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Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
- Zhitao Huang,
- Ruiqing Zheng,
- Pengzhen Jia,
- Xuhua Yan,
- Jinmiao Chen,
- and Min Li
Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
...between scRNA-seq and scATAC-seq pose challenges for identifying different cell types, which hinders the discovery of novel types. In this study, we propose a new label transfer tool scSHEFT, which simultaneously considers gene expression count data, peak count data, and Gene Activity Scores as inputs...
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Method: Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses
- Xiuhao Fu,
- Chao Yang,
- Chunyan Cui,
- Aoyun Geng,
- Yidi Sun,
- Chao Zha,
- Feifei Cui,
- Leyi Wei,
- Quan Zou,
- Xin Gao,
- and Zilong Zhang
Genome Res. March 26, 2026 gr.281523.125; Published in Advance March 26, 2026, doi:10.1101/gr.281523.125
...), King Abdullah University of Science and Technology (KAUST), Thuwal, 239556900, Saudi Arabia 3Centre for Artificial Intelligence driven Drug Discovery, Faculty of Applied Science, Macao Polytechnic University, Macao SAR, China 4Institute of Fundamental and Frontier Sciences, University of Electronic...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...). However, because MGEs are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short term and long term. By combining comparative...
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Research: Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
- Héloïse Muller,
- Rosina Savisaar,
- Jean Peccoud,
- Sylvain Charlat,
- and Clément Gilbert
Genome Res. September 2025 35: 2011-2022; Published in Advance August 8, 2025, doi:10.1101/gr.280432.125
...considered similar to each other). We then compared the mean number of transfers per pair of species occupying similar habitats to that measured per pair of species occupying different habitats. To account for the confounding effect of species relatedness on transfer rates, comparisons were restricted...
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Resource: The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
- Simon Bray,
- John Chilton,
- Matthias Bernt,
- Nicola Soranzo,
- Marius van den Beek,
- Bérénice Batut,
- Helena Rasche,
- Martin Čech,
- Peter J.A. Cock,
- Björn Grüning,
- and Anton Nekrutenko
Genome Res. February 2023 33: 261-268; Published in Advance February 24, 2023, doi:10.1101/gr.276963.122
..., United Kingdom ↵7 These authors contributed equally to this work. Corresponding author: aun1@psu.eduAbstractThere are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing...
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Method: Predicting transfer RNA gene activity from sequence and genome context
- Bryan P. Thornlow,
- Joel Armstrong,
- Andrew D. Holmes,
- Jonathan M. Howard,
- Russell B. Corbett-Detig,
- and Todd M. Lowe
Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
...Predicting transfer RNA gene activity from sequence and context Bryan P. Thornlow1, Joel Armstrong1,2, Andrew D. Holmes1, Jonathan M. Howard1, Russell B. Corbett-Detig1,2 and Todd M. Lowe1,2 1Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA; 2...
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Resource: EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow
- Wagner C.S. Magalhães,
- Nathalia M. Araujo,
- Thiago P. Leal,
- Gilderlanio S. Araujo,
- Paula J.S. Viriato,
- Fernanda S. Kehdy,
- Gustavo N. Costa,
- Mauricio L. Barreto,
- Bernardo L. Horta,
- Maria Fernanda Lima-Costa,
- Alexandre C. Pereira,
- Eduardo Tarazona-Santos,
- Maíra R. Rodrigues,
- and The Brazilian EPIGEN Consortium
Genome Res. July 2018 28: 1090-1095; Published in Advance June 14, 2018, doi:10.1101/gr.225458.117
...). This limits the worldwide flow of bioinformatics knowledge necessary to build and train research groups with a solid bioinformatics background. Although there are several claims for more transparency and reproducibility of all the scientific process in biomedical literature (Sandve et al. 2013; Kolker et al...
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Research: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
- Young Seok Ju,
- Jose M.C. Tubio,
- William Mifsud,
- Beiyuan Fu,
- Helen R. Davies,
- Manasa Ramakrishna,
- Yilong Li,
- Lucy Yates,
- Gunes Gundem,
- Patrick S. Tarpey,
- Sam Behjati,
- Elli Papaemmanuil,
- Sancha Martin,
- Anthony Fullam,
- Moritz Gerstung,
- ICGC Prostate Cancer Working Group,
- ICGC Bone Cancer Working Group,
- ICGC Breast Cancer Working Group,
- Jyoti Nangalia,
- Anthony R. Green,
- Carlos Caldas,
- Åke Borg,
- Andrew Tutt,
- Ming Ta Michael Lee,
- Laura J. van't Veer,
- Benita K.T. Tan,
- Samuel Aparicio,
- Paul N. Span,
- John W.M. Martens,
- Stian Knappskog,
- Anne Vincent-Salomon,
- Anne-Lise Børresen-Dale,
- Jórunn Erla Eyfjörd,
- Ola Myklebost,
- Adrienne M. Flanagan,
- Christopher Foster,
- David E. Neal,
- Colin Cooper,
- Rosalind Eeles,
- G. Steven Bova,
- Sunil R. Lakhani,
- Christine Desmedt,
- Gilles Thomas,
- Andrea L. Richardson,
- Colin A. Purdie,
- Alastair M. Thompson,
- Ultan McDermott,
- Fengtang Yang,
- Serena Nik-Zainal,
- Peter J. Campbell,
- and Michael R. Stratton
Genome Res. June 2015 25: 814-824; Published in Advance May 11, 2015, doi:10.1101/gr.190470.115
.... 1991), de novo nuclear transfer of mtDNA in animal somatic tissues has not previously been comprehensively studied to our knowledge. To investigate the possibility of somatic mitochondrial-nuclear DNA fusion, we analyzed next-generation paired-end DNA whole- sequencing data from559 primary cancers, 28...
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Research: Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla_KPC
- Angela Gomez-Simmonds,
- Medini K. Annavajhala,
- Dwayne Seeram,
- Todd W. Hokunson,
- Heekuk Park,
- and Anne-Catrin Uhlemann
Genome Res. November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124
....columbia.edu; agomezsimmonds@ucdavis.eduAbstractTransmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long...
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PERSPECTIVE: Grains of knowledge: Genomics of model cereals
- Andrew H. Paterson,
- Michael Freeling,
- and Takuji Sasaki
Genome Res. December 2005 15: 1643-1650; doi:10.1101/gr.3725905
...Grains of knowledge: Genomics of model cereals Andrew H. Paterson 1 , 4 , Michael Freeling 2 , and Takuji Sasaki 3 1 Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA 2 Department of Plant...

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