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LETTER: Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
- David C. King,
- James Taylor,
- Ying Zhang,
- Yong Cheng,
- Heather A. Lawson,
- Joel Martin,
- ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. June 2007 17: 775-786; doi:10.1101/gr.5592107
...in common in two or more species by alignment algorithms will be called conserved . Those that show a signal for purifying selection will be called constrained .) How often is that underlying assumption really true, and, when it is true, how strong is the signal for constraint in multispecies alignments...
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Resource: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
- Guanjue Xiang,
- Cheryl A. Keller,
- Elisabeth Heuston,
- Belinda M. Giardine,
- Lin An,
- Alexander Q. Wixom,
- Amber Miller,
- April Cockburn,
- Michael E.G. Sauria,
- Kathryn Weaver,
- Jens Lichtenberg,
- Berthold Göttgens,
- Qunhua Li,
- David Bodine,
- Shaun Mahony,
- James Taylor,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- Yong Cheng,
- Feng Yue,
- Jim Hughes,
- Douglas R. Higgs,
- Yu Zhang,
- and Ross C. Hardison
Genome Res. March 2020 30: 472-484; Published in Advance March 4, 2020, doi:10.1101/gr.255760.119
...to testable hypotheses about functions of genomic elements and mechanisms of regulatory processes. Our multilaboratory project called VISION (validated systematic integration of hematopoietic epis) is endeavoring to meet this challenge by focusing on an important biological system, hematopoietic...
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LETTER: Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
- Yong Cheng,
- David C. King,
- Louis C. Dore,
- Xinmin Zhang,
- Yuepin Zhou,
- Ying Zhang,
- Christine Dorman,
- Demesew Abebe,
- Swathi A. Kumar,
- Francesca Chiaromonte,
- Webb Miller,
- Roland D. Green,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2008 18: 1896-1905; Published in Advance September 25, 2008, doi:10.1101/gr.083089.108
...Abstract Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act...
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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
...that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has...
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LETTER: Experimental validation of predicted mammalian erythroid cis-regulatory modules
- Hao Wang,
- Ying Zhang,
- Yong Cheng,
- Yuepin Zhou,
- David C. King,
- James Taylor,
- Francesca Chiaromonte,
- Jyotsna Kasturi,
- Hanna Petrykowska,
- Brian Gibb,
- Christine Dorman,
- Webb Miller,
- Louis C. Dore,
- John Welch,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2006 16: 1480-1492; Published in Advance October 12, 2006, doi:10.1101/gr.5353806
...of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA Abstract Multiple alignments of genome sequences are helpful guides to functional analysis, but predicting cis -regulatory modules (CRMs) accurately from such alignments remains an elusive goal. We predict CRMs...
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12 Drosophila Genomes/Methods: Reliable prediction of regulator targets using 12 Drosophila genomes
- Pouya Kheradpour,
- Alexander Stark,
- Sushmita Roy,
- and Manolis Kellis
Genome Res. December 2007 17: 1919-1931; Published in Advance November 7, 2007, doi:10.1101/gr.7090407
...into a confidence measure for each motif instance, correcting for varying motif length, composition, and background conservation of the target regions. We predict targets of fly transcription factors and miRNAs in alignments of 12 recently sequenced Drosophila species. When compared to extensive genome...
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LETTER: Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
- David M. McGaughey,
- Ryan M. Vinton,
- Jimmy Huynh,
- Amr Al-Saif,
- Michael A. Beer,
- and Andrew S. McCallion
Genome Res. February 2008 18: 252-260; Published in Advance December 10, 2007, doi:10.1101/gr.6929408
.... , Chiaromonte, F. ( 2006 ) ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements . Genome Res. 16 : 1596 – 1604 . ↵ Trochet, D. , O’Brien, L.M. , Gozal, D. , Trang, H. , Nordenskjold, A. , Laudier, B. , Svensson, P.J. , Uhrig, S. , Cole, T. , Niemann, S. , et al...

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