Arend Sidow

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Concepts in solid tumor evolution
    Arend Sidow
    Departments of Pathology and of Genetics, Stanford University, Stanford, CA 94305, USA Electronic address
    Trends Genet 31:208-14. 2015
  2. pmc Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members
    Inna Hughes
    Department of Developmental Biology, Washington University School of Medicine, St, Louis, MO 63110, USA
    BMC Evol Biol 8:41. 2008
  3. pmc Constructing a meaningful evolutionary average at the phylogenetic center of mass
    Eric A Stone
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    BMC Bioinformatics 8:222. 2007
  4. ncbi request reprint Fruit fly family fun
    Arend Sidow
    Department of Pathology and Department of Genetics, SUMC L235, Stanford CA 94305 5324, USA
    Cell 131:1222-3. 2007
  5. ncbi request reprint A novel member of the F-box/WD40 gene family, encoding dactylin, is disrupted in the mouse dactylaplasia mutant
    A Sidow
    Departments of Pathology and Genetics, SUMC R248B, Stanford, California 94305 5324, USA
    Nat Genet 23:104-7. 1999
  6. ncbi request reprint Sequence first. Ask questions later
    Arend Sidow
    Department of Pathology, SUMC R248B, 300 Pasteur Drive, Stanford University, Stanford, CA 94305, USA
    Cell 111:13-6. 2002
  7. pmc Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 13:813-20. 2003
  8. pmc Distribution and intensity of constraint in mammalian genomic sequence
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 15:901-13. 2005
  9. pmc ABC: software for interactive browsing of genomic multiple sequence alignment data
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, CA 94305 9010, USA
    BMC Bioinformatics 5:192. 2004
  10. pmc Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
    David L Goode
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 20:301-10. 2010

Research Grants

  1. GENETIC ANALYSIS OF EARLY LIMB DEVELOPMENT
    Arend Sidow; Fiscal Year: 2004
  2. The ProPhylER Database and Web Resource
    Arend Sidow; Fiscal Year: 2006
  3. The Ciona savignyi Genetic Map
    Arend Sidow; Fiscal Year: 2008

