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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...Qinhu Zhang1,2, Siguo Wang1, Zhipeng Li1, Wenzheng Bao3, Wenjian Liu4 and De-Shuang Huang1,5 1Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo 315201, China; 2Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning, 530007, China; 3School...
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Method: ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods
- Jiaxin Luo,
- Minghua Deng,
- Xuegong Zhang,
- and Xiaoqiang Sun
Genome Res. October 2023 33: 1788-1805; Published in Advance October 12, 2023, doi:10.1101/gr.278001.123
...Bioinformatics Division of BNRIST and Department of Automation, MOE Key Lab of Bioinformatics, Tsinghua University, Beijing, 100084, China Corresponding author: sunxq6@mail.sysu.edu.cnAbstractCell-cell communication (CCC) is critical for determining cell fates and functions in multicellular organisms...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...Benjamin J. Auerbach1, Jian Hu2, Muredach P. Reilly3 and Mingyao Li2 1Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; 2Department of Biostatistics, Epidemiology and Informatics, University...
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Resource: H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa
- Nicola J. Mulder,
- Ezekiel Adebiyi,
- Raouf Alami,
- Alia Benkahla,
- James Brandful,
- Seydou Doumbia,
- Dean Everett,
- Faisal M. Fadlelmola,
- Fatima Gaboun,
- Simani Gaseitsiwe,
- Hassan Ghazal,
- Scott Hazelhurst,
- Winston Hide,
- Azeddine Ibrahimi,
- Yasmina Jaufeerally Fakim,
- C. Victor Jongeneel,
- Fourie Joubert,
- Samar Kassim,
- Jonathan Kayondo,
- Judit Kumuthini,
- Sylvester Lyantagaye,
- Julie Makani,
- Ahmed Mansour Alzohairy,
- Daniel Masiga,
- Ahmed Moussa,
- Oyekanmi Nash,
- Odile Ouwe Missi Oukem-Boyer,
- Ellis Owusu-Dabo,
- Sumir Panji,
- Hugh Patterton,
- Fouzia Radouani,
- Khalid Sadki,
- Fouad Seghrouchni,
- Özlem Tastan Bishop,
- Nicki Tiffin,
- Nzovu Ulenga,
- and The H3ABioNet Consortium
Genome Res. February 2016 26: 271-277; Published in Advance December 1, 2015, doi:10.1101/gr.196295.115
...Town, Cape Town, South Africa 7925; 2Covenant University Bioinformatics Research (CUBRe) and Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria, P.M.B. 1023; 3Centre National de Transfusion Sanguine, Rabat, Morocco 10100; 4Institute Pasteur of Tunis, Tunis...
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Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
- Vikram S. Shivakumar and
- Ben Langmead
Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
...Vikram S. Shivakumar and Ben Langmead Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding authors: vshivak1@jhu.edu, langmea@cs.jhu.eduAbstractPan collections are growing to hundreds of high-quality s. This necessitates scalable methods...
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Resource: A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
- Samia N. Naccache,
- Scot Federman,
- Narayanan Veeraraghavan,
- Matei Zaharia,
- Deanna Lee,
- Erik Samayoa,
- Jerome Bouquet,
- Alexander L. Greninger,
- Ka-Cheung Luk,
- Barryett Enge,
- Debra A. Wadford,
- Sharon L. Messenger,
- Gillian L. Genrich,
- Kristen Pellegrino,
- Gilda Grard,
- Eric Leroy,
- Bradley S. Schneider,
- Joseph N. Fair,
- Miguel A. Martínez,
- Pavel Isa,
- John A. Crump,
- Joseph L. DeRisi,
- Taylor Sittler,
- John Hackett, Jr.,
- Steve Miller,
- and Charles Y. Chiu
Genome Res. July 2014 24: 1180-1192; Published in Advance June 4, 2014, doi:10.1101/gr.171934.113
...by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (‘‘sequence-based ultrarapid pathogen identification’’), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
.... Bioinformatics 38: 3698–3702. doi:10.1093/bioinformatics/btac410 ↵Chandra G, Gibney D, Jain C. 2024. Haplotype-aware sequence alignment to pan graphs. Genome Res 34: 1265–1275. doi:10.1101/gr.279143.124 ↵Computational Pan-Genomics Consortium. 2018. Computational pan-genomics: status, promises and challenges...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...–5167. doi:10.1093/bioinformatics/btac671 ↵Lv H, Dao FY, Zhang D, Guan ZX, Yang H, Su W, Liu ML, Ding H, Chen W, Lin H. 2020. iDNA-MS: an integrated computational tool for detecting DNA modification sites in multiple s. iScience 23: 100991. doi:10.1016/j.isci.2020.100991 ↵Manavalan B, Basith S, Shin TH, Wei...
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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
...of sequence data. J Comput Biol 19: 577–590. doi:10.1089/cmb.2012.0084 ↵Bansal V, Bafna V. 2008. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24: i153–i159. doi:10.1093/bioinformatics/btn298 ↵Bengio Y, Louradour J, Collobert R, Weston J. 2009. Curriculum...
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Method: Minimizing reference bias with an imputed personalized reference
- Kavya Vaddadi,
- Mao-Jan Lin,
- Sina Majidian,
- Taher Mun,
- and Ben Langmead
Genome Res. March 5, 2026 gr.280989.125; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
...Kavya Vaddadi1, Mao-Jan Lin1, Sina Majidian1, Taher Mun1, Ben Langmead1 1. Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA Abstract Pan indexes reduce reference bias in sequencing data analysis. However, bias can be reduced...
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