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David A. Nix · SciRah

Researcher profile · Semantic Scholar

David A. Nix

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David A. Nix — researcher profile on SciRah

h-index: 26
Works: 53
Citations: 7,909

Most-cited papers

RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
P. Kapranov, Jill Cheng, S. Dike, David A. Nix +18 more
2007Science2,541 citations
Semantic Scholar
Conserved roles for murine DUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons
P. Hendrickson, Jessie A. Doráis, Edward J. Grow, Jennifer L. Whiddon +11 more
2017Nature Genetics665 citations Open access
Semantic Scholar
Genome-wide analysis of Polycomb targets in Drosophila melanogaster
Y. Schwartz, T. G. Kahn, David A. Nix, Xiao-Yong Li +3 more
2006Nature Genetics658 citations Open access
Semantic Scholar
Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.
J. Rowley, Andrew J. Oler, Neal D. Tolley, Benjamin Hunter +5 more
2011Blood593 citations Open access
Semantic Scholar
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Xiao-Yong Li, S. MacArthur, Richard Bourgon, David A. Nix +18 more
2008PLoS Biology533 citations Open access
Semantic Scholar
Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern
Magdalena E. Potok, David A. Nix, Timothy J. Parnell, B. Cairns
2013Cell382 citations Open access
Semantic Scholar
Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men.
S. S. Hammoud, David A. Nix, A. Hammoud, M. Gibson +2 more
2011Human Reproduction269 citations Open access
Semantic Scholar
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
Alan M. Moses, D. Pollard, David A. Nix, Venky N. Iyer +3 more
2006PLoS Comput. Biol.265 citations Open access
Semantic Scholar
Nuclear–Cytoplasmic Shuttling of the Focal Contact Protein, Zyxin: A Potential Mechanism for Communication between Sites of Cell Adhesion and the Nucleus
David A. Nix, M. Beckerle
1997Journal of Cell Biology258 citations Open access
Semantic Scholar
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
David A. Nix, Samir J. Courdy, K. Boucher
2008BMC Bioinformatics247 citations Open access
Semantic Scholar
Adenomatous polyposis coli protein contains two nuclear export signals and shuttles between the nucleus and cytoplasm.
Kristi L. Neufeld, David A. Nix, H. Bogerd, Yi-Bin Kang +3 more
2000Proceedings of the National Academy of Sciences of the United States of America172 citations Open access
Semantic Scholar
Targeting of Zyxin to Sites of Actin Membrane Interaction and to the Nucleus*
David A. Nix, J. Fradelizi, S. Bockholt, B. Menichi +3 more
2001Journal of Biological Chemistry169 citations Open access
Semantic Scholar
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
David S. Johnson, Wei Li, D. B. Gordon, A. Bhattacharjee +44 more
2008Genome Research147 citations Open access
Semantic Scholar
Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping
Natalie Dutrow, David A. Nix, Derick G. Holt, B. Milash +4 more
2008Nature Genetics117 citations Open access
Semantic Scholar
Potential role for snoRNAs in PKR activation during metabolic stress
Osama Youssef, S. A. Safran, Takahisa Nakamura, David A. Nix +2 more
2015Proceedings of the National Academy of Sciences of the United States of America112 citations Open access
Semantic Scholar
Targeted Disruption of the Murine zyxin Gene
Laura M. Hoffman, David A. Nix, Beverly A. Benson, R. Boot-Hanford +9 more
2003Molecular and Cellular Biology105 citations Open access
Semantic Scholar
GATA: a graphic alignment tool for comparative sequence analysis
David A. Nix, M. Eisen
2005BMC Bioinformatics84 citations Open access
Semantic Scholar
Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs.
