Research

There is an abundance of publicly available data about various biological systems, but it can be difficult to draw insight from individual datasets. Our lab develops algorithms that integrate these data to help model and understand complex biological systems. Doing this allows us to investigate many different biological conditions, including those with limited data, such as rare diseases. We recognize that our lab won’t have all the answers, or even all of the questions, so we aim to develop tools and processes that any biologist can reuse. Our approach to research prioritizes transparency, rigor, and reproducibility.

Showing all papers

2020

SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics
Halie M. Rando,  Casey S. Greene,  Michael P. Robson,  Simina M. Boca,  Nils Wellhausen,  Ronan Lordan,  Christian Brueffer,  Sadipan Ray,  Lucy D\'Agostino McGowan,  Anthony Gitter,  Ronnie M. Russell,  Anna Ada Dattoli,  Ryan Velazquez,  John P. Barton,  Jeffrey M. Field,  Bharath Ramsundar,  Adam L. MacLean,  Alexandra J. Lee,  Immunology Institute of the Icahn School Medicine,  Fengling Hu,  Nafisa M. Jadavji,  Elizabeth Sell,  Jinhui Wang,  Diane N. Rafizadeh,  Ashwin N. Skelly,  Marouen Ben Guebila,  Likhitha Kolla,  David Manheim,  Soumita Ghosh,  Matthias Fax,  James Brian Byrd,  YoSon Park,  Vikas Bansal,  Stephen Capone,  John J. Dziak,  YuCheng Sun,  Yanjun Qi,  Lamonica Shinholster,  Sergey Knyazev,  Dimitri Perrin,  Serghei Mangul,  Shikta Das,  Gregory L. Szeto
Manubot  ·  16 Sep 2020
COVID19
PhenomeXcan: Mapping the genome to the phenome through the transcriptome
Milton Pividori,  Padma S. Rajagopal,  Alvaro Barbeira,  Yanyu Liang,  Owen Melia,  Lisa Bastarache,  YoSon Park,  GTEx Consortium,  Xiaoquan Wen,  Hae K. Im
Science Advances  ·  01 Sep 2020
TWAS PrediXcan UK Biobank
Prognostic gene expression signature for high-grade serous ovarian cancer
J. Millstein,  T. Budden,  E.L. Goode,  M.S. Anglesio,  A. Talhouk,  M.P. Intermaggio,  H.S. Leong,  S. Chen,  W. Elatre,  B. Gilks,  T. Nazeran,  M. Volchek,  R.C. Bentley,  C. Wang,  D.S. Chiu,  S. Kommoss,  S.C.Y. Leung,  J. Senz,  A. Lum,  V. Chow,  H. Sudderuddin,  R. Mackenzie,  J. George,  S. Fereday,  J. Hendley,  N. Traficante,  H. Steed,  J.M. Koziak,  M. Köbel,  I.A. McNeish,  T. Goranova,  D. Ennis,  G. Macintyre,  D. Silva De Silva,  T. Ramón y Cajal,  J. García-Donas,  S. Hernando Polo,  G.C. Rodriguez,  K.L. Cushing-Haugen,  H.R. Harris,  C.S. Greene,  R.A. Zelaya,  S. Behrens,  R.T. Fortner,  P. Sinn,  E. Herpel,  J. Lester,  J. Lubiński,  O. Oszurek,  A. Tołoczko,  C. Cybulski,  J. Menkiszak,  C.L. Pearce,  M.C. Pike,  C. Tseng,  J. Alsop,  V. Rhenius,  H. Song,  M. Jimenez-Linan,  A.M. Piskorz,  A. Gentry-Maharaj,  C. Karpinskyj,  M. Widschwendter,  N. Singh,  C.J. Kennedy,  R. Sharma,  P.R. Harnett,  B. Gao,  S.E. Johnatty,  R. Sayer,  J. Boros,  S.J. Winham,  G.L. Keeney,  S.H. Kaufmann,  M.C. Larson,  H. Luk,  B.Y. Hernandez,  P.J. Thompson,  L.R. Wilkens,  M.E. Carney,  B. Trabert,  J. Lissowska,  L. Brinton,  M.E. Sherman,  C. Bodelon,  S. Hinsley,  L.A. Lewsley,  R. Glasspool,  S.N. Banerjee,  E.A. Stronach,  P. Haluska,  I. Ray-Coquard,  S. Mahner,  B. Winterhoff,  D. Slamon,  D.A. Levine,  L.E. Kelemen,  J. Benitez,  J. Chang-Claude,  J. Gronwald,  A.H. Wu,  U. Menon,  M.T. Goodman,  J.M. Schildkraut,  N. Wentzensen,  R. Brown,  A. Berchuck,  G. Chenevix-Trench,  A. deFazio,  S.A. Gayther,  M.J. García,  M.J. Henderson,  M.A. Rossing,  A. Beeghly-Fadiel,  P.A. Fasching,  S. Orsulic,  B.Y. Karlan,  G.E. Konecny,  D.G. Huntsman,  D.D. Bowtell,  J.D. Brenton,  J.A. Doherty,  P.D.P. Pharoah,  S.J. Ramus,  D. Bowtell,  G. Chenevix-Trench,  A. Green,  P. Webb,  A. DeFazio,  D. Gertig,  N. Traficante,  S. Fereday,  S. Moore,  J. Hung,  K. Harrap,  T. Sadkowsky,  N. Pandeya,  M. Malt,  A. Mellon,  R. Robertson,  T. Vanden Bergh,  M. Jones,  P. Mackenzie,  J. Maidens,  K. Nattress,  Y.E. Chiew,  A. Stenlake,  H. Sullivan,  B. Alexander,  P. Ashover,  S. Brown,  T. Corrish,  L. Green,  L. Jackman,  K. Ferguson,  K. Martin,  A. Martyn,  B. Ranieri,  J. White,  V. Jayde,  P. Mamers,  L. Bowes,  L. Galletta,  D. Giles,  J. Hendley,  K. Alsop,  T. Schmidt,  H. Shirley,  C. Ball,  C. Young,  S. Viduka,  Hoa Tran,  Sanela Bilic,  Lydia Glavinas,  Julia Brooks,  R. Stuart-Harris,  F. Kirsten,  J. Rutovitz,  P. Clingan,  A. Glasgow,  A. Proietto,  S. Braye,  G. Otton,  J. Shannon,  T. Bonaventura,  J. Stewart,  S. Begbie,  M. Friedlander,  D. Bell,  S. Baron-Hay,  A. Ferrier,a,  G. Gard,  D. Nevell,  N. Pavlakis,  S. Valmadre,  B. Young,  C. Camaris,  R. Crouch,  L. Edwards,  N. Hacker,  D. Marsden,  G. Robertson,  P. Beale,  J. Beith,  J. Carter,  C. Dalrymple,  R. Houghton,  P. Russell,  M. Links,  J. Grygiel,  J. Hill,  A. Brand,  K. Byth,  R. Jaworski,  P. Harnett,  R. Sharma,  G. Wain,  B. Ward,  D. Papadimos,  A. Crandon,  M. Cummings,  K. Horwood,  A. Obermair,  L. Perrin,  D. Wyld,  J. Nicklin,  M. Davy,  M.K. Oehler,  C. Hall,  T. Dodd,  T. Healy,  K. Pittman,  D. Henderson,  J. Miller,  J. Pierdes,  P. Blomfield,  D. Challis,  R. McIntosh,  A. Parker,  B. Brown,  R. Rome,  D. Allen,  P. Grant,  S. Hyde,  R. Laurie,  M. Robbie,  D. Healy,  T. Jobling,  T. Manolitsas,  J. McNealage,  P. Rogers,  B. Susil,  E. Sumithran,  I. Simpson,  K. Phillips,  D. Rischin,  S. Fox,  D. Johnson,  S. Lade,  M. Loughrey,  N. O’Callaghan,  W. Murray,  P. Waring,  V. Billson,  J. Pyman,  D. Neesham,  M. Quinn,  C. Underhill,  R. Bell,  L.F. Ng,  R. Blum,  V. Ganju,  I. Hammond,  Y. Leung,  A. McCartney,  M. Buck,  I. Haviv,  D. Purdie,  D. Whiteman,  N. Zeps
Annals of Oncology  ·  01 Sep 2020
ovarian cancer genomics
Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing
William E. Allen,  Han Altae-Tran,  James Briggs,  Xin Jin,  Glen McGee,  Andy Shi,  Rumya Raghavan,  Mireille Kamariza,  Nicole Nova,  Albert Pereta,  Chris Danford,  Amine Kamel,  Patrik Gothe,  Evrhet Milam,  Jean Aurambault,  Thorben Primke,  Weijie Li,  Josh Inkenbrandt,  Tuan Huynh,  Evan Chen,  Christina Lee,  Michael Croatto,  Helen Bentley,  Wendy Lu,  Robert Murray,  Mark Travassos,  Brent A. Coull,  John Openshaw,  Casey S. Greene,  Ophir Shalem,  Gary King,  Ryan Probasco,  David R. Cheng,  Ben Silbermann,  Feng Zhang,  Xihong Lin
Nature Human Behaviour  ·  26 Aug 2020
COVID19
The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment
Haendel Melissa,  Chute Christopher,  Gersing Kenneth
Journal of the American Medical Informatics Association  ·  17 Aug 2020
COVID19
Responsible, practical genomic data sharing that accelerates research
James Brian Byrd,  Anna C. Greene,  Deepashree Venkatesh Prasad,  Xiaoqian Jiang,  Casey S. Greene
Nature Reviews Genetics  ·  21 Jul 2020
open science data sharing
Constructing knowledge graphs and their biomedical applications
David N. Nicholson,  Casey S. Greene
Computational and Structural Biotechnology Journal  ·  02 Jun 2020
knowledge graphs
Building an international consortium for tracking coronavirus health status
Eran Segal,  Feng Zhang,  Xihong Lin,  Gary King,  Ophir Shalem,  Smadar Shilo,  William E. Allen,  Faisal Alquaddoomi,  Han Altae-Tran,  Simon Anders,  Ran Balicer,  Tal Bauman,  Ximena Bonilla,  Gisel Booman,  Andrew T. Chan,  Ori Cohen,  Silvano Coletti,  Natalie Davidson,  Yuval Dor,  David A. Drew,  Olivier Elemento,  Georgina Evans,  Phil Ewels,  Joshua Gale,  Amir Gavrieli,  Benjamin Geiger,  Yonatan H. Grad,  Casey S. Greene,  Iman Hajirasouliha,  Roman Jerala,  Andre Kahles,  Olli Kallioniemi,  Ayya Keshet,  Ljupco Kocarev,  Gregory Landua,  Tomer Meir,  Aline Muller,  Long H. Nguyen,  Matej Oresic,  Svetlana Ovchinnikova,  Hedi Peterson,  Jana Prodanova,  Jay Rajagopal,  Gunnar Rätsch,  Hagai Rossman,  Johan Rung,  Andrea Sboner,  Alexandros Sigaras,  Tim Spector,  Ron Steinherz,  Irene Stevens,  Jaak Vilo,  Paul Wilmes
Nature Medicine  ·  02 Jun 2020
Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE)
Aline Talhouk,  Joshy George,  Chen Wang,  Timothy Budden,  Tuan Zea Tan,  Derek S. Chiu,  Stefan Kommoss,  Huei San Leong,  Stephanie Chen,  Maria P. Intermaggio,  Blake Gilks,  Tayyebeh M. Nazeran,  Mila Volchek,  Wafaa Elatre,  Rex C. Bentley,  Janine Senz,  Amy Lum,  Veronica Chow,  Hanwei Sudderuddin,  Robertson Mackenzie,  Samuel C.Y. Leong,  Geyi Liu,  Dustin Johnson,  Billy Chen,  AOCS Group,  Jennifer Alsop,  Susana N. Banerjee,  Sabine Behrens,  Clara Bodelon,  Alison H. Brand,  Louise Brinton,  Michael E. Carney,  Yoke-Eng Chiew,  Kara L. Cushing-Haugen,  Cezary Cybulski,  Darren Ennis,  Sian Fereday,  Renée T. Fortner,  Jesús García-Donas,  Aleksandra Gentry-Maharaj,  Rosalind Glasspool,  Teodora Goranova,  Casey S. Greene,  Paul Haluska,  Holly R. Harris,  Joy Hendley,  Brenda Y. Hernandez,  Esther Herpel,  Mercedes Jimenez-Linan,  Chloe Karpinskyj,  Scott H. Kaufmann,  Gary L. Keeney,  Catherine J. Kennedy,  Martin Köbel,  Jennifer M Koziak,  Melissa C. Larson,  Jenny Lester,  Liz-Anne Lewsley,  Jolanta Lissowska,  Jan Lubiński,  Hugh Luk,  Geoff Macintyre,  Sven Mahner,  Iain A. McNeish,  Janusz Menkiszak,  Nikilyn Nevins,  Ana Osorio,  Oleg Oszurek,  José Palacios,  Samantha Hinsley,  Celeste L. Pearce,  Malcolm C. Pike,  Anna M. Piskorz,  Isabelle Ray-Coquard,  Valerie Rhenius,  Cristina Rodriguez-Antona,  Raghwa Sharma,  Mark E. Sherman,  Dilrini De Silva,  Naveena Singh,  Peter Sinn,  Dennis Slamon,  Honglin Song,  Helen Steed,  Euan A. Stronach,  Pamela J. Thompson,  Aleksandra Tołoczko,  Britton Trabert,  Nadia Traficante,  Chiu-Chen Tseng,  Martin Widschwendter,  Lynne R. Wilkens,  Stacey J. Winham,  Boris Winterhoff,  Alicia Beeghly-Fadiel,  Javier Benitez,  Andrew Berchuck,  James D. Brenton,  Robert Brown,  Jenny Chang-Claude,  Georgia Chenevix-Trench,  Anna deFazio,  Peter A. Fasching,  María J. García,  Simon A. Gayther,  Marc T. Goodman,  Jacek Gronwald,  Michelle J. Henderson,  Beth Y. Karlan,  Linda E. Kelemen,  Usha Menon,  Sandra Orsulic,  Paul D.P. Pharoah,  Nicolas Wentzensen,  Anna H. Wu,  Joellen M. Schildkraut,  Mary Anne Rossing,  Gottfried E. Konecny,  David G. Huntsman,  Ruby Yun-Ju Huang,  Ellen L. Goode,  Susan J. Ramus,  Jennifer A. Doherty,  David D. Bowtell,  Michael S. Anglesio
Clinical Cancer Research  ·  17 Jun 2020
ovarian cancer genomics
Recommendations to enhance rigor and reproducibility in biomedical research
Jaqueline J Brito,  Jun Li,  Jason H Moore,  Casey S Greene,  Nicole A Nogoy,  Lana X Garmire,  Serghei Mangul
GigaScience  ·  01 Jun 2020
Incorporating biological structure into machine learning models in biomedicine
Jake Crawford,  Casey S Greene
Current Opinion in Biotechnology  ·  01 Jun 2020
Correcting for experiment-specific variability in expression compendia can remove underlying signals
Alexandra J. Lee,  YoSon Park,  Georgia Doing,  Deborah A. Hogan,  Casey S. Greene
Cold Spring Harbor Laboratory  ·  03 May 2020
genomics machine learning data integration
Specific histone modifications associate with alternative exon selection during mammalian development
Qiwen Hu,  Casey S Greene,  Elizabeth A Heller
Nucleic Acids Research  ·  21 May 2020
genomics machine learning
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Gregory P. Way,  Michael Zietz,  Vincent Rubinetti,  Daniel S. Himmelstein,  Casey S. Greene
Genome Biology  ·  11 May 2020
machine learning genomics
Analysis of ISCB honorees and keynotes reveals disparities
Trang T. Le,  Daniel S. Himmelstein,  Ariel A. Hippen Anderson,  Matthew R. Gazzara,  Casey S. Greene
bioRxiv  ·  14 Apr 2020
machine learning diversity
Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1
Jineta Banerjee,  Robert J Allaway,  Jaclyn N Taroni,  Aaron Baker,  Xiaochun Zhang,  Chang In Moon,  Christine A Pratilas,  Jaishri O Blakeley,  Justin Guinney,  Angela Hirbe,  Casey S Greene,  Sara JC Gosline
Genes  ·  21 Feb 2020
machine learning rare diseases
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping
Diana L Cousminer,  Yadav Wagley,  James Pippin,  Ahmed Elhakeem,  Gregory Way,  Shana McCormack,  Alessandra Chesi,  Jonathan Mitchell,  Joeseph Kindler,  Denis Baird,  April Hartley,  Laura D Howe,  Heidi Kalkwarf,  Joan Lappe,  Sumei Lu,  Michelle Leonard,  Matthew Johnson,  Hakon Hakonarson,  Vicente Gilsanz,  John Shepherd,  Sharon Oberfield,  Casey Greene,  Andrea Kelly,  Deborah Lawlor,  Benjamin Franklin Voight,  Andrew Wells,  Babette Zemel,  Kurt Hankenson,  Struan Grant
medRxiv  ·  20 Feb 2020
genetics
Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment
Mai T. Dang,  Michael Gonzalez,  Krutika S. Gaonkar,  Komal S. Rathi,  Patricia Young,  Sherjeel Arif,  Li Zhai,  Md Zahidul Alam,  Samir Devalaraja,  Tsun Ki To,  Ian W. Folkert,  Pichai Ramen,  Jo Lynne Rokita,  Daniel Martinez,  Jaclyn N. Taroni,  Joshua Shapiro,  Casey S. Greene,  Candace Savonen,  Hakon Hakonarson,  Tom Curran,  Malay Haldar
bioRxiv  ·  13 Feb 2020
genomics rare diseases
Transparency and reproducibility in artificial intelligence
Benjamin Haibe-Kains,  George Alexandru Adam,  Ahmed Hosny,  Farnoosh Khodakarami,  Levi Waldron,  Bo Wang,  Chris McIntosh,  Anna Goldenberg,  Anshul Kundaje,  Casey S. Greene,  Tamara Broderick,  Michael M. Hoffman,  Jeffrey T. Leek,  Keegan Korthauer,  Wolfgang Huber,  Alvis Brazma,  Joelle Pineau,  Robert Tibshirani,  Trevor Hastie,  John P. A. Ioannidis,  John Quackenbush,  Hugo J. W. L. Aerts,  
Nature  ·  14 Oct 2020
Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts
David N. Nicholson,  Daniel S. Himmelstein,  Casey S. Greene
bioRxiv  ·  31 Jan 2020
knowledge graphs open science
Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin
Michelle E. Clay,  John H. Hammond,  Fangfang Zhong,  Xiaolei Chen,  Caitlin H. Kowalski,  Alexandra J. Lee,  Monique S. Porter,  Thomas H. Hampton,  Casey S. Greene,  Ekaterina V. Pletneva,  Deborah A. Hogan
Proceedings of the National Academy of Sciences  ·  24 Jan 2020
Graph biased feature selection of genes is better than random for many genes
Jake Crawford,  Casey S. Greene
bioRxiv  ·  21 Jan 2020
machine learning genomics