Detail Information

Publications50

  1. pmc Concepts in solid tumor evolution
    Arend Sidow
    Departments of Pathology and of Genetics, Stanford University, Stanford, CA 94305, USA Electronic address
    Trends Genet 31:208-14. 2015
    ....
  2. pmc Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members
    Inna Hughes
    Department of Developmental Biology, Washington University School of Medicine, St, Louis, MO 63110, USA
    BMC Evol Biol 8:41. 2008
    ..Vertebrate Otop1 and its paralogues Otop2 and Otop3 define a new gene family with homology to the invertebrate Domain of Unknown Function 270 genes (DUF270; pfam03189)...
  3. pmc Constructing a meaningful evolutionary average at the phylogenetic center of mass
    Eric A Stone
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    BMC Bioinformatics 8:222. 2007
    ..Here we propose a remedy that weighs the contribution of each species according to its phylogenetic placement...
  4. ncbi request reprint Fruit fly family fun
    Arend Sidow
    Department of Pathology and Department of Genetics, SUMC L235, Stanford CA 94305 5324, USA
    Cell 131:1222-3. 2007
    ..2007) reveals a comprehensive picture of the evolution of small animal genomes and greatly improves computational predictions of functional elements in the D. melanogaster reference sequence...
  5. ncbi request reprint A novel member of the F-box/WD40 gene family, encoding dactylin, is disrupted in the mouse dactylaplasia mutant
    A Sidow
    Departments of Pathology and Genetics, SUMC R248B, Stanford, California 94305 5324, USA
    Nat Genet 23:104-7. 1999
    ..In conjuction with recent biochemical studies, this report demonstrates the importance of this gene family in vertebrate embryonic development...
  6. ncbi request reprint Sequence first. Ask questions later
    Arend Sidow
    Department of Pathology, SUMC R248B, 300 Pasteur Drive, Stanford University, Stanford, CA 94305, USA
    Cell 111:13-6. 2002
    ..Functional changes that set us apart from apes are identifiable, as are functional constraints in proteins and genomic elements that arose in our relatively distant phylogenetic past...
  7. pmc Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 13:813-20. 2003
    ..Estimates of the neutral divergence in these data suggest that a small number of diverse mammalian genomes in addition to human, mouse, and rat would allow single nucleotide resolution in comparative sequence analyses...
  8. pmc Distribution and intensity of constraint in mammalian genomic sequence
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 15:901-13. 2005
    ..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer...
  9. pmc ABC: software for interactive browsing of genomic multiple sequence alignment data
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, CA 94305 9010, USA
    BMC Bioinformatics 5:192. 2004
    ..Visualization and browsing of results can be difficult, and there are currently limited software options for performing this task...
  10. pmc Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
    David L Goode
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 20:301-10. 2010
    ..These observations show that common, noncoding alleles contribute substantially to human phenotypes and that constraint-based analyses will be of value to identify phenotypically relevant variants in individual genomes...
  11. pmc Identifying a high fraction of the human genome to be under selective constraint using GERP++
    Eugene V Davydov
    Department of Computer Science, Stanford University, Stanford, California, United States of America
    PLoS Comput Biol 6:e1001025. 2010
    ..GERP++ is an efficient and effective tool to provide both nucleotide- and element-level constraint scores within deep multiple sequence alignments...
  12. pmc The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution
    Matthew M Hill
    Department of Pathology, SUMC, Stanford, CA 94305 5324, USA
    Genome Res 18:1369-79. 2008
    ..These results, when considered in light of the neutral theory, suggest fundamentally different modes of evolution of animal species with large versus small population sizes...
  13. pmc Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
    Anshul Kundaje
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1735-47. 2012
    ..Meta-analyses of the signal profiles revealed a common vocabulary of chromatin signals shared across multiple cell lines and binding proteins...
  14. pmc Automated whole-genome multiple alignment of rat, mouse, and human
    Michael Brudno
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 14:685-92. 2004
    ..5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present...
  15. pmc Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance
    David S Johnson
    Department of Pathology, Stanford University Medical Center, Stanford, California 94305 5324, USA
    Genome Res 14:2448-56. 2004
    ..This work demonstrates the power of comparative sequence analysis between the two Ciona species for guiding gene regulatory experiments...
  16. pmc A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
    Kerrin S Small
    Department of Pathology, Stanford University Medical Center, Stanford, California 94305 5324, USA
    Genome Biol 8:R41. 2007
    ..In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved...
  17. ncbi request reprint Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
    Eric A Stone
    Department of Statistics, Stanford University, Stanford, California 94305, USA
    Annu Rev Genomics Hum Genet 6:143-64. 2005
    ..We consider the impact of an expanding diversity of orthologous sequences on our ability to resolve functional elements. This impact is assessed through both recent comparative analyses of deep alignments and mathematical modeling...
