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Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
...Shuangshuang Feng1,2,3, Maitena Tellaetxe-Abete4,7, Yujie Zhang2,3,7, Yan Peng2,3,5, Han Zhou2, Mingjie Dong2, Erika Larrea2,3,6, Liang Xue2,3, Li Zhang2 and Magdalena J. Koziol1,2,3 1State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China; 2...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...existing data sets to expand the resolution of elongation rate analysis.In summary, our enhanced method provides a robust, high-resolution tool to accurately measure RNAPII elongation rates at the individual gene level, facilitating discovery of global or novel gene-specific regulators of RNAPII elongation...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...gene expression and fewer regulated target genes. Our user-friendly web-accessible interface, the Muscle Multiome Browser, facilitates interrogating gene, chromatin, TFs, and regulatory circuits of interest to any investigator (https://rstudio-connect.hpc.mssm.edu/muscle-multiome/).View larger version...
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Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
...) using ∼12 CPU hours and ∼29 GB of memory per sample. The read alignments to each subgraph are summarized as a vector of the number of reads mapped to each node/k-mer. When normalized by global read depth, these represent mapping dosage used as input for eQTL mapping of the 100-kb cis-windows of genes...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...plays a major role in the accuracy of ab initio gene prediction; that is, mistakes in assemblies can lead to the erroneous addition and/or subtraction of gene annotations (Han et al. 2013). Thus far, as most of the nematode annotations are still based on automated annotation pipelines...
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Method: A novel synthetic-genetic-array–based yeast one-hybrid system for high discovery rate and short processing time
- Chung-Shu Yeh,
- Zhifeng Wang,
- Fang Miao,
- Hongyan Ma,
- Chung-Ting Kao,
- Tzu-Shu Hsu,
- Jhong-He Yu,
- Er-Tsi Hung,
- Chia-Chang Lin,
- Chen-Yu Kuan,
- Ni-Chiao Tsai,
- Chenguang Zhou,
- Guan-Zheng Qu,
- Jing Jiang,
- Guifeng Liu,
- Jack P. Wang,
- Wei Li,
- Vincent L. Chiang,
- Tien-Hsien Chang,
- and Ying-Chung Jimmy Lin
Genome Res. August 2019 29: 1343-1351; Published in Advance June 11, 2019, doi:10.1101/gr.245951.118
...27695, USA ↵6 These authors contributed equally to this work. Corresponding authors: ycjimmylin@ntu.edu.tw, chang108@gate.sinica.edu.tw, weili2015@nefu.edu.cn, vchiang@ncsu.eduAbstractEukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
...aligned raw reads from the GTEx RNA-seq data per the TCGA pipeline. We processed the tumor and normal aligned files to generate coverage files that were used to identify 3′-UTR differences. We assessed the extent of differential batch effects by comparing the variation in expression of housekeeping genes...
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METHODS: Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes
- Piero Carninci,
- Yuko Shibata,
- Norihito Hayatsu,
- Yuichi Sugahara,
- Kazuhiro Shibata,
- Masayoshi Itoh,
- Hideaki Konno,
- Yasushi Okazaki,
- Masami Muramatsu,
- and Yoshihide Hayashizaki
Genome Res. October 1, 2000 10: 1617-1630; doi:10.1101/gr.145100
...Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes Piero Carninci 1 , Yuko Shibata , Norihito Hayatsu , Yuichi Sugahara , Kazuhiro Shibata , Masayoshi Itoh...
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Method: Discovery of recurrent structural variants in nasopharyngeal carcinoma
- Anton Valouev,
- Ziming Weng,
- Robert T. Sweeney,
- Sushama Varma,
- Quynh-Thu Le,
- Christina Kong,
- Arend Sidow,
- and Robert B. West
Genome Res. February 2014 24: 300-309; Published in Advance November 8, 2013, doi:10.1101/gr.156224.113
...contributed equally to this work. Abstract We present the discovery of genes recurrently involved in structural variation in nasopharyngeal carcinoma (NPC) and the identification of a novel type of somatic structural variant. We identified the variants with high complexity mate-pair libraries...
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RESOURCE: High-Throughput Gene Discovery in the Rat
- Todd E. Scheetz,
- Jennifer J. Laffin,
- Brian Berger,
- Sara Holte,
- Susan A. Baumes,
- Robert Brown II,
- Shereen Chang,
- Justin Coco,
- Jim Conklin,
- Keith Crouch,
- Micca Donohue,
- Greg Doonan,
- Chris Estes,
- Mari Eyestone,
- Katrina Fishler,
- Jack Gardiner,
- Lankai Guo,
- Brad Johnson,
- Catherine Keppel,
- Rikki Kreger,
- Mark Lebeck,
- Rudy Marcelino,
- Vladan Miljkovich,
- Mindee Perdue,
- Ling Qui,
- Joshua Rehmann,
- Rebecca S. Reiter,
- Bridgette Rhoads,
- Kelly Schaefer,
- Christina Smith,
- Ivana Sunjevaric,
- Kurtis Trout,
- Ning Wu,
- Clayton L. Birkett,
- Jared Bischof,
- Barry Gackle,
- Allen Gavin,
- A. Jason Grundstad,
- Brian Mokrzycki,
- Chris Moressi,
- Brian O'Leary,
- Kevin Pedretti,
- Chad Roberts,
- Natalie L. Robinson,
- Michael Smith,
- Dylan Tack,
- Nishank Trivedi,
- Tamara Kucaba,
- Tom Freeman,
- Jim J.-C. Lin,
- Maria F. Bonaldo,
- Thomas L. Casavant,
- Val C. Sheffield,
- and M. Bento Soares
Genome Res. April 2004 14: 733-741; doi:10.1101/gr.1414204
...Abstract The rat is an important animal model for human diseases and is widely used in physiology. In this article we present a new strategy for gene discovery based on the production of ESTs from serially subtracted and normalized cDNA libraries, and we describe its application for the development...

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