2019

Voices in methods development
Polina Anikeeva,  Edward Boyden,  Clifford Brangwynne,  Ibrahim I. Cissé,  Oliver Fiehn,  Petra Fromme,  Anne-Claude Gingras,  Casey S. Greene,  Edith Heard,  Stefan W. Hell,  Elizabeth Hillman,  Grant Jay Jensen,  Rachel Karchin,  Laura L. Kiessling,  Benjamin P. Kleinstiver,  Rob Knight,  Philipp Kukura,  Madeline A. Lancaster,  Nicholas Loman,  Loren Looger,  Emma Lundberg,  Qingming Luo,  Atsushi Miyawaki,  Eugene W. Myers,  Garry P. Nolan,  Paola Picotti,  Wolf Reik,  Markus Sauer,  Alex K. Shalek,  Jay Shendure,  Nikolai Slavov,  Amos Tanay,  Olga Troyanskaya,  David van Valen,  Hong-Wei Wang,  Chengqi Yi,  Peng Yin,  Magdalena Zernicka-Goetz,  Xiaowei Zhuang
Nature Methods  ·  27 Sep 2019
Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning
Gregory P. Way,  Casey S. Greene
Annual Review of Biomedical Data Science  ·  20 Jul 2019
Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing
Brett K. Beaulieu-Jones,  Zhiwei Steven Wu,  Chris Williams,  Ran Lee,  Sanjeev P. Bhavnani,  James Brian Byrd,  Casey S. Greene
Circulation: Cardiovascular Quality and Outcomes  ·  01 Jul 2019
Open collaborative writing with Manubot
Daniel S. Himmelstein,  Vincent Rubinetti,  David R. Slochower,  Dongbo Hu,  Venkat S. Malladi,  Casey S. Greene,  Anthony Gitter
PLOS Computational Biology  ·  24 Jun 2019
Show me the models
Casey S. Greene
Nature Biotechnology  ·  28 May 2019
Learning and Imputation for Mass-spec Bias Reduction (LIMBR)
Alexander M Crowell,  Casey S Greene,  Jennifer J Loros,  Jay C Dunlap
Bioinformatics  ·  01 May 2019
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease
Jaclyn N. Taroni,  Peter C. Grayson,  Qiwen Hu,  Sean Eddy,  Matthias Kretzler,  Peter A. Merkel,  Casey S. Greene
Cell Systems  ·  01 May 2019
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution
Deanne M. Taylor,  Bruce J. Aronow,  Kai Tan,  Kathrin Bernt,  Nathan Salomonis,  Casey S. Greene,  Alina Frolova,  Sarah E. Henrickson,  Andrew Wells,  Liming Pei,  Jyoti K. Jaiswal,  Jeffrey Whitsett,  Kathryn E. Hamilton,  Sonya A. MacParland,  Judith Kelsen,  Robert O. Heuckeroth,  S. Steven Potter,  Laura A. Vella,  Natalie A. Terry,  Louis R. Ghanem,  Benjamin C. Kennedy,  Ingo Helbig,  Kathleen E. Sullivan,  Leslie Castelo-Soccio,  Arnold Kreigstein,  Florian Herse,  Martijn C. Nawijn,  Gerard H. Koppelman,  Melissa Haendel,  Nomi L. Harris,  Jo Lynne Rokita,  Yuanchao Zhang,  Aviv Regev,  Orit Rozenblatt-Rosen,  Jennifer E. Rood,  Timothy L. Tickle,  Roser Vento-Tormo,  Saif Alimohamed,  Monkol Lek,  Jessica C. Mar,  Kathleen M. Loomes,  David M. Barrett,  Prech Uapinyoying,  Alan H. Beggs,  Pankaj B. Agrawal,  Yi-Wen Chen,  Amanda B. Muir,  Lana X. Garmire,  Scott B. Snapper,  Javad Nazarian,  Steven H. Seeholzer,  Hossein Fazelinia,  Larry N. Singh,  Robert B. Faryabi,  Pichai Raman,  Noor Dawany,  Hongbo Michael Xie,  Batsal Devkota,  Sharon J. Diskin,  Stewart A. Anderson,  Eric F. Rappaport,  William Peranteau,  Kathryn A. Wikenheiser-Brokamp,  Sarah Teichmann,  Douglas Wallace,  Tao Peng,  Yang-yang Ding,  Man S. Kim,  Yi Xing,  Sek Won Kong,  Carsten G. Bönnemann,  Kenneth D. Mandl,  Peter S. White
Developmental Cell  ·  01 Apr 2019
Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx
Nicole R. Gay,  Michael Gloudemans,  Margaret L. Antonio,  Brunilda Balliu,  YoSon Park,  Alicia R. Martin,  Shaila Musharoff,  Abhiram Rao,  François Aguet,  Alvaro Barbeira,  Rodrigo Bonazzola,  Farhad Hormozdiari,  Kristin G. Ardlie,  Christopher D. Brown,  Hae Kyung Im,  Tuuli Lappalainen,  Xiaoquan Wen,  Stephen B. Montgomery,  
bioRxiv  ·  09 Nov 2019
Immune landscapes associated with different glioblastoma molecular subtypes
Maria Martinez-Lage,  Timothy M. Lynch,  Yingtao Bi,  Carolina Cocito,  Gregory P. Way,  Sharmistha Pal,  Josephine Haller,  Rachel E. Yan,  Amy Ziober,  Aivi Nguyen,  Manoj Kandpal,  Donald M. O’Rourke,  Jeffrey P. Greenfield,  Casey S. Greene,  Ramana V. Davuluri,  Nadia Dahmane
Acta Neuropathologica Communications  ·  29 Nov 2019
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Naihui Zhou,  Yuxiang Jiang,  Timothy R. Bergquist,  Alexandra J. Lee,  Balint Z. Kacsoh,  Alex W. Crocker,  Kimberley A. Lewis,  George Georghiou,  Huy N. Nguyen,  Md Nafiz Hamid,  Larry Davis,  Tunca Dogan,  Volkan Atalay,  Ahmet S. Rifaioglu,  Alperen Dalkıran,  Rengul Cetin Atalay,  Chengxin Zhang,  Rebecca L. Hurto,  Peter L. Freddolino,  Yang Zhang,  Prajwal Bhat,  Fran Supek,  José M. Fernández,  Branislava Gemovic,  Vladimir R. Perovic,  Radoslav S. Davidović,  Neven Sumonja,  Nevena Veljkovic,  Ehsaneddin Asgari,  Mohammad R.K. Mofrad,  Giuseppe Profiti,  Castrense Savojardo,  Pier Luigi Martelli,  Rita Casadio,  Florian Boecker,  Heiko Schoof,  Indika Kahanda,  Natalie Thurlby,  Alice C. McHardy,  Alexandre Renaux,  Rabie Saidi,  Julian Gough,  Alex A. Freitas,  Magdalena Antczak,  Fabio Fabris,  Mark N. Wass,  Jie Hou,  Jianlin Cheng,  Zheng Wang,  Alfonso E. Romero,  Alberto Paccanaro,  Haixuan Yang,  Tatyana Goldberg,  Chenguang Zhao,  Liisa Holm,  Petri Törönen,  Alan J. Medlar,  Elaine Zosa,  Itamar Borukhov,  Ilya Novikov,  Angela Wilkins,  Olivier Lichtarge,  Po-Han Chi,  Wei-Cheng Tseng,  Michal Linial,  Peter W. Rose,  Christophe Dessimoz,  Vedrana Vidulin,  Saso Dzeroski,  Ian Sillitoe,  Sayoni Das,  Jonathan Gill Lees,  David T. Jones,  Cen Wan,  Domenico Cozzetto,  Rui Fa,  Mateo Torres,  Alex Warwick Vesztrocy,  Jose Manuel Rodriguez,  Michael L. Tress,  Marco Frasca,  Marco Notaro,  Giuliano Grossi,  Alessandro Petrini,  Matteo Re,  Giorgio Valentini,  Marco Mesiti,  Daniel B. Roche,  Jonas Reeb,  David W. Ritchie,  Sabeur Aridhi,  Seyed Ziaeddin Alborzi,  Marie-Dominique Devignes,  Da Chen Emily Koo,  Richard Bonneau,  Vladimir Gligorijević,  Meet Barot,  Hai Fang,  Stefano Toppo,  Enrico Lavezzo,  Marco Falda,  Michele Berselli,  Silvio C.E. Tosatto,  Marco Carraro,  Damiano Piovesan,  Hafeez Ur Rehman,  Qizhong Mao,  Shanshan Zhang,  Slobodan Vucetic,  Gage S. Black,  Dane Jo,  Erica Suh,  Jonathan B. Dayton,  Dallas J. Larsen,  Ashton R. Omdahl,  Liam J. McGuffin,  Danielle A. Brackenridge,  Patricia C. Babbitt,  Jeffrey M. Yunes,  Paolo Fontana,  Feng Zhang,  Shanfeng Zhu,  Ronghui You,  Zihan Zhang,  Suyang Dai,  Shuwei Yao,  Weidong Tian,  Renzhi Cao,  Caleb Chandler,  Miguel Amezola,  Devon Johnson,  Jia-Ming Chang,  Wen-Hung Liao,  Yi-Wei Liu,  Stefano Pascarelli,  Yotam Frank,  Robert Hoehndorf,  Maxat Kulmanov,  Imane Boudellioua,  Gianfranco Politano,  Stefano Di Carlo,  Alfredo Benso,  Kai Hakala,  Filip Ginter,  Farrokh Mehryary,  Suwisa Kaewphan,  Jari Björne,  Hans Moen,  Martti E.E. Tolvanen,  Tapio Salakoski,  Daisuke Kihara,  Aashish Jain,  Tomislav Šmuc,  Adrian Altenhoff,  Asa Ben-Hur,  Burkhard Rost,  Steven E. Brenner,  Christine A. Orengo,  Constance J. Jeffery,  Giovanni Bosco,  Deborah A. Hogan,  Maria J. Martin,  Claire O’Donovan,  Sean D. Mooney,  Casey S. Greene,  Predrag Radivojac,  Iddo Friedberg
Genome Biology  ·  19 Nov 2019
Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma
Yu-Hsiu T. Lin,  Gregory P. Way,  Benjamin G. Barwick,  Margarette C. Mariano,  Makeba Marcoulis,  Ian D. Ferguson,  Christoph Driessen,  Lawrence H. Boise,  Casey S. Greene,  Arun P. Wiita
Blood Advances  ·  12 Nov 2019
Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design
Jo Lynne Rokita,  Komal S. Rathi,  Maria F. Cardenas,  Kristen A. Upton,  Joy Jayaseelan,  Katherine L. Cross,  Jacob Pfeil,  Laura E. Egolf,  Gregory P. Way,  Alvin Farrel,  Nathan M. Kendsersky,  Khushbu Patel,  Krutika S. Gaonkar,  Apexa Modi,  Esther R. Berko,  Gonzalo Lopez,  Zalman Vaksman,  Chelsea Mayoh,  Jonas Nance,  Kristyn McCoy,  Michelle Haber,  Kathryn Evans,  Hannah McCalmont,  Katerina Bendak,  Julia W. Böhm,  Glenn M. Marshall,  Vanessa Tyrrell,  Karthik Kalletla,  Frank K. Braun,  Lin Qi,  Yunchen Du,  Huiyuan Zhang,  Holly B. Lindsay,  Sibo Zhao,  Jack Shu,  Patricia Baxter,  Christopher Morton,  Dias Kurmashev,  Siyuan Zheng,  Yidong Chen,  Jay Bowen,  Anthony C. Bryan,  Kristen M. Leraas,  Sara E. Coppens,  HarshaVardhan Doddapaneni,  Zeineen Momin,  Wendong Zhang,  Gregory I. Sacks,  Lori S. Hart,  Kateryna Krytska,  Yael P. Mosse,  Gregory J. Gatto,  Yolanda Sanchez,  Casey S. Greene,  Sharon J. Diskin,  Olena Morozova Vaske,  David Haussler,  Julie M. Gastier-Foster,  E. Anders Kolb,  Richard Gorlick,  Xiao-Nan Li,  C. Patrick Reynolds,  Raushan T. Kurmasheva,  Peter J. Houghton,  Malcolm A. Smith,  Richard B. Lock,  Pichai Raman,  David A. Wheeler,  John M. Maris
Cell Reports  ·  01 Nov 2019
Embracing study heterogeneity for finding genetic interactions in large‐scale research consortia
Yulun Liu,  Jing Huang,  Ryan J. Urbanowicz,  Kun Chen,  Elisabetta Manduchi,  Casey S. Greene,  Jason H. Moore,  Paul Scheet,  Yong Chen
Genetic Epidemiology  ·  04 Oct 2019
Diverse transcriptomic signatures across human tissues identify functional rare genetic variation
Nicole M. Ferraro,  Benjamin J. Strober,  Jonah Einson,  Xin Li,  Francois Aguet,  Alvaro N. Barbeira,  Stephane E. Castel,  Joe R. Davis,  Austin T. Hilliard,  Bence Kotis,  YoSon Park,  Alexandra J. Scott,  Craig Smail,  Emily K. Tsang,  Kristin G. Ardlie,  Themistocles L. Assimes,  Ira Hall,  Hae Kyung Im,  Tuuli Lappalainen,  Pejman Mohammadi,  Stephen B. Montgomery,  Alexis Battle,  
bioRxiv  ·  03 Oct 2019
The GTEx Consortium atlas of genetic regulatory effects across human tissues
François Aguet,  Alvaro N Barbeira,  Rodrigo Bonazzola,  Andrew Brown,  Stephane E Castel,  Brian Jo,  Silva Kasela,  Sarah Kim-Hellmuth,  Yanyu Liang,  Meritxell Oliva,  Princy E Parsana,  Elise Flynn,  Laure Fresard,  Eric R Gaamzon,  Andrew R Hamel,  Yuan He,  Farhad Hormozdiari,  Pejman Mohammadi,  Manuel Muñoz-Aguirre,  YoSon Park,  Ashis Saha,  Ayellet V Segrć,  Benjamin J Strober,  Xiaoquan Wen,  Valentin Wucher,  Sayantan Das,  Diego Garrido-Martín,  Nicole R Gay,  Robert E Handsaker,  Paul J Hoffman,  Seva Kashin,  Alan Kwong,  Xiao Li,  Daniel MacArthur,  John M Rouhana,  Matthew Stephens,  Ellen Todres,  Ana Viñuela,  Gao Wang,  Yuxin Zou,  Christopher D Brown,  Nancy Cox,  Emmanouil Dermitzakis,  Barbara E Engelhardt,  Gad Getz,  Roderic Guigo,  Stephen B Montgomery,  Barbara E Stranger,  Hae Kyung Im,  Alexis Battle,  Kristin G Ardlie,  Tuuli Lappalainen,  
bioRxiv  ·  03 Oct 2019
Long non-coding RNA gene regulation and trait associations across human tissues
O. M. de Goede,  N. M. Ferraro,  D. C. Nachun,  A. S. Rao,  F. Aguet,  A. N. Barbeira,  S. E. Castel,  S. Kim-Hellmuth,  Y. Park,  A. J. Scott,  B. J. Strober,  C. D. Brown,  X. Wen,  I. M. Hall,  A. Battle,  T. Lappalainen,  H. K. Im,  K. G. Ardlie,  T. Quertermous,  K. Kirkegaard,  S. B. Montgomery,  
bioRxiv  ·  03 Oct 2019
Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits
Alvaro N Barbeira,  Rodrigo Bonazzola,  Eric R Gamazon,  Yanyu Liang,  YoSon Park,  Sarah Kim-Hellmuth,  Gao Wang,  Zhuoxun Jiang,  Dan Zhou,  Farhad Hormozdiari,  Boxiang Liu,  Abhiram Rao,  Andrew R Hamel,  Milton D Pividori,  François Aguet,  Lisa Bastarache,  Daniel M Jordan,  Marie Verbanck,  Ron Do,  Matthew Stephens,  Kristin Ardlie,  Mark McCarthy,  Stephen B Montgomery,  Ayellet Segré,  Christopher D Brown,  Tuuli Lappalainen,  Xiaoquan Wen,  Hae Kyung Im
bioRxiv  ·  22 Oct 2019
Technologies to watch in 2019
Marissa Fessenden
Nature  ·  23 Jan 2019
New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods
Balint Z. Kacsoh,  Stephen Barton,  Yuxiang Jiang,  Naihui Zhou,  Sean D. Mooney,  Iddo Friedberg,  Predrag Radivojac,  Casey S. Greene,  Giovanni Bosco
G3: Genes|Genomes|Genetics  ·  01 Jan 2019