  18. pmc Characterization of evolutionary rates and constraints in three Mammalian genomes
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 14:539-48. 2004
    ..At least 5% of the human genome is under substantial constraint, most of which is noncoding...
  19. pmc ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses
    Jonathan Binkley
    Stanford University School of Medicine, Departments of Pathology and Genetics, Stanford, California 94305, USA
    Genome Res 20:142-54. 2010
    ..The high accuracy of ProPhylER's regional analysis complements the high resolution of its single-site analysis to effectively guide and inform structure-function investigations and predict the impact of polymorphisms...
  20. pmc Inference of tumor phylogenies with improved somatic mutation discovery
    Raheleh Salari
    1 Department of Computer Science, Stanford University, Stanford, California
    J Comput Biol 20:933-44. 2013
    ..Experimental analyses demonstrate that our method achieves up to 32% improvement for somatic SNV calling of multiple, related samples over the accuracy of GATK's Unified Genotyper, the state-of-the-art multisample SNV caller...
  21. pmc Mammalian comparative sequence analysis of the Agrp locus
    Christopher B Kaelin
    Department of Genetics, Stanford University, Stanford, California, United States of America
    PLoS ONE 2:e702. 2007
    ..Conserved sequences within these elements suggest a role for homeodomain proteins in the regulation of Agrp and provide additional targets for functional evaluation...
  22. ncbi request reprint Functional architecture and evolution of transcriptional elements that drive gene coexpression
    Christopher D Brown
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 317:1557-60. 2007
    ..Thus, the syntactical rules governing this regulatory function are flexible but become highly constrained evolutionarily once they are established in a particular element...
  23. pmc Extreme genomic variation in a natural population
    Kerrin S Small
    Departments of Genetics and Pathology, Stanford University Medical Center, Stanford, CA 94305 5324, USA
    Proc Natl Acad Sci U S A 104:5698-703. 2007
    ..These results constitute in-depth insight into the dynamics of highly polymorphic genomes and provide important empirical support of population genetic theory as it pertains to population size, heterozygosity, and natural selection...
  24. pmc ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    Stephen G Landt
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1813-31. 2012
    ..All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals...
  25. ncbi request reprint Genomic regulatory regions: insights from comparative sequence analysis
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, CA 94305 9010, USA
    Curr Opin Genet Dev 13:604-10. 2003
    ....
  26. pmc Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
    Anton Valouev
    Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, California 94305, USA
    Nat Methods 5:829-34. 2008
    ..By combining QuEST analyses with Gene Ontology (GO) annotations and expression data, we illustrate how general functions of transcription factors can be inferred...
  27. pmc Read clouds uncover variation in complex regions of the human genome
    Alex Bishara
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 25:1570-80. 2015
    ....
  28. pmc Constraint and divergence of global gene expression in the mammalian embryo
    Noah Spies
    Department of Pathology, Stanford University School of Medicine, Stanford, United States
    elife 4:e05538. 2015
    ..The widespread effect of maternal and embryonic genotype in conjunction with the purifying selection we uncovered suggests that embryogenesis is an important and understudied reservoir of phenotypic variation. ..
  29. pmc LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA
    Michael Brudno
    Department of Computer Science, Stanford University, Stanford, California 94305 9010, USA
    Genome Res 13:721-31. 2003
    ..Multi-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evolutionary distance. Our systems are publicly available at http://lagan.stanford.edu...
  30. pmc The integrity of a cholesterol-binding pocket in Niemann-Pick C2 protein is necessary to control lysosome cholesterol levels
    Dennis C Ko
    Department of Developmental Biology, Beckman Center B300, 279 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305 5329, USA
    Proc Natl Acad Sci U S A 100:2518-25. 2003
    ..On the basis of evolutionary analysis and mutagenesis, three other regions of the NPC2 protein emerged as important, including one required for efficient secretion...
  31. pmc Determinants of nucleosome organization in primary human cells
    Anton Valouev
    Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA
    Nature 474:516-20. 2011
    ..Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells...
  32. pmc Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
    Eric A Stone
    Department of Statistics, Stanford University, Stanford, California 94305 5324, USA
    Genome Res 15:978-86. 2005
    ....
  33. pmc Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta
    Elizabeth H Finn
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, United States
    Dev Biol 390:80-92. 2014
    ..In all, we observe a striking preference for maternal transcription in the midgestation mouse placenta and a dynamic imprinting landscape in extraembryonic tissues, reflecting the complex nature of epigenetic pathways in the placenta. ..
