Analyses

  • Analysis |

    A new standard allows the accuracy of variant calls to be assessed and compared across different technologies, variant types and genomic regions.

    • Peter Krusche
    • , Len Trigg
    • , Paul C. Boutros
    • , Christopher E. Mason
    • , Francisco M. De La Vega
    • , Benjamin L. Moore
    • , Mar Gonzalez-Porta
    • , Michael A. Eberle
    • , Zivana Tezak
    • , Samir Lababidi
    • , Rebecca Truty
    • , George Asimenos
    • , Birgit Funke
    • , Mark Fleharty
    • , Brad A. Chapman
    • , Marc Salit
    •  & Justin M. Zook
  • Analysis |

    Systems-wide analysis of HeLa cell lines from 13 labs identifies substantial molecular and phenotypic variability.

    • Yansheng Liu
    • , Yang Mi
    • , Torsten Mueller
    • , Saskia Kreibich
    • , Evan G. Williams
    • , Audrey Van Drogen
    • , Christelle Borel
    • , Max Frank
    • , Pierre-Luc Germain
    • , Isabell Bludau
    • , Martin Mehnert
    • , Michael Seifert
    • , Mario Emmenlauer
    • , Isabel Sorg
    • , Fedor Bezrukov
    • , Frederique Sloan Bena
    • , Hu Zhou
    • , Christoph Dehio
    • , Giuseppe Testa
    • , Julio Saez-Rodriguez
    • , Stylianos E. Antonarakis
    • , Wolf-Dietrich Hardt
    •  & Ruedi Aebersold
  • Analysis |

    A benchmarking analysis on single-cell RNA-seq and mass cytometry data reveals the best-performing technique for dimensionality reduction.

    • Etienne Becht
    • , Leland McInnes
    • , John Healy
    • , Charles-Antoine Dutertre
    • , Immanuel W H Kwok
    • , Lai Guan Ng
    • , Florent Ginhoux
    •  & Evan W Newell
  • Analysis |

    Pattern recognition in imaging data by >300,000 players of a global, online, commercial computer game is combined with deep learning to improve the accuracy of annotation of subcellular protein localization.

    • Devin P Sullivan
    • , Casper F Winsnes
    • , Lovisa Åkesson
    • , Martin Hjelmare
    • , Mikaela Wiking
    • , Rutger Schutten
    • , Linzi Campbell
    • , Hjalti Leifsson
    • , Scott Rhodes
    • , Andie Nordgren
    • , Kevin Smith
    • , Bernard Revaz
    • , Bergur Finnbogason
    • , Attila Szantner
    •  & Emma Lundberg
  • Analysis |

    Testing 21 different fecal DNA extraction protocols in multiple laboratories results in a standardized protocol with the potential to improve comparability across human gut microbiome studies.

    • Paul I Costea
    • , Georg Zeller
    • , Shinichi Sunagawa
    • , Eric Pelletier
    • , Adriana Alberti
    • , Florence Levenez
    • , Melanie Tramontano
    • , Marja Driessen
    • , Rajna Hercog
    • , Ferris-Elias Jung
    • , Jens Roat Kultima
    • , Matthew R Hayward
    • , Luis Pedro Coelho
    • , Emma Allen-Vercoe
    • , Laurie Bertrand
    • , Michael Blaut
    • , Jillian R M Brown
    • , Thomas Carton
    • , Stéphanie Cools-Portier
    • , Michelle Daigneault
    • , Muriel Derrien
    • , Anne Druesne
    • , Willem M de Vos
    • , B Brett Finlay
    • , Harry J Flint
    • , Francisco Guarner
    • , Masahira Hattori
    • , Hans Heilig
    • , Ruth Ann Luna
    • , Johan van Hylckama Vlieg
    • , Jana Junick
    • , Ingeborg Klymiuk
    • , Philippe Langella
    • , Emmanuelle Le Chatelier
    • , Volker Mai
    • , Chaysavanh Manichanh
    • , Jennifer C Martin
    • , Clémentine Mery
    • , Hidetoshi Morita
    • , Paul W O'Toole
    • , Céline Orvain
    • , Kiran Raosaheb Patil
    • , John Penders
    • , Søren Persson
    • , Nicolas Pons
    • , Milena Popova
    • , Anne Salonen
    • , Delphine Saulnier
    • , Karen P Scott
    • , Bhagirath Singh
    • , Kathleen Slezak
    • , Patrick Veiga
    • , James Versalovic
    • , Liping Zhao
    • , Erwin G Zoetendal
    • , S Dusko Ehrlich
    • , Joel Dore
    •  & Peer Bork
  • Analysis |

