Kyle Ellrott

Affiliations

Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA.

ORCID: http://orcid.org/0000-0002-6573-5900

Publications (11)

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Nature communications

Avec: Matthew H Bailey , William U Meyerson , Lewis Jonathan Dursi , Liang-Bo Wang , Guanlan Dong , Wen-Wei Liang , Amila Weerasinghe , Shantao Li , Yize Li , Sean Kelso , Auteur inconnu , Auteur inconnu , Gordon Saksena , Kyle Ellrott , Michael C Wendl , David A Wheeler , Gad Getz , Jared T Simpson , Mark B Gerstein , Li Ding , Auteur inconnu

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.

Genome biology

Avec: Kyle Ellrott , Alex Buchanan , Allison Creason , Michael Mason , Thomas Schaffter , Bruce Hoff , James Eddy , John M Chilton , Thomas Yu , Joshua M Stuart , Julio Saez-Rodriguez , Gustavo Stolovitzky , Paul C Boutros , Justin Guinney

recountmethylation enables flexible analysis of public blood DNA methylation array data.

Bioinformatics advances

Avec: Sean K Maden , Brian Walsh , Kyle Ellrott , Kasper D Hansen , Reid F Thompson , Abhinav Nellore

Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.

Nature biotechnology

Avec: Adriana Salcedo , Maxime Tarabichi , Alex Buchanan , Shadrielle M G Espiritu , Hongjiu Zhang , Kaiyi Zhu , Tai-Hsien Ou Yang , Ignaty Leshchiner , Dimitris Anastassiou , Yuanfang Guan , Gun Ho Jang , Mohammed F E Mootor , Kerstin Haase , Amit G Deshwar , William Zou , Imaad Umar , Stefan Dentro , Jeff A Wintersinger , Kami Chiotti , Jonas Demeulemeester , Clemency Jolly , Lesia Sycza , Minjeong Ko , Auteur inconnu , Auteur inconnu , David C Wedge , Quaid D Morris , Kyle Ellrott , Peter Van Loo , Paul C Boutros

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.

Nature genetics

Avec: Alex H Wagner , Brian Walsh , Georgia Mayfield , David Tamborero , Dmitriy Sonkin , Kilannin Krysiak , Jordi Deu-Pons , Ryan P Duren , Jianjiong Gao , Julie McMurry , Sara Patterson , Catherine Del Vecchio Fitz , Beth A Pitel , Ozman U Sezerman , Kyle Ellrott , Jeremy L Warner , Damian T Rieke , Tero Aittokallio , Ethan Cerami , Deborah I Ritter , Lynn M Schriml , Robert R Freimuth , Melissa Haendel , Gordana Raca , Subha Madhavan , Michael Baudis , Jacques S Beckmann , Rodrigo Dienstmann , Debyani Chakravarty , Xuan Shirley Li , Susan Mockus , Olivier Elemento , Nikolaus Schultz , Nuria Lopez-Bigas , Mark Lawler , Jeremy Goecks , Malachi Griffith , Obi L Griffith , Adam A Margolin , Auteur inconnu

neoepiscope improves neoepitope prediction with multivariant phasing.

Bioinformatics (Oxford, England)

Avec: Mary A Wood , Austin Nguyen , Adam J Struck , Kyle Ellrott , Abhinav Nellore , Reid F Thompson

Exploring Integrative Analysis Using the BioMedical Evidence Graph.

JCO clinical cancer informatics

Avec: Adam Struck , Brian Walsh , Alexander Buchanan , Jordan A Lee , Ryan Spangler , Joshua M Stuart , Kyle Ellrott

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Nature communications

Avec: Matthew H Bailey , William U Meyerson , Lewis Jonathan Dursi , Liang-Bo Wang , Guanlan Dong , Wen-Wei Liang , Amila Weerasinghe , Shantao Li , Yize Li , Sean Kelso , Auteur inconnu , Auteur inconnu , Gordon Saksena , Kyle Ellrott , Michael C Wendl , David A Wheeler , Gad Getz , Jared T Simpson , Mark B Gerstein , Li Ding , Auteur inconnu

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.