  34. pmc De novo discovery of a tissue-specific gene regulatory module in a chordate
    David S Johnson
    Department of Pathology, Stanford University Medical Center, Stanford, California 94305 5324, USA
    Genome Res 15:1315-24. 2005
    ..As final biological validation of the discovered muscle regulatory module, we implement a novel algorithm to search the genome for instances of the module and identify seven novel enhancers...
  35. doi request reprint A research roadmap for next-generation sequencing informatics
    Russ B Altman
    Bioengineering, Genetics, and Medicine, Stanford University, Stanford, CA 94305, USA
    Sci Transl Med 8:335ps10. 2016
    ..Next-generation sequencing technologies are fueling a wave of new diagnostic tests. Progress on a key set of nine research challenge areas will help generate the knowledge required to advance effectively these diagnostics to the clinic. ..
  36. ncbi request reprint Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail
    Rami Aburomia
    Department of Pathology, Stanford University Medical Center, Room 248B, 300 Pasteur Drive, Stanford, CA 94305 5324, USA
    J Struct Funct Genomics 3:45-52. 2003
    ..We discuss analyses of two gene families whose regulatory and structural evolution shed light on the connection between gene duplication and increases in organismal complexity...
  37. pmc 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples
    Andrew H Beck
    Department of Pathology, Stanford University Medical Center, Stanford, California, United States of America
    PLoS ONE 5:e8768. 2010
    ..These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research...
  38. pmc Genome evolution during progression to breast cancer
    Daniel E Newburger
    Biomedical Informatics Training Program, Stanford, California 94305, USA
    Genome Res 23:1097-108. 2013
    ..Aneuploidies that occur in common ancestors of neoplastic and tumor cells are the earliest events that affect a large number of genes and may predispose breast tissue to eventual development of invasive carcinoma. ..
  39. pmc Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses
    Daniela Kenzelmann Broz
    Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
    Genes Dev 27:1016-31. 2013
    ..Together, our data highlight an intimate connection between p53 and autophagy through a vast transcriptional network and indicate that autophagy contributes to p53-dependent apoptosis and cancer suppression...
  40. doi request reprint svviz: a read viewer for validating structural variants
    Noah Spies
    Department of Genetics, Stanford University, Department of Pathology, Stanford University, Genome Scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, USA and
    Bioinformatics 31:3994-6. 2015
    ..svviz supports data from most modern sequencing platforms...
  41. pmc Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines
    Joseph W Foley
    Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, California 94305, USA
    BMC Genomics 14:720. 2013
    ..HOT regions were initially defined in invertebrate model organisms, and we here show that they are a ubiquitous feature of the human gene-regulation landscape...
  42. pmc Inference of functional regions in proteins by quantification of evolutionary constraints
    Alexander L Simon
    Program in Cancer Biology and Department of Pathology, Stanford University Medical School, Stanford, CA 94305 5324, USA
    Proc Natl Acad Sci U S A 99:2912-7. 2002
    ..The methodology has significant predictive power and may be used to guide structure--function studies for any protein represented by a modest number of homologs in sequence databases...
  43. pmc A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
    Anton Valouev
    Departments of Pathology and Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 18:1051-63. 2008
    ..We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome...
  44. pmc An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo
    Lia E Gracey
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Epigenetics Chromatin 3:13. 2010
    ....
  45. pmc Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells
    Jamy C Peng
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 139:1290-302. 2009
    ..Our findings illuminate a mechanism of histone methylation regulation in pluripotent cells and during early cell-fate transitions...
  46. pmc Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence
    Carl S Kashuk
    McKusick Nathans Institute of Genetic Medicine and Department of Comparative Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 102:8949-54. 2005
    ....
  47. pmc Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins
    Pilgrim J Jackson
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Chem Biol 13:1297-305. 2006
    ....
  48. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
    ..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization...
  49. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  50. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...

Research Grants3

  1. GENETIC ANALYSIS OF EARLY LIMB DEVELOPMENT
    Arend Sidow; Fiscal Year: 2004
    ..Because Dac is likely to be the mouse ortholog of the human Split Hand/Foot Malformation 3 gene, this project may also bear direct relevance to understanding and diagnosis of congenital limb diseases. ..
  2. The ProPhylER Database and Web Resource
    Arend Sidow; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  3. The Ciona savignyi Genetic Map
    Arend Sidow; Fiscal Year: 2008
    ..Insights into the molecular mechanisms of regulation and development using Ciona as a model are highly effective and relevant to the homologous processes in human. ..