    The Microbiome Quality Control project consortium reports outcomes of a baseline study (MBQC) that will guide future improvements in reproducibility of microbiome analyses.

    • Rashmi Sinha
    • , Galeb Abu-Ali
    • , Emily Vogtmann
    • , Anthony A Fodor
    • , Boyu Ren
    • , Amnon Amir
    • , Emma Schwager
    • , Jonathan Crabtree
    • , Siyuan Ma
    • , The Microbiome Quality Control Project Consortium
    • , Christian C Abnet
    • , Rob Knight
    • , Owen White
    •  & Curtis Huttenhower
  • Analysis |

    The global effects of epistasis on protein and RNA function are revealed by an unsupervised model of amino acid co-conservation in evolutionary sequence variation.

    • Thomas A Hopf
    • , John B Ingraham
    • , Frank J Poelwijk
    • , Charlotta P I Schärfe
    • , Michael Springer
    • , Chris Sander
    •  & Debora S Marks
  • Analysis |

    LFQbench, a software tool to assess the quality of label-free quantitative proteomics analyses, enables developers to benchmark and improve analytic methods.

    • Pedro Navarro
    • , Jörg Kuharev
    • , Ludovic C Gillet
    • , Oliver M Bernhardt
    • , Brendan MacLean
    • , Hannes L Röst
    • , Stephen A Tate
    • , Chih-Chiang Tsou
    • , Lukas Reiter
    • , Ute Distler
    • , George Rosenberger
    • , Yasset Perez-Riverol
    • , Alexey I Nesvizhskii
    • , Ruedi Aebersold
    •  & Stefan Tenzer
  • Analysis |

    Sources of error and bias in PCR amplification of microbial samples for 16S rRNA gene sequencing are systematically evaluated, and best-practice recommendations for reliable amplification are made.

    • Daryl M Gohl
    • , Pajau Vangay
    • , John Garbe
    • , Allison MacLean
    • , Adam Hauge
    • , Aaron Becker
    • , Trevor J Gould
    • , Jonathan B Clayton
    • , Timothy J Johnson
    • , Ryan Hunter
    • , Dan Knights
    •  & Kenneth B Beckman
  • Analysis | | open

    A multicenter comparison of DNA methylation assays identifies robust methods for translational research and clinical diagnostics.

