Winston Timp

Affiliations
  • Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

Publications (67)

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms.

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
Avec: Rebecca Yee , Florian P Breitwieser , Stephanie Hao , Belita N A Opene , Rachael E Workman , Pranita D Tamma , Jennifer Dien-Bard , Winston Timp , Patricia J Simner

Beyond mass spectrometry, the next step in proteomics.

Science advances
Avec: Winston Timp , Gregory Timp

Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region.

medRxiv : the preprint server for health sciences
Avec: Peter M Thielen , Shirlee Wohl , Thomas Mehoke , Srividya Ramakrishnan , Melanie Kirsche , Oluwaseun Falade-Nwulia , Nídia S Trovão , Amanda Ernlund , Craig Howser , Norah Sadowski , Paul Morris , Mark Hopkins , Matthew Schwartz , Yunfan Fan , Victoria Gniazdowski , Justin Lessler , Lauren Sauer , Michael C Schatz , Jared D Evans , Stuart C Ray , Winston Timp , Heba H Mostafa

MiR-203a is differentially expressed during branching morphogenesis and EMT in breast progenitor cells and is a repressor of peroxidasin.

Mechanisms of development
Avec: Eirikur Briem , Zuzana Budkova , Anna Karen Sigurdardottir , Bylgja Hilmarsdottir , Jennifer Kricker , Winston Timp , Magnus Karl Magnusson , Gunnhildur Asta Traustadottir , Thorarinn Gudjonsson

Characterization of human telomerase reverse transcriptase promoter methylation and transcription factor binding in differentiated thyroid cancer cell lines.

Genes, chromosomes & cancer
Avec: Brittany A Avin , Yongchun Wang , Timothy Gilpatrick , Rachael E Workman , Isac Lee , Winston Timp , Christopher B Umbricht , Martha A Zeiger

Epigenetically regulated digital signaling defines epithelial innate immunity at the tissue level.

Nature communications
Avec: Helen R Clark , Connor McKenney , Nathan M Livingston , Ariel Gershman , Seema Sajjan , Isaac S Chan , Andrew J Ewald , Winston Timp , Bin Wu , Abhyudai Singh , Sergi Regot

Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area.

JCI insight
Avec: Peter M Thielen , Shirlee Wohl , Thomas Mehoke , Srividya Ramakrishnan , Melanie Kirsche , Oluwaseun Falade-Nwulia , Nídia S Trovão , Amanda Ernlund , Craig Howser , Norah Sadowski , C Paul Morris , Mark Hopkins , Matthew Schwartz , Yunfan Fan , Victoria Gniazdowski , Justin Lessler , Lauren Sauer , Michael C Schatz , Jared D Evans , Stuart C Ray , Winston Timp , Heba H Mostafa

Comprehensive screening of a light-inducible split Cre recombinase with domain insertion profiling.

bioRxiv : the preprint server for biology
Avec: Nathan Tague , Virgile Andreani , Yunfan Fan , Winston Timp , Mary J Dunlop

Sustained ERK signaling promotes G2 cell cycle exit and primes cells for whole-genome duplication.

Developmental cell
Avec: Adler Guerrero Zuniga , Timothy J Aikin , Connor McKenney , Yovel Lendner , Alain Phung , Paul W Hook , Amy Meltzer , Winston Timp , Sergi Regot

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.

bioRxiv : the preprint server for biology
Avec: Sam Kovaka , Paul W Hook , Katharine M Jenike , Vikram Shivakumar , Luke B Morina , Roham Razaghi , Winston Timp , Michael C Schatz

Subcloning induces changes in the DNA-methylation pattern of outgrowing Chinese hamster ovary cell colonies.

Biotechnology journal
Avec: Marcus Weinguny , Gerald Klanert , Peter Eisenhut , Isac Lee , Winston Timp , Nicole Borth

Nanopore native RNA sequencing of a human poly(A) transcriptome.

Nature methods
Avec: Rachael E Workman , Alison D Tang , Paul S Tang , Miten Jain , John R Tyson , Roham Razaghi , Philip C Zuzarte , Timothy Gilpatrick , Alexander Payne , Joshua Quick , Norah Sadowski , Nadine Holmes , Jaqueline Goes de Jesus , Karen L Jones , Cameron M Soulette , Terrance P Snutch , Nicholas Loman , Benedict Paten , Matthew Loose , Jared T Simpson , Hugh E Olsen , Angela N Brooks , Mark Akeson , Winston Timp

Telomere-to-telomere assembly of a complete human X chromosome.

Nature
Avec: Karen H Miga , Sergey Koren , Arang Rhie , Mitchell R Vollger , Ariel Gershman , Andrey Bzikadze , Shelise Brooks , Edmund Howe , David Porubsky , Glennis A Logsdon , Valerie A Schneider , Tamara Potapova , Jonathan Wood , William Chow , Joel Armstrong , Jeanne Fredrickson , Evgenia Pak , Kristof Tigyi , Milinn Kremitzki , Christopher Markovic , Valerie Maduro , Amalia Dutra , Gerard G Bouffard , Alexander M Chang , Nancy F Hansen , Amy B Wilfert , Françoise Thibaud-Nissen , Anthony D Schmitt , Jon-Matthew Belton , Siddarth Selvaraj , Megan Y Dennis , Daniela C Soto , Ruta Sahasrabudhe , Gulhan Kaya , Josh Quick , Nicholas J Loman , Nadine Holmes , Matthew Loose , Urvashi Surti , Rosa Ana Risques , Tina A Graves Lindsay , Robert Fulton , Ira Hall , Benedict Paten , Kerstin Howe , Winston Timp , Alice Young , James C Mullikin , Pavel A Pevzner , Jennifer L Gerton , Beth A Sullivan , Evan E Eichler , Adam M Phillippy

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome.