Cell systems

Avec: Allison Creason , David Haan , Kristen Dang , Kami E Chiotti , Matthew Inkman , Andrew Lamb , Thomas Yu , Yin Hu , Thea C Norman , Alex Buchanan , Marijke J van Baren , Ryan Spangler , M Rick Rollins , Paul T Spellman , Dmitri Rozanov , Jin Zhang , Christopher A Maher , Cristian Caloian , John D Watson , Sebastian Uhrig , Brian J Haas , Miten Jain , Mark Akeson , Mehmet Eren Ahsen , Auteur inconnu , Gustavo Stolovitzky , Justin Guinney , Paul C Boutros , Joshua M Stuart , Kyle Ellrott

A community effort to create standards for evaluating tumor subclonal reconstruction.

Nature biotechnology

Avec: Adriana Salcedo , Maxime Tarabichi , Shadrielle Melijah G Espiritu , Amit G Deshwar , Matei David , Nathan M Wilson , Stefan Dentro , Jeff A Wintersinger , Lydia Y Liu , Minjeong Ko , Srinivasan Sivanandan , Hongjiu Zhang , Kaiyi Zhu , Tai-Hsien Ou Yang , John M Chilton , Alex Buchanan , Christopher M Lalansingh , Christine P'ng , Catalina V Anghel , Imaad Umar , Bryan Lo , William Zou , Auteur inconnu , Jared T Simpson , Joshua M Stuart , Dimitris Anastassiou , Yuanfang Guan , Adam D Ewing , Kyle Ellrott , David C Wedge , Quaid Morris , Peter Van Loo , Paul C Boutros

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space.

Cell genomics

Avec: Michael C Schatz , Anthony A Philippakis , Enis Afgan , Eric Banks , Vincent J Carey , Robert J Carroll , Alessandro Culotti , Kyle Ellrott , Jeremy Goecks , Robert L Grossman , Ira M Hall , Kasper D Hansen , Jonathan Lawson , Jeffrey T Leek , Anne O'Donnell Luria , Stephen Mosher , Martin Morgan , Anton Nekrutenko , Brian D O'Connor , Kevin Osborn , Benedict Paten , Candace Patterson , Frederick J Tan , Casey Overby Taylor , Jennifer Vessio , Levi Waldron , Ting Wang , Kristin Wuichet

