Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A.
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.
Nat Methods. 2008 Sep; 5:(9):829-35.
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Hill MM, Broman KW, Stupka E, Smith WC, Jiang D, Sidow A
The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution
Genome Res. 2008 Aug;18(8):1369-79.
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Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham P, Zeng C, Malek JA, Costa G, McKernan K, Sidow A, Fire A, and Johnson SM
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.
Genome Res. 2008 Jul;18(7):1051-63.
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Sidow A, Lacroute P.
Fruit fly family fun.
Cell 2007 Dec 28, 131(7):1222-1223.
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Stone EA, Sidow A.
Constructing a meaningful evolutionary average at the phylogenetic center of mass.
BMC Bioinformatics. 2007 Jun 26;8:222.
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Kaelin CB, Cooper GM, Sidow A, Barsh GS.
Mammalian comparative sequence analysis of the Agrp locus.
PLoS ONE. 2007 Aug 8;2(1):e702.
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Brown CD, Johnson DS, Sidow A.
Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression.
Science 2007 Sept 14, 317:1557-1560.
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Marguiles EH, Cooper GM, .....Encode Comparative Analysis Group ... Sidow A.
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Genome Research 2007, 17:760-774.
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Small KS, Brudno M, Hill MM, Sidow A
Extreme genomic variation in a natural population.
Proc Natl Acad Sci U S A. 2007 Mar 27;104:5698-5703.
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Small KS, Brudno M, Hill MM, Sidow A
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome.
Genome Biology 2007, 8:R41;1-14.
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Encode Project Consortium.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature 2007 447:799-816.

Jackson PJ, Douglas NR, Chai B, Binkley J, Sidow A, Barsh GS, Millhauser GL
Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins.
Chemistry and Biology 2006, Dec;13:1297-1305
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Johnson DS, Zhou Q, Yagi K, Satoh N, Wong W, Sidow A
De novo discovery of a tissue-specific gene regulatory module in a chordate.
Genome Res. 2005, Oct;15:1315-24
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Stone EA, Cooper GM, Sidow A
Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.
Annual Review of Genomics and Human Genetics 2005 6:143-64
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Stone EA, Sidow A
Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity.
Genome Res. 2005, Jul;15:978-986
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Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A
Distribution and intensity of constraint in mammalian genomic sequence.
Genome Res. 2005, Jul;15:901-913
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Kashuk CS, Stone EA, Grice EA, Portnoy ME, Green ED, Sidow A, Chakravarti A, McCallion AS
Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence.
Proc Natl Acad Sci U S A. 2005 Jun;102(25):8949-54.
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