2018

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
Kathleen M. Chen,  Jie Tan,  Gregory P. Way,  Georgia Doing,  Deborah A. Hogan,  Casey S. Greene
BioData Mining  ·  03 Jul 2018
Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay*
Gary E. Weissman,  Rebecca A. Hubbard,  Lyle H. Ungar,  Michael O. Harhay,  Casey S. Greene,  Blanca E. Himes,  Scott D. Halpern
Critical Care Medicine  ·  01 Jul 2018
Metabolic pathways and immunometabolism in rare kidney diseases
Peter C Grayson,  Sean Eddy,  Jaclyn N Taroni,  Yaíma L Lightfoot,  Laura Mariani,  Hemang Parikh,  Maja T Lindenmeyer,  Wenjun Ju,  Casey S Greene,  Brad Godfrey,  Clemens D Cohen,  Jeffrey Krischer,  Matthias Kretzler,  Peter A Merkel
Annals of the Rheumatic Diseases  ·  03 May 2018
Opportunities and obstacles for deep learning in biology and medicine
Travers Ching,  Daniel S. Himmelstein,  Brett K. Beaulieu-Jones,  Alexandr A. Kalinin,  Brian T. Do,  Gregory P. Way,  Enrico Ferrero,  Paul-Michael Agapow,  Michael Zietz,  Michael M. Hoffman,  Wei Xie,  Gail L. Rosen,  Benjamin J. Lengerich,  Johnny Israeli,  Jack Lanchantin,  Stephen Woloszynek,  Anne E. Carpenter,  Avanti Shrikumar,  Jinbo Xu,  Evan M. Cofer,  Christopher A. Lavender,  Srinivas C. Turaga,  Amr M. Alexandari,  Zhiyong Lu,  David J. Harris,  Dave DeCaprio,  Yanjun Qi,  Anshul Kundaje,  Yifan Peng,  Laura K. Wiley,  Marwin H. S. Segler,  Simina M. Boca,  S. Joshua Swamidass,  Austin Huang,  Anthony Gitter,  Casey S. Greene
Journal of The Royal Society Interface  ·  04 Apr 2018
Oncogenic Signaling Pathways in The Cancer Genome Atlas
Francisco Sanchez-Vega,  Marco Mina,  Joshua Armenia,  Walid K. Chatila,  Augustin Luna,  Konnor C. La,  Sofia Dimitriadoy,  David L. Liu,  Havish S. Kantheti,  Sadegh Saghafinia,  Debyani Chakravarty,  Foysal Daian,  Qingsong Gao,  Matthew H. Bailey,  Wen-Wei Liang,  Steven M. Foltz,  Ilya Shmulevich,  Li Ding,  Zachary Heins,  Angelica Ochoa,  Benjamin Gross,  Jianjiong Gao,  Hongxin Zhang,  Ritika Kundra,  Cyriac Kandoth,  Istemi Bahceci,  Leonard Dervishi,  Ugur Dogrusoz,  Wanding Zhou,  Hui Shen,  Peter W. Laird,  Gregory P. Way,  Casey S. Greene,  Han Liang,  Yonghong Xiao,  Chen Wang,  Antonio Iavarone,  Alice H. Berger,  Trever G. Bivona,  Alexander J. Lazar,  Gary D. Hammer,  Thomas Giordano,  Lawrence N. Kwong,  Grant McArthur,  Chenfei Huang,  Aaron D. Tward,  Mitchell J. Frederick,  Frank McCormick,  Matthew Meyerson,  Eliezer M. Van Allen,  Andrew D. Cherniack,  Giovanni Ciriello,  Chris Sander,  Nikolaus Schultz,  Samantha J. Caesar-Johnson,  John A. Demchok,  Ina Felau,  Melpomeni Kasapi,  Martin L. Ferguson,  Carolyn M. Hutter,  Heidi J. Sofia,  Roy Tarnuzzer,  Zhining Wang,  Liming Yang,  Jean C. Zenklusen,  Jiashan (Julia) Zhang,  Sudha Chudamani,  Jia Liu,  Laxmi Lolla,  Rashi Naresh,  Todd Pihl,  Qiang Sun,  Yunhu Wan,  Ye Wu,  Juok Cho,  Timothy DeFreitas,  Scott Frazer,  Nils Gehlenborg,  Gad Getz,  David I. Heiman,  Jaegil Kim,  Michael S. Lawrence,  Pei Lin,  Sam Meier,  Michael S. Noble,  Gordon Saksena,  Doug Voet,  Hailei Zhang,  Brady Bernard,  Nyasha Chambwe,  Varsha Dhankani,  Theo Knijnenburg,  Roger Kramer,  Kalle Leinonen,  Yuexin Liu,  Michael Miller,  Sheila Reynolds,  Ilya Shmulevich,  Vesteinn Thorsson,  Wei Zhang,  Rehan Akbani,  Bradley M. Broom,  Apurva M. Hegde,  Zhenlin Ju,  Rupa S. Kanchi,  Anil Korkut,  Jun Li,  Han Liang,  Shiyun Ling,  Wenbin Liu,  Yiling Lu,  Gordon B. Mills,  Kwok-Shing Ng,  Arvind Rao,  Michael Ryan,  Jing Wang,  John N. Weinstein,  Jiexin Zhang,  Adam Abeshouse,  Joshua Armenia,  Debyani Chakravarty,  Walid K. Chatila,  Ino de Bruijn,  Jianjiong Gao,  Benjamin E. Gross,  Zachary J. Heins,  Ritika Kundra,  Konnor La,  Marc Ladanyi,  Augustin Luna,  Moriah G. Nissan,  Angelica Ochoa,  Sarah M. Phillips,  Ed Reznik,  Francisco Sanchez-Vega,  Chris Sander,  Nikolaus Schultz,  Robert Sheridan,  S. Onur Sumer,  Yichao Sun,  Barry S. Taylor,  Jioajiao Wang,  Hongxin Zhang,  Pavana Anur,  Myron Peto,  Paul Spellman,  Christopher Benz,  Joshua M. Stuart,  Christopher K. Wong,  Christina Yau,  D. Neil Hayes,  Joel S. Parker,  Matthew D. Wilkerson,  Adrian Ally,  Miruna Balasundaram,  Reanne Bowlby,  Denise Brooks,  Rebecca Carlsen,  Eric Chuah,  Noreen Dhalla,  Robert Holt,  Steven J.M. Jones,  Katayoon Kasaian,  Darlene Lee,  Yussanne Ma,  Marco A. Marra,  Michael Mayo,  Richard A. Moore,  Andrew J. Mungall,  Karen Mungall,  A. Gordon Robertson,  Sara Sadeghi,  Jacqueline E. Schein,  Payal Sipahimalani,  Angela Tam,  Nina Thiessen,  Kane Tse,  Tina Wong,  Ashton C. Berger,  Rameen Beroukhim,  Andrew D. Cherniack,  Carrie Cibulskis,  Stacey B. Gabriel,  Galen F. Gao,  Gavin Ha,  Matthew Meyerson,  Steven E. Schumacher,  Juliann Shih,  Melanie H. Kucherlapati,  Raju S. Kucherlapati,  Stephen Baylin,  Leslie Cope,  Ludmila Danilova,  Moiz S. Bootwalla,  Phillip H. Lai,  Dennis T. Maglinte,  David J. Van Den Berg,  Daniel J. Weisenberger,  J. Todd Auman,  Saianand Balu,  Tom Bodenheimer,  Cheng Fan,  Katherine A. Hoadley,  Alan P. Hoyle,  Stuart R. Jefferys,  Corbin D. Jones,  Shaowu Meng,  Piotr A. Mieczkowski,  Lisle E. Mose,  Amy H. Perou,  Charles M. Perou,  Jeffrey Roach,  Yan Shi,  Janae V. Simons,  Tara Skelly,  Matthew G. Soloway,  Donghui Tan,  Umadevi Veluvolu,  Huihui Fan,  Toshinori Hinoue,  Peter W. Laird,  Hui Shen,  Wanding Zhou,  Michelle Bellair,  Kyle Chang,  Kyle Covington,  Chad J. Creighton,  Huyen Dinh,  HarshaVardhan Doddapaneni,  Lawrence A. Donehower,  Jennifer Drummond,  Richard A. Gibbs,  Robert Glenn,  Walker Hale,  Yi Han,  Jianhong Hu,  Viktoriya Korchina,  Sandra Lee,  Lora Lewis,  Wei Li,  Xiuping Liu,  Margaret Morgan,  Donna Morton,  Donna Muzny,  Jireh Santibanez,  Margi Sheth,  Eve Shinbrot,  Linghua Wang,  Min Wang,  David A. Wheeler,  Liu Xi,  Fengmei Zhao,  Julian Hess,  Elizabeth L. Appelbaum,  Matthew Bailey,  Matthew G. Cordes,  Li Ding,  Catrina C. Fronick,  Lucinda A. Fulton,  Robert S. Fulton,  Cyriac Kandoth,  Elaine R. Mardis,  Michael D. McLellan,  Christopher A. Miller,  Heather K. Schmidt,  Richard K. Wilson,  Daniel Crain,  Erin Curley,  Johanna Gardner,  Kevin Lau,  David Mallery,  Scott Morris,  Joseph Paulauskis,  Robert Penny,  Candace Shelton,  Troy Shelton,  Mark Sherman,  Eric Thompson,  Peggy Yena,  Jay Bowen,  Julie M. Gastier-Foster,  Mark Gerken,  Kristen M. Leraas,  Tara M. Lichtenberg,  Nilsa C. Ramirez,  Lisa Wise,  Erik Zmuda,  Niall Corcoran,  Tony Costello,  Christopher Hovens,  Andre L. Carvalho,  Ana C. de Carvalho,  José H. Fregnani,  Adhemar Longatto-Filho,  Rui M. Reis,  Cristovam Scapulatempo-Neto,  Henrique C.S. Silveira,  Daniel O. Vidal,  Andrew Burnette,  Jennifer Eschbacher,  Beth Hermes,  Ardene Noss,  Rosy Singh,  Matthew L. Anderson,  Patricia D. Castro,  Michael Ittmann,  David Huntsman,  Bernard Kohl,  Xuan Le,  Richard Thorp,  Chris Andry,  Elizabeth R. Duffy,  Vladimir Lyadov,  Oxana Paklina,  Galiya Setdikova,  Alexey Shabunin,  Mikhail Tavobilov,  Christopher McPherson,  Ronald Warnick,  Ross Berkowitz,  Daniel Cramer,  Colleen Feltmate,  Neil Horowitz,  Adam Kibel,  Michael Muto,  Chandrajit P. Raut,  Andrei Malykh,  Jill S. Barnholtz-Sloan,  Wendi Barrett,  Karen Devine,  Jordonna Fulop,  Quinn T. Ostrom,  Kristen Shimmel,  Yingli Wolinsky,  Andrew E. Sloan,  Agostino De Rose,  Felice Giuliante,  Marc Goodman,  Beth Y. Karlan,  Curt H. Hagedorn,  John Eckman,  Jodi Harr,  Jerome Myers,  Kelinda Tucker,  Leigh Anne Zach,  Brenda Deyarmin,  Hai Hu,  Leonid Kvecher,  Caroline Larson,  Richard J. Mural,  Stella Somiari,  Ales Vicha,  Tomas Zelinka,  Joseph Bennett,  Mary Iacocca,  Brenda Rabeno,  Patricia Swanson,  Mathieu Latour,  Louis Lacombe,  Bernard Têtu,  Alain Bergeron,  Mary McGraw,  Susan M. Staugaitis,  John Chabot,  Hanina Hibshoosh,  Antonia Sepulveda,  Tao Su,  Timothy Wang,  Olga Potapova,  Olga Voronina,  Laurence Desjardins,  Odette Mariani,  Sergio Roman-Roman,  Xavier Sastre,  Marc-Henri Stern,  Feixiong Cheng,  Sabina Signoretti,  Andrew Berchuck,  Darell Bigner,  Eric Lipp,  Jeffrey Marks,  Shannon McCall,  Roger McLendon,  Angeles Secord,  Alexis Sharp,  Madhusmita Behera,  Daniel J. Brat,  Amy Chen,  Keith Delman,  Seth Force,  Fadlo Khuri,  Kelly Magliocca,  Shishir Maithel,  Jeffrey J. Olson,  Taofeek Owonikoko,  Alan Pickens,  Suresh Ramalingam,  Dong M. Shin,  Gabriel Sica,  Erwin G. Van Meir,  Hongzheng Zhang,  Wil Eijckenboom,  Ad Gillis,  Esther Korpershoek,  Leendert Looijenga,  Wolter Oosterhuis,  Hans Stoop,  Kim E. van Kessel,  Ellen C. Zwarthoff,  Chiara Calatozzolo,  Lucia Cuppini,  Stefania Cuzzubbo,  Francesco DiMeco,  Gaetano Finocchiaro,  Luca Mattei,  Alessandro Perin,  Bianca Pollo,  Chu Chen,  John Houck,  Pawadee Lohavanichbutr,  Arndt Hartmann,  Christine Stoehr,  Robert Stoehr,  Helge Taubert,  Sven Wach,  Bernd Wullich,  Witold Kycler,  Dawid Murawa,  Maciej Wiznerowicz,  Ki Chung,  W. Jeffrey Edenfield,  Julie Martin,  Eric Baudin,  Glenn Bubley,  Raphael Bueno,  Assunta De Rienzo,  William G. Richards,  Steven Kalkanis,  Tom Mikkelsen,  Houtan Noushmehr,  Lisa Scarpace,  Nicolas Girard,  Marta Aymerich,  Elias Campo,  Eva Giné,  Armando López Guillermo,  Nguyen Van Bang,  Phan Thi Hanh,  Bui Duc Phu,  Yufang Tang,  Howard Colman,  Kimberley Evason,  Peter R. Dottino,  John A. Martignetti,  Hani Gabra,  Hartmut Juhl,  Teniola Akeredolu,  Serghei Stepa,  Dave Hoon,  Keunsoo Ahn,  Koo Jeong Kang,  Felix Beuschlein,  Anne Breggia,  Michael Birrer,  Debra Bell,  Mitesh Borad,  Alan H. Bryce,  Erik Castle,  Vishal Chandan,  John Cheville,  John A. Copland,  Michael Farnell,  Thomas Flotte,  Nasra Giama,  Thai Ho,  Michael Kendrick,  Jean-Pierre Kocher,  Karla Kopp,  Catherine Moser,  David Nagorney,  Daniel O’Brien,  Brian Patrick O’Neill,  Tushar Patel,  Gloria Petersen,  Florencia Que,  Michael Rivera,  Lewis Roberts,  Robert Smallridge,  Thomas Smyrk,  Melissa Stanton,  R. Houston Thompson,  Michael Torbenson,  Ju Dong Yang,  Lizhi Zhang,  Fadi Brimo,  Jaffer A. Ajani,  Ana Maria Angulo Gonzalez,  Carmen Behrens,  Jolanta Bondaruk,  Russell Broaddus,  Bogdan Czerniak,  Bita Esmaeli,  Junya Fujimoto,  Jeffrey Gershenwald,  Charles Guo,  Alexander J. Lazar,  Christopher Logothetis,  Funda Meric-Bernstam,  Cesar Moran,  Lois Ramondetta,  David Rice,  Anil Sood,  Pheroze Tamboli,  Timothy Thompson,  Patricia Troncoso,  Anne Tsao,  Ignacio Wistuba,  Candace Carter,  Lauren Haydu,  Peter Hersey,  Valerie Jakrot,  Hojabr Kakavand,  Richard Kefford,  Kenneth Lee,  Georgina Long,  Graham Mann,  Michael Quinn,  