CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. - Adam A. Margolin; Joel Greshock; Tara L. Naylor; Yael Mosse; John M. Maris; Graham Bignell; Alexander I. Saeed; John Quackenbush; Barbara L. Weber (Bioinform., 2005)

Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. - Kai Wang 045; Ilya Nemenman; Nilanjana Banerjee; Adam A. Margolin; Andrea Califano (RECOMB, 2006)

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context. - Adam A. Margolin; Ilya Nemenman; Katia Basso; Chris Wiggins 001; Gustavo Stolovitzky; Riccardo Dalla Favera; Andrea Califano (BMC Bioinform., 2006)

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding. - Adam A. Margolin; Teresa Palomero; Adolfo A. Ferrando; Andrea Califano; Gustavo Stolovitzky (BMC Bioinform., 2007)

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)

Kernelized Bayesian Transfer Learning. - Mehmet Gönen; Adam A. Margolin (AAAI, 2014)

Localized Data Fusion for Kernel k-Means Clustering with Application to Cancer Biology. - Mehmet Gönen; Adam A. Margolin (NIPS, 2014)

Systematic Assessment of Analytical Methods for Drug Sensitivity Prediction from Cancer Cell Line Data. - In Sock Jang; Elias Chaibub Neto; Justin Guinney; Stephen H. Friend; Adam A. Margolin (Pacific Symposium on Biocomputing, 2014)

The Stream Algorithm: Computationally Efficient Ridge-Regression via Bayesian Model Averaging, and Applications to Pharmacogenomic Prediction of Cancer Cell Line Sensitivity. - Elias Chaibub Neto; In Sock Jang; Stephen H. Friend; Adam A. Margolin (Pacific Symposium on Biocomputing, 2014)

Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. - Mehmet Gönen; Adam A. Margolin (Bioinform., 2014)

Session Introduction. - Søren Brunak; Francisco M. de la Vega; Adam A. Margolin; Benjamin J. Raphael; Gunnar Rätsch; Joshua M. Stuart (Pacific Symposium on Biocomputing, 2015)

Stepwise Group Sparse Regression (SGSR): Gene-Set-Based Pharmacogenomic Predictive Models with Stepwise Selection of Functional Priors. - In Sock Jang; Rodrigo Dienstmann; Adam A. Margolin; Justin Guinney (Pacific Symposium on Biocomputing, 2015)

The NIH BD2K center for big data in translational genomics. - Benedict Paten; Mark Diekhans; Brian J. Druker; Stephen H. Friend; Justin Guinney; Nadine Gassner; Mitchell Guttman; W. James Kent; Patrick Mantey; Adam A. Margolin; Matt Massie; Adam M. Novak; et al. (J. Am. Medical Informatics Assoc., 2015)

Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics. - Young Hwan Chang; Guillaume Thibault; Vahid Azimi; Brett Johnson; Danielle Jorgens; Jason Link; Adam A. Margolin; Joe W. Gray (EMBC, 2016)

Deep learning based Nucleus Classification in pancreas histological images. - Young Hwan Chang; Guillaume Thibault; Owen Madin; Vahid Azimi; Cole Meyers; Brett Johnson; Jason Link; Adam A. Margolin; Joe W. Gray (EMBC, 2017)

Multiplexed immunohistochemistry image analysis using sparse coding. - Young Hwan Chang; Takahiro Tsujikawa; Adam A. Margolin; Lisa M. Coussens; Joe W. Gray (EMBC, 2017)

Breast cancer histopathology image analysis pipeline for tumor purity estimation. - Vahid Azimi; Young Hwan Chang; Guillaume Thibault; Jaclyn Smith; Takahiro Tsujikawa; Benjamin Kukull; Bradden Jensen; Christopher Corless; Adam A. Margolin; Joe W. Gray (ISBI, 2017)

Integrative analysis on histopathological image for identifying cellular heterogeneity. - Young Hwan Chang; Guillaume Thibault; Brett Johnson; Adam A. Margolin; Joe W. Gray (Digital Pathology, 2017)

Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies. - Olga Nikolova; Russell Moser; Christopher Kemp; Mehmet Gönen; Adam A. Margolin (Bioinform., 2017)

SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks. - Erik A. Burlingame; Adam A. Margolin; Joe W. Gray; Young Hwan Chang (Digital Pathology, 2018)

Valection: design optimization for validation and verification studies. - Christopher I Cooper; Delia Yao; Dorota H. Sendorek; Takafumi N. Yamaguchi; Christine P'ng; Kathleen E. Houlahan; Cristian Caloian; Michael Fraser; Kyle Ellrott; Adam A. Margolin; Robert G. Bristow; Joshua M. Stuart; et al. (BMC Bioinform., 2018)

Germline contamination and leakage in whole genome somatic single nucleotide variant detection. - Dorota H. Sendorek; Cristian Caloian; Kyle Ellrott; J. Christopher Bare; Takafumi N. Yamaguchi; Adam D. Ewing; Kathleen E. Houlahan; Thea C. Norman; Adam A. Margolin; Joshua M. Stuart; Paul C. Boutros (BMC Bioinform., 2018)

svpluscnv: analysis and visualization of complex structural variation data. - Gonzalo López; Laura E. Egolf; Federico M. Giorgi; Sharon J. Diskin; Adam A. Margolin (Bioinform., 2021)