Réseau de co-auteurs

None None 11 collaborations

Alex Buchanan 4 collaborations

Joshua M Stuart 4 collaborations

Paul C Boutros 4 collaborations

Jared T Simpson 3 collaborations

Brian Walsh 3 collaborations

Matthew H Bailey 2 collaborations

William U Meyerson 2 collaborations

Lewis Jonathan Dursi 2 collaborations

Liang-Bo Wang 2 collaborations

Guanlan Dong 2 collaborations

Wen-Wei Liang 2 collaborations

Amila Weerasinghe 2 collaborations

Shantao Li 2 collaborations

Yize Li 2 collaborations

Sean Kelso 2 collaborations

Gordon Saksena 2 collaborations

Michael C Wendl 2 collaborations

David A Wheeler 2 collaborations

Gad Getz 2 collaborations

Mark B Gerstein 2 collaborations

Li Ding 2 collaborations

Allison Creason 2 collaborations

John M Chilton 2 collaborations

Thomas Yu 2 collaborations

Gustavo Stolovitzky 2 collaborations

Justin Guinney 2 collaborations

Kasper D Hansen 2 collaborations

Reid F Thompson 2 collaborations

Abhinav Nellore 2 collaborations

Adriana Salcedo 2 collaborations

Maxime Tarabichi 2 collaborations

Hongjiu Zhang 2 collaborations

Kaiyi Zhu 2 collaborations

Tai-Hsien Ou Yang 2 collaborations

Dimitris Anastassiou 2 collaborations

Yuanfang Guan 2 collaborations

Amit G Deshwar 2 collaborations

William Zou 2 collaborations

Imaad Umar 2 collaborations

Stefan Dentro 2 collaborations

Jeff A Wintersinger 2 collaborations

Minjeong Ko 2 collaborations

David C Wedge 2 collaborations

Peter Van Loo 2 collaborations

Jeremy Goecks 2 collaborations

Ryan Spangler 2 collaborations

Michael Mason 1 collaboration

Thomas Schaffter 1 collaboration

Bruce Hoff 1 collaboration

James Eddy 1 collaboration

Julio Saez-Rodriguez 1 collaboration

Sean K Maden 1 collaboration

Shadrielle M G Espiritu 1 collaboration

Ignaty Leshchiner 1 collaboration

Gun Ho Jang 1 collaboration

Mohammed F E Mootor 1 collaboration

Kerstin Haase 1 collaboration

Kami Chiotti 1 collaboration

Jonas Demeulemeester 1 collaboration

Clemency Jolly 1 collaboration

Lesia Sycza 1 collaboration

Quaid D Morris 1 collaboration

Alex H Wagner 1 collaboration

Georgia Mayfield 1 collaboration

David Tamborero 1 collaboration

Dmitriy Sonkin 1 collaboration

Kilannin Krysiak 1 collaboration

Jordi Deu-Pons 1 collaboration

Ryan P Duren 1 collaboration

Jianjiong Gao 1 collaboration

Julie McMurry 1 collaboration

Sara Patterson 1 collaboration

Catherine Del Vecchio Fitz 1 collaboration

Beth A Pitel 1 collaboration

Ozman U Sezerman 1 collaboration

Jeremy L Warner 1 collaboration

Damian T Rieke 1 collaboration

Tero Aittokallio 1 collaboration

Ethan Cerami 1 collaboration

Deborah I Ritter 1 collaboration

Lynn M Schriml 1 collaboration

Robert R Freimuth 1 collaboration

Melissa Haendel 1 collaboration

Gordana Raca 1 collaboration

Subha Madhavan 1 collaboration

Michael Baudis 1 collaboration

Jacques S Beckmann 1 collaboration

Rodrigo Dienstmann 1 collaboration

Debyani Chakravarty 1 collaboration

Xuan Shirley Li 1 collaboration

Susan Mockus 1 collaboration

Olivier Elemento 1 collaboration

Nikolaus Schultz 1 collaboration

Nuria Lopez-Bigas 1 collaboration

Mark Lawler 1 collaboration

Malachi Griffith 1 collaboration

Obi L Griffith 1 collaboration

Adam A Margolin 1 collaboration

Mary A Wood 1 collaboration

Austin Nguyen 1 collaboration

Adam J Struck 1 collaboration

Adam Struck 1 collaboration

Alexander Buchanan 1 collaboration

Jordan A Lee 1 collaboration

David Haan 1 collaboration

Kristen Dang 1 collaboration

Kami E Chiotti 1 collaboration

Matthew Inkman 1 collaboration

Andrew Lamb 1 collaboration

Yin Hu 1 collaboration

Thea C Norman 1 collaboration

Marijke J van Baren 1 collaboration

M Rick Rollins 1 collaboration

Paul T Spellman 1 collaboration

Dmitri Rozanov 1 collaboration

Jin Zhang 1 collaboration

Christopher A Maher 1 collaboration

Cristian Caloian 1 collaboration

John D Watson 1 collaboration

Sebastian Uhrig 1 collaboration

Brian J Haas 1 collaboration

Miten Jain 1 collaboration

Mark Akeson 1 collaboration

Mehmet Eren Ahsen 1 collaboration

Shadrielle Melijah G Espiritu 1 collaboration

Matei David 1 collaboration

Nathan M Wilson 1 collaboration

Lydia Y Liu 1 collaboration

Srinivasan Sivanandan 1 collaboration

Christopher M Lalansingh 1 collaboration

Christine P'ng 1 collaboration

Catalina V Anghel 1 collaboration

Bryan Lo 1 collaboration

Adam D Ewing 1 collaboration

Quaid Morris 1 collaboration

Michael C Schatz 1 collaboration

Anthony A Philippakis 1 collaboration

Enis Afgan 1 collaboration

Eric Banks 1 collaboration

Vincent J Carey 1 collaboration

Robert J Carroll 1 collaboration

Alessandro Culotti 1 collaboration

Robert L Grossman 1 collaboration

Ira M Hall 1 collaboration

Jonathan Lawson 1 collaboration

Jeffrey T Leek 1 collaboration

Anne O'Donnell Luria 1 collaboration

Stephen Mosher 1 collaboration

Martin Morgan 1 collaboration

Anton Nekrutenko 1 collaboration

Brian D O'Connor 1 collaboration

Kevin Osborn 1 collaboration

Benedict Paten 1 collaboration

Candace Patterson 1 collaboration

Frederick J Tan 1 collaboration

Casey Overby Taylor 1 collaboration

Jennifer Vessio 1 collaboration

Levi Waldron 1 collaboration

Ting Wang 1 collaboration

Kristin Wuichet 1 collaboration