GigaScience
Avec: Annarita Marrano , Monica Britton , Paulo A Zaini , Aleksey V Zimin , Rachael E Workman , Daniela Puiu , Luca Bianco , Erica Adele Di Pierro , Brian J Allen , Sandeep Chakraborty , Michela Troggio , Charles A Leslie , Winston Timp , Abhaya Dandekar , Steven L Salzberg , David B Neale

Targeted nanopore sequencing with Cas9-guided adapter ligation.

Nature biotechnology
Avec: Timothy Gilpatrick , Isac Lee , James E Graham , Etienne Raimondeau , Rebecca Bowen , Andrew Heron , Bradley Downs , Saraswati Sukumar , Fritz J Sedlazeck , Winston Timp

The American lobster genome reveals insights on longevity, neural, and immune adaptations.

Science advances
Avec: Jennifer M Polinski , Aleksey V Zimin , K Fraser Clark , Andrea B Kohn , Norah Sadowski , Winston Timp , Andrey Ptitsyn , Prarthana Khanna , Daria Y Romanova , Peter Williams , Spencer J Greenwood , Leonid L Moroz , David R Walt , Andrea G Bodnar

A Reference Genome Sequence for Giant Sequoia.

G3 (Bethesda, Md.)
Avec: Alison D Scott , Aleksey V Zimin , Daniela Puiu , Rachael Workman , Monica Britton , Sumaira Zaman , Madison Caballero , Andrew C Read , Adam J Bogdanove , Emily Burns , Jill Wegrzyn , Winston Timp , Steven L Salzberg , David B Neale

The complete sequence of a human genome.

Science (New York, N.Y.)
Avec: Sergey Nurk , Sergey Koren , Arang Rhie , Mikko Rautiainen , Andrey V Bzikadze , Alla Mikheenko , Mitchell R Vollger , Nicolas Altemose , Lev Uralsky , Ariel Gershman , Sergey Aganezov , Savannah J Hoyt , Mark Diekhans , Glennis A Logsdon , Michael Alonge , Stylianos E Antonarakis , Matthew Borchers , Gerard G Bouffard , Shelise Y Brooks , Gina V Caldas , Nae-Chyun Chen , Haoyu Cheng , Chen-Shan Chin , William Chow , Leonardo G de Lima , Philip C Dishuck , Richard Durbin , Tatiana Dvorkina , Ian T Fiddes , Giulio Formenti , Robert S Fulton , Arkarachai Fungtammasan , Erik Garrison , Patrick G S Grady , Tina A Graves-Lindsay , Ira M Hall , Nancy F Hansen , Gabrielle A Hartley , Marina Haukness , Kerstin Howe , Michael W Hunkapiller , Chirag Jain , Miten Jain , Erich D Jarvis , Peter Kerpedjiev , Melanie Kirsche , Mikhail Kolmogorov , Jonas Korlach , Milinn Kremitzki , Heng Li , Valerie V Maduro , Tobias Marschall , Ann M McCartney , Jennifer McDaniel , Danny E Miller , James C Mullikin , Eugene W Myers , Nathan D Olson , Benedict Paten , Paul Peluso , Pavel A Pevzner , David Porubsky , Tamara Potapova , Evgeny I Rogaev , Jeffrey A Rosenfeld , Steven L Salzberg , Valerie A Schneider , Fritz J Sedlazeck , Kishwar Shafin , Colin J Shew , Alaina Shumate , Ying Sims , Arian F A Smit , Daniela C Soto , Ivan Sović , Jessica M Storer , Aaron Streets , Beth A Sullivan , Françoise Thibaud-Nissen , James Torrance , Justin Wagner , Brian P Walenz , Aaron Wenger , Jonathan M D Wood , Chunlin Xiao , Stephanie M Yan , Alice C Young , Samantha Zarate , Urvashi Surti , Rajiv C McCoy , Megan Y Dennis , Ivan A Alexandrov , Jennifer L Gerton , Rachel J O'Neill , Winston Timp , Justin M Zook , Michael C Schatz , Evan E Eichler , Karen H Miga , Adam M Phillippy

A primordial DNA store and compute engine.

Nature nanotechnology
Avec: Kevin N Lin , Kevin Volkel , Cyrus Cao , Paul W Hook , Rachel E Polak , Andrew S Clark , Adriana San Miguel , Winston Timp , James M Tuck , Orlin D Velev , Albert J Keung

Genomic insights into metabolic flux in hummingbirds.

Genome research
Avec: Ariel Gershman , Quinn Hauck , Morag Dick , Jerrica M Jamison , Michael Tassia , Xabier Agirrezabala , Saad Muhammad , Raafay Ali , Rachael E Workman , Mikel Valle , G William Wong , Kenneth C Welch , Winston Timp

IVT generation of guideRNAs for Cas9-enrichment Nanopore Sequencing.

bioRxiv : the preprint server for biology
Avec: Timothy Gilpatrick , Josh Zhiyong Wang , David Weiss , Alexis L Norris , James Eshleman , Winston Timp

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

mSystems
Avec: Eric Sakowski , Gherman Uritskiy , Rachel Cooper , Maya Gomes , Michael R McLaren , Jacquelyn S Meisel , Rebecca L Mickol , C David Mintz , Emmanuel F Mongodin , Mihai Pop , Mohammad Arifur Rahman , Alvaro Sanchez , Winston Timp , Jeseth Delgado Vela , Carly Muletz Wolz , Joseph P Zackular , Jessica Chopyk , Seth Commichaux , Meghan Davis , Douglas Dluzen , Sukirth M Ganesan , Muyideen Haruna , Dan Nasko , Mary J Regan , Saul Sarria , Nidhi Shah , Brook Stacy , Dylan Taylor , Jocelyne DiRuggiero , Sarah P Preheim

Epigenetic Changes Induced by

Infection and immunity
Avec: Jawara Allen , Stephanie Hao , Cynthia L Sears , Winston Timp

Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries.