Noah C. Welker, Derek M. Pavelec, David A. Nix, T. Duchaine +2 more
2010RNA: A publication of the RNA Society82 citations Open access
Semantic Scholar
Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array
F. Biemar, David A. Nix, J. Piel, Brant Peterson +5 more
2006Proceedings of the National Academy of Sciences of the United States of America65 citations Open access
Semantic Scholar
Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants
M. Vallée, Tonya DiSera, David A. Nix, A. Paquette +7 more
2016Human Mutation61 citations Open access
Semantic Scholar
Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing
S. Hellwig, David A. Nix, Keith M. Gligorich, John M O'Shea +6 more
2018PLoS ONE57 citations Open access
Semantic Scholar
Pluripotency Transcription Factor Oct4 Mediates Stepwise Nucleosome Demethylation and Depletion
A. Shakya, Catherine Callister, Alon Goren, N. Yosef +5 more
2015Molecular and Cellular Biology51 citations Open access
Semantic Scholar
Next generation tools for genomic data generation, distribution, and visualization
David A. Nix, Tonya DiSera, Brian K. Dalley, B. Milash +3 more
2010BMC Bioinformatics51 citations Open access
Semantic Scholar
Genome-wide profiling of the C. elegans dsRNAome
Joseph M. Whipple, Osama Youssef, P. Aruscavage, David A. Nix +3 more
2015RNA: A publication of the RNA Society48 citations Open access
Semantic Scholar
The actin-regulating kinase Prk1p negatively regulates Scd5p, a suppressor of clathrin deficiency, in actin organization and endocytosis.
Kenneth R. Henry, K. D'hondt, J. Chang, David A. Nix +4 more
2003Current Biology44 citations Open access
Semantic Scholar
DNA methylation profiling in zebrafish.
Shan-Fu Wu, Haiying Zhang, S. S. Hammoud, Magdalena E. Potok +3 more
2011Methods in Cell Biology32 citations
Semantic Scholar
ENCODE Tiling Array Analysis Identifies Differentially Expressed Annotated and Novel 5′ Capped RNAs in Hepatitis C Infected Liver
M. Folkers, D. Delker, Christopher I. Maxwell, Cassie A. Nelson +3 more
2011PLoS ONE21 citations Open access
Semantic Scholar
Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes.
A. Willingham, Sujit Dike, Jill Cheng, J. Manak +14 more
2006Cold Spring Harbor Symposia on Quantitative Biology20 citations Open access
Semantic Scholar
Detection of circulating tumor DNA without a tumor-informed search using next-generation sequencing is a prognostic biomarker in pancreatic ductal adenocarcinoma
Kajsa E. Affolter, S. Hellwig, David A. Nix, M. Bronner +7 more
2021Neoplasia14 citations Open access
Semantic Scholar
The stochastic nature of errors in next-generation sequencing of circulating cell-free DNA
David A. Nix, S. Hellwig, Christopher C. Conley, Alun Thomas +7 more
2020PLoS ONE14 citations Open access
Semantic Scholar
Replicative Instability Drives Cancer Progression
Benjamin B. Morris, Jason Paul Smith, Qi Zhang, Zhijie Jiang +27 more
2022bioRxiv8 citations Open access
Semantic Scholar
Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing
C. Gorbea, T. Mosbruger, David A. Nix, Demián Cazalla
2019eLife7 citations Open access
Semantic Scholar
Germline epigenetics, and reprogramming in zebrafish early embryos
Magdalena E. Potok, David A. Nix, Timothy J. Parnell, B. Cairns
2013Epigenetics & Chromatin6 citations Open access
Semantic Scholar
Correction: Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Xiao-Yong Li, S. MacArthur, Richard Bourgon, David A. Nix +18 more
2008PLoS Biology6 citations Open access
Semantic Scholar
Genome-wide analysis of Polycomb targets in Drosophila
Y. Schwartz, T. G. Kahn, David A. Nix, Xiao-Yong Li +3 more
20064 citations
Semantic Scholar