    • The BLUEPRINT consortium
    • , Christoph Bock
    • , Florian Halbritter
    • , Francisco J Carmona
    • , Sascha Tierling
    • , Paul Datlinger
    • , Yassen Assenov
    • , María Berdasco
    • , Anke K Bergmann
    • , Keith Booher
    • , Florence Busato
    • , Mihaela Campan
    • , Christina Dahl
    • , Christina M Dahmcke
    • , Dinh Diep
    • , Agustín F Fernández
    • , Clarissa Gerhauser
    • , Andrea Haake
    • , Katharina Heilmann
    • , Thomas Holcomb
    • , Dianna Hussmann
    • , Mitsuteru Ito
    • , Ruth Kläver
    • , Martin Kreutz
    • , Marta Kulis
    • , Virginia Lopez
    • , Shalima S Nair
    • , Dirk S Paul
    • , Nongluk Plongthongkum
    • , Wenjia Qu
    • , Ana C Queirós
    • , Frank Reinicke
    • , Guido Sauter
    • , Thorsten Schlomm
    • , Aaron Statham
    • , Clare Stirzaker
    • , Ruslan Strogantsev
    • , Rocío G Urdinguio
    • , Kimberly Walter
    • , Dieter Weichenhan
    • , Daniel J Weisenberger
    • , Stephan Beck
    • , Susan J Clark
    • , Manel Esteller
    • , Anne C Ferguson-Smith
    • , Mario F Fraga
    • , Per Guldberg
    • , Lise Lotte Hansen
    • , Peter W Laird
    • , José I Martín-Subero
    • , Anders O H Nygren
    • , Ralf Peist
    • , Christoph Plass
    • , David S Shames
    • , Reiner Siebert
    • , Xueguang Sun
    • , Jörg Tost
    • , Jörn Walter
    •  & Kun Zhang
  • Analysis |

    The effects of drugs on the immune system is predicted by a data integration method.

    • Brian A Kidd
    • , Aleksandra Wroblewska
    • , Mary R Boland
    • , Judith Agudo
    • , Miriam Merad
    • , Nicholas P Tatonetti
    • , Brian D Brown
    •  & Joel T Dudley
  • Analysis |

    An analysis of the HLA class I loci in 7,930 tumor samples detects recurrent mutation 'hotspots' in these genes.

    • Sachet A Shukla
    • , Michael S Rooney
    • , Mohini Rajasagi
    • , Grace Tiao
    • , Philip M Dixon
    • , Michael S Lawrence
    • , Jonathan Stevens
    • , William J Lane
    • , Jamie L Dellagatta
    • , Scott Steelman
    • , Carrie Sougnez
    • , Kristian Cibulskis
    • , Adam Kiezun
    • , Nir Hacohen
    • , Vladimir Brusic
    • , Catherine J Wu
    •  & Gad Getz
  • Analysis | | open

    Crowdsourcing analysis improves computational prediction of cytotoxic responses in humans.

