Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. - Scott H. Robertson; Chris K. Smith; Anna L. Langhans; Sara E. McLinden; Matthew A. Oberhardt; Karoly R. Jakab; Bette Dzamba; Douglas W. DeSimone; Jason A. Papin; Shayn M. Peirce (BMC Syst. Biol., 2007)

Predicting biological system objectives de novo from internal state measurements. - Erwin P. Gianchandani; Matthew A. Oberhardt; Anthony P. Burgard; Costas D. Maranas; Jason A. Papin (BMC Bioinform., 2008)

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology. - Jacek Puchalka; Matthew A. Oberhardt; Miguel Godinho; Agata Bielecka; Daniela Regenhardt; Kenneth N. Timmis; Jason A. Papin; Vítor A. P. Martins dos Santos (PLoS Comput. Biol., 2008)

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis. - Matthew A. Oberhardt; Jacek Puchalka; Vítor A. P. Martins dos Santos; Jason A. Papin (PLoS Comput. Biol., 2011)

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. - Raphy Zarecki; Matthew A. Oberhardt; Leah Reshef; Uri Gophna; Eytan Ruppin (PLoS Comput. Biol., 2014)

Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. - Noam Auslander; Allon Wagner; Matthew A. Oberhardt; Eytan Ruppin (PLoS Comput. Biol., 2016)

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. - Matthew A. Oberhardt; Raphy Zarecki; Leah Reshef; Fangfang Xia; Miquel Duran-Frigola; Rachel Schreiber; Christopher S. Henry; Nir Ben-Tal; Daniel J. Dwyer; Uri Gophna; Eytan Ruppin (PLoS Comput. Biol., 2016)

Reducing Variation in Core Measures data through Automation. - Matthew A. Oberhardt; Hojjat Salmasian; Dena Goffman; David K. Vawdrey (AMIA, 2017)

Predicting Intramuscular Injection of Antipsychotics in the Psychiatric Emergency Service. - Matthew A. Oberhardt; Dianna Dragatsi; David K. Vawdrey; Sean Luo (AMIA, 2018)

Developing an informatics framework for responding to an outbreak of Burkholderia cenocepacia. - Matthew A. Oberhardt; Lisa Saiman; William Greendyke; Alexandra Hill-Ricciuti; David K. Vawdrey; Yoko Furuya (AMIA, 2018)

A principled framework for phenotyping postpartum hemorrhage across multiple levels of severity. - Matthew A. Oberhardt; Alexander Friedman; Rimma Perotte; Jean-Ju Sheen; Alan Kessler; David K. Vawdrey; Robert A. Green; Mary D'Alton; Dena Goffman (AMIA, 2019)