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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...lies in the difficulty in the prediction of precise TAD boundaries. We solve this problem by introducing a novel algorithm, called BINDER, which conducts a boundary consensus approach, and then precisely locate hierarchical TAD boundaries by developing a multifaceted boundary characterization strategy...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...of the pathogenesis—is similar in the different disease-relevant cell types. This is possible in principle, because all these cell types are subject to effects from the same causative gene, which has the same kind of function (e.g., methylates histones) and is disrupted by the same germline variant. We focus on mouse...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...-promoter connections involving HOT sites. We also found a substantial number of closed chromatin regions with multiple DAPs bound, and explored their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic...
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Method: Characterization of network hierarchy reflects cell state specificity in genome organization
- Jingyao Wang,
- Yue Xue,
- Yueying He,
- Hui Quan,
- Jun Zhang,
- and Yi Qin Gao
Genome Res. February 2023 33: 247-260; Published in Advance February 24, 2023, doi:10.1101/gr.277206.122
...Characterization of network hierarchy reflects cell state specificity in organization Jingyao Wang1,4, Yue Xue1,4, Yueying He1, Hui Quan1, Jun Zhang3 and Yi Qin Gao1,2,3 1Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...to characterize sample-specific APA using the corresponding RNA-seq data, but suffered from high error rate on both polyadenylation site (PAS) identification and quantification of PAS usage (PAU), and bias toward 3′ untranslated regions. Here we developed a tool for APA identification and quantification (APAIQ...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
...by different combinations of TFs/motifs. Current approaches do not take into account this issue of combinatorial diversity. We present a new statistical framework, cisDIVERSITY, which models regions as diverse modules characterized by combinations of motifs while simultaneously learning the motifs themselves...
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Method: Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data
- Matthew D. Parker,
- Benjamin B. Lindsey,
- Shay Leary,
- Silvana Gaudieri,
- Abha Chopra,
- Matthew Wyles,
- Adrienn Angyal,
- Luke R. Green,
- Paul Parsons,
- Rachel M. Tucker,
- Rebecca Brown,
- Danielle Groves,
- Katie Johnson,
- Laura Carrilero,
- Joe Heffer,
- David G. Partridge,
- Cariad Evans,
- Mohammad Raza,
- Alexander J. Keeley,
- Nikki Smith,
- Ana Da Silva Filipe,
- James G. Shepherd,
- Chris Davis,
- Sahan Bennett,
- Vattipally B. Sreenu,
- Alain Kohl,
- Elihu Aranday-Cortes,
- Lily Tong,
- Jenna Nichols,
- Emma C. Thomson,
- The COVID-19 Genomics UK (COG-UK) Consortium,
- Dennis Wang,
- Simon Mallal,
- and Thushan I. de Silva
Genome Res. April 2021 31: 645-658; Published in Advance March 15, 2021, doi:10.1101/gr.268110.120
...RNA intermediates (Stern and Kennedy 1980; Sola et al. 2015). sgRNAs are produced through discontinuous transcription during negative-strand synthesis followed by positive-strand synthesis to form mRNA. The resulting sgRNAs contain a leader sequence derived from the 5′ untranslated region of the and a transcription...
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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
.... Some topics with high probability in too few cells to be used for clustering may characterize cell types that are rare or that were less successfully isolated. In addition, topics with more diffuse probability across cells could correspond to other phenomena, for example, to different kinds...
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Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
- Rui Yokomori,
- Kotaro Shimai,
- Koki Nishitsuji,
- Yutaka Suzuki,
- Takehiro G. Kusakabe,
- and Kenta Nakai
Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
...Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis Rui Yokomori 1 , Kotaro Shimai 2 , Koki Nishitsuji 3 , Yutaka Suzuki 1 , Takehiro G. Kusakabe 2 , 4...

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