    • Federica Eduati
    • , Lara M Mangravite
    • , Tao Wang
    • , Hao Tang
    • , J Christopher Bare
    • , Ruili Huang
    • , Thea Norman
    • , Mike Kellen
    • , Michael P Menden
    • , Jichen Yang
    • , Xiaowei Zhan
    • , Rui Zhong
    • , Guanghua Xiao
    • , Menghang Xia
    • , Nour Abdo
    • , Oksana Kosyk
    • , The NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration
    • , Federica Eduati
    • , Lara M Mangravite
    • , Tao Wang
    • , Hao Tang
    • , J Christopher Bare
    • , Ruili Huang
    • , Thea Norman
    • , Mike Kellen
    • , Michael P Menden
    • , Jichen Yang
    • , Xiaowei Zhan
    • , Rui Zhong
    • , Guanghua Xiao
    • , Menghang Xia
    • , Nour Abdo
    • , Oksana Kosyk
    • , Stephen Friend
    • , Allen Dearry
    • , Anton Simeonov
    • , Raymond R Tice
    • , Ivan Rusyn
    • , Fred A Wright
    • , Gustavo Stolovitzky
    • , Yang Xie
    • , Julio Saez-Rodriguez
    • , Tero Aittokallio
    • , Salvatore Alaimo
    • , Alicia Amadoz
    • , Muhammad Ammad-ud-din
    • , Chloé-Agathe Azencott
    • , Jaume Bacardit
    • , Pelham Barron
    • , Elsa Bernard
    • , Andreas Beyer
    • , Shao Bin
    • , Alena van Bömmel
    • , Karsten Borgwardt
    • , April M Brys
    • , Brian Caffrey
    • , Jeffrey Chang
    • , Jungsoo Chang
    • , Himanshu Chheda
    • , Eleni G Christodoulou
    • , Mathieu Clément-Ziza
    • , Trevor Cohen
    • , Marianne Cowherd
    • , Sofie Demeyer
    • , Joaquin Dopazo
    • , Joel D Elhard
    • , Andre O Falcao
    • , Alfredo Ferro
    • , David A Friedenberg
    • , Rosalba Giugno
    • , Yunguo Gong
    • , Jenni W Gorospe
    • , Courtney A Granville
    • , Dominik Grimm
    • , Matthias Heinig
    • , Rosa D Hernansaiz
    • , Petteri Hintsanen
    • , Sepp Hochreiter
    • , Liang-Chin Huang
    • , Matthew Huska
    • , Alok Jaiswal
    • , Yunlong Jiao
    • , Samuel Kaski
    • , Ismeet Kaur
    • , Suleiman Ali Khana
    • , Günter Klambauer
    • , Natalio Krasnogor
    • , Michael Kuhn
    • , Miron Bartosz Kursa
    • , Rintu Kutum
    • , Nicola Lazzarini
    • , Inhan Lee
    • , Michael K K Leung
    • , Weng Khong Lim
    • , Charlie Liu
    • , Felipe Llinares López
    • , Alessandro Mammana
    • , Andreas Mayr
    • , Tom Michoel
    • , Misael Mongiovì
    • , Jonathan D Moore
    • , John-Patrick Mpindi
    • , Ravi Narasimhan
    • , Stephen O Opiyo
    • , Gaurav Pandey
    • , Andrea L Peabody
    • , Juliane Perner
    • , Antti Poso
    • , Alfredo Pulvirenti
    • , Konrad Rawlik
    • , Susanne Reinhardt
    • , Carol G Riffle
    • , Douglas Ruderfer
    • , Aaron J Sander
    • , Richard S Savage
    • , Erwan Scornet
    • , Patricia Sebastian-Leon
    • , Roded Sharan
    • , Carl Johann Simon-Gabriel
    • , Veronique Stoven
    • , Jingchun Sun
    • , Jing Tang
    • , Ana L Teixeira
    • , Albert Tenesa
    • , Jean-Philippe Vert
    • , Martin Vingron
    • , Thomas Walter
    • , Krister Wennerberg
    • , Sean Whalen
    • , Zofia Wiśniewska
    • , Yonghui Wu
    • , Hua Xu
    • , Shihua Zhang
    • , Junfei Zhao
    • , W Jim Zheng
    • , Dai Ziwei
    • , Stephen Friend
    • , Allen Dearry
    • , Anton Simeonov
    • , Raymond R Tice
    • , Ivan Rusyn
    • , Fred A Wright
    • , Gustavo Stolovitzky
    • , Yang Xie
    •  & Julio Saez-Rodriguez
  • Analysis |

    Computational analysis of antigen-specific T cell subsets highlights individual-level variation in immune response quality.

    • Lin Lin
    • , Greg Finak
    • , Kevin Ushey
    • , Chetan Seshadri
    • , Thomas R Hawn
    • , Nicole Frahm
    • , Thomas J Scriba
    • , Hassan Mahomed
    • , Willem Hanekom
    • , Pierre-Alexandre Bart
    • , Giuseppe Pantaleo
    • , Georgia D Tomaras
    • , Supachai Rerks-Ngarm
    • , Jaranit Kaewkungwal
    • , Sorachai Nitayaphan
    • , Punnee Pitisuttithum
    • , Nelson L Michael
    • , Jerome H Kim
    • , Merlin L Robb
    • , Robert J O'Connell
    • , Nicos Karasavvas
    • , Peter Gilbert
    • , Stephen C De Rosa
    • , M Juliana McElrath
    •  & Raphael Gottardo
  • Analysis |

    RNA-seq data from single cells are mapped to their location in complex tissues using gene expression atlases based on in situ hybridization.