Nucleic acids research
Avec: Jory Lietard , Adrien Leger , Yaniv Erlich , Norah Sadowski , Winston Timp , Mark M Somoza

Cell-Cycle-Dependent ERK Signaling Dynamics Direct Fate Specification in the Mammalian Preimplantation Embryo.

Developmental cell
Avec: Michael J Pokrass , Kathleen A Ryan , Tianchi Xin , Brittany Pielstick , Winston Timp , Valentina Greco , Sergi Regot

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.

Nature biotechnology
Avec: Sam Kovaka , Yunfan Fan , Bohan Ni , Winston Timp , Michael C Schatz

De novo genome assembly of the tobacco hornworm moth (Manduca sexta).

G3 (Bethesda, Md.)
Avec: Ariel Gershman , Tatiana G Romer , Yunfan Fan , Roham Razaghi , Wendy A Smith , Winston Timp

Complete genomic and epigenetic maps of human centromeres.

Science (New York, N.Y.)
Avec: Nicolas Altemose , Glennis A Logsdon , Andrey V Bzikadze , Pragya Sidhwani , Sasha A Langley , Gina V Caldas , Savannah J Hoyt , Lev Uralsky , Fedor D Ryabov , Colin J Shew , Michael E G Sauria , Matthew Borchers , Ariel Gershman , Alla Mikheenko , Valery A Shepelev , Tatiana Dvorkina , Olga Kunyavskaya , Mitchell R Vollger , Arang Rhie , Ann M McCartney , Mobin Asri , Ryan Lorig-Roach , Kishwar Shafin , Julian K Lucas , Sergey Aganezov , Daniel Olson , Leonardo Gomes de Lima , Tamara Potapova , Gabrielle A Hartley , Marina Haukness , Peter Kerpedjiev , Fedor Gusev , Kristof Tigyi , Shelise Brooks , Alice Young , Sergey Nurk , Sergey Koren , Sofie R Salama , Benedict Paten , Evgeny I Rogaev , Aaron Streets , Gary H Karpen , Abby F Dernburg , Beth A Sullivan , Aaron F Straight , Travis J Wheeler , Jennifer L Gerton , Evan E Eichler , Adam M Phillippy , Winston Timp , Megan Y Dennis , Rachel J O'Neill , Justin M Zook , Michael C Schatz , Pavel A Pevzner , Mark Diekhans , Charles H Langley , Ivan A Alexandrov , Karen H Miga

Direct detection of RNA modifications and structure using single-molecule nanopore sequencing.

Cell genomics
Avec: William Stephenson , Roham Razaghi , Steven Busan , Kevin M Weeks , Winston Timp , Peter Smibert

The complete sequence of a human Y chromosome.

Nature
Avec: Arang Rhie , Sergey Nurk , Monika Cechova , Savannah J Hoyt , Dylan J Taylor , Nicolas Altemose , Paul W Hook , Sergey Koren , Mikko Rautiainen , Ivan A Alexandrov , Jamie Allen , Mobin Asri , Andrey V Bzikadze , Nae-Chyun Chen , Chen-Shan Chin , Mark Diekhans , Paul Flicek , Giulio Formenti , Arkarachai Fungtammasan , Carlos Garcia Giron , Erik Garrison , Ariel Gershman , Jennifer L Gerton , Patrick G S Grady , Andrea Guarracino , Leanne Haggerty , Reza Halabian , Nancy F Hansen , Robert Harris , Gabrielle A Hartley , William T Harvey , Marina Haukness , Jakob Heinz , Thibaut Hourlier , Robert M Hubley , Sarah E Hunt , Stephen Hwang , Miten Jain , Rupesh K Kesharwani , Alexandra P Lewis , Heng Li , Glennis A Logsdon , Julian K Lucas , Wojciech Makalowski , Christopher Markovic , Fergal J Martin , Ann M Mc Cartney , Rajiv C McCoy , Jennifer McDaniel , Brandy M McNulty , Paul Medvedev , Alla Mikheenko , Katherine M Munson , Terence D Murphy , Hugh E Olsen , Nathan D Olson , Luis F Paulin , David Porubsky , Tamara Potapova , Fedor Ryabov , Steven L Salzberg , Michael E G Sauria , Fritz J Sedlazeck , Kishwar Shafin , Valery A Shepelev , Alaina Shumate , Jessica M Storer , Likhitha Surapaneni , Angela M Taravella Oill , Françoise Thibaud-Nissen , Winston Timp , Marta Tomaszkiewicz , Mitchell R Vollger , Brian P Walenz , Allison C Watwood , Matthias H Weissensteiner , Aaron M Wenger , Melissa A Wilson , Samantha Zarate , Yiming Zhu , Justin M Zook , Evan E Eichler , Rachel J O'Neill , Michael C Schatz , Karen H Miga , Kateryna D Makova , Adam M Phillippy

LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins.

bioRxiv : the preprint server for biology
Avec: James A Saba , Zixuan Huang , Kate L Schole , Xianwen Ye , Shrey D Bhatt , Yi Li , Winston Timp , Jingdong Cheng , Rachel Green

FrameD: framework for DNA-based data storage design, verification, and validation.

Bioinformatics (Oxford, England)
Avec: Kevin D Volkel , Kevin N Lin , Paul W Hook , Winston Timp , Albert J Keung , James M Tuck

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.

