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Papers 2001 to 2010

Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S.
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++.
PLoS Comput Biol. 2010 Dec 2;6(12):e1001025

Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A.
Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes.
Genome Res. 2010 Mar;20(3):301-310.
<pdf><supplemental material>

Binkley J, Karra K, Kirby A, Hosobuchi M, Stone EA, Sidow A.
ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses.
Genome Res. 2010 Jan; 20(1):142-154.

Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J.
Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells.
Cell 2009 Dec 24; 139(7):1290-1302.

Rumble SM, Lacroute P, Dalca A, Fiume M, Sidow A, Brudno M
SHRiMP: Accurate Mapping of Short Color-space Reads.

PLoS Computational Biology 2009 May; 5(5):e1000386.

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.

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.

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.

Sidow A, Lacroute P.
Fruit fly family fun.
Cell 2007 Dec 28, 131(7):1222-1223.

Stone EA, Sidow A.
Constructing a meaningful evolutionary average at the phylogenetic center of mass.
BMC Bioinformatics. 2007 Jun 26;8:222.

Kaelin CB, Cooper GM, Sidow A, Barsh GS.
Mammalian comparative sequence analysis of the Agrp locus.
PLoS ONE. 2007 Aug 8;2(1):e702.

Brown CD, Johnson DS, Sidow A.
Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression.
Science 2007 Sept 14, 317:1557-1560.
<pdf> <supp>

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.

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.

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.

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

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

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

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

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

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.

Encode Project Consortium
The ENCODE (ENCyclopedia Of DNA Elements) project.
Science. 2004 Oct 22;306(5696):636-40.

Johnson DS, Davidson B, Brown CD, Smith WC, Sidow A.
Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance.
Genome Res. 2004 Dec;14(12):2448-56.

Sundarajan M, Brudno M, Small K, Sidow A, Batzoglou S.
Chaining algorithms for alignment of draft sequence.
WABI 2004, LNBI 3240, pp. 326–37.

Cooper GM, Singaravelu SAG, Sidow A
ABC: software for interactive browsing of genomic multiple sequence alignment data.
BMC Bioinformatics 2004, 5:192

Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A.
Characterization of evolutionary rates and constraints in three mammalian genomes.
Genome Res. 2004 Apr;14(4):539-48.

Rat Genome Sequencing Project Consortium.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature. 2004 Apr 1;428(6982):493-521.

Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I.
Automated whole-genome multiple alignment of rat, mouse, and human.
Genome Res. 2004 Apr;14(4):685-92.

Cooper GM, Sidow A.
Genomic regulatory regions: insights from comparative sequence analysis.
Curr Opin Genet Dev. 2003 Dec;13(6):604-10.

Aburomia R, Khaner O, Sidow A.
Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail.
J Struct Funct Genomics. 2003;3(1-4):45-52.

Cooper GM, Brudno M, Green ED, Batzoglou S, Sidow A.
Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.
Genome Res. 2003 May;13(5):813-20.

Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S.
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
Genome Res. 2003 Apr;13(4):721-31.

Ko DC, Binkley J, Sidow A, Scott MP.
The integrity of a cholesterol-binding pocket in Niemann-Pick C2 protein is necessary to control lysosome cholesterol levels.
Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2518-25.

Sidow A.
Sequence first. Ask questions later.
Cell. 2002 Oct 4;111(1):13-6.

Simon AL, Stone EA, Sidow A.
Inference of functional regions in proteins by quantification of evolutionary constraints.
Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2912-7.

Serluca FC, Sidow A, Mably JD, Fishman MC.
Partitioning of tissue expression accompanies multiple duplications of the Na+/K+ ATPase alpha subunit gene.
Genome Res. 2001 Oct;11(10):1625-31.

Rieger DK, Reichenberger E, McLean W, Sidow A, Olsen BR.
A double-deletion mutation in the Pitx3 gene causes arrested lens development in aphakia mice.
Genomics. 2001 Feb 15;72(1):61-72.

Arend's old papers from previous lives