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Methods: Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites
- George A. Follows,
- Pawan Dhami,
- Berthold Göttgens,
- Alexander W. Bruce,
- Peter J. Campbell,
- Shane C. Dillon,
- Aileen M. Smith,
- Christoph Koch,
- Ian J. Donaldson,
- Mike A. Scott,
- Ian Dunham,
- Mary E. Janes,
- David Vetrie,
- and Anthony R. Green
Genome Res. October 2006 16: 1310-1319; Published in Advance September 8, 2006, doi:10.1101/gr.5373606
...Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites George A. Follows 1 , 4 , Pawan Dhami 2 , Berthold Göttgens 1 , Alexander W. Bruce 2 , Peter J. Campbell 1 , Shane C. Dillon 2...
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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
...onto a NextSeq 500/550 High Output v2 kit (300 cycles) flow cell and sequenced on a NextSeq 500 instrument.We performed transcript-level abundance quantification by pseudo-aligning RNA-seq reads to the coding sequences of a Saccharomyces Genome Database (SGD) yeast reference gene set, using kallisto (v...
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LETTER: Representational Oligonucleotide Microarray Analysis: A High-Resolution Method to Detect Genome Copy Number Variation
- Robert Lucito,
- John Healy,
- Joan Alexander,
- Andrew Reiner,
- Diane Esposito,
- Maoyen Chi,
- Linda Rodgers,
- Amy Brady,
- Jonathan Sebat,
- Jennifer Troge,
- Joseph A. West,
- Seth Rostan,
- Ken C.Q. Nguyen,
- Scott Powers,
- Kenneth Q. Ye,
- Adam Olshen,
- Ennapadam Venkatraman,
- Larry Norton,
- and Michael Wigler
Genome Res. October 2003 13: 2291-2305; Published in Advance January 1, 2003, doi:10.1101/gr.1349003
...genes or oncogenes, respectively. We describe here our success with ROMA (representational oligonucleotide microarray analysis), a technique that evolved from an earlier method, RDA (representational difference analysis; Lisitsyn et al. 1993 ). Like RDA, ROMA detects differences present in cancer s...
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LETTER: Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis
- Justen Andrews,
- Gerard G. Bouffard,
- Chris Cheadle,
- Jining Lü,
- Kevin G. Becker,
- and Brian Oliver
Genome Res. December 1, 2000 10: 2030-2043; doi:10.1101/gr.159800
...in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, &gt;80% of the genes expressed in the testis showed onefold overexpression relative to ovaries...
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REVIEW: Copy number variation: New insights in genome diversity
- Jennifer L. Freeman,
- George H. Perry,
- Lars Feuk,
- Richard Redon,
- Steven A. McCarroll,
- David M. Altshuler,
- Hiroyuki Aburatani,
- Keith W. Jones,
- Chris Tyler-Smith,
- Matthew E. Hurles,
- Nigel P. Carter,
- Stephen W. Scherer,
- and Charles Lee
Genome Res. August 2006 16: 949-961; Published in Advance June 29, 2006, doi:10.1101/gr.3677206
...% in a given population. In our preferred nomenclature, a CNV represents a copy number change involving a DNA fragment that is ∼1 kilobases (kb) or larger ( Feuk et al. 2006a ). At a recent workshop (“The effects of genomic structural variation on gene expression and human disease,” The Wellcome Trust Sanger...
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Methods: Sensitive and accurate detection of copy number variants using read depth of coverage
- Seungtai Yoon,
- Zhenyu Xuan,
- Vladimir Makarov,
- Kenny Ye,
- and Jonathan Sebat
Genome Res. September 2009 19: 1586-1592; Published in Advance August 5, 2009, doi:10.1101/gr.092981.109
.... 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851– 1858. Lucito R, West J, Reiner A, Alexander J, Esposito D, Mishra B, Powers S, Norton L, Wigler M. 2000. Detecting gene copy number fluctuations in tumor cells by microarray analysis...
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Methods: Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
- Daisuke Komura,
- Fan Shen,
- Shumpei Ishikawa,
- Karen R. Fitch,
- Wenwei Chen,
- Jane Zhang,
- Guoying Liu,
- Sigeo Ihara,
- Hiroshi Nakamura,
- Matthew E. Hurles,
- Charles Lee,
- Stephen W. Scherer,
- Keith W. Jones,
- Michael H. Shapero,
- Jing Huang,
- and Hiroyuki Aburatani
Genome Res. December 2006 16: 1575-1584; Published in Advance November 22, 2006, doi:10.1101/gr.5629106
...been used to detect -wide DNA copy number changes that include loss of heterozygosity (LOH), deletions, and gene amplification events ( Bignell et al. 2004 ; Huang et al. 2004 , 2006 ; Zhao et al. 2004 ; Ishikawa et al. 2005 ; Laframboise et al. 2005 ; Nannya et al. 2005 ; Slater et al. 2005...
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Research: Multidimensional regulation of gene expression in the C. elegans embryo
- John Isaac Murray,
- Thomas J. Boyle,
- Elicia Preston,
- Dionne Vafeados,
- Barbara Mericle,
- Peter Weisdepp,
- Zhongying Zhao,
- Zhirong Bao,
- Max Boeck,
- and Robert H. Waterston
Genome Res. July 2012 22: 1282-1294; Published in Advance April 16, 2012, doi:10.1101/gr.131920.111
...Max, Boeck Murray, John Isaac Zhao Zhongying Dionne Vafeados Vafeados Weisdepp, P John Isaac, Murray 10.1101/gr.131920.111 1088-9051 genome;gr.131920.111 Multidimensional regulation of gene expression in the C. elegans embryo Research Multidimensional regulation of gene expression in the C. elegans...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...is to detect CNEs that are specific to a certain gene family. To assess the specificity of our predictions, we used the set of PCNEs generated from real gene families, and searched for similarity both in the original genomic sequences that generated the PCNEs andwithin a second randomized gene family. Across...
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ARTICLE: Genomic Regionality in Rates of Evolution Is Not Explained by Clustering of Genes of Comparable Expression Profile
- Martin J. Lercher,
- Jean-Vincent Chamary,
- and Laurence D. Hurst
Genome Res. June 2004 14: 1002-1013; doi:10.1101/gr.1597404
...representation of expression rates, the latter are estimated from SAGE and microarray data alone. Further, recent evidence suggests that in GC-rich regions, the substitution process may well be affected by both mutation and biased gene conversion ( Eyre-Walker 1999 ; Smith and Eyre-Walker 2001 ; Duret et al...

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