Arend Sidow

Publications

• Genome Evolution during Progression to Breast Cancer. Newburger DE, Kashef-Haghighi D, Weng Z, Salari R, Sweeney RT, Brunner AL, Zhu SX, Guo X, Varma S, Troxell ML, West RB, Batzoglou S, Sidow A. Genome Res. 2013
• The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, Macarthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G. Genome Res. 2013; 23 (5): 749-61
• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. Genome Res. 2012; 22 (9): 1813-31
• Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Genome Res. 2012; 22 (9): 1735-47
• Determinants of nucleosome organization in primary human cells. Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Nature. 2011; 474 (7352): 516-20
• Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A. Genome Res. 2010; 20 (3): 301-10
• Identifying a high fraction of the human genome to be under selective constraint using GERP++. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. PLoS Comput Biol. 2010; 6 (12): e1001025
• ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses. Binkley J, Karra K, Kirby A, Hosobuchi M, Stone EA, Sidow A. Genome Res. 2010; 20 (1): 142-54
• Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J. Cell. 2009; 139 (7): 1290-302
• 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
• Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Nat Methods. 2008; 5 (9): 829-34
• 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
• 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
• 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
• Fruit fly family fun. Sidow A, Lacroute P. Cell. 2007; 131 (7): 1222-3
• Functional architecture and evolution of transcriptional elements that drive gene coexpression. Brown CD, Johnson DS, Sidow A. Science. 2007; 317 (5844): 1557-60
• Mammalian comparative sequence analysis of the Agrp locus. Kaelin CB, Cooper GM, Sidow A, Barsh GS. PLoS One. 2007; 2 (8): e702
• 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
• 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
• 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
• 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
• ABC: software for interactive browsing of genomic multiple sequence alignment data. Cooper GM, Singaravelu SA, Sidow A. BMC Bioinformatics. 2004: 5 192
• 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
• 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
• Genome sequence of the brown Norway rat yields insights into mammalian evolution Sidow A, Nature. 2004 428
• 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
• 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
• Genomic regulatory regions: insights from comparative sequence analysis. Cooper GM, Sidow A. Curr Opin Genet Dev. 2003; 13 (6): 604-10
• 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
• 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
• 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
• 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
• Sequence first. Ask questions later. Sidow A, Cell. 2002; 111 (1): 13-6
• 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