Nature methods
Avec: Mikhail Kolmogorov , Kimberley J Billingsley , Mira Mastoras , Melissa Meredith , Jean Monlong , Ryan Lorig-Roach , Mobin Asri , Pilar Alvarez Jerez , Laksh Malik , Ramita Dewan , Xylena Reed , Rylee M Genner , Kensuke Daida , Sairam Behera , Kishwar Shafin , Trevor Pesout , Jeshuwin Prabakaran , Paolo Carnevali , Jianzhi Yang , Arang Rhie , Sonja W Scholz , Bryan J Traynor , Karen H Miga , Miten Jain , Winston Timp , Adam M Phillippy , Mark Chaisson , Fritz J Sedlazeck , Cornelis Blauwendraat , Benedict Paten

Tn-seq of the Candida glabrata reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin.

G3 (Bethesda, Md.)
Avec: Timothy J Nickels , Andrew N Gale , Abigail A Harrington , Winston Timp , Kyle W Cunningham

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing.

Genome research
Avec: Sergey Aganezov , Sara Goodwin , Rachel M Sherman , Fritz J Sedlazeck , Gayatri Arun , Sonam Bhatia , Isac Lee , Melanie Kirsche , Robert Wappel , Melissa Kramer , Karen Kostroff , David L Spector , Winston Timp , W Richard McCombie , Michael C Schatz

Epigenetic comparison of CHO hosts and clones reveals divergent methylation and transcription patterns across lineages.

Biotechnology and bioengineering
Avec: Meiping Chang , Amit Kumar , Swetha Kumar , Steven Huhn , Winston Timp , Michael Betenbaugh , Zhimei Du

Plasma virome and the risk of blood-borne infection in persons with substance use disorder.

Nature communications
Avec: Abraham J Kandathil , Andrea L Cox , Kimberly Page , David Mohr , Roham Razaghi , Khalil G Ghanem , Susan A Tuddenham , Yu-Hsiang Hsieh , Jennifer L Evans , Kelly E Coller , Winston Timp , David D Celentano , Stuart C Ray , David L Thomas

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.

Nature methods
Avec: Isac Lee , Roham Razaghi , Timothy Gilpatrick , Michael Molnar , Ariel Gershman , Norah Sadowski , Fritz J Sedlazeck , Kasper D Hansen , Jared T Simpson , Winston Timp

Segmental duplications and their variation in a complete human genome.

Science (New York, N.Y.)
Avec: Mitchell R Vollger , Xavi Guitart , Philip C Dishuck , Ludovica Mercuri , William T Harvey , Ariel Gershman , Mark Diekhans , Arvis Sulovari , Katherine M Munson , Alexandra P Lewis , Kendra Hoekzema , David Porubsky , Ruiyang Li , Sergey Nurk , Sergey Koren , Karen H Miga , Adam M Phillippy , Winston Timp , Mario Ventura , Evan E Eichler

PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation.

Genome biology
Avec: Medhat Mahmoud , Harshavardhan Doddapaneni , Winston Timp , Fritz J Sedlazeck

Long read mitochondrial genome sequencing using Cas9-guided adaptor ligation.

Mitochondrion
Avec: Amy R Vandiver , Brittany Pielstick , Timothy Gilpatrick , Austin N Hoang , Hillary J Vernon , Jonathan Wanagat , Winston Timp

Treatment of Sindbis Virus-Infected Neurons with Antibody to E2 Alters Synthesis of Complete and nsP1-Expressing Defective Viral RNAs.

mBio
Avec: Jane X Yeh , Yunfan Fan , Maggie L Bartlett , Xiaoyan Zhang , Norah Sadowski , Debra A Hauer , Winston Timp , Diane E Griffin

Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification.

Plant physiology
Avec: Junhui Zhou , Muzi Li , Yongping Li , Yuwei Xiao , Xi Luo , Shenglan Gao , Zhimin Ma , Norah Sadowski , Winston Timp , Chris Dardick , Ann Callahan , Stephen M Mount , Zhongchi Liu

Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like

JAC-antimicrobial resistance
Avec: Patricia J Simner , Yehudit Bergman , Yunfan Fan , Emily B Jacobs , Srividya Ramakrishnan , Jennifer Lu , Shawna Lewis , Ann Hanlon , Pranita D Tamma , Michael C Schatz , Winston Timp , Karen C Carroll

Beyond assembly: the increasing flexibility of single-molecule sequencing technology.

Nature reviews. Genetics
Avec: Paul W Hook , Winston Timp

A Genome Sequence for the Threatened Whitebark Pine.

bioRxiv : the preprint server for biology
Avec: David B Neale , Aleksey V Zimin , Amy Meltzer , Akriti Bhattarai , Maurice Amee , Laura Figueroa Corona , Brian J Allen , Daniela Puiu , Jessica Wright , Amanda R De La Torre , Patrick E McGuire , Winston Timp , Steven L Salzberg , Jill L Wegrzyn

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.

bioRxiv : the preprint server for biology
Avec: Mikhail Kolmogorov , Kimberley J Billingsley , Mira Mastoras , Melissa Meredith , Jean Monlong , Ryan Lorig-Roach , Mobin Asri , Pilar Alvarez Jerez , Laksh Malik , Ramita Dewan , Xylena Reed , Rylee M Genner , Kensuke Daida , Sairam Behera , Kishwar Shafin , Trevor Pesout , Jeshuwin Prabakaran , Paolo Carnevali , Auteur inconnu , Jianzhi Yang , Arang Rhie , Sonja W Scholz , Bryan J Traynor , Karen H Miga , Miten Jain , Winston Timp , Adam M Phillippy , Mark Chaisson , Fritz J Sedlazeck , Cornelis Blauwendraat , Benedict Paten

A Genome Sequence for the Threatened Whitebark Pine.

