Microarray Standard Data Set and Figures of Merit for Comparing Data Processing Methods and Experiment Designs. - Yudong D. He; Hongyue Dai; Eric E. Schadt; Guy Cavet; Stephen W. Edwards; Sergey B. Stepaniants; Sven Duenwald; Robert Kleinhanz; Allan R. Jones; Daniel D. Shoemaker; Roland B. Stoughton (Bioinform., 2003)

Statistical power of phylo-HMM for evolutionarily conserved element detection. - Xiaodan Fan; Jun Zhu; Eric E. Schadt; Jun S. Liu (BMC Bioinform., 2007)

Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations. - Jun Zhu; Matthew C. Wiener; Chunsheng Zhang; Arthur Fridman; Eric Minch; Pek Y. Lum; Jeffrey R. Sachs; Eric E. Schadt (PLoS Comput. Biol., 2007)

Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases. - Kai Wang 045; Manikandan Narayanan; Hua Zhong; Martin Tompa; Eric E. Schadt; Jun Zhu (PLoS Comput. Biol., 2009)

Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets. - Manikandan Narayanan; Adrian Vetta; Eric E. Schadt; Jun Zhu (PLoS Comput. Biol., 2010)

An Integrative Multi-Network and Multi-Classifier Approach to Predict Genetic Interactions. - Gaurav Pandey 002; Bin Zhang 002; Aaron N. Chang; Chad L. Myers; Jun Zhu; Vipin Kumar 001; Eric E. Schadt (PLoS Comput. Biol., 2010)

A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules. - Wei Zhang; Jun Zhu; Eric E. Schadt; Jun S. Liu (PLoS Comput. Biol., 2010)

Characterizing Dynamic Changes in the Human Blood Transcriptional Network. - Jun Zhu; Yanqing Chen; Amy S. Leonardson; Kai Wang 045; John R. Lamb; Valur Emilsson; Eric E. Schadt (PLoS Comput. Biol., 2010)

Correction for Hidden Confounders in the Genetic Analysis of Gene Expression (Abstract). - Jennifer Listgarten; Carl Myers Kadie; Eric E. Schadt; David Heckerman (UAI, 2011)

COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. - Haisu Ma; Eric E. Schadt; Lee M. Kaplan; Hongyu Zhao 003 (Bioinform., 2011)

Inferring causal genomic alterations in breast cancer using gene expression data. - Linh M. Tran; Bin Zhang 002; Zhan Zhang; Chunsheng Zhang; Tao Xie 002; John R. Lamb; Hongyue Dai; Eric E. Schadt; Jun Zhu (BMC Syst. Biol., 2011)

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. - Kenneth Lo; Adrian E. Raftery; Kenneth M. Dombek; Jun Zhu; Eric E. Schadt; Roger Eugene Bumgarner; Ka Yee Yeung (BMC Syst. Biol., 2012)

Mining the digital universe of data to develop personalized cancer therapies. - Eric E. Schadt (KDD, 2013)

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling. - Erhan Bilal; Janusz Dutkowski; Justin Guinney; In Sock Jang; Benjamin A. Logsdon; Gaurav Pandey 002; Benjamin A. Sauerwine; Yishai Shimoni; Hans Kristian Moen Vollan; Brigham H. Mecham; Oscar M. Rueda; Jorg Tost; et al. (PLoS Comput. Biol., 2013)

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic. - Zhixing Feng; Gang Fang; Jonas Korlach; Tyson Clark; Khai Luong; Xuegong Zhang; Wing Wong; Eric E. Schadt (PLoS Comput. Biol., 2013)

A data driven approach to diagnosing and treating disease. - Eric E. Schadt (KDD, 2014)

lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R. - Gabriel E. Hoffman; Jason G. Mezey; Eric E. Schadt (Bioinform., 2014)

MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis. - Seungyeul Yoo; Tao Huang; Joshua D. Campbell; Eunjee Lee; Zhidong Tu; Mark W. Geraci; Charles A. Powell; Eric E. Schadt; Avrum Spira; Jun Zhu (PLoS Comput. Biol., 2014)

Causal Inference in Biology Networks with Integrated Belief Propagation. - Rui Chang; Jonathan R. Karr; Eric E. Schadt (Pacific Symposium on Biocomputing, 2015)

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. - Benjamin S. Glicksberg; Li Li 062; Marcus A. Badgeley; Khader Shameer; Roman Kosoy; Noam D. Beckmann; Nam Pho; Jörg Hakenberg; Meng Ma; Kristin L. Ayers; Gabriel E. Hoffman; Shuyu Dan Li; et al. (Bioinform., 2016)

Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers. - Eunjee Lee; Koichi Ito; Yong Zhao; Eric E. Schadt; Hanna Y. Irie; Jun Zhu (Bioinform., 2016)

variancePartition: interpreting drivers of variation in complex gene expression studies. - Gabriel E. Hoffman; Eric E. Schadt (BMC Bioinform., 2016)

