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RESOURCE: 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
- Webb Miller,
- Kate Rosenbloom,
- Ross C. Hardison,
- Minmei Hou,
- James Taylor,
- Brian Raney,
- Richard Burhans,
- David C. King,
- Robert Baertsch,
- Daniel Blankenberg,
- Sergei L. Kosakovsky Pond,
- Anton Nekrutenko,
- Belinda Giardine,
- Robert S. Harris,
- Svitlana Tyekucheva,
- Mark Diekhans,
- Thomas H. Pringle,
- William J. Murphy,
- Arthur Lesk,
- George M. Weinstock,
- Kerstin Lindblad-Toh,
- Richard A. Gibbs,
- Eric S. Lander,
- Adam Siepel,
- David Haussler,
- and W. James Kent
Genome Res. December 2007 17: 1797-1808; Published in Advance November 5, 2007, doi:10.1101/gr.6761107
...28-Way vertebrate alignment and conservation track in the UCSC Genome Browser Webb Miller 1 , 11 , Kate Rosenbloom 2 , Ross C. Hardison 1 , Minmei Hou 1 , James Taylor 3 , Brian Raney 2 , Richard Burhans 1 , David C...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...that collate and integrate many different sources of data and databases because ease of use and reliability are key.Three types of tools should be applied in parallel: – Genome browsers with multiple annotation tracks, especially the unrivalled University of California at Santa Cruz (UCSC) browser (Perez et al...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...WigToBedGraph from UCSC Genome Browser utilities (Kent et al. 2010) and sorted by chromosome and start position. Finally, peaks were called from the sorted bedGraphs using MACS2 bdgpeakcall command (version 2.2.9.1) (Zhang et al. 2008) with a minimum score threshold of 1 to filter low-confidence regions...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...1, Raony Cardenas1, Thyago Cardoso1, Luis F. Paulin2, Philippe Sanio2, Joseph Mafofo1, Haiguo Wu1, Val Zvereff1, Albarah El-Khani1, Fahed Al Marzooqi1, Tiago R. Magalhães1, Fritz J. Sedlazeck2,3,4 and Javier Quilez1 1M42, Abu Dhabi, United Arab Emirates; 2Human Genome Sequencing Center, Baylor...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...effectively. Moreover, ScPGE greatly reduces computational demands for modeling by using discrete cCREs instead of the entire genomic region flanking target genes, facilitating rapid training and deployment for new cell types. To quantify its computational demand, we systematically evaluated the model...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...)–normalized and Z-score-normalized heatmaps from differential analysis of H3K27me3 over genes between 1-day-old cell types. (E–H) UCSC Genome Browser tracks of repressed domains in the three cell types in young guts. (E) The ANTP-C domain is shared between all three cell types. (F–H) A domain encompassing the pi...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...-positives (Garretson et al. 2025). Specifically, putative dnSNVs were excluded if they (1) overlapped with any of the following annotations defined by the RepeatMasker track accessed from the UCSC Genome Browser (low complexity regions, rRNA, satellite DNA, scRNA, simple repeats, snRNA, srpRNA, and tRNA) (Kent et al...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...-Cas9 RE deletionsPaired sgRNAs (5′- and 3′-sgRNAs) were designed to target both ends of selected candidate REs in the human DNAJC9 locus to create a deletion. sgRNA with on-target high predicted cleavage and a low number of off-targets was carefully selected using the UCSC Genome Browser (hg38) (Perez...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
...Rashid Al-Abri1,2 and Gamze Gürsoy1,2,3 1Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA; 2New York Genome Center, New York, New York 10013, USA; 3Department of Computer Science, Columbia University, New York, New York 10027, USA Corresponding author: gamze...
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