G3 (Bethesda, Md.)
Avec: David B Neale , Aleksey V Zimin , Amy Meltzer , Akriti Bhattarai , Maurice Amee , Laura Figueroa Corona , Brian J Allen , Daniela Puiu , Jessica Wright , Amanda R De La Torre , Patrick E McGuire , Winston Timp , Steven L Salzberg , Jill L Wegrzyn

Long-Read Nanopore-Based Sequencing of Anelloviruses.

Viruses
Avec: Raghavendran Anantharam , Dylan Duchen , Andrea L Cox , Winston Timp , David L Thomas , Steven J Clipman , Abraham J Kandathil

Identification of Essential Genes and Fluconazole Susceptibility Genes in

G3 (Bethesda, Md.)
Avec: Andrew N Gale , Rima M Sakhawala , Anton Levitan , Roded Sharan , Judith Berman , Winston Timp , Kyle W Cunningham

The full-length transcriptome of

Genome research
Avec: Nathan P Roach , Norah Sadowski , Amelia F Alessi , Winston Timp , James Taylor , John K Kim

Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome.

Nature methods
Avec: Rachael E Workman , Alison D Tang , Paul S Tang , Miten Jain , John R Tyson , Roham Razaghi , Philip C Zuzarte , Timothy Gilpatrick , Alexander Payne , Joshua Quick , Norah Sadowski , Nadine Holmes , Jaqueline Goes de Jesus , Karen L Jones , Cameron M Soulette , Terrance P Snutch , Nicholas Loman , Benedict Paten , Matthew Loose , Jared T Simpson , Hugh E Olsen , Angela N Brooks , Mark Akeson , Winston Timp

Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates.

Antimicrobial agents and chemotherapy
Avec: Pranita D Tamma , Yunfan Fan , Yehudit Bergman , Geo Pertea , Abida Q Kazmi , Shawna Lewis , Karen C Carroll , Michael C Schatz , Winston Timp , Patricia J Simner

Transmission and clearance of potential procarcinogenic bacteria during fecal microbiota transplantation for recurrent Clostridioides difficile.

JCI insight
Avec: Julia L Drewes , Alina Corona , Uriel Sanchez , Yunfan Fan , Suchitra K Hourigan , Melissa Weidner , Sarah D Sidhu , Patricia J Simner , Hao Wang , Winston Timp , Maria Oliva-Hemker , Cynthia L Sears

Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection.

Genes and immunity
Avec: Candelaria Vergara , Priya Duggal , Chloe L Thio , Ana Valencia , Thomas R O'Brien , Rachel Latanich , Winston Timp , Eric O Johnson , Alex H Kral , Alessandra Mangia , James J Goedert , Valeria Piazzola , Shruti H Mehta , Gregory D Kirk , Marion G Peters , Sharyne M Donfield , Brian R Edlin , Michael P Busch , Graeme Alexander , Edward L Murphy , Arthur Y Kim , Georg M Lauer , Raymond T Chung , Matthew E Cramp , Andrea L Cox , Salim I Khakoo , Hugo R Rosen , Laurent Alric , Sarah J Wheelan , Genevieve L Wojcik , David L Thomas , Margaret A Taub

A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor.

PLoS pathogens
Avec: Jay Vornhagen , Christine M Bassis , Srividya Ramakrishnan , Robert Hein , Sophia Mason , Yehudit Bergman , Nicole Sunshine , Yunfan Fan , Caitlyn L Holmes , Winston Timp , Michael C Schatz , Vincent B Young , Patricia J Simner , Michael A Bachman

Genome and transcriptome of a pathogenic yeast, Candida nivariensis.

G3 (Bethesda, Md.)
Avec: Yunfan Fan , Andrew N Gale , Anna Bailey , Kali Barnes , Kiersten Colotti , Michal Mass , Luke B Morina , Bailey Robertson , Remy Schwab , Niki Tselepidakis , Winston Timp

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.

Microbiome
Avec: Nathan D Olson , M Senthil Kumar , Shan Li , Domenick J Braccia , Stephanie Hao , Winston Timp , Marc L Salit , O Colin Stine , Hector Corrada Bravo

Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing.

Genome research
Avec: Samantha L Sholes , Kayarash Karimian , Ariel Gershman , Thomas J Kelly , Winston Timp , Carol W Greider

Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin.

G3 (Bethesda, Md.)
Avec: David B Neale , Aleksey V Zimin , Sumaira Zaman , Alison D Scott , Bikash Shrestha , Rachael E Workman , Daniela Puiu , Brian J Allen , Zane J Moore , Manoj K Sekhwal , Amanda R De La Torre , Patrick E McGuire , Emily Burns , Winston Timp , Jill L Wegrzyn , Steven L Salzberg

Epigenetic patterns in a complete human genome.

Science (New York, N.Y.)
Avec: Ariel Gershman , Michael E G Sauria , Xavi Guitart , Mitchell R Vollger , Paul W Hook , Savannah J Hoyt , Miten Jain , Alaina Shumate , Roham Razaghi , Sergey Koren , Nicolas Altemose , Gina V Caldas , Glennis A Logsdon , Arang Rhie , Evan E Eichler , Michael C Schatz , Rachel J O'Neill , Adam M Phillippy , Karen H Miga , Winston Timp

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.

Science (New York, N.Y.)
Avec: Savannah J Hoyt , Jessica M Storer , Gabrielle A Hartley , Patrick G S Grady , Ariel Gershman , Leonardo G de Lima , Charles Limouse , Reza Halabian , Luke Wojenski , Matias Rodriguez , Nicolas Altemose , Arang Rhie , Leighton J Core , Jennifer L Gerton , Wojciech Makalowski , Daniel Olson , Jeb Rosen , Arian F A Smit , Aaron F Straight , Mitchell R Vollger , Travis J Wheeler , Michael C Schatz , Evan E Eichler , Adam M Phillippy , Winston Timp , Karen H Miga , Rachel J O'Neill

Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas.