    • Rahul Satija
    • , Jeffrey A Farrell
    • , David Gennert
    • , Alexander F Schier
    •  & Aviv Regev
  • Analysis |

    Combining four years of field data with computer modeling reveals that development of resistance to Bacillus thuringiensis insecticidal proteins (Bt) in cotton bollworm can be delayed by refuges of non-Bt host plants other than cotton, but that these so-called ‘natural refuges’ are not as effective as non-Bt cotton refuges.

    • Lin Jin
    • , Haonan Zhang
    • , Yanhui Lu
    • , Yihua Yang
    • , Kongming Wu
    • , Bruce E Tabashnik
    •  & Yidong Wu
  • Analysis |

    A comparison of different ways of generating induced pluripotent stem cells helps researchers choose the most appropriate method for particular applications.

    • Thorsten M Schlaeger
    • , Laurence Daheron
    • , Thomas R Brickler
    • , Samuel Entwisle
    • , Karrie Chan
    • , Amelia Cianci
    • , Alexander DeVine
    • , Andrew Ettenger
    • , Kelly Fitzgerald
    • , Michelle Godfrey
    • , Dipti Gupta
    • , Jade McPherson
    • , Prerana Malwadkar
    • , Manav Gupta
    • , Blair Bell
    • , Akiko Doi
    • , Namyoung Jung
    • , Xin Li
    • , Maureen S Lynes
    • , Emily Brookes
    • , Anne B C Cherry
    • , Didem Demirbas
    • , Alexander M Tsankov
    • , Leonard I Zon
    • , Lee L Rubin
    • , Andrew P Feinberg
    • , Alexander Meissner
    • , Chad A Cowan
    •  & George Q Daley
  • Analysis |

    A community computational challenge generates algorithms to predict activity of drug combinations.

    • Mukesh Bansal
    • , Jichen Yang
    • , Charles Karan
    • , Michael P Menden
    • , James C Costello
    • , Hao Tang
    • , Guanghua Xiao
    • , Yajuan Li
    • , Jeffrey Allen
    • , Rui Zhong
    • , Beibei Chen
    • , Minsoo Kim
    • , Tao Wang
    • , Laura M Heiser
    • , Ronald Realubit
    • , Michela Mattioli
    • , Mariano J Alvarez
    • , Yao Shen
    • , NCI-DREAM Community
    • , Jean-Paul Abbuehl
    • , Jeffrey Allen
    • , Russ B Altman
    • , Shawn Balcome
    • , Mukesh Bansal
    • , Ana Bell
    • , Andreas Bender
    • , Bonnie Berger
    • , Jonathan Bernard
    • , Andrew A Bieberich
    • , Giorgos Borboudakis
    • , Andrea Califano
    • , Christina Chan
    • , Beibei Chen
    • , Ting-Huei Chen
    • , Jaejoon Choi
    • , Luis Pedro Coelho
    • , James C Costello
    • , Chad J Creighton
    • , Will Dampier
    • , V Jo Davisson
    • , Raamesh Deshpande
    • , Lixia Diao
    • , Barbara Di Camillo
    • , Murat Dundar
    • , Adam Ertel
    • , Cellworks Group
    • , Daniel Gallahan
    • , Chirayu P Goswami
    • , Assaf Gottlieb
    • , Michael N Gould
    • , Jonathan Goya
    • , Michael Grau
    • , Joe W Gray
    • , Laura M Heiser
    • , Hussein A Hejase
    • , Michael F Hoffmann
    • , Krisztian Homicsko
    • , Max Homilius
    • , Woochang Hwang
    • , Adriaan P Ijzerman
    • , Olli Kallioniemi
    • , Bilge Karacali
    • , Charles Karan
    • , Samuel Kaski
    • , Junho Kim
    • , Minsoo Kim
    • , Arjun Krishnan
    • , Junehawk Lee
    • , Young-Suk Lee
    • , Eelke B Lenselink
    • , Peter Lenz
    • , Lang Li
    • , Jun Li
    • , Yajuan Li
    • , Han Liang
    • , Michela Mattioli
    • , Michael P Menden
    • , John-Patrick Mpindi
    • , Chad L Myers
    • , Michael A Newton
    • , John P Overington
    • , Juuso Parkkinen
    • , Robert J Prill
    • , Jian Peng
    • , Richard Pestell
    • , Peng Qiu
    • , Bartek Rajwa
    • , Ronald Realubit
    • , Anguraj Sadanandam
    • , Julio Saez-Rodriguez
    • , Francesco Sambo
    • , Dinah Singer
    • , Gustavo Stolovitzky
    • , Arvind Sridhar
    • , Wei Sun
    • , Hao Tang
    • , Gianna M Toffolo
    • , Aydin Tozeren
    • , Olga G Troyanskaya
    • , Ioannis Tsamardinos
    • , Herman W T van Vlijmen
    • , Tao Wang
    • , Wen Wang
    • , Joerg K Wegner
    • , Krister Wennerberg
    • , Gerard J P van Westen
    • , Tian Xia
    • , Guanghua Xiao
    • , Yang Xie
    • , Jichen Yang
    • , Yang Yang
    • , Victoria Yao
    • , Yuan Yuan
    • , Haoyang Zeng
    • , Shihua Zhang
    • , Junfei Zhao
    • , Jian Zhou
    • , Rui Zhong
    • , Daniel Gallahan
    • , Dinah Singer
    • , Julio Saez-Rodriguez
    • , Yang Xie
    • , Gustavo Stolovitzky
    •  & Andrea Califano
  • Analysis |

