David A Nix

Summary

Affiliation: University of Utah
Country: USA

Publications

  1. pmc Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
    David A Nix
    Huntsman Cancer Institute, Department of Research Informatics, University of Utah, Salt Lake City, Utah, 84105, USA
    BMC Bioinformatics 9:523. 2008
  2. pmc Next generation tools for genomic data generation, distribution, and visualization
    David A Nix
    Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA
    BMC Bioinformatics 11:455. 2010
  3. pmc Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men
    Saher Sue Hammoud
    Department of Oncological Sciences, Howard Hughes Medical Institute, Salt Lake City, UT, USA
    Hum Reprod 26:2558-69. 2011
  4. pmc Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern
    Magdalena E Potok
    Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
    Cell 153:759-72. 2013
  5. pmc Potential role for snoRNAs in PKR activation during metabolic stress
    Osama A Youssef
    Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
    Proc Natl Acad Sci U S A 112:5023-8. 2015
  6. pmc Genome-wide profiling of the C. elegans dsRNAome
    Joseph M Whipple
    Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112 5650, USA
    RNA 21:786-800. 2015
  7. pmc ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver
    Milan E Folkers
    Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America
    PLoS ONE 6:e14697. 2011
  8. pmc Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs
    Noah C Welker
    1Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
    RNA 16:893-903. 2010
  9. pmc Distinctive chromatin in human sperm packages genes for embryo development
    Saher Sue Hammoud
    Howard Hughes Medical Institute, Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
    Nature 460:473-8. 2009
  10. pmc Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes
    Jesse W Rowley
    Program in Molecular Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
    Blood 118:e101-11. 2011

Collaborators

  • Changjin Hong
  • Christian C Yost
  • Jason J Schwartz
  • Haiying Zhang
  • Don A Delker
  • D T Carrell
  • Saher Sue Hammoud
  • Osama A Youssef
  • Brenda L Bass
  • Bradley R Cairns
  • Joseph M Whipple
  • Magdalena E Potok
  • Milan E Folkers
  • Jesse W Rowley
  • Noah C Welker
  • Gokhan S Hotamisligil
  • W Evan Johnson
  • Takahisa Nakamura
  • P Joseph Aruscavage
  • Sarah A Safran
  • Timothy J Parnell
  • Andrew J Oler
  • Curt H Hagedorn
  • Mark Gibson
  • Ahmad O Hammoud
  • Benjamin N Hunter
  • Christopher I Maxwell
  • Andrew S Weyrich
  • Elizabeth N Low
  • Guy A Zimmerman
  • Neal D Tolley
  • Cassie A Nelson
  • Derek M Pavelec
  • Scott Kennedy
  • Thomas F Duchaine
  • Jahnvi Purwar

Detail Information

Publications10

  1. pmc Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
    David A Nix
    Huntsman Cancer Institute, Department of Research Informatics, University of Utah, Salt Lake City, Utah, 84105, USA
    BMC Bioinformatics 9:523. 2008
    ....
  2. pmc Next generation tools for genomic data generation, distribution, and visualization
    David A Nix
    Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA
    BMC Bioinformatics 11:455. 2010
    ....
  3. pmc Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men
    Saher Sue Hammoud
    Department of Oncological Sciences, Howard Hughes Medical Institute, Salt Lake City, UT, USA
    Hum Reprod 26:2558-69. 2011
    ..We hypothesize that changes in chromatin packaging may be associated with poor reproductive outcome...
  4. pmc Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern
    Magdalena E Potok
    Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
    Cell 153:759-72. 2013
    ..Thus, zebrafish achieve a totipotent chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming...
  5. pmc Potential role for snoRNAs in PKR activation during metabolic stress
    Osama A Youssef
    Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
    Proc Natl Acad Sci U S A 112:5023-8. 2015
    ..Our results suggest an unprecedented and unexpected model whereby snoRNAs play a role in the activation of PKR under metabolic stress. ..
  6. pmc Genome-wide profiling of the C. elegans dsRNAome
    Joseph M Whipple
    Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112 5650, USA
    RNA 21:786-800. 2015
    ..By combining RNA-seq with freely available bioinformatics tools, our workflow provides an easily accessible approach for the identification of dsRNAs, and more importantly, a catalog of the C. elegans dsRNAome. ..
  7. pmc ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver
    Milan E Folkers
    Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America
    PLoS ONE 6:e14697. 2011
    ....
  8. pmc Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs
    Noah C Welker
    1Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
    RNA 16:893-903. 2010
    ....
  9. pmc Distinctive chromatin in human sperm packages genes for embryo development
    Saher Sue Hammoud
    Howard Hughes Medical Institute, Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
    Nature 460:473-8. 2009
    ..Furthermore, developmental promoters are generally DNA hypomethylated in sperm, but acquire methylation during differentiation. Taken together, epigenetic marking in sperm is extensive, and correlated with developmental regulators...
  10. pmc Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes
    Jesse W Rowley
    Program in Molecular Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
    Blood 118:e101-11. 2011
    ..The sequencing dataset will be useful in the design of mouse models of hemostasis and a catalyst for discovery of new functions of platelets. Access to the dataset is found in the "Introduction."..