Publications by authors named "Timothy Harkins"

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de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project.
Jeffrey K Ng, Pankaj Vats, Elyn Fritz-Waters, Stephanie Sarkar, Eleanor I Sams, Timothy T Harkins

Hum Mutat· December 2022

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A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study.
Giovanna Carpi, Lev Gorenstein, Timothy T Harkins, Mehrzad Samadi, Pankaj Vats

Brief Bioinform· September 2022

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Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples.
Phillip A Morin, Brenna R Forester, Karin A Forney, Carla A Crossman, Brittany L Hancock-Hanser, Timothy Harkins

Mol Ecol· March 2021

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Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum.
Yacine Ben Chehida, Julie Thumloup, Cassie Schumacher, Timothy Harkins, Alex Aguilar

Sci Rep· September 2020

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Detection of endometrial precancer by a targeted gynecologic cancer liquid biopsy.
John A Martignetti, Deep Pandya, Nimesh Nagarsheth, Ying Chen, Olga Camacho, Timothy T Harkins

Cold Spring Harb Mol Case Stud· December 2018

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ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data.
Nick Kamps-Hughes, Andrew McUsic, Laurie Kurihara, Timothy T Harkins, Prithwish Pal

PLoS One· July 2018

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Applying Precision Medicine to Ovarian Cancer: Proof-of-Principle for a "Molecular Second Look".
Melissa Schwartz, Olga Camacho-Vanegas, Ashley M Wood, Matthew Dashkoff, Courtney Whitelock, Timothy T Harkins

Int J Gynecol Cancer· March 2018

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Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Timothy T Harkins

Science· August 2017

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Genomic 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.
Navya Nair, Olga Camacho-Vanegas, Dmitry Rykunov, Matthew Dashkoff, Sandra Catalina Camacho, Timothy T Harkins

PLoS Med· December 2016

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The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments.
Joanna L Kelley, Muh-Ching Yee, Anthony P Brown, Rhea R Richardson, Andrey Tatarenkov, Timothy T Harkins

Genome Biol Evol· August 2016

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Erratum for Salipante et al., Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling.
Stephen J Salipante, Toana Kawashima, Christopher Rosenthal, Daniel R Hoogestraat, Lisa A Cummings, Timothy T Harkins

Appl Environ Microbiol· July 2016

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Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome.
Evangelos Giamarellos-Bourboulis, Jie Tang, Emmannouil Pyleris, Aikaterini Pistiki, Charalambos Barbatzas, Timothy T Harkins

Scand J Gastroenterol· March 2016

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Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs.
Adam H Freedman, Rena M Schweizer, Diego Ortega-Del Vecchyo, Eunjung Han, Brian W Davis, Timothy T Harkins

PLoS Genet· March 2016

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Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling.
Stephen J Salipante, Toana Kawashima, Christopher Rosenthal, Daniel R Hoogestraat, Lisa A Cummings, Timothy T Harkins

Appl Environ Microbiol· December 2014

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Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.
Elza C de Bruin, Nicholas McGranahan, Richard Mitter, Max Salm, David C Wedge, Timothy T Harkins

Science· October 2014

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Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.
Yan Wei Lim, Daniel A Cuevas, Genivaldo Gueiros Z Silva, Kristen Aguinaldo, Elizabeth A Dinsdale, Timothy T Harkins

PeerJ· September 2014

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Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions.
Bas E Dutilh, Cristiane C Thompson, Ana C P Vicente, Michel A Marin, Clarence Lee, Timothy T Harkins

BMC Genomics· August 2014

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Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis.
Henne Holstege, Wayne Pfeiffer, Daoud Sie, Marc Hulsman, Thomas J Nicholas, Timothy T Harkins

Genome Res· May 2014

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Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe.
Martin Sikora, Meredith L Carpenter, Andres Moreno-Estrada, Brenna M Henn, Peter A Underhill, Timothy T Harkins

PLoS Genet· May 2014

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Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.
Marlous Hoogstraat, Mirjam S de Pagter, Geert A Cirkel, Markus J van Roosmalen, Timothy T Harkins

Genome Res· February 2014

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Detection of circulating tumor DNA in early- and late-stage human malignancies.
Chetan Bettegowda, Mark Sausen, Rebecca J Leary, Isaac Kinde, Yuxuan Wang, Timothy T Harkins

Sci Transl Med· February 2014

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Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.
Stephen J Salipante, Dhruba J Sengupta, Christopher Rosenthal, Gina Costa, Jessica Spangler, Timothy T Harkins

PLoS One· January 2014

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A comprehensive assay for CFTR mutational analysis using next-generation sequencing.
Ahmad N Abou Tayoun, Christopher D Tunkey, Trevor J Pugh, Tristen Ross, Minita Shah, Timothy T Harkins

Clin Chem· October 2013

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Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era.
Robert Alan Edwards, John Matthew Haggerty, Noriko Cassman, Julia Christine Busch, Kristen Aguinaldo, Timothy T Harkins

BMC Genomics· September 2013

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