Robyn Saw,  Richard Scolyer,  Kerwin Shannon,  Andrew Spillane,  Jonathan Stretch,  Maria Synott,  John Thompson,  James Wilmott,  Hikmat Al-Ahmadie,  Timothy A. Chan,  Ronald Ghossein,  Anuradha Gopalan,  Douglas A. Levine,  Victor Reuter,  Samuel Singer,  Bhuvanesh Singh,  Nguyen Viet Tien,  Thomas Broudy,  Cyrus Mirsaidi,  Praveen Nair,  Paul Drwiega,  Judy Miller,  Jennifer Smith,  Howard Zaren,  Joong-Won Park,  Nguyen Phi Hung,  Electron Kebebew,  W. Marston Linehan,  Adam R. Metwalli,  Karel Pacak,  Peter A. Pinto,  Mark Schiffman,  Laura S. Schmidt,  Cathy D. Vocke,  Nicolas Wentzensen,  Robert Worrell,  Hannah Yang,  Marc Moncrieff,  Chandra Goparaju,  Jonathan Melamed,  Harvey Pass,  Natalia Botnariuc,  Irina Caraman,  Mircea Cernat,  Inga Chemencedji,  Adrian Clipca,  Serghei Doruc,  Ghenadie Gorincioi,  Sergiu Mura,  Maria Pirtac,  Irina Stancul,  Diana Tcaciuc,  Monique Albert,  Iakovina Alexopoulou,  Angel Arnaout,  John Bartlett,  Jay Engel,  Sebastien Gilbert,  Jeremy Parfitt,  Harman Sekhon,  George Thomas,  Doris M. Rassl,  Robert C. Rintoul,  Carlo Bifulco,  Raina Tamakawa,  Walter Urba,  Nicholas Hayward,  Henri Timmers,  Anna Antenucci,  Francesco Facciolo,  Gianluca Grazi,  Mirella Marino,  Roberta Merola,  Ronald de Krijger,  Anne-Paule Gimenez-Roqueplo,  Alain Piché,  Simone Chevalier,  Ginette McKercher,  Kivanc Birsoy,  Gene Barnett,  Cathy Brewer,  Carol Farver,  Theresa Naska,  Nathan A. Pennell,  Daniel Raymond,  Cathy Schilero,  Kathy Smolenski,  Felicia Williams,  Carl Morrison,  Jeffrey A. Borgia,  Michael J. Liptay,  Mark Pool,  Christopher W. Seder,  Kerstin Junker,  Larsson Omberg,  Mikhail Dinkin,  George Manikhas,  Domenico Alvaro,  Maria Consiglia Bragazzi,  Vincenzo Cardinale,  Guido Carpino,  Eugenio Gaudio,  David Chesla,  Sandra Cottingham,  Michael Dubina,  Fedor Moiseenko,  Renumathy Dhanasekaran,  Karl-Friedrich Becker,  Klaus-Peter Janssen,  Julia Slotta-Huspenina,  Mohamed H. Abdel-Rahman,  Dina Aziz,  Sue Bell,  Colleen M. Cebulla,  Amy Davis,  Rebecca Duell,  J. Bradley Elder,  Joe Hilty,  Bahavna Kumar,  James Lang,  Norman L. Lehman,  Randy Mandt,  Phuong Nguyen,  Robert Pilarski,  Karan Rai,  Lynn Schoenfield,  Kelly Senecal,  Paul Wakely,  Paul Hansen,  Ronald Lechan,  James Powers,  Arthur Tischler,  William E. Grizzle,  Katherine C. Sexton,  Alison Kastl,  Joel Henderson,  Sima Porten,  Jens Waldmann,  Martin Fassnacht,  Sylvia L. Asa,  Dirk Schadendorf,  Marta Couce,  Markus Graefen,  Hartwig Huland,  Guido Sauter,  Thorsten Schlomm,  Ronald Simon,  Pierre Tennstedt,  Oluwole Olabode,  Mark Nelson,  Oliver Bathe,  Peter R. Carroll,  June M. Chan,  Philip Disaia,  Pat Glenn,  Robin K. Kelley,  Charles N. Landen,  Joanna Phillips,  Michael Prados,  Jeffry Simko,  Karen Smith-McCune,  Scott VandenBerg,  Kevin Roggin,  Ashley Fehrenbach,  Ady Kendler,  Suzanne Sifri,  Ruth Steele,  Antonio Jimeno,  Francis Carey,  Ian Forgie,  Massimo Mannelli,  Michael Carney,  Brenda Hernandez,  Benito Campos,  Christel Herold-Mende,  Christin Jungk,  Andreas Unterberg,  Andreas von Deimling,  Aaron Bossler,  Joseph Galbraith,  Laura Jacobus,  Michael Knudson,  Tina Knutson,  Deqin Ma,  Mohammed Milhem,  Rita Sigmund,  Andrew K. Godwin,  Rashna Madan,  Howard G. Rosenthal,  Clement Adebamowo,  Sally N. Adebamowo,  Alex Boussioutas,  David Beer,  Thomas Giordano,  Anne-Marie Mes-Masson,  Fred Saad,  Therese Bocklage,  Lisa Landrum,  Robert Mannel,  Kathleen Moore,  Katherine Moxley,  Russel Postier,  Joan Walker,  Rosemary Zuna,  Michael Feldman,  Federico Valdivieso,  Rajiv Dhir,  James Luketich,  Edna M. Mora Pinero,  Mario Quintero-Aguilo,  Carlos Gilberto Carlotti,  Jose Sebastião Dos Santos,  Rafael Kemp,  Ajith Sankarankuty,  Daniela Tirapelli,  James Catto,  Kathy Agnew,  Elizabeth Swisher,  Jenette Creaney,  Bruce Robinson,  Carl Simon Shelley,  Eryn M. Godwin,  Sara Kendall,  Cassaundra Shipman,  Carol Bradford,  Thomas Carey,  Andrea Haddad,  Jeffey Moyer,  Lisa Peterson,  Mark Prince,  Laura Rozek,  Gregory Wolf,  Rayleen Bowman,  Kwun M. Fong,  Ian Yang,  Robert Korst,  W. Kimryn Rathmell,  J. Leigh Fantacone-Campbell,  Jeffrey A. Hooke,  Albert J. Kovatich,  Craig D. Shriver,  John DiPersio,  Bettina Drake,  Ramaswamy Govindan,  Sharon Heath,  Timothy Ley,  Brian Van Tine,  Peter Westervelt,  Mark A. Rubin,  Jung Il Lee,  Natália D. Aredes,  Armaz Mariamidze
Cell  ·  01 Apr 2018
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas
Gregory P. Way,  Francisco Sanchez-Vega,  Konnor La,  Joshua Armenia,  Walid K. Chatila,  Augustin Luna,  Chris Sander,  Andrew D. Cherniack,  Marco Mina,  Giovanni Ciriello,  Nikolaus Schultz,  Yolanda Sanchez,  Casey S. Greene,  Samantha J. Caesar-Johnson,  John A. Demchok,  Ina Felau,  Melpomeni Kasapi,  Martin L. Ferguson,  Carolyn M. Hutter,  Heidi J. Sofia,  Roy Tarnuzzer,  Zhining Wang,  Liming Yang,  Jean C. Zenklusen,  Jiashan (Julia) Zhang,  Sudha Chudamani,  Jia Liu,  Laxmi Lolla,  Rashi Naresh,  Todd Pihl,  Qiang Sun,  Yunhu Wan,  Ye Wu,  Juok Cho,  Timothy DeFreitas,  Scott Frazer,  Nils Gehlenborg,  Gad Getz,  David I. Heiman,  Jaegil Kim,  Michael S. Lawrence,  Pei Lin,  Sam Meier,  Michael S. Noble,  Gordon Saksena,  Doug Voet,  Hailei Zhang,  Brady Bernard,  Nyasha Chambwe,  Varsha Dhankani,  Theo Knijnenburg,  Roger Kramer,  Kalle Leinonen,  Yuexin Liu,  Michael Miller,  Sheila Reynolds,  Ilya Shmulevich,  Vesteinn Thorsson,  Wei Zhang,  Rehan Akbani,  Bradley M. Broom,  Apurva M. Hegde,  Zhenlin Ju,  Rupa S. Kanchi,  Anil Korkut,  Jun Li,  Han Liang,  Shiyun Ling,  Wenbin Liu,  Yiling Lu,  Gordon B. Mills,  Kwok-Shing Ng,  Arvind Rao,  Michael Ryan,  Jing Wang,  John N. Weinstein,  Jiexin Zhang,  Adam Abeshouse,  Joshua Armenia,  Debyani Chakravarty,  Walid K. Chatila,  Ino de Bruijn,  Jianjiong Gao,  Benjamin E. Gross,  Zachary J. Heins,  Ritika Kundra,  Konnor La,  Marc Ladanyi,  Augustin Luna,  Moriah G. Nissan,  Angelica Ochoa,  Sarah M. Phillips,  Ed Reznik,  Francisco Sanchez-Vega,  Chris Sander,  Nikolaus Schultz,  Robert Sheridan,  S. Onur Sumer,  Yichao Sun,  Barry S. Taylor,  Jioajiao Wang,  Hongxin Zhang,  Pavana Anur,  Myron Peto,  Paul Spellman,  Christopher Benz,  Joshua M. Stuart,  Christopher K. Wong,  Christina Yau,  D. Neil Hayes,  Joel S. Parker,  Matthew D. Wilkerson,  Adrian Ally,  Miruna Balasundaram,  Reanne Bowlby,  Denise Brooks,  Rebecca Carlsen,  Eric Chuah,  Noreen Dhalla,  Robert Holt,  Steven J.M. Jones,  Katayoon Kasaian,  Darlene Lee,  Yussanne Ma,  Marco A. Marra,  Michael Mayo,  Richard A. Moore,  Andrew J. Mungall,  Karen Mungall,  A. Gordon Robertson,  Sara Sadeghi,  Jacqueline E. Schein,  Payal Sipahimalani,  Angela Tam,  Nina Thiessen,  Kane Tse,  Tina Wong,  Ashton C. Berger,  Rameen Beroukhim,  Andrew D. Cherniack,  Carrie Cibulskis,  Stacey B. Gabriel,  Galen F. Gao,  Gavin Ha,  Matthew Meyerson,  Steven E. Schumacher,  Juliann Shih,  Melanie H. Kucherlapati,  Raju S. Kucherlapati,  Stephen Baylin,  Leslie Cope,  Ludmila Danilova,  Moiz S. Bootwalla,  Phillip H. Lai,  Dennis T. Maglinte,  David J. Van Den Berg,  Daniel J. Weisenberger,  J. Todd Auman,  Saianand Balu,  Tom Bodenheimer,  Cheng Fan,  Katherine A. Hoadley,  Alan P. Hoyle,  Stuart R. Jefferys,  Corbin D. Jones,  Shaowu Meng,  Piotr A. Mieczkowski,  Lisle E. Mose,  Amy H. Perou,  Charles M. Perou,  Jeffrey Roach,  Yan Shi,  Janae V. Simons,  Tara Skelly,  Matthew G. Soloway,  Donghui Tan,  Umadevi Veluvolu,  Huihui Fan,  Toshinori Hinoue,  Peter W. Laird,  Hui Shen,  Wanding Zhou,  Michelle Bellair,  Kyle Chang,  Kyle Covington,  Chad J. Creighton,  Huyen Dinh,  HarshaVardhan Doddapaneni,  Lawrence A. Donehower,  Jennifer Drummond,  Richard A. Gibbs,  Robert Glenn,  Walker Hale,  Yi Han,  Jianhong Hu,  Viktoriya Korchina,  Sandra Lee,  Lora Lewis,  Wei Li,  Xiuping Liu,  Margaret Morgan,  Donna Morton,  Donna Muzny,  Jireh Santibanez,  Margi Sheth,  Eve Shinbrot,  Linghua Wang,  Min Wang,  David A. Wheeler,  Liu Xi,  Fengmei Zhao,  Julian Hess,  Elizabeth L. Appelbaum,  Matthew Bailey,  Matthew G. Cordes,  Li Ding,  Catrina C. Fronick,  Lucinda A. Fulton,  Robert S. Fulton,  Cyriac Kandoth,  Elaine R. Mardis,  Michael D. McLellan,  Christopher A. Miller,  Heather K. Schmidt,  Richard K. Wilson,  Daniel Crain,  Erin Curley,  Johanna Gardner,  Kevin Lau,  David Mallery,  Scott Morris,  Joseph Paulauskis,  Robert Penny,  Candace Shelton,  Troy Shelton,  Mark Sherman,  Eric Thompson,  Peggy Yena,  Jay Bowen,  Julie M. Gastier-Foster,  Mark Gerken,  Kristen M. Leraas,  Tara M. Lichtenberg,  Nilsa C. Ramirez,  Lisa Wise,  Erik Zmuda,  Niall Corcoran,  Tony Costello,  Christopher Hovens,  Andre L. Carvalho,  Ana C. de Carvalho,  José H. Fregnani,  Adhemar Longatto-Filho,  Rui M. Reis,  Cristovam Scapulatempo-Neto,  Henrique C.S. Silveira,  Daniel O. Vidal,  Andrew Burnette,  Jennifer Eschbacher,  Beth Hermes,  Ardene Noss,  Rosy Singh,  Matthew L. Anderson,  Patricia D. Castro,  Michael Ittmann,  David Huntsman,  Bernard Kohl,  Xuan Le,  Richard Thorp,  Chris Andry,  Elizabeth R. Duffy,  Vladimir Lyadov,  Oxana Paklina,  Galiya Setdikova,  Alexey Shabunin,  Mikhail Tavobilov,  Christopher McPherson,  Ronald Warnick,  Ross Berkowitz,  Daniel Cramer,  Colleen Feltmate,  Neil Horowitz,  Adam Kibel,  Michael Muto,  Chandrajit P. Raut,  Andrei Malykh,  Jill S. Barnholtz-Sloan,  Wendi Barrett,  Karen Devine,  Jordonna Fulop,  Quinn T. Ostrom,  Kristen Shimmel,  Yingli Wolinsky,  Andrew E. Sloan,  Agostino De Rose,  Felice Giuliante,  Marc Goodman,  Beth Y. Karlan,  Curt H. Hagedorn,  John Eckman,  Jodi Harr,  Jerome Myers,  Kelinda Tucker,  Leigh Anne Zach,  Brenda Deyarmin,  Hai Hu,  Leonid Kvecher,  Caroline Larson,  Richard J. Mural,  Stella Somiari,  Ales Vicha,  Tomas Zelinka,  Joseph Bennett,  Mary Iacocca,  Brenda Rabeno,  Patricia Swanson,  Mathieu Latour,  Louis Lacombe,  Bernard Têtu,  Alain Bergeron,  Mary McGraw,  Susan M. Staugaitis,  John Chabot,  Hanina Hibshoosh,  Antonia Sepulveda,  Tao Su,  Timothy Wang,  Olga Potapova,  Olga Voronina,  Laurence Desjardins,  Odette Mariani,  Sergio Roman-Roman,  Xavier Sastre,  Marc-Henri Stern,  Feixiong Cheng,  Sabina Signoretti,  Andrew Berchuck,  Darell Bigner,  Eric Lipp,  Jeffrey Marks,  Shannon McCall,  Roger McLendon,  Angeles Secord,  Alexis Sharp,  Madhusmita Behera,  Daniel J. Brat,  Amy Chen,  Keith Delman,  Seth Force,  Fadlo Khuri,  Kelly Magliocca,  Shishir Maithel,  Jeffrey J. Olson,  Taofeek Owonikoko,  Alan Pickens,  Suresh Ramalingam,  Dong M. Shin,  Gabriel Sica,  Erwin G. Van Meir,  