    An open competition to predict the progression of amyotrophic lateral sclerosis (ALS, also known as Lou Gehrig's disease) disease from the largest database of ALS clinical trial data yields potential new biomarkers and algorithms that outperform human clinicians.

    • Robert Küffner
    • , Neta Zach
    • , Raquel Norel
    • , Johann Hawe
    • , David Schoenfeld
    • , Liuxia Wang
    • , Guang Li
    • , Lilly Fang
    • , Lester Mackey
    • , Orla Hardiman
    • , Merit Cudkowicz
    • , Alexander Sherman
    • , Gokhan Ertaylan
    • , Moritz Grosse-Wentrup
    • , Torsten Hothorn
    • , Jules van Ligtenberg
    • , Jakob H Macke
    • , Timm Meyer
    • , Bernhard Schölkopf
    • , Linh Tran
    • , Rubio Vaughan
    • , Gustavo Stolovitzky
    •  & Melanie L Leitner
  • Analysis |

    A new approach overcomes the hurdles of identifying large, complex structural variants in cancer genomes by directly comparing tumor and normal genome sequencing reads.

    • Valentí Moncunill
    • , Santi Gonzalez
    • , Sílvia Beà
    • , Lise O Andrieux
    • , Itziar Salaverria
    • , Cristina Royo
    • , Laura Martinez
    • , Montserrat Puiggròs
    • , Maia Segura-Wang
    • , Adrian M Stütz
    • , Alba Navarro
    • , Romina Royo
    • , Josep L Gelpí
    • , Ivo G Gut
    • , Carlos López-Otín
    • , Modesto Orozco
    • , Jan O Korbel
    • , Elias Campo
    • , Xose S Puente
    •  & David Torrents
  • Analysis |

    An elegant mathematical model supported by experiments in Escherichia coli demonstrates how clustering enzymes can efficiently channel intermediates from one enzyme to the next, facilitating rational engineering of metabolism.

    • Michele Castellana
    • , Maxwell Z Wilson
    • , Yifan Xu
    • , Preeti Joshi
    • , Ileana M Cristea
    • , Joshua D Rabinowitz
    • , Zemer Gitai
    •  & Ned S Wingreen
  • Analysis |

    Li et al. identify the top-performing methods to improve cross-site differential gene expression analysis with RNA-seq.

