERα) for proliferation, but little is known about its transcriptional regulation in these tumors. We generate epigenomics, transcriptomics, and Hi-C datastreams in healthy and tumor endometrial tissues, identifying robust ERα reprogramming and profound alterations in