Bayesian infinite mixture model based clustering of gene expression profiles. - Mario Medvedovic; Siva Sivaganesan (Bioinform., 2002)

Bayesian Model-Averaging in Unsupervised Learning From Microarray Data. - Mario Medvedovic; Junhai Guo (BIOKDD, 2004)

Bayesian mixture model based clustering of replicated microarray data. - Mario Medvedovic; Ka Yee Yeung; Roger Eugene Bumgarner (Bioinform., 2004)

Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset. - Xiangdong Liu; Siva Sivaganesan; Ka Yee Yeung; Junhai Guo; Roger Eugene Bumgarner; Mario Medvedovic (Bioinform., 2006)

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. - Maureen A. Sartor; Craig R. Tomlinson; Scott C. Wesselkamper; Siva Sivaganesan; George D. Leikauf; Mario Medvedovic (BMC Bioinform., 2006)

Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. - Xiangdong Liu; Walter J. Jessen; Siva Sivaganesan; Bruce J. Aronow; Mario Medvedovic (BMC Bioinform., 2007)

LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. - Maureen A. Sartor; George D. Leikauf; Mario Medvedovic (Bioinform., 2009)

CLEAN: CLustering Enrichment ANalysis. - Johannes M. Freudenberg; Vineet K. Joshi; Zhen Hu; Mario Medvedovic (BMC Bioinform., 2009)

Prior Information Based Bayesian Infinite Mixture Model. - Zhen Hu; Siva Sivaganesan; Mario Medvedovic (ISAIM, 2010)

A semi-parametric Bayesian model for unsupervised differential co-expression analysis. - Johannes M. Freudenberg; Siva Sivaganesan; Michael Wagner 010; Mario Medvedovic (BMC Bioinform., 2010)

Generalized random set framework for functional enrichment analysis using primary genomics datasets. - Johannes M. Freudenberg; Siva Sivaganesan; Mukta Phatak; Kaustubh Shinde; Mario Medvedovic (Bioinform., 2011)

WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results. - Vineet K. Joshi; Johannes M. Freudenberg; Zhen Hu; Mario Medvedovic (Source Code Biol. Medicine, 2011)

Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules. - Jing Chen 021; Zhen Hu; Mukta Phatak; John Reichard; Johannes M. Freudenberg; Siva Sivaganesan; Mario Medvedovic (PLoS Comput. Biol., 2013)

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. - Amar Koleti; Raymond Terryn; Vasileios Stathias; Caty Chung; Daniel J. Cooper; John Paul Turner; Dusica Vidovic; Michele Forlin; Tanya T. Kelley; Alessandro D'Urso; Bryce K. Allen; Denis Torre; et al. (Nucleic Acids Res., 2018)

Predicting mechanism of action of cellular perturbations with pathway activity signatures. - Yan Ren; Siva Sivaganesan; Nicholas A. Clark; Lixia Zhang; Jacek Biesiada; Wen Niu; David R. Plas; Mario Medvedovic (Bioinform., 2020)

piNET: a versatile web platform for downstream analysis and visualization of proteomics data. - Behrouz Shamsaei; Szymon Chojnacki; Marcin Pilarczyk; Mehdi Fazel-Najafabadi; Wen Niu; Chuming Chen; Karen Ross; Andrea Matlock; Jeremy Muhlich; Somchai Chutipongtanate; Jie Zheng 001; John Turner; et al. (Nucleic Acids Res., 2020)

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. - Vasileios Stathias; John Paul Turner; Amar Koleti; Dusica Vidovic; Daniel J. Cooper; Mehdi Fazel-Najafabadi; Marcin Pilarczyk; Raymond Terryn; Caty Chung; Afoma Umeano; Daniel J. B. Clarke; Alexander Lachmann; et al. (Nucleic Acids Res., 2020)

SigCom LINCS: data and metadata search engine for a million gene expression signatures. - John Erol Evangelista; Daniel J. B. Clarke; Zhuorui Xie; Alexander Lachmann; Minji Jeon; Kerwin Chen; Kathleen M. Jagodnik; Sherry L. Jenkins; Maxim V. Kuleshov; Megan L. Wojciechowicz; Stephan C. Schürer; Mario Medvedovic; et al. (Nucleic Acids Res., 2022)