Science advances
Avec: Deanna M Tiek , Beril Erdogdu , Roham Razaghi , Lu Jin , Norah Sadowski , Carla Alamillo-Ferrer , J Robert Hogg , Bassem R Haddad , David H Drewry , Carrow I Wells , Julie E Pickett , Xiao Song , Anshika Goenka , Bo Hu , Samuel A Goldlust , William J Zuercher , Mihaela Pertea , Winston Timp , Shi-Yuan Cheng , Rebecca B Riggins

Similar evolutionary trajectories in an environmental

Proceedings of the National Academy of Sciences of the United States of America
Avec: Poppy Sephton-Clark , Scott A McConnell , Nina Grossman , Rosanna P Baker , Quigly Dragotakes , Yunfan Fan , Man Shun Fu , Gracen Gerbig , Seth Greengo , J Marie Hardwick , Madhura Kulkarni , Stuart M Levitz , Joshua D Nosanchuk , Shmuel Shoham , Daniel F Q Smith , Piotr Stempinski , Winston Timp , Maggie P Wear , Christina A Cuomo , Arturo Casadevall

Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging.

Aging cell
Avec: Amy R Vandiver , Austin N Hoang , Allen Herbst , Cathy C Lee , Judd M Aiken , Debbie McKenzie , Michael A Teitell , Winston Timp , Jonathan Wanagat

Comprehensive Screening of a Light-Inducible Split Cre Recombinase with Domain Insertion Profiling.

ACS synthetic biology
Avec: Nathan Tague , Virgile Andreani , Yunfan Fan , Winston Timp , Mary J Dunlop

Tn-seq of the

bioRxiv : the preprint server for biology
Avec: Timothy J Nickels , Andrew P Gale , Abigail A Harrington , Winston Timp , Kyle W Cunningham