Hongzheng Zhang,  Wil Eijckenboom,  Ad Gillis,  Esther Korpershoek,  Leendert Looijenga,  Wolter Oosterhuis,  Hans Stoop,  Kim E. van Kessel,  Ellen C. Zwarthoff,  Chiara Calatozzolo,  Lucia Cuppini,  Stefania Cuzzubbo,  Francesco DiMeco,  Gaetano Finocchiaro,  Luca Mattei,  Alessandro Perin,  Bianca Pollo,  Chu Chen,  John Houck,  Pawadee Lohavanichbutr,  Arndt Hartmann,  Christine Stoehr,  Robert Stoehr,  Helge Taubert,  Sven Wach,  Bernd Wullich,  Witold Kycler,  Dawid Murawa,  Maciej Wiznerowicz,  Ki Chung,  W. Jeffrey Edenfield,  Julie Martin,  Eric Baudin,  Glenn Bubley,  Raphael Bueno,  Assunta De Rienzo,  William G. Richards,  Steven Kalkanis,  Tom Mikkelsen,  Houtan Noushmehr,  Lisa Scarpace,  Nicolas Girard,  Marta Aymerich,  Elias Campo,  Eva Giné,  Armando López Guillermo,  Nguyen Van Bang,  Phan Thi Hanh,  Bui Duc Phu,  Yufang Tang,  Howard Colman,  Kimberley Evason,  Peter R. Dottino,  John A. Martignetti,  Hani Gabra,  Hartmut Juhl,  Teniola Akeredolu,  Serghei Stepa,  Dave Hoon,  Keunsoo Ahn,  Koo Jeong Kang,  Felix Beuschlein,  Anne Breggia,  Michael Birrer,  Debra Bell,  Mitesh Borad,  Alan H. Bryce,  Erik Castle,  Vishal Chandan,  John Cheville,  John A. Copland,  Michael Farnell,  Thomas Flotte,  Nasra Giama,  Thai Ho,  Michael Kendrick,  Jean-Pierre Kocher,  Karla Kopp,  Catherine Moser,  David Nagorney,  Daniel O’Brien,  Brian Patrick O’Neill,  Tushar Patel,  Gloria Petersen,  Florencia Que,  Michael Rivera,  Lewis Roberts,  Robert Smallridge,  Thomas Smyrk,  Melissa Stanton,  R. Houston Thompson,  Michael Torbenson,  Ju Dong Yang,  Lizhi Zhang,  Fadi Brimo,  Jaffer A. Ajani,  Ana Maria Angulo Gonzalez,  Carmen Behrens,  Jolanta Bondaruk,  Russell Broaddus,  Bogdan Czerniak,  Bita Esmaeli,  Junya Fujimoto,  Jeffrey Gershenwald,  Charles Guo,  Alexander J. Lazar,  Christopher Logothetis,  Funda Meric-Bernstam,  Cesar Moran,  Lois Ramondetta,  David Rice,  Anil Sood,  Pheroze Tamboli,  Timothy Thompson,  Patricia Troncoso,  Anne Tsao,  Ignacio Wistuba,  Candace Carter,  Lauren Haydu,  Peter Hersey,  Valerie Jakrot,  Hojabr Kakavand,  Richard Kefford,  Kenneth Lee,  Georgina Long,  Graham Mann,  Michael Quinn,  Robyn Saw,  Richard Scolyer,  Kerwin Shannon,  Andrew Spillane,  Jonathan Stretch,  Maria Synott,  John Thompson,  James Wilmott,  Hikmat Al-Ahmadie,  Timothy A. Chan,  Ronald Ghossein,  Anuradha Gopalan,  Douglas A. Levine,  Victor Reuter,  Samuel Singer,  Bhuvanesh Singh,  Nguyen Viet Tien,  Thomas Broudy,  Cyrus Mirsaidi,  Praveen Nair,  Paul Drwiega,  Judy Miller,  Jennifer Smith,  Howard Zaren,  Joong-Won Park,  Nguyen Phi Hung,  Electron Kebebew,  W. Marston Linehan,  Adam R. Metwalli,  Karel Pacak,  Peter A. Pinto,  Mark Schiffman,  Laura S. Schmidt,  Cathy D. Vocke,  Nicolas Wentzensen,  Robert Worrell,  Hannah Yang,  Marc Moncrieff,  Chandra Goparaju,  Jonathan Melamed,  Harvey Pass,  Natalia Botnariuc,  Irina Caraman,  Mircea Cernat,  Inga Chemencedji,  Adrian Clipca,  Serghei Doruc,  Ghenadie Gorincioi,  Sergiu Mura,  Maria Pirtac,  Irina Stancul,  Diana Tcaciuc,  Monique Albert,  Iakovina Alexopoulou,  Angel Arnaout,  John Bartlett,  Jay Engel,  Sebastien Gilbert,  Jeremy Parfitt,  Harman Sekhon,  George Thomas,  Doris M. Rassl,  Robert C. Rintoul,  Carlo Bifulco,  Raina Tamakawa,  Walter Urba,  Nicholas Hayward,  Henri Timmers,  Anna Antenucci,  Francesco Facciolo,  Gianluca Grazi,  Mirella Marino,  Roberta Merola,  Ronald de Krijger,  Anne-Paule Gimenez-Roqueplo,  Alain Piché,  Simone Chevalier,  Ginette McKercher,  Kivanc Birsoy,  Gene Barnett,  Cathy Brewer,  Carol Farver,  Theresa Naska,  Nathan A. Pennell,  Daniel Raymond,  Cathy Schilero,  Kathy Smolenski,  Felicia Williams,  Carl Morrison,  Jeffrey A. Borgia,  Michael J. Liptay,  Mark Pool,  Christopher W. Seder,  Kerstin Junker,  Larsson Omberg,  Mikhail Dinkin,  George Manikhas,  Domenico Alvaro,  Maria Consiglia Bragazzi,  Vincenzo Cardinale,  Guido Carpino,  Eugenio Gaudio,  David Chesla,  Sandra Cottingham,  Michael Dubina,  Fedor Moiseenko,  Renumathy Dhanasekaran,  Karl-Friedrich Becker,  Klaus-Peter Janssen,  Julia Slotta-Huspenina,  Mohamed H. Abdel-Rahman,  Dina Aziz,  Sue Bell,  Colleen M. Cebulla,  Amy Davis,  Rebecca Duell,  J. Bradley Elder,  Joe Hilty,  Bahavna Kumar,  James Lang,  Norman L. Lehman,  Randy Mandt,  Phuong Nguyen,  Robert Pilarski,  Karan Rai,  Lynn Schoenfield,  Kelly Senecal,  Paul Wakely,  Paul Hansen,  Ronald Lechan,  James Powers,  Arthur Tischler,  William E. Grizzle,  Katherine C. Sexton,  Alison Kastl,  Joel Henderson,  Sima Porten,  Jens Waldmann,  Martin Fassnacht,  Sylvia L. Asa,  Dirk Schadendorf,  Marta Couce,  Markus Graefen,  Hartwig Huland,  Guido Sauter,  Thorsten Schlomm,  Ronald Simon,  Pierre Tennstedt,  Oluwole Olabode,  Mark Nelson,  Oliver Bathe,  Peter R. Carroll,  June M. Chan,  Philip Disaia,  Pat Glenn,  Robin K. Kelley,  Charles N. Landen,  Joanna Phillips,  Michael Prados,  Jeffry Simko,  Karen Smith-McCune,  Scott VandenBerg,  Kevin Roggin,  Ashley Fehrenbach,  Ady Kendler,  Suzanne Sifri,  Ruth Steele,  Antonio Jimeno,  Francis Carey,  Ian Forgie,  Massimo Mannelli,  Michael Carney,  Brenda Hernandez,  Benito Campos,  Christel Herold-Mende,  Christin Jungk,  Andreas Unterberg,  Andreas von Deimling,  Aaron Bossler,  Joseph Galbraith,  Laura Jacobus,  Michael Knudson,  Tina Knutson,  Deqin Ma,  Mohammed Milhem,  Rita Sigmund,  Andrew K. Godwin,  Rashna Madan,  Howard G. Rosenthal,  Clement Adebamowo,  Sally N. Adebamowo,  Alex Boussioutas,  David Beer,  Thomas Giordano,  Anne-Marie Mes-Masson,  Fred Saad,  Therese Bocklage,  Lisa Landrum,  Robert Mannel,  Kathleen Moore,  Katherine Moxley,  Russel Postier,  Joan Walker,  Rosemary Zuna,  Michael Feldman,  Federico Valdivieso,  Rajiv Dhir,  James Luketich,  Edna M. Mora Pinero,  Mario Quintero-Aguilo,  Carlos Gilberto Carlotti,  Jose Sebastião Dos Santos,  Rafael Kemp,  Ajith Sankarankuty,  Daniela Tirapelli,  James Catto,  Kathy Agnew,  Elizabeth Swisher,  Jenette Creaney,  Bruce Robinson,  Carl Simon Shelley,  Eryn M. Godwin,  Sara Kendall,  Cassaundra Shipman,  Carol Bradford,  Thomas Carey,  Andrea Haddad,  Jeffey Moyer,  Lisa Peterson,  Mark Prince,  Laura Rozek,  Gregory Wolf,  Rayleen Bowman,  Kwun M. Fong,  Ian Yang,  Robert Korst,  W. Kimryn Rathmell,  J. Leigh Fantacone-Campbell,  Jeffrey A. Hooke,  Albert J. Kovatich,  Craig D. Shriver,  John DiPersio,  Bettina Drake,  Ramaswamy Govindan,  Sharon Heath,  Timothy Ley,  Brian Van Tine,  Peter Westervelt,  Mark A. Rubin,  Jung Il Lee,  Natália D. Aredes,  Armaz Mariamidze
Cell Reports  ·  01 Apr 2018
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Theo A. Knijnenburg,  Linghua Wang,  Michael T. Zimmermann,  Nyasha Chambwe,  Galen F. Gao,  Andrew D. Cherniack,  Huihui Fan,  Hui Shen,  Gregory P. Way,  Casey S. Greene,  Yuexin Liu,  Rehan Akbani,  Bin Feng,  Lawrence A. Donehower,  Chase Miller,  Yang Shen,  Mostafa Karimi,  Haoran Chen,  Pora Kim,  Peilin Jia,  Eve Shinbrot,  Shaojun Zhang,  Jianfang Liu,  Hai Hu,  Matthew H. Bailey,  Christina Yau,  Denise Wolf,  Zhongming Zhao,  John N. Weinstein,  Lei Li,  Li Ding,  Gordon B. Mills,  Peter W. Laird,  David A. Wheeler,  Ilya Shmulevich,  Raymond J. Monnat,  Yonghong Xiao,  Chen Wang,  Samantha J. Caesar-Johnson,  John A. Demchok,  Ina Felau,  Melpomeni Kasapi,  Martin L. Ferguson,  Carolyn M. Hutter,  Heidi J. Sofia,  Roy Tarnuzzer,  Zhining Wang,  Liming Yang,  Jean C. Zenklusen,  Jiashan (Julia) Zhang,  Sudha Chudamani,  Jia Liu,  Laxmi Lolla,  Rashi Naresh,  Todd Pihl,  Qiang Sun,  Yunhu Wan,  Ye Wu,  Juok Cho,  Timothy DeFreitas,  Scott Frazer,  Nils Gehlenborg,  Gad Getz,  David I. Heiman,  Jaegil Kim,  Michael S. Lawrence,  Pei Lin,  Sam Meier,  Michael S. Noble,  Gordon Saksena,  Doug Voet,  Hailei Zhang,  Brady Bernard,  Nyasha Chambwe,  Varsha Dhankani,  Theo Knijnenburg,  Roger Kramer,  Kalle Leinonen,  Yuexin Liu,  Michael Miller,  Sheila Reynolds,  Ilya Shmulevich,  Vesteinn Thorsson,  Wei Zhang,  Rehan Akbani,  Bradley M. Broom,  Apurva M. Hegde,  Zhenlin Ju,  Rupa S. Kanchi,  Anil Korkut,  Jun Li,  Han Liang,  Shiyun Ling,  Wenbin Liu,  Yiling Lu,  Gordon B. Mills,  Kwok-Shing Ng,  Arvind Rao,  Michael Ryan,  Jing Wang,  John N. Weinstein,  Jiexin Zhang,  Adam Abeshouse,  Joshua Armenia,  Debyani Chakravarty,  Walid K. Chatila,  Ino de Bruijn,  Jianjiong Gao,  Benjamin E. Gross,  Zachary J. Heins,  Ritika Kundra,  Konnor La,  Marc Ladanyi,  Augustin Luna,  Moriah G. Nissan,  Angelica Ochoa,  Sarah M. Phillips,  Ed Reznik,  Francisco Sanchez-Vega,  Chris Sander,  Nikolaus Schultz,  Robert Sheridan,  S. Onur Sumer,  Yichao Sun,  Barry S. Taylor,  Jioajiao Wang,  Hongxin Zhang,  Pavana Anur,  Myron Peto,  Paul Spellman,  Christopher Benz,  Joshua M. Stuart,  Christopher K. Wong,  Christina Yau,  D. Neil Hayes,  Joel S. Parker,  Matthew D. Wilkerson,  Adrian Ally,  Miruna Balasundaram,  Reanne Bowlby,  Denise Brooks,  Rebecca Carlsen,  Eric Chuah,  Noreen Dhalla,  Robert Holt,  Steven J.M. Jones,  Katayoon Kasaian,  Darlene Lee,  Yussanne Ma,  Marco A. Marra,  Michael Mayo,  Richard A. Moore,  Andrew J. Mungall,  Karen Mungall,  A. Gordon Robertson,  Sara Sadeghi,  Jacqueline E. Schein,  Payal Sipahimalani,  Angela Tam,  Nina Thiessen,  Kane Tse,  Tina Wong,  Ashton C. Berger,  Rameen Beroukhim,  Andrew D. Cherniack,  Carrie Cibulskis,  Stacey B. Gabriel,  Galen F. Gao,  Gavin Ha,  Matthew Meyerson,  Steven E. Schumacher,  Juliann Shih,  Melanie H. Kucherlapati,  Raju S. Kucherlapati,  Stephen Baylin,  Leslie Cope,  Ludmila Danilova,  Moiz S. Bootwalla,  Phillip H. Lai,  Dennis T. Maglinte,  David J. Van Den Berg,  Daniel J. Weisenberger,  J. Todd Auman,  Saianand Balu,  Tom Bodenheimer,  Cheng Fan,  Katherine A. Hoadley,  Alan P. Hoyle,  Stuart R. Jefferys,  Corbin D. Jones,  Shaowu Meng,  Piotr A. Mieczkowski,  Lisle E. Mose,  Amy H. Perou,  Charles M. Perou,  Jeffrey Roach,  Yan Shi,  Janae V. Simons,  Tara Skelly,  Matthew G. Soloway,  Donghui Tan,  Umadevi Veluvolu,  Huihui Fan,  Toshinori Hinoue,  Peter W. Laird,  Hui Shen,  Wanding Zhou,  Michelle Bellair,  Kyle Chang,  Kyle Covington,  Chad J. Creighton,  Huyen Dinh,  HarshaVardhan Doddapaneni,  Lawrence A. Donehower,  Jennifer Drummond,  Richard A. Gibbs,  Robert Glenn,  Walker Hale,  Yi Han,  Jianhong Hu,  Viktoriya Korchina,  Sandra Lee,  Lora Lewis,  Wei Li,  Xiuping Liu,  Margaret Morgan,  Donna Morton,  Donna Muzny,  Jireh Santibanez,  Margi Sheth,  Eve Shinbrot,  Linghua Wang,  Min Wang,  David A. Wheeler,  Liu Xi,  Fengmei Zhao,  Julian Hess,  Elizabeth