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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...of genomic signals on individual TE loci where we extend the WashU Epi Browser to display user-selected datasets and TE loci. These features could help to close the gaps in our understanding of the repetitive sequences and their putative regulatory functions and aid investigators in formulating new...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...regions around TE-derived TSSs were generated using deepTools (Ramírez et al. 2016). HOMER (Heinz et al. 2010) was used to perform motif enrichment analysis around TE-derived TSSs. Examples of TE-derived alternative promoters were visualized using the WashU Epi Browser (Li et al. 2019). The Integrative...
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Method: Epigenomic differences in the human and chimpanzee genomes are associated with structural variation
- Xiaoyu Zhuo,
- Alan Y. Du,
- Erica C. Pehrsson,
- Daofeng Li,
- and Ting Wang
Genome Res. February 2021 31: 279-290; Published in Advance December 10, 2020, doi:10.1101/gr.263491.120
...IP-seq data were normalized to reads per genomic content (RPGC) using deepTools bamcoverage (Ramírez et al. 2016). Binding profiles and heatmaps were generated using deepTools2 (Supplemental Methods; Ramírez et al. 2016).Data accessAll processed data are accessible on the WashU Comparative Epi browser: (https://epigateway.wustl.edu/browser...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...by optimally weighting diverse genomic features (Shihab et al. 2015). To streamline the annotation process, PhD-SNPg, a lightweight, sequence-based machine learning tool, enables efficient analysis of SNPs and indels across coding and noncoding regions (Capriotti and Fariselli 2023). With advancements in SV...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...Madden Hyung Joo Lee Xing, Xiaoyun genome;gr.156539.113 10.1101/gr.156539.113 1088-9051 Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&amp;M algorithm Method Functional DNA methylation differences between tissues, cell types, and across...
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Method: Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing
- Wai Lim Ku,
- Lixia Pan,
- Yaqiang Cao,
- Weiwu Gao,
- and Keji Zhao
Genome Res. October 2021 31: 1831-1842; Published in Advance April 14, 2021, doi:10.1101/gr.260893.120
...analysis of the single-cell dataVisualization in browserFor H3K4me3 and H3K27me3, 2000 single cells were randomly selected (MATLAB command: randperm [N, 2000]) and pooled together as the pseudo-bulk-cell data. This pseudo-bulk-cell data was visualized using the WashU Epi Browser (Figs. 2A, 4A; Zhou et al...
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Research: The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
- Xianglin Zhang,
- Xuehui Liu,
- Zhenhai Du,
- Lei Wei,
- Huan Fang,
- Qiongye Dong,
- Jing Niu,
- Yanda Li,
- Juntao Gao,
- Michael Q. Zhang,
- Wei Xie,
- and Xiaowo Wang
Genome Res. July 2021 31: 1121-1135; Published in Advance June 17, 2021, doi:10.1101/gr.275235.121
...were pooled except for special note. Interaction matrices and other genomic data were uploaded to the WashU Epi Browser for visualization (Zhou et al. 2013). DNA replication timing (wgEncodeUwRepliSeqBjWaveSignal) and CTCF binding sites (wgEncodeUwTfbsBjInputStdRaw) of the BJ cell line and TF binding...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...of enriched top GO terms associated with the highly regulated genes linked to each peak cluster in A. (C,D) On the left, WashU Epi Browser views show aggregated and normalized snRNA-seq signals (pink tracks) and snATAC-seq signals (blue tracks) across time points surrounding genes inhbaa and il11a in MES...
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Research: Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations
- Phillippa C. Taberlay,
- Joanna Achinger-Kawecka,
- Aaron T.L. Lun,
- Fabian A. Buske,
- Kenneth Sabir,
- Cathryn M. Gould,
- Elena Zotenko,
- Saul A. Bert,
- Katherine A. Giles,
- Denis C. Bauer,
- Gordon K. Smyth,
- Clare Stirzaker,
- Sean I. O'Donoghue,
- and Susan J. Clark
Genome Res. June 2016 26: 719-731; Published in Advance April 6, 2016, doi:10.1101/gr.201517.115
...in cancer cells. CNV regions visualized as relative copy-number estimates for each cell type (presented in green) are aligned with chromatin interaction heat maps (presented as normalized interaction counts visualized in WashU Epi Browser) and TADs, demonstrating that cancer-specific domain boundaries...
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Method: High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
- Marie-Odile Baudement,
- Axel Cournac,
- Franck Court,
- Marie Seveno,
- Hugues Parrinello,
- Christelle Reynes,
- Robert Sabatier,
- Tristan Bouschet,
- Zhou Yi,
- Sephora Sallis,
- Mathilde Tancelin,
- Cosette Rebouissou,
- Guy Cathala,
- Annick Lesne,
- Julien Mozziconacci,
- Laurent Journot,
- and Thierry Forné
Genome Res. November 2018 28: 1733-1746; Published in Advance October 4, 2018, doi:10.1101/gr.237073.118
...in ESCs. Tracks displaying DNase I–sensitive sites, RNA PolII peaks as well as ChIP-seq data for the indicated epigenetic marks (ENCODE E14 ESC data) were plotted using the WashU EpiGenome Browser. (B) Heat map depicting the Pearson correlation coefficients obtained between ESC HRSs and sequences (10-kb...

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