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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...integrative summary of such data sets. Here, we present the ENCODE4 Catalog of Segway Annotations, a set of sample-specific -wide chromatin state annotations of 234 human biosamples inferred from 1,794 genomics experiments. This catalog identifies genomic elements, accurately captures cell type...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...Genomics and Transcriptomics Laboratory, Biological and Medical Research Center, Heinrich Heine University and West German Genome Center, 40225 Düsseldorf, Germany; 7Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; 8Institute for Pharmaceutical...
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Research: Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma
- Winnie S. Liang,
- William Hendricks,
- Jeffrey Kiefer,
- Jessica Schmidt,
- Shobana Sekar,
- John Carpten,
- David W. Craig,
- Jonathan Adkins,
- Lori Cuyugan,
- Zarko Manojlovic,
- Rebecca F. Halperin,
- Adrienne Helland,
- Sara Nasser,
- Christophe Legendre,
- Laurence H. Hurley,
- Karthigayini Sivaprakasam,
- Douglas B. Johnson,
- Holly Crandall,
- Klaus J. Busam,
- Victoria Zismann,
- Valerie Deluca,
- Jeeyun Lee,
- Aleksandar Sekulic,
- Charlotte E. Ariyan,
- Jeffrey Sosman,
- and Jeffrey Trent
Genome Res. April 2017 27: 524-532; doi:10.1101/gr.213348.116
...lentiginous melanoma (ALM), a rare sun-shielded melanoma subtype associated with worse survival than CM, is needed to delineate non-UV oncogenic mechanisms. We thus performed comprehensive genomic and transcriptomic analysis of 34 ALM patients. Unlike CM, somatic alterations were dominated by structural...
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Research: Cell-type–specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes
- Tongwu Zhang,
- Jiyeon Choi,
- Michael A. Kovacs,
- Jianxin Shi,
- Mai Xu,
- NISC Comparative Sequencing Program,
- Melanoma Meta-Analysis Consortium,
- Alisa M. Goldstein,
- Adam J. Trower,
- D. Timothy Bishop,
- Mark M. Iles,
- David L. Duffy,
- Stuart MacGregor,
- Laufey T. Amundadottir,
- Matthew H. Law,
- Stacie K. Loftus,
- William J. Pavan,
- and Kevin M. Brown
Genome Res. November 2018 28: 1621-1635; Published in Advance October 17, 2018, doi:10.1101/gr.233304.117
...-wide association studies. Melanocyte eQTLs also colocalized with melanoma GWAS variants in five known loci. Finally, a transcriptome-wide association study using melanocyte eQTLs uncovered four novel susceptibility loci, where imputed expression levels of five genes (ZFP90, HEBP1, MSC, CBWD1, and RP11...
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Research: LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
- Jan Attig,
- George R. Young,
- Louise Hosie,
- David Perkins,
- Vesela Encheva-Yokoya,
- Jonathan P. Stoye,
- Ambrosius P. Snijders,
- Nicola Ternette,
- and George Kassiotis
Genome Res. October 2019 29: 1578-1590; Published in Advance September 19, 2019, doi:10.1101/gr.248922.119
...(Laumont et al. 2018). As our analysis of the melanoma immunopeptidome shows, such unconventional transcripts and ORFs therein hold great promise for cancer-specific antigens.Although the annotated LTR transcriptome has been increasingly implicated in cancer (Romanish et al. 2010; Kassiotis and Stoye 2017...
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Method: Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations
- Yu-Jui Ho,
- Naishitha Anaparthy,
- David Molik,
- Grinu Mathew,
- Toby Aicher,
- Ami Patel,
- James Hicks,
- and Molly Gale Hammell
Genome Res. September 2018 28: 1353-1363; Published in Advance July 30, 2018, doi:10.1101/gr.234062.117
...statistically significant genes (P < 0.01) shown in black, showing highly similar results.For comparison, BRAFi-resistant cells for a second melanoma cell line also carrying the BRAF V600E mutation, A375, were derived using the same strategy (Supplemental Fig. S2B). Bulk RNA transcriptomes from the two cell...
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Method: INTEGRATE: gene fusion discovery using whole genome and transcriptome data
- Jin Zhang,
- Nicole M. White,
- Heather K. Schmidt,
- Robert S. Fulton,
- Chad Tomlinson,
- Wesley C. Warren,
- Richard K. Wilson,
- and Christopher A. Maher
Genome Res. January 2016 26: 108-118; Published in Advance November 10, 2015, doi:10.1101/gr.186114.114
...INTEGRATE: gene fusion discovery using whole genome and transcriptome data Jin Zhang 1 , 2 , Nicole M. White 2 , Heather K. Schmidt 1 , Robert S. Fulton 1 , 3 , Chad Tomlinson 1 , Wesley C. Warren 1 , Richard K. Wilson 1...
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Research: BRAF^V600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration
- Ross J. Flockhart,
- Dan E. Webster,
- Kun Qu,
- Nicholas Mascarenhas,
- Joanna Kovalski,
- Markus Kretz,
- and Paul A. Khavari
Genome Res. June 2012 22: 1006-1014; Published in Advance May 11, 2012, doi:10.1101/gr.140061.112
...BRAF V600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration Ross J. Flockhart , Dan E. Webster , Kun Qu , Nicholas Mascarenhas , Joanna Kovalski , Markus Kretz and Paul A. Khavari...
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Research: Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
- Can Cenik,
- Elif Sarinay Cenik,
- Gun W. Byeon,
- Fabian Grubert,
- Sophie I. Candille,
- Damek Spacek,
- Bilal Alsallakh,
- Hagen Tilgner,
- Carlos L. Araya,
- Hua Tang,
- Emiliano Ricci,
- and Michael P. Snyder
Genome Res. November 2015 25: 1610-1621; Published in Advance August 21, 2015, doi:10.1101/gr.193342.115
...have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...of the Austrian Academy of Sciences, 1090 Vienna, Austria; 11Eric and Wendy Schmidt Center, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA Corresponding author: valentina.boeva@inf.ethz.chAbstractGene signature scoring is integral to single-cell RNA sequencing (scRNA-seq) data analysis...
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