L. Appelbaum,  Matthew Bailey,  Matthew G. Cordes,  Li Ding,  Catrina C. Fronick,  Lucinda A. Fulton,  Robert S. Fulton,  Cyriac Kandoth,  Elaine R. Mardis,  Michael D. McLellan,  Christopher A. Miller,  Heather K. Schmidt,  Richard K. Wilson,  Daniel Crain,  Erin Curley,  Johanna Gardner,  Kevin Lau,  David Mallery,  Scott Morris,  Joseph Paulauskis,  Robert Penny,  Candace Shelton,  Troy Shelton,  Mark Sherman,  Eric Thompson,  Peggy Yena,  Jay Bowen,  Julie M. Gastier-Foster,  Mark Gerken,  Kristen M. Leraas,  Tara M. Lichtenberg,  Nilsa C. Ramirez,  Lisa Wise,  Erik Zmuda,  Niall Corcoran,  Tony Costello,  Christopher Hovens,  Andre L. Carvalho,  Ana C. de Carvalho,  José H. Fregnani,  Adhemar Longatto-Filho,  Rui M. Reis,  Cristovam Scapulatempo-Neto,  Henrique C.S. Silveira,  Daniel O. Vidal,  Andrew Burnette,  Jennifer Eschbacher,  Beth Hermes,  Ardene Noss,  Rosy Singh,  Matthew L. Anderson,  Patricia D. Castro,  Michael Ittmann,  David Huntsman,  Bernard Kohl,  Xuan Le,  Richard Thorp,  Chris Andry,  Elizabeth R. Duffy,  Vladimir Lyadov,  Oxana Paklina,  Galiya Setdikova,  Alexey Shabunin,  Mikhail Tavobilov,  Christopher McPherson,  Ronald Warnick,  Ross Berkowitz,  Daniel Cramer,  Colleen Feltmate,  Neil Horowitz,  Adam Kibel,  Michael Muto,  Chandrajit P. Raut,  Andrei Malykh,  Jill S. Barnholtz-Sloan,  Wendi Barrett,  Karen Devine,  Jordonna Fulop,  Quinn T. Ostrom,  Kristen Shimmel,  Yingli Wolinsky,  Andrew E. Sloan,  Agostino De Rose,  Felice Giuliante,  Marc Goodman,  Beth Y. Karlan,  Curt H. Hagedorn,  John Eckman,  Jodi Harr,  Jerome Myers,  Kelinda Tucker,  Leigh Anne Zach,  Brenda Deyarmin,  Hai Hu,  Leonid Kvecher,  Caroline Larson,  Richard J. Mural,  Stella Somiari,  Ales Vicha,  Tomas Zelinka,  Joseph Bennett,  Mary Iacocca,  Brenda Rabeno,  Patricia Swanson,  Mathieu Latour,  Louis Lacombe,  Bernard Têtu,  Alain Bergeron,  Mary McGraw,  Susan M. Staugaitis,  John Chabot,  Hanina Hibshoosh,  Antonia Sepulveda,  Tao Su,  Timothy Wang,  Olga Potapova,  Olga Voronina,  Laurence Desjardins,  Odette Mariani,  Sergio Roman-Roman,  Xavier Sastre,  Marc-Henri Stern,  Feixiong Cheng,  Sabina Signoretti,  Andrew Berchuck,  Darell Bigner,  Eric Lipp,  Jeffrey Marks,  Shannon McCall,  Roger McLendon,  Angeles Secord,  Alexis Sharp,  Madhusmita Behera,  Daniel J. Brat,  Amy Chen,  Keith Delman,  Seth Force,  Fadlo Khuri,  Kelly Magliocca,  Shishir Maithel,  Jeffrey J. Olson,  Taofeek Owonikoko,  Alan Pickens,  Suresh Ramalingam,  Dong M. Shin,  Gabriel Sica,  Erwin G. Van Meir,  Hongzheng Zhang,  Wil Eijckenboom,  Ad Gillis,  Esther Korpershoek,  Leendert Looijenga,  Wolter Oosterhuis,  Hans Stoop,  Kim E. van Kessel,  Ellen C. Zwarthoff,  Chiara Calatozzolo,  Lucia Cuppini,  Stefania Cuzzubbo,  Francesco DiMeco,  Gaetano Finocchiaro,  Luca Mattei,  Alessandro Perin,  Bianca Pollo,  Chu Chen,  John Houck,  Pawadee Lohavanichbutr,  Arndt Hartmann,  Christine Stoehr,  Robert Stoehr,  Helge Taubert,  Sven Wach,  Bernd Wullich,  Witold Kycler,  Dawid Murawa,  Maciej Wiznerowicz,  Ki Chung,  W. Jeffrey Edenfield,  Julie Martin,  Eric Baudin,  Glenn Bubley,  Raphael Bueno,  Assunta De Rienzo,  William G. Richards,  Steven Kalkanis,  Tom Mikkelsen,  Houtan Noushmehr,  Lisa Scarpace,  Nicolas Girard,  Marta Aymerich,  Elias Campo,  Eva Giné,  Armando López Guillermo,  Nguyen Van Bang,  Phan Thi Hanh,  Bui Duc Phu,  Yufang Tang,  Howard Colman,  Kimberley Evason,  Peter R. Dottino,  John A. Martignetti,  Hani Gabra,  Hartmut Juhl,  Teniola Akeredolu,  Serghei Stepa,  Dave Hoon,  Keunsoo Ahn,  Koo Jeong Kang,  Felix Beuschlein,  Anne Breggia,  Michael Birrer,  Debra Bell,  Mitesh Borad,  Alan H. Bryce,  Erik Castle,  Vishal Chandan,  John Cheville,  John A. Copland,  Michael Farnell,  Thomas Flotte,  Nasra Giama,  Thai Ho,  Michael Kendrick,  Jean-Pierre Kocher,  Karla Kopp,  Catherine Moser,  David Nagorney,  Daniel O’Brien,  Brian Patrick O’Neill,  Tushar Patel,  Gloria Petersen,  Florencia Que,  Michael Rivera,  Lewis Roberts,  Robert Smallridge,  Thomas Smyrk,  Melissa Stanton,  R. Houston Thompson,  Michael Torbenson,  Ju Dong Yang,  Lizhi Zhang,  Fadi Brimo,  Jaffer A. Ajani,  Ana Maria Angulo Gonzalez,  Carmen Behrens,  Jolanta Bondaruk,  Russell Broaddus,  Bogdan Czerniak,  Bita Esmaeli,  Junya Fujimoto,  Jeffrey Gershenwald,  Charles Guo,  Alexander J. Lazar,  Christopher Logothetis,  Funda Meric-Bernstam,  Cesar Moran,  Lois Ramondetta,  David Rice,  Anil Sood,  Pheroze Tamboli,  Timothy Thompson,  Patricia Troncoso,  Anne Tsao,  Ignacio Wistuba,  Candace Carter,  Lauren Haydu,  Peter Hersey,  Valerie Jakrot,  Hojabr Kakavand,  Richard Kefford,  Kenneth Lee,  Georgina Long,  Graham Mann,  Michael Quinn,  Robyn Saw,  Richard Scolyer,  Kerwin Shannon,  Andrew Spillane,  Jonathan Stretch,  Maria Synott,  John Thompson,  James Wilmott,  Hikmat Al-Ahmadie,  Timothy A. Chan,  Ronald Ghossein,  Anuradha Gopalan,  Douglas A. Levine,  Victor Reuter,  Samuel Singer,  Bhuvanesh Singh,  Nguyen Viet Tien,  Thomas Broudy,  Cyrus Mirsaidi,  Praveen Nair,  Paul Drwiega,  Judy Miller,  Jennifer Smith,  Howard Zaren,  Joong-Won Park,  Nguyen Phi Hung,  Electron Kebebew,  W. Marston Linehan,  Adam R. Metwalli,  Karel Pacak,  Peter A. Pinto,  Mark Schiffman,  Laura S. Schmidt,  Cathy D. Vocke,  Nicolas Wentzensen,  Robert Worrell,  Hannah Yang,  Marc Moncrieff,  Chandra Goparaju,  Jonathan Melamed,  Harvey Pass,  Natalia Botnariuc,  Irina Caraman,  Mircea Cernat,  Inga Chemencedji,  Adrian Clipca,  Serghei Doruc,  Ghenadie Gorincioi,  Sergiu Mura,  Maria Pirtac,  Irina Stancul,  Diana Tcaciuc,  Monique Albert,  Iakovina Alexopoulou,  Angel Arnaout,  John Bartlett,  Jay Engel,  Sebastien Gilbert,  Jeremy Parfitt,  Harman Sekhon,  George Thomas,  Doris M. Rassl,  Robert C. Rintoul,  Carlo Bifulco,  Raina Tamakawa,  Walter Urba,  Nicholas Hayward,  Henri Timmers,  Anna Antenucci,  Francesco Facciolo,  Gianluca Grazi,  Mirella Marino,  Roberta Merola,  Ronald de Krijger,  Anne-Paule Gimenez-Roqueplo,  Alain Piché,  Simone Chevalier,  Ginette McKercher,  Kivanc Birsoy,  Gene Barnett,  Cathy Brewer,  Carol Farver,  Theresa Naska,  Nathan A. Pennell,  Daniel Raymond,  Cathy Schilero,  Kathy Smolenski,  Felicia Williams,  Carl Morrison,  Jeffrey A. Borgia,  Michael J. Liptay,  Mark Pool,  Christopher W. Seder,  Kerstin Junker,  Larsson Omberg,  Mikhail Dinkin,  George Manikhas,  Domenico Alvaro,  Maria Consiglia Bragazzi,  Vincenzo Cardinale,  Guido Carpino,  Eugenio Gaudio,  David Chesla,  Sandra Cottingham,  Michael Dubina,  Fedor Moiseenko,  Renumathy Dhanasekaran,  Karl-Friedrich Becker,  Klaus-Peter Janssen,  Julia Slotta-Huspenina,  Mohamed H. Abdel-Rahman,  Dina Aziz,  Sue Bell,  Colleen M. Cebulla,  Amy Davis,  Rebecca Duell,  J. Bradley Elder,  Joe Hilty,  Bahavna Kumar,  James Lang,  Norman L. Lehman,  Randy Mandt,  Phuong Nguyen,  Robert Pilarski,  Karan Rai,  Lynn Schoenfield,  Kelly Senecal,  Paul Wakely,  Paul Hansen,  Ronald Lechan,  James Powers,  Arthur Tischler,  William E. Grizzle,  Katherine C. Sexton,  Alison Kastl,  Joel Henderson,  Sima Porten,  Jens Waldmann,  Martin Fassnacht,  Sylvia L. Asa,  Dirk Schadendorf,  Marta Couce,  Markus Graefen,  Hartwig Huland,  Guido Sauter,  Thorsten Schlomm,  Ronald Simon,  Pierre Tennstedt,  Oluwole Olabode,  Mark Nelson,  Oliver Bathe,  Peter R. Carroll,  June M. Chan,  Philip Disaia,  Pat Glenn,  Robin K. Kelley,  Charles N. Landen,  Joanna Phillips,  Michael Prados,  Jeffry Simko,  Karen Smith-McCune,  Scott VandenBerg,  Kevin Roggin,  Ashley Fehrenbach,  Ady Kendler,  Suzanne Sifri,  Ruth Steele,  Antonio Jimeno,  Francis Carey,  Ian Forgie,  Massimo Mannelli,  Michael Carney,  Brenda Hernandez,  Benito Campos,  Christel Herold-Mende,  Christin Jungk,  Andreas Unterberg,  Andreas von Deimling,  Aaron Bossler,  Joseph Galbraith,  Laura Jacobus,  Michael Knudson,  Tina Knutson,  Deqin Ma,  Mohammed Milhem,  Rita Sigmund,  Andrew K. Godwin,  Rashna Madan,  Howard G. Rosenthal,  Clement Adebamowo,  Sally N. Adebamowo,  Alex Boussioutas,  David Beer,  Thomas Giordano,  Anne-Marie Mes-Masson,  Fred Saad,  Therese Bocklage,  Lisa Landrum,  Robert Mannel,  Kathleen Moore,  Katherine Moxley,  Russel Postier,  Joan Walker,  Rosemary Zuna,  Michael Feldman,  Federico Valdivieso,  Rajiv Dhir,  James Luketich,  Edna M. Mora Pinero,  Mario Quintero-Aguilo,  Carlos Gilberto Carlotti,  Jose Sebastião Dos Santos,  Rafael Kemp,  Ajith Sankarankuty,  Daniela Tirapelli,  James Catto,  Kathy Agnew,  Elizabeth Swisher,  Jenette Creaney,  Bruce Robinson,  Carl Simon Shelley,  Eryn M. Godwin,  Sara Kendall,  Cassaundra Shipman,  Carol Bradford,  Thomas Carey,  Andrea Haddad,  Jeffey Moyer,  Lisa Peterson,  Mark Prince,  Laura Rozek,  Gregory Wolf,  Rayleen Bowman,  Kwun M. Fong,  Ian Yang,  Robert Korst,  W. Kimryn Rathmell,  J. Leigh Fantacone-Campbell,  Jeffrey A. Hooke,  Albert J. Kovatich,  Craig D. Shriver,  John DiPersio,  Bettina Drake,  Ramaswamy Govindan,  Sharon Heath,  Timothy Ley,  Brian Van Tine,  Peter Westervelt,  Mark A. Rubin,  Jung Il Lee,  Natália D. Aredes,  Armaz Mariamidze
Cell Reports  ·  01 Apr 2018
A Multimodal Strategy Used by a Large c-di-GMP Network
Kurt M. Dahlstrom,  Alan J. Collins,  Georgia Doing,  Jaclyn N. Taroni,  Timothy J. Gauvin,  Casey S. Greene,  Deborah A. Hogan,  George A. O'Toole
Journal of Bacteriology  ·  26 Mar 2018
Sci-Hub provides access to nearly all scholarly literature
Daniel S Himmelstein,  Ariel Rodriguez Romero,  Jacob G Levernier,  Thomas Anthony Munro,  Stephen Reid McLaughlin,  Bastian Greshake Tzovaras,  Casey S Greene
eLife  ·  01 Mar 2018
A parasite's perspective on data sharing
YoSon Park,  Casey S Greene
GigaScience  ·  05 Nov 2018
Bayesian deep learning for single-cell analysis
Gregory P. Way,  Casey S. Greene
Nature Methods  ·  30 Nov 2018
Enter the Matrix: Factorization Uncovers Knowledge from Omics
Genevieve L. Stein-O’Brien,  Raman Arora,  Aedin C. Culhane,  Alexander V. Favorov,  Lana X. Garmire,  Casey S. Greene,  Loyal A. Goff,  Yifeng Li,  Aloune Ngom,  Michael F. Ochs,  Yanxun Xu,  Elana J. Fertig
Trends in Genetics  ·  01 Oct 2018
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses
Lia X Harrington,  Gregory P Way,  Jennifer A Doherty,  Casey S Greene
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  ·  01 Jan 2018
Advances in Text Mining and Visualization for Precision Medicine.
Graciela Gonzalez-Hernandez,  Abeed Sarker,  Karen O'Connor,  Casey Greene,  Hongfang Liu
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  ·  01 Jan 2018

