Cristian Coarfa

Summary

Affiliation: Baylor College of Medicine
Country: USA

Publications

  1. pmc Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood
    Matthew N Davies
    Institute of Psychiatry, King s College London, De Crespigny Park, London, UK
    Genome Biol 13:R43. 2012
  2. pmc Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
    BMC Genomics 12:277. 2011
  3. pmc Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
    Cristian Coarfa
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA
    BMC Bioinformatics 11:572. 2010
  4. pmc Atlas2 Cloud: a framework for personal genome analysis in the cloud
    Uday S Evani
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Genomics 13:S19. 2012
  5. doi request reprint Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
    Govindarajan Kunde-Ramamoorthy
    Department of Pediatrics, Baylor College of Medicine, USDA ARS Children s Nutrition Research Center, Houston, TX 77030, USA, Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Nucleic Acids Res 42:e43. 2014
  6. pmc The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
    Kevin Riehle
    Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Bioinformatics 13:S11. 2012
  7. pmc An integrative variant analysis suite for whole exome next-generation sequencing data
    Danny Challis
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA
    BMC Bioinformatics 13:8. 2012
  8. doi request reprint CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma
    Kalpana Kannan
    Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Genet 10:e1004216. 2014

Collaborators

  • Aleksandar Milosavljevic
  • Kjersti Aagaard
  • Jun Ma
  • Richard A Gibbs
  • Danny Challis
  • Sameer Paithankar
  • Uday S Evani
  • Kalpana Kannan
  • Govindarajan Kunde-Ramamoorthy
  • R Alan Harris
  • Kevin Riehle
  • Andrew R Jackson
  • Jin Yu
  • Fuli Yu
  • Matthew N Davies
  • Preethi H Gunaratne
  • Martin M Matzuk
  • Shannon M Hawkins
  • Noah J Kessler
  • Kimal Rajapakshe
  • Laising Yen
  • Mingchu Xu
  • Rui Chen
  • Lanlan Shen
  • Robert A Waterland
  • Eleonora Laritsky
  • María Alejandra Díaz
  • Claire Troakes
  • Matthew N Bainbridge
  • Safa Al-Sarraj
  • Peter Pham
  • Ruth Pidsley
  • Toni Ann Mistretta
  • Leonard C Schalkwyk
  • Sriram Raghuraman
  • Jonathan Mill
  • Andrew Jackson
  • Richard Dobson
  • Manuela Volta
  • Adinarayana Jakkamsetti
  • Sabeen Raza
  • Robert Shulman
  • Arpit Tandon
  • James Versalovic
  • Delphine Saulnier
  • Katie Lunnon
  • Abhishek Dixit
  • Simon Lovestone
  • David F Clayton
  • Ashley L Benham
  • Jong H Kim
  • Jenny Drnevich
  • Sam Griffiths-Jones
  • Ya Chi Lin
  • Chad J Creighton
  • Michael Watson
  • Jayantha B Tennakoon

Detail Information

Publications8

  1. pmc Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood
    Matthew N Davies
    Institute of Psychiatry, King s College London, De Crespigny Park, London, UK
    Genome Biol 13:R43. 2012
    ..We characterized intra- and inter-individual methylomic variation across whole blood and multiple regions of the brain from multiple donors...
  2. pmc Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
    BMC Genomics 12:277. 2011
    ..To test this, we used massively parallel Illumina sequencing to analyse small RNAs from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence...
  3. pmc Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
    Cristian Coarfa
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA
    BMC Bioinformatics 11:572. 2010
    ..Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing...
  4. pmc Atlas2 Cloud: a framework for personal genome analysis in the cloud
    Uday S Evani
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Genomics 13:S19. 2012
    ..To this end, the cloud computing and Software-as-a-Service (SaaS) technologies can help address these issues...
  5. doi request reprint Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
    Govindarajan Kunde-Ramamoorthy
    Department of Pediatrics, Baylor College of Medicine, USDA ARS Children s Nutrition Research Center, Houston, TX 77030, USA, Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Nucleic Acids Res 42:e43. 2014
    ..Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage. ..
  6. pmc The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
    Kevin Riehle
    Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Bioinformatics 13:S11. 2012
    ..Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings...
  7. pmc An integrative variant analysis suite for whole exome next-generation sequencing data
    Danny Challis
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA
    BMC Bioinformatics 13:8. 2012
    ..Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data...
  8. doi request reprint CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma
    Kalpana Kannan
    Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Genet 10:e1004216. 2014
    ..CDKN2D-WDFY2 fusion could be an important molecular signature for understanding and classifying sub-lineages among heterogeneous high-grade serous ovarian carcinomas. ..