Réseau de co-auteurs

Yunfan Fan 13 collaborations
Michael C Schatz 13 collaborations
Ariel Gershman 12 collaborations
Norah Sadowski 11 collaborations
Roham Razaghi 9 collaborations
Karen H Miga 9 collaborations
Adam M Phillippy 9 collaborations
Arang Rhie 8 collaborations
Fritz J Sedlazeck 8 collaborations
Rachael E Workman 7 collaborations
Timothy Gilpatrick 7 collaborations
Paul W Hook 7 collaborations
Miten Jain 7 collaborations
Benedict Paten 7 collaborations
Mitchell R Vollger 7 collaborations
Evan E Eichler 7 collaborations
Steven L Salzberg 7 collaborations
Sergey Koren 6 collaborations
Aleksey V Zimin 6 collaborations
Patricia J Simner 5 collaborations
Isac Lee 5 collaborations
Glennis A Logsdon 5 collaborations
Jennifer L Gerton 5 collaborations
Daniela Puiu 5 collaborations
David B Neale 5 collaborations
Nicolas Altemose 5 collaborations
Savannah J Hoyt 5 collaborations
Kishwar Shafin 5 collaborations
Rachel J O'Neill 5 collaborations
Srividya Ramakrishnan 4 collaborations
Melanie Kirsche 4 collaborations
David Porubsky 4 collaborations
Tamara Potapova 4 collaborations
Brian J Allen 4 collaborations
Sergey Nurk 4 collaborations
Mark Diekhans 4 collaborations
Gabrielle A Hartley 4 collaborations
Mobin Asri 4 collaborations
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Pranita D Tamma 3 collaborations
Stuart C Ray 3 collaborations
Sergi Regot 3 collaborations
Amy Meltzer 3 collaborations
Nadine Holmes 3 collaborations
Matthew Loose 3 collaborations
Jared T Simpson 3 collaborations
Hugh E Olsen 3 collaborations
Nancy F Hansen 3 collaborations
Françoise Thibaud-Nissen 3 collaborations
Megan Y Dennis 3 collaborations
Pavel A Pevzner 3 collaborations
Beth A Sullivan 3 collaborations
Andrey V Bzikadze 3 collaborations
Alla Mikheenko 3 collaborations
Sergey Aganezov 3 collaborations
Gina V Caldas 3 collaborations
Patrick G S Grady 3 collaborations
Marina Haukness 3 collaborations
Mikhail Kolmogorov 3 collaborations
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Alaina Shumate 3 collaborations
Jessica M Storer 3 collaborations
Ivan A Alexandrov 3 collaborations
Justin M Zook 3 collaborations
Michael E G Sauria 3 collaborations
Ryan Lorig-Roach 3 collaborations
Andrew N Gale 3 collaborations
Kyle W Cunningham 3 collaborations
Andrea L Cox 3 collaborations
David L Thomas 3 collaborations
Yehudit Bergman 3 collaborations
Amanda R De La Torre 3 collaborations
Patrick E McGuire 3 collaborations
Jill L Wegrzyn 3 collaborations
Peter M Thielen 2 collaborations
Shirlee Wohl 2 collaborations
Thomas Mehoke 2 collaborations
Oluwaseun Falade-Nwulia 2 collaborations
Nídia S Trovão 2 collaborations
Amanda Ernlund 2 collaborations
Craig Howser 2 collaborations
Mark Hopkins 2 collaborations
Matthew Schwartz 2 collaborations
Victoria Gniazdowski 2 collaborations
Justin Lessler 2 collaborations
Lauren Sauer 2 collaborations
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Heba H Mostafa 2 collaborations
Connor McKenney 2 collaborations
Nathan Tague 2 collaborations
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Sam Kovaka 2 collaborations
Luke B Morina 2 collaborations
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Paul S Tang 2 collaborations
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Philip C Zuzarte 2 collaborations
Alexander Payne 2 collaborations
Joshua Quick 2 collaborations
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Angela N Brooks 2 collaborations
Mark Akeson 2 collaborations
Shelise Brooks 2 collaborations
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William Chow 2 collaborations
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Gerard G Bouffard 2 collaborations
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James C Mullikin 2 collaborations
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Sumaira Zaman 2 collaborations
Emily Burns 2 collaborations
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Lev Uralsky 2 collaborations
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Nae-Chyun Chen 2 collaborations
Chen-Shan Chin 2 collaborations
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Philip C Dishuck 2 collaborations
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Heng Li 2 collaborations
Ann M McCartney 2 collaborations
Jennifer McDaniel 2 collaborations
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James M Tuck 2 collaborations
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Daniel Olson 2 collaborations
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Reza Halabian 2 collaborations
William T Harvey 2 collaborations
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Wojciech Makalowski 2 collaborations
Katherine M Munson 2 collaborations
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Mira Mastoras 2 collaborations
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Jean Monlong 2 collaborations
Pilar Alvarez Jerez 2 collaborations
Laksh Malik 2 collaborations
Ramita Dewan 2 collaborations
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Rylee M Genner 2 collaborations
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Paolo Carnevali 2 collaborations
Jianzhi Yang 2 collaborations
Sonja W Scholz 2 collaborations
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Mark Chaisson 2 collaborations
Cornelis Blauwendraat 2 collaborations
Timothy J Nickels 2 collaborations
Abigail A Harrington 2 collaborations
Abraham J Kandathil 2 collaborations
Xavi Guitart 2 collaborations
Amy R Vandiver 2 collaborations
Austin N Hoang 2 collaborations
Jonathan Wanagat 2 collaborations
Shawna Lewis 2 collaborations
Karen C Carroll 2 collaborations
Akriti Bhattarai 2 collaborations
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Jessica Wright 2 collaborations
Rebecca Yee 1 collaboration
Florian P Breitwieser 1 collaboration
Belita N A Opene 1 collaboration
Jennifer Dien-Bard 1 collaboration
Gregory Timp 1 collaboration
Paul Morris 1 collaboration
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Anna Karen Sigurdardottir 1 collaboration
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Martha A Zeiger 1 collaboration
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Nathan M Livingston 1 collaboration
Seema Sajjan 1 collaboration
Isaac S Chan 1 collaboration
Andrew J Ewald 1 collaboration
Bin Wu 1 collaboration
Abhyudai Singh 1 collaboration
C Paul Morris 1 collaboration
Adler Guerrero Zuniga 1 collaboration
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Alain Phung 1 collaboration
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Marcus Weinguny 1 collaboration
Gerald Klanert 1 collaboration
Peter Eisenhut 1 collaboration
Nicole Borth 1 collaboration
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Edmund Howe 1 collaboration
Jonathan Wood 1 collaboration
Joel Armstrong 1 collaboration
Jeanne Fredrickson 1 collaboration
Evgenia Pak 1 collaboration
Valerie Maduro 1 collaboration
Amalia Dutra 1 collaboration
Alexander M Chang 1 collaboration
Amy B Wilfert 1 collaboration
Anthony D Schmitt 1 collaboration
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Josh Quick 1 collaboration
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K Fraser Clark 1 collaboration
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Peter Williams 1 collaboration
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David R Walt 1 collaboration
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Andrew C Read 1 collaboration
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Michael Alonge 1 collaboration
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Haoyu Cheng 1 collaboration
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Chirag Jain 1 collaboration
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Danny E Miller 1 collaboration
Eugene W Myers 1 collaboration
Paul Peluso 1 collaboration