Author response: Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing
C. Gorbea, T. Mosbruger, David A. Nix, Demián Cazalla
20191 citations Open access
Semantic Scholar
Targeted Gene Sequencing in Children with Crohn’s Disease and Their Parents: Implications for Missing Heritability
Jiun-Sheng Chen, Fu-Lan Hu, S. Kugathasan, L. Jorde +7 more
2018G3: Genes, Genomes, Genetics1 citations Open access
Semantic Scholar
Del genoma humano a su pangenoma pasando por los consorcios ENCODE y T2T
M. Claros, Catherine Choo, Caroline Ucla, Carine Manzano +238 more
2022Encuentros en la Biología0 citations Open access
Semantic Scholar
Inherited germline variants in urothelial cancer: A multicenter whole-exome sequencing analysis.
W. Kohlmann, David A. Nix, Aaron E. Atkinson, K. Boucher +16 more
2022Journal of Clinical Oncology0 citations
Semantic Scholar
Abstract 580: The broad surveillance and unbiased detection of circulating tumor DNA using next-generation sequencing withouta prioriknowledge of somatic mutations is a prognostically significant biomarker in pancreatic ductal adenocarcinoma
Kajsa E. Affolter, S. Hellwig, David A. Nix, M. Bronner +7 more
2021Clinical research0 citations
Semantic Scholar
Abstract 286: Smyd1 is Required for Cell Survival During Glucose Deprivation
Amira D. Sabry, Keiko M. Cawley, Katie J. Sciuto, Amanda Horiuchi +5 more
2019Circulation Research0 citations
Semantic Scholar
Abstract 2220: Benchmarking of somatic variant calling algorithms for detection of circulating tumor DNA
P. Bhetariya, S. Hellwig, David A. Nix, G. Marth +2 more
2019Clinical research0 citations
Semantic Scholar
Abstract 441: The stochastic nature of errors in next-generation sequencing of circulating cell-free DNA
H. Underhill, P. Bhetariya, S. Hellwig, David A. Nix +3 more
2019Clinical research0 citations
Semantic Scholar
COMP-10. THE MUTATIONAL PROFILE OF GLIOBLASTOMA-DERIVED CELL-FREE DNA IN PLASMA REPRESENTS A DISTINCT SUBSET OF THE SOMATIC MUTATIONS PRESENT IN GLIOBLASTOMA SOLID TUMOR DNA
H. Underhill, David A. Nix, Christian J Davidson, S. Hellwig +4 more
2019Neuro-Oncology0 citations Open access
Semantic Scholar
COMP-20. THE NON-INVASIVE DETECTION OF GLIOBLASTOMA-DERIVED CELL-FREE DNA IN PLASMA USING NEXT-GENERATION SEQUENCING AND AN UNTARGETED VARIANT SEARCH
H. Underhill, S. Hellwig, David A. Nix, P. Bhetariya +5 more
2018Neuro-Oncology0 citations Open access
Semantic Scholar
Abstract 4590: Larger family sizes improve stochastic error correction during untargeted searches of very-low frequency variant alleles in circulating cell-free DNA (ccfDNA)
P. Bhetariya, David A. Nix, S. Hellwig, G. Marth +2 more
2018Clinical research0 citations
Semantic Scholar
Abstract 129: Smyd1 is an Essential Regulator of Adaptive Response to Glucose Starvation in Cardiomyocytes
Junco S. Warren, Amira D. Sabry, Keiko M. Cawley, Aman Makaju +5 more
20170 citations
Semantic Scholar
Germline epigenetics, and reprogramming in zebrafish early embryos
Magdalena E. Potok, David A. Nix, Timothy J. Parnell, Brad R. Cairns
2013Epigenetics & Chromatin0 citations Open access
Semantic Scholar
473 RNA-Sequencing Analysis of 5′ Capped RNA in HCV Infected Cirrhotic Liver, Acutely HCV Infected Huh 7.5 Cells, and Control Specimens Identifies Common Upregulated Known and Novel Genes
Christopher I. Maxwell, D. Delker, Shuang-Hu Liu, Cassie A. Nelson +3 more
20100 citations
Semantic Scholar
T1999 Gene Expression Changes in Hepatitis C Infected Liver as Measured by Encode Tiling Array Analysis of Both 5′ CAP and 3′ poly(A) RNA
M. Folkers, D. Delker, Christopher I. Maxwell, Cassie A. Nelson +2 more
20100 citations Open access
Semantic Scholar

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