Casey S. Greene

Overview

Best Publications

• Oncogenic Signaling Pathways in The Cancer Genome Atlas

  Francisco Sanchez-Vega;Marco Mina;Joshua Armenia;Walid K. Chatila

  3193
  Citations

• Opportunities and obstacles for deep learning in biology and medicine.

  Travers Ching;Daniel S. Himmelstein;Brett K. Beaulieu-Jones;Alexandr A. Kalinin

  2372
  Citations

• Understanding multicellular function and disease with human tissue-specific networks

  Casey S Greene;Arjun Krishnan;Aaron K Wong;Emanuela Ricciotti

  961
  Citations

• The importance of transparency and reproducibility in artificial intelligence research

  Benjamin Haibe-Kains;George Alexandru Adam;Ahmed Hosny;Farnoosh Khodakarami

  474
  Citations

• An expanded evaluation of protein function prediction methods shows an improvement in accuracy

  Yuxiang Jiang;Tal Ronnen Oron;Wyatt T. Clark;Asma R. Bankapur

  453
  Citations

• 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

  449
  Citations

• Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing.

  Brett K. Beaulieu-Jones;Zhiwei Steven Wu;Chris Williams;Ran Lee

  416
  Citations

• 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

  333
  Citations

• Failure to Replicate a Genetic Association May Provide Important Clues About Genetic Architecture

  Casey S. Greene;Nadia M. Penrod;Scott M. Williams;Jason H. Moore

  308
  Citations

• An expanded evaluation of protein function prediction methods shows an improvement in accuracy

  Yuxiang Jiang;Tal Ronnen Oron;Wyatt T Clark;Asma R Bankapur

  302
  Citations

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

  Gregory P. Way;Casey S. Greene

  294
  Citations

• Defining cell-type specificity at the transcriptional level in human disease.

  Wenjun Ju;Casey S. Greene;Casey S. Greene;Felix Eichinger;Viji Nair

  278
  Citations

• Enter the Matrix: Factorization Uncovers Knowledge from Omics

  Genevieve L. Stein-O’Brien;Raman Arora;Aedin C. Culhane;Alexander V. Favorov

  252
  Citations

• Big Data Bioinformatics

  Casey S. Greene;Jie Tan;Matthew Ung;Jason H. Moore

  246
  Citations

• Constructing knowledge graphs and their biomedical applications.

  David N. Nicholson;Casey S. Greene

  246
  Citations

• Semi-supervised learning of the electronic health record for phenotype stratification.

  Brett K Beaulieu-Jones;Casey S Greene

  203
  Citations

• Reproducibility standards for machine learning in the life sciences.

  Benjamin J. Heil;Michael M. Hoffman;Florian Markowetz;Su In Lee

  199
  Citations

• Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery

  Graciela H. Gonzalez;Tasnia Tahsin;Britton C. Goodale;Anna C. Greene

  195
  Citations

• Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

  Gregory P Way;Francisco Sanchez-Vega;Konnor La;Joshua Armenia

  179
  Citations

• Spatially uniform relieff (SURF) for computationally-efficient filtering of gene-gene interactions.

  Casey S Greene;Nadia M Penrod;Jeff Kiralis;Jason H Moore

  173
  Citations

• 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 Ailo Bongo

  171
  Citations

• Transparency and reproducibility in artificial intelligence.

  Benjamin Haibe-Kains;George Alexandru Adam;Ahmed Hosny;Farnoosh Khodakarami;Farnoosh Khodakarami

  82
  Citations

• Additional file 1 of An expanded evaluation of protein function prediction methods shows an improvement in accuracy

  Yuxiang Jiang;Tal Ronnen Oron;Wyatt T. Clark;Asma R. Bankapur

  1
  Citations