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.

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, Sandipan Ray, Lucy D'Agostino McGowan, Anthony Gitter, 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, James Brian Byrd, YoSon Park, Vikas Bansal, Stephen Capone, John J. Dziak, Yuchen Sun, Yanjun Qi, Lamonica Shinholster, Temitayo Lukan, Sergey Knyazev, Dimitri Perrin, Serghei Mangul, Shikta Das, Gregory L. Szeto, Tiago Lubiana

Manubot  ·  17 Nov 2020

COVID19
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

Lukas M. Weber, Ariel A. Hippen, Peter F. Hickey, Kristofer C. Berrett, Jason Gertz, Jennifer Anne Doherty, Casey S. Greene, Stephanie C. Hicks

Cold Spring Harbor Laboratory  ·  07 Nov 2020

cancer single cell ovarian cancer
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

GigaScience  ·  03 Nov 2020

genomics machine learning data integration
Biologically Informed Neural Networks Predict Drug Responses

Casey S. Greene, James C. Costello

Cancer Cell  ·  01 Nov 2020

cancer machine learning
Expanding and Remixing the Metadata Landscape

Ariel A. Hippen, Casey S. Greene

Trends in Cancer  ·  01 Nov 2020

cancer open science machine learning
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

Analysis of ISCB honorees and keynotes reveals disparities

Trang T. Le, Daniel S. Himmelstein, Ariel A. Hippen Anderson, Matthew R. Gazzara, Casey S. Greene

Cold Spring Harbor Laboratory  ·  22 Sep 2020

machine learning diversity
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

Melissa A Haendel, Christopher G Chute, Kenneth Gersing

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
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
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

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

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
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 A. Pippin, Ahmed Elhakeem, Gregory P. Way, Shana E. McCormack, Alessandra Chesi, Jonathan A. Mitchell, Joseph M. Kindler, Denis Baird, April Hartley, Laura Howe, Heidi J. Kalkwarf, Joan M. Lappe, Sumei Lu, Michelle Leonard, Matthew E. Johnson, Hakon Hakonarson, Vicente Gilsanz, John A. Shepherd, Sharon E. Oberfield, Casey S. Greene, Andrea Kelly, Deborah Lawlor, Benjamin F. Voight, Andrew D. Wells, Babette S. Zemel, Kurt Hankenson, Struan F. A. Grant

Cold Spring Harbor Laboratory  ·  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

Cold Spring Harbor Laboratory  ·  13 Feb 2020

genomics rare diseases
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

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

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

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

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

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,

Cold Spring Harbor Laboratory  ·  03 Oct 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

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

Bayesian deep learning for single-cell analysis

Gregory P. Way, Casey S. Greene

Nature Methods  ·  30 Nov 2018

A parasite's perspective on data sharing

YoSon Park, Casey S Greene

GigaScience  ·  05 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

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

Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders

Gregory P. Way, Casey S. Greene

World Scientific Pub Co Pte Lt  ·  01 Jan 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

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

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

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

Cold Spring Harbor Laboratory  ·  09 Oct 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

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

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

A stromal focus reveals tumor immune signatures

Casey S. Greene

Science Translational Medicine  ·  28 Sep 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

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

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

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

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

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

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

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

Big Data Bioinformatics

Casey S. Greene, Jie Tan, Matthew Ung, Jason H. Moore, Chao Cheng

Journal of Cellular Physiology  ·  01 Dec 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

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

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

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

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

Chapter 2: Data-Driven View of Disease Biology

Casey S. Greene, Olga G. Troyanskaya

PLoS Computational Biology  ·  27 Dec 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

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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.