2017

Implicating candidate genes at GWAS signals by leveraging topologically associating domains
Gregory P Way,  Daniel W Youngstrom,  Kurt D Hankenson,  Casey S Greene,  Struan FA Grant
European Journal of Human Genetics  ·  09 Aug 2017
Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes
Jennifer Anne Doherty,  Lauren Cole Peres,  Chen Wang,  Gregory P. Way,  Casey S. Greene,  Joellen M. Schildkraut
Current Epidemiology Reports  ·  10 Jul 2017
Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks
Jie Tan,  Georgia Doing,  Kimberley A. Lewis,  Courtney E. Price,  Kathleen M. Chen,  Kyle C. Cady,  Barret Perchuk,  Michael T. Laub,  Deborah A. Hogan,  Casey S. Greene
Cell Systems  ·  01 Jul 2017
Data-Sharing Models
New England Journal of Medicine  ·  08 Jun 2017
Celebrating parasites
Casey S Greene,  Lana X Garmire,  Jack A Gilbert,  Marylyn D Ritchie,  Lawrence E Hunter
Nature Genetics  ·  01 Apr 2017
A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis
Jaclyn N. Taroni,  Casey S. Greene,  Viktor Martyanov,  Tammara A. Wood,  Romy B. Christmann,  Harrison W. Farber,  Robert A. Lafyatis,  Christopher P. Denton,  Monique E. Hinchcliff,  Patricia A. Pioli,  J. Matthew Mahoney,  Michael L. Whitfield
Genome Medicine  ·  23 Mar 2017
Reproducibility of computational workflows is automated using continuous analysis
Brett K Beaulieu-Jones,  Casey S Greene
Nature Biotechnology  ·  13 Mar 2017
Tell me your neighbors, and I will tell you what you are
Casey S. Greene
Science Translational Medicine  ·  08 Feb 2017
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
Gregory P. Way,  Robert J. Allaway,  Stephanie J. Bouley,  Camilo E. Fadul,  Yolanda Sanchez,  Casey S. Greene
BMC Genomics  ·  06 Feb 2017
A Pilot Characterization of the Human Chronobiome
Carsten Skarke,  Nicholas F. Lahens,  Seth D. Rhoades,  Amy Campbell,  Kyle Bittinger,  Aubrey Bailey,  Christian Hoffmann,  Randal S. Olson,  Lihong Chen,  Guangrui Yang,  Thomas S. Price,  Jason H. Moore,  Frederic D. Bushman,  Casey S. Greene,  Gregory R. Grant,  Aalim M. Weljie,  Garret A. FitzGerald
Scientific Reports  ·  07 Dec 2017
ADAGE signature analysis: differential expression analysis with data-defined gene sets
Jie Tan,  Matthew Huyck,  Dongbo Hu,  René A. Zelaya,  Deborah A. Hogan,  Casey S. Greene
BMC Bioinformatics  ·  22 Nov 2017
Tribe: The collaborative platform for reproducible web-based analysis of gene sets
René A. Zelaya,  Aaron K. Wong,  Alex T. Frase,  Marylyn D. Ritchie,  Casey S. Greene
bioRxiv  ·  09 Oct 2017
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules
Xiaohui Yao,  Jingwen Yan,  Kefei Liu,  Sungeun Kim,  Kwangsik Nho,  Shannon L. Risacher,  Casey S. Greene,  Jason H. Moore,  Andrew J. Saykin,  Li Shen,  
Bioinformatics  ·  15 Oct 2017
NO-BOUNDARY THINKING IN BIOINFORMATICS
JASON H. MOORE,  STEVEN F. JENNINGS,  CASEY S. GREENE,  LAWRENCE E. HUNTER,  ANDY D. PERKINS,  CLARLYNDA WILLIAMS-DEVANE,  DONALD C. WUNSCH,  ZHONGMING ZHAO,  XIUZHEN HUANG
World Scientific Pub Co Pte Lt  ·  01 Jan 2017

