Publications
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The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution.
Hill MM,
Broman KW, Stupka E, Smith WC, Jiang D, Sidow A.
Genome Res.
2008;
18
(8):
1369-79
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A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.
Valouev A,
Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM.
Genome Res.
2008;
18
(7):
1051-63
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A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome.
Small KS,
Brudno M, Hill MM, Sidow A.
Genome Biol.
2007;
8
(3):
R41
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Functional architecture and evolution of transcriptional elements that drive gene coexpression.
Brown CD,
Johnson DS, Sidow A.
Science.
2007;
317
(5844):
1557-60
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Extreme genomic variation in a natural population.
Small KS,
Brudno M, Hill MM, Sidow A.
Proc Natl Acad Sci U S A.
2007;
104
(13):
5698-703
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Mammalian comparative sequence analysis of the Agrp locus.
Kaelin CB,
Cooper GM, Sidow A, Barsh GS.
PLoS One.
2007;
2
(1):
e702
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Fruit fly family fun.
Sidow A,
Lacroute P.
Cell.
2007;
131
(7):
1222-3
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De novo discovery of a tissue-specific gene regulatory module in a chordate.
Johnson DS,
Zhou Q, Yagi K, Satoh N, Wong W, Sidow A.
Genome Res.
2005;
15
(10):
1315-24
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Distribution and intensity of constraint in mammalian genomic sequence.
Cooper GM,
Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A.
Genome Res.
2005;
15
(7):
901-13
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Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.
Stone EA,
Cooper GM, Sidow A.
Annu Rev Genomics Hum Genet.
2005:
6
143-64
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Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity.
Stone EA,
Sidow A.
Genome Res.
2005;
15
(7):
978-86
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Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance.
Johnson DS,
Davidson B, Brown CD, Smith WC, Sidow A.
Genome Res.
2004;
14
(12):
2448-56
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ABC: software for interactive browsing of genomic multiple sequence alignment data.
Cooper GM,
Singaravelu SA, Sidow A.
BMC Bioinformatics.
2004:
5
192
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Genome sequence of the brown Norway rat yields insights into mammalian evolution
Sidow A,
Nature.
2004
428
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Automated whole-genome multiple alignment of rat, mouse, and human.
Brudno M,
Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I.
Genome Res.
2004;
14
(4):
685-92
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Characterization of evolutionary rates and constraints in three Mammalian genomes.
Cooper GM,
Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A.
Genome Res.
2004;
14
(4):
539-48
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The integrity of a cholesterol-binding pocket in Niemann-Pick C2 protein is necessary to control lysosome cholesterol levels.
Ko DC,
Binkley J, Sidow A, Scott MP.
Proc Natl Acad Sci U S A.
2003;
100
(5):
2518-25
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LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
Brudno M,
Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S.
Genome Res.
2003;
13
(4):
721-31
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Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.
Cooper GM,
Brudno M, Green ED, Batzoglou S, Sidow A.
Genome Res.
2003;
13
(5):
813-20
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Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail.
Aburomia R,
Khaner O, Sidow A.
J Struct Funct Genomics.
2003;
3
(1-4):
45-52
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Genomic regulatory regions: insights from comparative sequence analysis.
Cooper GM,
Sidow A.
Curr Opin Genet Dev.
2003;
13
(6):
604-10
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Inference of functional regions in proteins by quantification of evolutionary constraints.
Simon AL,
Stone EA, Sidow A.
Proc Natl Acad Sci U S A.
2002;
99
(5):
2912-7
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Sequence first. Ask questions later.
Sidow A,
Cell.
2002;
111
(1):
13-6
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A novel member of the F-box/WD40 gene family, encoding dactylin, is disrupted in the mouse dactylaplasia mutant.
Sidow A,
Bulotsky MS, Kerrebrock AW, Birren BW, Altshuler D, Jaenisch R, Johnson KR, Lander ES.
Nat Genet.
1999;
23
(1):
104-7
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