Exploring the Reproducibility of Probabilistic Causal Molecular Network Models>. - Ariella Cohain; Aparna A. Divaraniya; Kuixi Zhu; Joseph R. Scarpa; Andrew Kasarskis; Jun Zhu; Rui Chang; Joel T. Dudley; Eric E. Schadt (PSB, 2017)

Identify Cancer Driver Genes Through Shared Mendelian Disease Pathogenic Variants and Cancer Somatic Mutations. - Meng Ma; Changchang Wang; Benjamin S. Glicksberg; Eric E. Schadt; Shuyu Dan Li; Rong Chen 006 (PSB, 2017)

Methods for Clustering Time Series Data Acquired from Mobile Health Apps. - Nicole L. Tignor; Pei Wang 014; Nicholas Genes; Linda Rogers; Steven G. Hershman; Erick R. Scott; Micol Zweig; Yu-Feng Yvonne Chan; Eric E. Schadt (PSB, 2017)

STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts. - Nicholas K. Akers; Eric E. Schadt; Bojan Losic (Bioinform., 2018)

From smartphone to EHR: a case report on integrating patient-generated health data. - Nicholas Genes; Samantha Violante; Christine Cetrangol; Linda Rogers; Eric E. Schadt; Yu-Feng Yvonne Chan (npj Digit. Medicine, 2018)

ORE identifies extreme expression effects enriched for rare variants. - Felix Richter 002; Gabriel E. Hoffman; K. B. Manheimer; Nihir Patel; A J. Sharp; D. McKean; Sarah U. Morton; S. DePalma; J. Gorham; A Kitaygorodksy; George A. Porter; A Giardini; et al. (Bioinform., 2019)

DxTree: a visual analytics tool for hierarchical representation of disease cohort counts for clinical trials. - Mingwei Zhang; Zongzhi Liu; Meng Ma; Kyeryoung Lee; Yun Mai; Scott Jones; Chris Gilman; Ying Ru; Matthew Deitz; Yunrou Gong; Xiang Zhou; Krish Ghosh; et al. (AMIA, 2020)

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness. - Ivan Carcamo-Orive; Marc Y. R. Henrion; Kuixi Zhu; Noam D. Beckmann; Paige Cundiff; Sara Moein; Zenan Zhang; Melissa Alamprese; Sunita L. D'Souza; Martin Wabitsch; Eric E. Schadt; Thomas Quertermous; et al. (PLoS Comput. Biol., 2020)

The Real-World Trend Analysis of Cancer Drugs Empowered by Natural Language Processing. - Meng Ma; Kyeryoung Lee; Yun Mai; Chris Gilman; Zongzhi Liu; Mingwei Zhang; Minghao Li; Arielle Redfern; Tommy Mullaney; Tony Prentice; Paul McDonagh; Qi Pan; et al. (AMIA, 2021)

Applying Bayesian hyperparameter optimization towards accurate and efficient topic modeling in clinical notes. - Minghao Li; Kyeryoung Lee; Zongzhi Liu; Meng Ma; Qi Pan; Rong Chen 006; Eric E. Schadt; Xiaoyan Wang (ICHI, 2021)

Improving postpartum hemorrhage risk prediction using longitudinal electronic medical records. - Amanda B. Zheutlin; Luciana Vieira; Ryan A. Shewcraft; Shilong Li; Zichen Wang 002; Emilio Schadt; Susan Gross; Siobhan M. Dolan; Joanne Stone; Eric E. Schadt; Li Li 062 (J. Am. Medical Informatics Assoc., 2022)

A comprehensive digital phenotype for postpartum hemorrhage. - Amanda B. Zheutlin; Luciana Vieira; Ryan A. Shewcraft; Shilong Li; Zichen Wang 002; Emilio Schadt; Yu-Han Kao; Susan Gross; Siobhan M. Dolan; Joanne Stone; Eric E. Schadt; Li Li 062 (J. Am. Medical Informatics Assoc., 2022)

Better Understanding of the Metamorphosis of Pregnancy (BUMP): protocol for a digital feasibility study in women from preconception to postpartum. - Sarah M. Goodday; E. Karlin; A. Brooks; C. Chapman; Daniel R. Karlin; Luca Foschini 002; E. Kipping; M. Wildman; M. Francis; H. Greenman; Li Li 062; Eric E. Schadt; et al. (npj Digit. Medicine, 2022)

Improving preeclampsia risk prediction by modeling pregnancy trajectories from routinely collected electronic medical record data. - Shilong Li; Zichen Wang 002; Luciana Vieira; Amanda B. Zheutlin; Boshu Ru; Emilio Schadt; Pei Wang 014; Alan B. Copperman; Joanne Stone; Susan Gross; Yu-Han Kao; Yan Kwan Lau; et al. (npj Digit. Medicine, 2022)