    • Sheng Li
    • , Paweł P Łabaj
    • , Paul Zumbo
    • , Peter Sykacek
    • , Wei Shi
    • , Leming Shi
    • , John Phan
    • , Po-Yen Wu
    • , May Wang
    • , Charles Wang
    • , Danielle Thierry-Mieg
    • , Jean Thierry-Mieg
    • , David P Kreil
    •  & Christopher E Mason
  • Analysis |

    For several cancer types analyzed by The Cancer Genome Atlas project, predictions of patient survival were not substantially improved by using common data mining approaches to combine traditional clinical variables with molecular profiling data.

    • Yuan Yuan
    • , Eliezer M Van Allen
    • , Larsson Omberg
    • , Nikhil Wagle
    • , Ali Amin-Mansour
    • , Artem Sokolov
    • , Lauren A Byers
    • , Yanxun Xu
    • , Kenneth R Hess
    • , Lixia Diao
    • , Leng Han
    • , Xuelin Huang
    • , Michael S Lawrence
    • , John N Weinstein
    • , Josh M Stuart
    • , Gordon B Mills
    • , Levi A Garraway
    • , Adam A Margolin
    • , Gad Getz
    •  & Han Liang
  • Analysis |

    A community of researchers report the lessons learned from applying 44 algorithms to predict drug sensitivity in cancer cell lines using genomic, epigenetic and proteomic datasets

    • James C Costello
    • , Laura M Heiser
    • , Elisabeth Georgii
    • , Mehmet Gönen
    • , Michael P Menden
    • , Nicholas J Wang
    • , Mukesh Bansal
    • , Muhammad Ammad-ud-din
    • , Petteri Hintsanen
    • , Suleiman A Khan
    • , John-Patrick Mpindi
    • , Olli Kallioniemi
    • , Antti Honkela
    • , Tero Aittokallio
    • , Krister Wennerberg
    • , NCI DREAM Community
    • , Jean-Paul Abbuehl
    • , Tero Aittokallio
    • , Jeffrey Allen
    • , Russ B Altman
    • , Muhammad Ammad-ud-din
    • , Shawn Balcome
    • , Mukesh Bansal
    • , Alexis Battle
    • , Andreas Bender
    • , Bonnie Berger
    • , Jonathan Bernard
    • , Madhuchhanda Bhattacharjee
    • , Krithika Bhuvaneshwar
    • , Andrew A Bieberich
    • , Fred Boehm
    • , Andrea Califano
    • , Christina Chan
    • , Beibei Chen
    • , Ting-Huei Chen
    • , Jaejoon Choi
    • , Luis Pedro Coelho
    • , Thomas Cokelaer
    • , James C Collins
    • , James C Costello
    • , Chad J Creighton
    • , Jike Cui
    • , Will Dampier
    • , V Jo Davisson
    • , Bernard De Baets
    • , Raamesh Deshpande
    • , Barbara DiCamillo
    • , Murat Dundar
    • , Zhana Duren
    • , Adam Ertel
    • , Haoyang Fan
    • , Hongbin Fang
    • , Dan Gallahan
    • , Robinder Gauba
    • , Elisabeth Georgii
    • , Mehmet Gönen
    • , Assaf Gottlieb
    • , Michael Grau
    • , Joe W Gray
    • , Yuriy Gusev
    • , Min Jin Ha
    • , Leng Han
    • , Michael Harris
    • , Laura M Heiser
    • , Nicholas Henderson
    • , Hussein A Hejase
    • , Petteri Hintsanen
    • , Krisztian Homicsko
    • , Antti Honkela
    • , Jack P Hou
    • , Woochang Hwang
    • , Adriaan P IJzerman
    • , Olli Kallioniemi
    • , Bilge Karacali
    • , Samuel Kaski
    • , Sunduz Keles
    • , Christina Kendziorski
    • , Suleiman A Khan
    • , Junho Kim
    • , Min Kim
    • , Youngchul Kim
    • , David A Knowles
    • , Daphne Koller
    • , Junehawk Lee
    • , Jae K Lee
    • , Eelke B Lenselink
    • , Biao Li
    • , Bin Li
    • , Jun Li
    • , Han Liang
    • , Jian Ma
    • , Subha Madhavan
    • , Michael P Menden
    • , Sean Mooney
    • , John-Patrick Mpindi
    • , Chad L Myers
    • , Michael A Newton
    • , John P Overington
    • , Ranadip Pal
    • , Jian Peng
    • , Richard Pestell
    • , Robert J Prill
    • , Peng Qiu
    • , Bartek Rajwa
    • , Anguraj Sadanandam
    • , Julio Saez-Rodriguez
    • , Francesco Sambo
    • , Hyunjin Shin
    • , Dinah Singer
    • , Jiuzhou Song
    • , Lei Song
    • , Arvind Sridhar
    • , Michiel Stock
    • , Gustavo Stolovitzky
    • , Wei Sun
    • , Tram Ta
    • , Mahlet Tadesse
    • , Ming Tan
    • , Hao Tang
    • , Dan Theodorescu
    • , Gianna Maria Toffolo
    • , Aydin Tozeren
    • , William Trepicchio
    • , Nelle Varoquaux
    • , Jean-Philippe Vert
    • , Willem Waegeman
    • , Thomas Walter
    • , Qian Wan
    • , Difei Wang
    • , Nicholas J Wang
    • , Wen Wang
    • , Yong Wang
    • , Zhishi Wang
    • , Joerg K Wegner
    • , Krister Wennerberg
    • , Tongtong Wu
    • , Tian Xia
    • , Guanghua Xiao
    • , Yang Xie
    • , Yanxun Xu
    • , Jichen Yang
    • , Yuan Yuan
    • , Shihua Zhang
    • , Xiang-Sun Zhang
    • , Junfei Zhao
    • , Chandler Zuo
    • , Herman W T van Vlijmen
    • , Gerard J P van Westen
    • , James J Collins
    • , Dan Gallahan
    • , Dinah Singer
    • , Julio Saez-Rodriguez
    • , Samuel Kaski
    • , Joe W Gray
    •  & Gustavo Stolovitzky
  • Analysis |