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Ying Sims 1 collaboration
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Justin Wagner 1 collaboration
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Kevin Volkel 1 collaboration
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Michael Tassia 1 collaboration
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Saad Muhammad 1 collaboration
Raafay Ali 1 collaboration
Mikel Valle 1 collaboration
G William Wong 1 collaboration
Kenneth C Welch 1 collaboration
Josh Zhiyong Wang 1 collaboration
David Weiss 1 collaboration
Alexis L Norris 1 collaboration
James Eshleman 1 collaboration
Eric Sakowski 1 collaboration
Gherman Uritskiy 1 collaboration
Rachel Cooper 1 collaboration
Maya Gomes 1 collaboration
Michael R McLaren 1 collaboration
Jacquelyn S Meisel 1 collaboration
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C David Mintz 1 collaboration
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Mihai Pop 1 collaboration
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Meghan Davis 1 collaboration
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Dan Nasko 1 collaboration
Mary J Regan 1 collaboration
Saul Sarria 1 collaboration
Nidhi Shah 1 collaboration
Brook Stacy 1 collaboration
Dylan Taylor 1 collaboration
Jocelyne DiRuggiero 1 collaboration
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Jawara Allen 1 collaboration
Jory Lietard 1 collaboration
Adrien Leger 1 collaboration
Yaniv Erlich 1 collaboration
Mark M Somoza 1 collaboration
Michael J Pokrass 1 collaboration
Kathleen A Ryan 1 collaboration
Tianchi Xin 1 collaboration
Valentina Greco 1 collaboration
Bohan Ni 1 collaboration
Tatiana G Romer 1 collaboration
Wendy A Smith 1 collaboration
Pragya Sidhwani 1 collaboration
Sasha A Langley 1 collaboration
Fedor D Ryabov 1 collaboration
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Leonardo Gomes de Lima 1 collaboration
Fedor Gusev 1 collaboration
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Gary H Karpen 1 collaboration
Abby F Dernburg 1 collaboration
Charles H Langley 1 collaboration
William Stephenson 1 collaboration
Steven Busan 1 collaboration
Kevin M Weeks 1 collaboration
Peter Smibert 1 collaboration
Monika Cechova 1 collaboration
Dylan J Taylor 1 collaboration
Jamie Allen 1 collaboration
Paul Flicek 1 collaboration
Carlos Garcia Giron 1 collaboration
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Leanne Haggerty 1 collaboration
Robert Harris 1 collaboration
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Thibaut Hourlier 1 collaboration
Robert M Hubley 1 collaboration
Sarah E Hunt 1 collaboration
Stephen Hwang 1 collaboration
Rupesh K Kesharwani 1 collaboration
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Ann M Mc Cartney 1 collaboration
Brandy M McNulty 1 collaboration
Paul Medvedev 1 collaboration
Terence D Murphy 1 collaboration
Luis F Paulin 1 collaboration
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Aaron M Wenger 1 collaboration
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James A Saba 1 collaboration
Zixuan Huang 1 collaboration
Kate L Schole 1 collaboration
Xianwen Ye 1 collaboration
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Yi Li 1 collaboration
Jingdong Cheng 1 collaboration
Rachel Green 1 collaboration
Kevin D Volkel 1 collaboration
Sara Goodwin 1 collaboration
Rachel M Sherman 1 collaboration
Gayatri Arun 1 collaboration
Sonam Bhatia 1 collaboration
Robert Wappel 1 collaboration
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David L Spector 1 collaboration
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Meiping Chang 1 collaboration
Amit Kumar 1 collaboration
Swetha Kumar 1 collaboration
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Kimberly Page 1 collaboration
David Mohr 1 collaboration
Khalil G Ghanem 1 collaboration
Susan A Tuddenham 1 collaboration
Yu-Hsiang Hsieh 1 collaboration
Jennifer L Evans 1 collaboration
Kelly E Coller 1 collaboration
David D Celentano 1 collaboration
Michael Molnar 1 collaboration
Kasper D Hansen 1 collaboration
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Ruiyang Li 1 collaboration
Mario Ventura 1 collaboration
Medhat Mahmoud 1 collaboration
Harshavardhan Doddapaneni 1 collaboration
Hillary J Vernon 1 collaboration
Jane X Yeh 1 collaboration
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Xiaoyan Zhang 1 collaboration
Debra A Hauer 1 collaboration
Diane E Griffin 1 collaboration
Junhui Zhou 1 collaboration
Muzi Li 1 collaboration
Yongping Li 1 collaboration
Yuwei Xiao 1 collaboration
Xi Luo 1 collaboration
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Zhimin Ma 1 collaboration
Chris Dardick 1 collaboration
Ann Callahan 1 collaboration
Stephen M Mount 1 collaboration
Zhongchi Liu 1 collaboration
Emily B Jacobs 1 collaboration
Jennifer Lu 1 collaboration
Ann Hanlon 1 collaboration
None None 1 collaboration
Raghavendran Anantharam 1 collaboration
Dylan Duchen 1 collaboration
Steven J Clipman 1 collaboration
Rima M Sakhawala 1 collaboration
Anton Levitan 1 collaboration
Roded Sharan 1 collaboration
Judith Berman 1 collaboration
Nathan P Roach 1 collaboration
Amelia F Alessi 1 collaboration
James Taylor 1 collaboration
John K Kim 1 collaboration
Geo Pertea 1 collaboration
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Julia L Drewes 1 collaboration
Alina Corona 1 collaboration
Uriel Sanchez 1 collaboration
Suchitra K Hourigan 1 collaboration
Melissa Weidner 1 collaboration
Sarah D Sidhu 1 collaboration
Hao Wang 1 collaboration
Maria Oliva-Hemker 1 collaboration
Candelaria Vergara 1 collaboration
Priya Duggal 1 collaboration
Chloe L Thio 1 collaboration
Ana Valencia 1 collaboration
Thomas R O'Brien 1 collaboration
Rachel Latanich 1 collaboration
Eric O Johnson 1 collaboration
Alex H Kral 1 collaboration
Alessandra Mangia 1 collaboration
James J Goedert 1 collaboration
Valeria Piazzola 1 collaboration
Shruti H Mehta 1 collaboration
Gregory D Kirk 1 collaboration
Marion G Peters 1 collaboration
Sharyne M Donfield 1 collaboration
Brian R Edlin 1 collaboration
Michael P Busch 1 collaboration
Graeme Alexander 1 collaboration
Edward L Murphy 1 collaboration
Arthur Y Kim 1 collaboration
Georg M Lauer 1 collaboration
Raymond T Chung 1 collaboration
Matthew E Cramp 1 collaboration
Salim I Khakoo 1 collaboration
Hugo R Rosen 1 collaboration
Laurent Alric 1 collaboration
Sarah J Wheelan 1 collaboration
Genevieve L Wojcik 1 collaboration
Margaret A Taub 1 collaboration
Jay Vornhagen 1 collaboration
Christine M Bassis 1 collaboration
Robert Hein 1 collaboration
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Caitlyn L Holmes 1 collaboration
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Anna Bailey 1 collaboration
Kali Barnes 1 collaboration
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Shan Li 1 collaboration
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Marc L Salit 1 collaboration
O Colin Stine 1 collaboration
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Thomas J Kelly 1 collaboration
Carol W Greider 1 collaboration
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Charles Limouse 1 collaboration
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Jeb Rosen 1 collaboration
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Beril Erdogdu 1 collaboration
Lu Jin 1 collaboration
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Bassem R Haddad 1 collaboration
David H Drewry 1 collaboration
Carrow I Wells 1 collaboration
Julie E Pickett 1 collaboration
Xiao Song 1 collaboration
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Bo Hu 1 collaboration
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Scott A McConnell 1 collaboration
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Allen Herbst 1 collaboration
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