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Author Details

Timothy T Harkins
NVIDIA Corporation
1994
68
45
PMIDPaper TitleJournal TitlePublished Year
35945154A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study.Brief Bioinform2022
36054329de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project.Hum Mutat2022
33544423Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples.Mol Ecol2021
32938978Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum.Sci Rep2020
29324546Applying Precision Medicine to Ovarian Cancer: Proof-of-Principle for a "Molecular Second Look".Int J Gynecol Cancer2018
30301868Detection of endometrial precancer by a targeted gynecologic cancer liquid biopsy.Cold Spring Harb Mol Case Stud2018
29630678ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data.PLoS One2018
28798132Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.Science2017
26943675Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs.PLoS Genet2016
28027320Genomic Analysis of Uterine Lavage Fluid Detects Early Endometrial Cancers and Reveals a Prevalent Landscape of Driver Mutations in Women without Histopathologic Evidence of Cancer: A Prospective Cross-Sectional Study.PLoS Med2016
27364849Erratum for Salipante et al., Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling.Appl Environ Microbiol2016
27324916The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments.Genome Biol Evol2016
25865706Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome.Scand J Gastroenterol2015
24221193Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.Genome Res2014
25261520Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling.Appl Environ Microbiol2014
25301630Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.Science2014
25096633Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions.BMC Genomics2014
25177534Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.PeerJ2014
24809476Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe.PLoS Genet2014
24760347Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis.Genome Res2014
24908277Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.Nat Biotechnol2014
24553385Detection of circulating tumor DNA in early- and late-stage human malignancies.Sci Transl Med2014
24453982Genome sequencing highlights the dynamic early history of dogs.PLoS Genet2014
23590730Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.BMC Genomics2013
24007365Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era.BMC Genomics2013
23636849Somatic alterations contributing to metastasis of a castration-resistant prostate cancer.Hum Mutat2013
23775370A comprehensive assay for CFTR mutational analysis using next-generation sequencing.Clin Chem2013
23734239Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.PLoS One2013
22426219New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing.Nat Commun2012
23040067Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes.Cell Metab2012
23133345Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency.PLoS Comput Biol2012
22723055The possibility of de novo assembly of the genome and population genomics of the mangrove rivulus, Kryptolebias marmoratus.Integr Comp Biol2012
22848480Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.PLoS One2012
22841627Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl.Dev Biol2012
22529356Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle.Proc Natl Acad Sci U S A2012
22523606The Cassava Genome: Current Progress, Future Directions.Trop Plant Biol2012
22495314The clonal and mutational evolution spectrum of primary triple-negative breast cancers.Nature2012
21186353The genome of woodland strawberry (Fragaria vesca).Nat Genet2011
21746916Tumor-specific silencing of COPZ2 gene encoding coatomer protein complex subunit ζ 2 renders tumor cells dependent on its paralogous gene COPZ1.Proc Natl Acad Sci U S A2011
21347285The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.PLoS Genet2011
21429141Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids.Mol Ecol Resour2011
19823874A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.Hum Genet2010
20838655Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.PLoS Biol2010
20950470Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.).BMC Genomics2010
20885794An insect herbivore microbiome with high plant biomass-degrading capacity.PLoS Genet2010
20522740The landscape of C. elegans 3'UTRs.Science2010
20164927Complete Khoisan and Bantu genomes from southern Africa.Nature2010
20368428Function-based gene identification using enzymatically generated normalized shRNA library and massive parallel sequencing.Proc Natl Acad Sci U S A2010
20413674Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species.Genome Res2010
20044575The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer.Science2010
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Collaborators

Regeneron Pharmaceuticals, Inc.
Co-authored papers 10
Stanford University
Co-authored papers 6
GE Global Research Center
Co-authored papers 4
Co-authored papers 4
Co-authored papers 4
Co-authored papers 3
Co-authored papers 3
Bilkent University
Co-authored papers 3
Salk Institute for Biological Studies
Co-authored papers 3
Co-authored papers 3
Frederick National Laboratory for Cancer Research
Co-authored papers 3
Co-authored papers 3
Co-authored papers 3
Dana-Farber Cancer Institute, Harvard Medical School
Co-authored papers 3
Co-authored papers 3
Center for Public Health Genomics, University of Virginia
Co-authored papers 3
Virginia Tech
Co-authored papers 2
National Cancer Institute, National Institutes of Health
Co-authored papers 2
Co-authored papers 2
Co-authored papers 2
Co-authored papers 2
Georgia Institute of Technology
Co-authored papers 2
Co-authored papers 2
Co-authored papers 2
University of Wisconsin-Madison
Co-authored papers 2
Co-authored papers 2
Michigan Center for Translational Pathology, University of Michigan ann arbor
Co-authored papers 2
National Cancer Institute, Frederick National Laboratory for Cancer Research
Co-authored papers 2
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Joint Genome Institute
Co-authored papers 2