    When applied in large scale to electronic medical record data, the PheWAS approach replicates GWAS associations and reveals potentially new pleiotropic associations.

    • Joshua C Denny
    • , Lisa Bastarache
    • , Marylyn D Ritchie
    • , Robert J Carroll
    • , Raquel Zink
    • , Jonathan D Mosley
    • , Julie R Field
    • , Jill M Pulley
    • , Andrea H Ramirez
    • , Erica Bowton
    • , Melissa A Basford
    • , David S Carrell
    • , Peggy L Peissig
    • , Abel N Kho
    • , Jennifer A Pacheco
    • , Luke V Rasmussen
    • , David R Crosslin
    • , Paul K Crane
    • , Jyotishman Pathak
    • , Suzette J Bielinski
    • , Sarah A Pendergrass
    • , Hua Xu
    • , Lucia A Hindorff
    • , Rongling Li
    • , Teri A Manolio
    • , Christopher G Chute
    • , Rex L Chisholm
    • , Eric B Larson
    • , Gail P Jarvik
    • , Murray H Brilliant
    • , Catherine A McCarty
    • , Iftikhar J Kullo
    • , Jonathan L Haines
    • , Dana C Crawford
    • , Daniel R Masys
    •  & Dan M Roden
  • Analysis |

    The functional composition of microbial community samples from several environments is predicted based on 16S ribosomal RNA gene sequencing data.

    • Morgan G I Langille
    • , Jesse Zaneveld
    • , J Gregory Caporaso
    • , Daniel McDonald
    • , Dan Knights
    • , Joshua A Reyes
    • , Jose C Clemente
    • , Deron E Burkepile
    • , Rebecca L Vega Thurber
    • , Rob Knight
    • , Robert G Beiko
    •  & Curtis Huttenhower