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Method: Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
- Alexandre Lomsadze,
- Karl Gemayel,
- Shiyuyun Tang,
- and Mark Borodovsky
Genome Res. July 2018 28: 1079-1089; Published in Advance May 17, 2018, doi:10.1101/gr.230615.117
..., all genomic segments predicted and labeled as ‘protein-coding’ are collected into a training set to estimate the parameters of the ‘typical’ model. To reduce the chance of including noncoding ORFs into the training set, predicted genes shorter than 300 nt and those predicted as incomplete CDS...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...-1 footprint was detected at the locus encoding kinesin family member 3B (Kif3b)—a gene predicted to control intracellular transport (Fig. 1F). Although the mouse Kif3b knockout is embryonic-lethal (Nonaka et al. 1998), little is known about the function and regulation of this protein...
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Research: Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model
- Hassan Bukhari,
- Vanitha Nithianandam,
- Rachel A. Battaglia,
- Anthony Cicalo,
- Souvarish Sarkar,
- Aram Comjean,
- Yanhui Hu,
- Matthew J. Leventhal,
- Xianjun Dong,
- and Mel B. Feany
Genome Res. April 2024 34: 590-605; Published in Advance April 10, 2024, doi:10.1101/gr.278576.123
...Dong2,3,4 and Mel B. Feany1,2 1Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; 2Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA; 3Genomics and Bioinformatics Hub, Brigham...
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Resource: Benchmark and integration of resources for the estimation of human transcription factor activities
- Luz Garcia-Alonso,
- Christian H. Holland,
- Mahmoud M. Ibrahim,
- Denes Turei,
- and Julio Saez-Rodriguez
Genome Res. August 2019 29: 1363-1375; Published in Advance July 24, 2019, doi:10.1101/gr.240663.118
...of Nephrology, RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany Corresponding author: julio.saez@bioquant.uni-heidelberg.deAbstractThe prediction of transcription factor (TF) activities from the gene expression of their targets (i.e., TF regulon) is becoming a widely used approach...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...has fallen from 708 in 2013 (Hammonds et al. 2013), for a variety of reasons, including revised gene models and reassignment to other nucleic acid-associated proteins. Strains were not generated for TFs with complex genomic organization where there was no BAC containing the predicted TF...
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Method: Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data
- Shuze Wang,
- Mary P. Lee,
- Scott Jones,
- Jie Liu,
- and Joerg Waldhaus
Genome Res. October 2021 31: 1885-1899; Published in Advance April 9, 2021, doi:10.1101/gr.271080.120
...the epigenetic landscape of a given cell and direct differentiation through tight transcriptional control of downstream target genes, commonly summarized as regulons. We predicted TF-specific regulons at the whole-transcriptome level by leveraging the scRNA-seq and scATAC-seq data sets. First, coexpression...
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Research: Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver
- Ullas V. Chembazhi,
- Sushant Bangru,
- Mikel Hernaez,
- and Auinash Kalsotra
Genome Res. April 2021 31: 576-591; Published in Advance March 1, 2021, doi:10.1101/gr.267013.120
...individual cells by integrating co-expression data with transcription factor motif enrichment analysis, generating a “regulon,” which refers to an expressed transcription factor and all of its co-expressed target genes. We obtained the predicted regulon activities using AUCell, which ranks targets of each...
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Resource: Transcriptional milestones in Dictyostelium development
- Mariko Katoh-Kurasawa,
- Karin Hrovatin,
- Shigenori Hirose,
- Amanda Webb,
- Hsing-I Ho,
- Blaž Zupan,
- and Gad Shaulsky
Genome Res. August 2021 31: 1498-1511; Published in Advance June 28, 2021, doi:10.1101/gr.275496.121
...transitions, we identified 1371 milestone genes whose expression changes sharply between consecutive transitions. We also identified 1099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations. The gene...
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Resource: Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury
- Qiuyun Yang,
- Lingxuan Zhang,
- Manrui Li,
- Yang Xu,
- Xiaogang Chen,
- Ruixuan Yuan,
- Xiaofeng Ou,
- Min He,
- Miao Liao,
- Lin Zhang,
- Hao Dai,
- Meili Lv,
- Xiaoqi Xie,
- Weibo Liang,
- and Xiameng Chen
Genome Res. October 2023 33: 1818-1832; Published in Advance September 20, 2023, doi:10.1101/gr.277881.123
...count proportion of seven major cell types in the control and mTBI group. (B) Pie chart showing the proportion of cells in 16 clusters in the control and mTBI group. (C) Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the major cell types. (D) GO analysis showing enriched terms in seven major...
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Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
- Charlie George Barker,
- Eirini Petsalaki,
- Girolamo Giudice,
- Julia Sero,
- Emmanuel Nsa Ekpenyong,
- Chris Bakal,
- and Evangelia Petsalaki
Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
...the sensing of mechanical stimuli and regulation of NF-kB activity, with specific relevance to cell shape in breast cancer.The study of cancer has long been associated with changes in cell shape as morphology can be a reliable way to subtype cancer and predict patient prognosis (Wu et al. 2020). Recent...
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