2016

Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations
Arjun Krishnan,  Jaclyn N. Taroni,  Casey S. Greene
Current Genetic Medicine Reports  ·  09 Sep 2016
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Yuxiang Jiang,  Tal Ronnen Oron,  Wyatt T. Clark,  Asma R. Bankapur,  Daniel D’Andrea,  Rosalba Lepore,  Christopher S. Funk,  Indika Kahanda,  Karin M. Verspoor,  Asa Ben-Hur,  Da Chen Emily Koo,  Duncan Penfold-Brown,  Dennis Shasha,  Noah Youngs,  Richard Bonneau,  Alexandra Lin,  Sayed M. E. Sahraeian,  Pier Luigi Martelli,  Giuseppe Profiti,  Rita Casadio,  Renzhi Cao,  Zhaolong Zhong,  Jianlin Cheng,  Adrian Altenhoff,  Nives Skunca,  Christophe Dessimoz,  Tunca Dogan,  Kai Hakala,  Suwisa Kaewphan,  Farrokh Mehryary,  Tapio Salakoski,  Filip Ginter,  Hai Fang,  Ben Smithers,  Matt Oates,  Julian Gough,  Petri Törönen,  Patrik Koskinen,  Liisa Holm,  Ching-Tai Chen,  Wen-Lian Hsu,  Kevin Bryson,  Domenico Cozzetto,  Federico Minneci,  David T. Jones,  Samuel Chapman,  Dukka BKC,  Ishita K. Khan,  Daisuke Kihara,  Dan Ofer,  Nadav Rappoport,  Amos Stern,  Elena Cibrian-Uhalte,  Paul Denny,  Rebecca E. Foulger,  Reija Hieta,  Duncan Legge,  Ruth C. Lovering,  Michele Magrane,  Anna N. Melidoni,  Prudence Mutowo-Meullenet,  Klemens Pichler,  Aleksandra Shypitsyna,  Biao Li,  Pooya Zakeri,  Sarah ElShal,  Léon-Charles Tranchevent,  Sayoni Das,  Natalie L. Dawson,  David Lee,  Jonathan G. Lees,  Ian Sillitoe,  Prajwal Bhat,  Tamás Nepusz,  Alfonso E. Romero,  Rajkumar Sasidharan,  Haixuan Yang,  Alberto Paccanaro,  Jesse Gillis,  Adriana E. Sedeño-Cortés,  Paul Pavlidis,  Shou Feng,  Juan M. Cejuela,  Tatyana Goldberg,  Tobias Hamp,  Lothar Richter,  Asaf Salamov,  Toni Gabaldon,  Marina Marcet-Houben,  Fran Supek,  Qingtian Gong,  Wei Ning,  Yuanpeng Zhou,  Weidong Tian,  Marco Falda,  Paolo Fontana,  Enrico Lavezzo,  Stefano Toppo,  Carlo Ferrari,  Manuel Giollo,  Damiano Piovesan,  Silvio C.E. Tosatto,  Angela del Pozo,  José M. Fernández,  Paolo Maietta,  Alfonso Valencia,  Michael L. Tress,  Alfredo Benso,  Stefano Di Carlo,  Gianfranco Politano,  Alessandro Savino,  Hafeez Ur Rehman,  Matteo Re,  Marco Mesiti,  Giorgio Valentini,  Joachim W. Bargsten,  Aalt D. J. van Dijk,  Branislava Gemovic,  Sanja Glisic,  Vladmir Perovic,  Veljko Veljkovic,  Nevena Veljkovic,  Danillo C. Almeida-e-Silva,  Ricardo Z. N. Vencio,  Malvika Sharan,  Jörg Vogel,  Lakesh Kansakar,  Shanshan Zhang,  Slobodan Vucetic,  Zheng Wang,  Michael J. E. Sternberg,  Mark N. Wass,  Rachael P. Huntley,  Maria J. Martin,  Claire O’Donovan,  Peter N. Robinson,  Yves Moreau,  Anna Tramontano,  Patricia C. Babbitt,  Steven E. Brenner,  Michal Linial,  Christine A. Orengo,  Burkhard Rost,  Casey S. Greene,  Sean D. Mooney,  Iddo Friedberg,  Predrag Radivojac
Genome Biology  ·  07 Sep 2016
A stromal focus reveals tumor immune signatures
Casey S. Greene
Science Translational Medicine  ·  28 Sep 2016
Gut check
Casey S. Greene
Science Translational Medicine  ·  17 Aug 2016
The future is unsupervised
Casey S. Greene
Science Translational Medicine  ·  06 Jul 2016
Nothing but a hound dog
Casey S. Greene
Science Translational Medicine  ·  25 May 2016
CoINcIDE: All together now
Casey S. Greene
Science Translational Medicine  ·  13 Apr 2016
Genetic Association–Guided Analysis of Gene Networks for the Study of Complex Traits
Casey S. Greene,  Daniel S. Himmelstein
Circulation: Cardiovascular Genetics  ·  01 Apr 2016
Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites
Robert J. Allaway,  Dawn A. Fischer,  Francine B. de Abreu,  Timothy B. Gardner,  Stuart R. Gordon,  Richard J. Barth,  Thomas A. Colacchio,  Matthew Wood,  Balint Z. Kacsoh,  Stephanie J. Bouley,  Jingxuan Cui,  Joanna Hamilton,  Jungbin A. Choi,  Joshua T. Lange,  Jason D. Peterson,  Vijayalakshmi Padmanabhan,  Craig R. Tomlinson,  Gregory J. Tsongalis,  Arief A. Suriawinata,  Casey S. Greene,  Yolanda Sanchez,  Kerrington D. Smith
Oncotarget  ·  25 Feb 2016
Cheap-seq
C. S. Greene
Science Translational Medicine  ·  21 Dec 2016
Semi-supervised learning of the electronic health record for phenotype stratification
Brett K. Beaulieu-Jones,  Casey S. Greene
Journal of Biomedical Informatics  ·  01 Dec 2016
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes
Gregory P. Way,  James Rudd,  Chen Wang,  Habib Hamidi,  Brooke L. Fridley,  Gottfried E. Konecny,  Ellen L. Goode,  Casey S. Greene,  Jennifer A. Doherty
G3: Genes|Genomes|Genetics  ·  01 Dec 2016
How to know what we dont
C. S. Greene
Science Translational Medicine  ·  09 Nov 2016
Pathway and network-based strategies to translate genetic discoveries into effective therapies
Casey S. Greene,  Benjamin F. Voight
Human Molecular Genetics  ·  01 Oct 2016
Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer’s disease: a study of ADNI cohorts
Ailin Song,  Jingwen Yan,  Sungeun Kim,  Shannon Leigh Risacher,  Aaron K. Wong,  Andrew J. Saykin,  Li Shen,  Casey S. Greene
BioData Mining  ·  19 Jan 2016
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery
Graciela H. Gonzalez,  Tasnia Tahsin,  Britton C. Goodale,  Anna C. Greene,  Casey S. Greene
Briefings in Bioinformatics  ·  01 Jan 2016
Adapting bioinformatics curricula for big data
Anna C. Greene,  Kristine A. Giffin,  Casey S. Greene,  Jason H. Moore
Briefings in Bioinformatics  ·  01 Jan 2016
COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES
Casey S Greene,  James A Foster,  Bruce A Stanton,  Deborah A Hogan,  Yana Bromberg
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  ·  01 Jan 2016

2015

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways
Heather J. Cordell,  Younghun Han,  George F. Mells,  Yafang Li,  Gideon M. Hirschfield,  Casey S. Greene,  Gang Xie,  Brian D. Juran,  Dakai Zhu,  David C. Qian,  James A. B. Floyd,  Katherine I. Morley,  Daniele Prati,  Ana Lleo,  Daniele Cusi,  M. Eric Gershwin,  Carl A. Anderson,  Konstantinos N. Lazaridis,  Pietro Invernizzi,  Michael F. Seldin,  Richard N. Sandford,  Christopher I. Amos,  Katherine A. Siminovitch,   ,   ,  
Nature Communications  ·  22 Sep 2015
Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study
Jiang Gui,  Casey S. Greene,  Con Sullivan,  Walter Taylor,  Jason H. Moore,  Carol Kim
BioData Mining  ·  17 Jun 2015
Understanding multicellular function and disease with human tissue-specific networks
Casey S Greene,  Arjun Krishnan,  Aaron K Wong,  Emanuela Ricciotti,  Rene A Zelaya,  Daniel S Himmelstein,  Ran Zhang,  Boris M Hartmann,  Elena Zaslavsky,  Stuart C Sealfon,  Daniel I Chasman,  Garret A FitzGerald,  Kara Dolinski,  Tilo Grosser,  Olga G Troyanskaya
Nature Genetics  ·  27 Apr 2015
Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions
David C. Qian,  Jinyoung Byun,  Younghun Han,  Casey S. Greene,  John K. Field,  Rayjean J. Hung,  Yonathan Brhane,  John R. Mclaughlin,  Gordon Fehringer,  Maria Teresa Landi,  Albert Rosenberger,  Heike Bickeböller,  Jyoti Malhotra,  Angela Risch,  Joachim Heinrich,  David J. Hunter,  Brian E. Henderson,  Christopher A. Haiman,  Fredrick R. Schumacher,  Rosalind A. Eeles,  Douglas F. Easton,  Daniela Seminara,  Christopher I. Amos
Human Molecular Genetics  ·  20 Dec 2015
Leveraging global gene expression patterns to predict expression of unmeasured genes
James Rudd,  René A. Zelaya,  Eugene Demidenko,  Ellen L. Goode,  Casey S. Greene,  Jennifer A. Doherty
BMC Genomics  ·  15 Dec 2015
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
J. Matthew Mahoney,  Jaclyn Taroni,  Viktor Martyanov,  Tammara A. Wood,  Casey S. Greene,  Patricia A. Pioli,  Monique E. Hinchcliff,  Michael L. Whitfield
PLoS Computational Biology  ·  08 Jan 2015
Targeted exploration and analysis of large cross-platform human transcriptomic compendia
Qian Zhu,  Aaron K Wong,  Arjun Krishnan,  Miriam R Aure,  Alicja Tadych,  Ran Zhang,  David C Corney,  Casey S Greene,  Lars A Bongo,  Vessela N Kristensen,  Moses Charikar,  Kai Li,  Olga G Troyanskaya
Nature Methods  ·  12 Jan 2015
Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders
Jie Tan,  Matthew Ung,  Chao Cheng,  Casey S Greene
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  ·  01 Jan 2015

2014

Computational genetics analysis of grey matter density in Alzheimer’s disease
Amanda L Zieselman,  Jonathan M Fisher,  Ting Hu,  Peter C Andrews,  Casey S Greene,  Li Shen,  Andrew J Saykin,  Jason H Moore,  
BioData Mining  ·  22 Aug 2014
Big Data Bioinformatics
Casey S. Greene,  Jie Tan,  Matthew Ung,  Jason H. Moore,  Chao Cheng
Journal of Cellular Physiology  ·  01 Dec 2014
Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity
Nadia M Penrod,  Casey S Greene,  Jason H Moore
Genome Medicine  ·  01 Jan 2014

2013

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes
Christopher Y. Park,  Aaron K. Wong,  Casey S. Greene,  Jessica Rowland,  Yuanfang Guan,  Lars A. Bongo,  Rebecca D. Burdine,  Olga G. Troyanskaya
PLoS Computational Biology  ·  14 Mar 2013
Defining cell-type specificity at the transcriptional level in human disease
Wenjun Ju,  Casey S. Greene,  Felix Eichinger,  Viji Nair,  Jeffrey B. Hodgin,  Markus Bitzer,  Young-suk Lee,  Qian Zhu,  Masami Kehata,  Min Li,  Song Jiang,  Maria Pia Rastaldi,  Clemens D. Cohen,  Olga G. Troyanskaya,  Matthias Kretzler
Genome Research  ·  01 Nov 2013
Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments
Jie Tan,  Gavin D. Grant,  Michael L. Whitfield,  Casey S. Greene
Lecture Notes in Computer Science  ·  01 Jan 2013

2012

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
Aaron K. Wong,  Christopher Y. Park,  Casey S. Greene,  Lars A. Bongo,  Yuanfang Guan,  Olga G. Troyanskaya
Nucleic Acids Research  ·  01 Jul 2012
Accurate evaluation and analysis of functional genomics data and methods
Casey S. Greene,  Olga G. Troyanskaya
Annals of the New York Academy of Sciences  ·  01 Jul 2012
Chapter 2: Data-Driven View of Disease Biology
Casey S. Greene,  Olga G. Troyanskaya
PLoS Computational Biology  ·  27 Dec 2012

More

More on PubMed More on Google Scholar

The citations on this page were generated automatically from just identifiers using the Manubot cite utility developed right here in the Greene Lab!


Our recent research, compressed into sketch form by YoSon Park during the 2016 [#PennGenRetreat](https://twitter.com/search?f=tweets&vertical=default&q=%23PennGenRetreat&src=typd).
Our recent research, compressed into sketch form by YoSon Park during the 2016 #PennGenRetreat.