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. Macrophage mediated recognition and clearance of Borrelia burgdorferinelicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation., 2019.

Preprint Project

. Benchmarking Time-Series Data Discretization on Inference Methods. Bioinformatics, Jan 18 2019. doi: 10.1093/bioinformatics/btz036. PMID: 30657860, 2019.

Preprint PDF Code Project

. Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin. Scientific Reports. Volume 7, Article number: 14466, 2017.

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. CD169+ marginal zone macrophages orchestrate innate immune responses to bacterial infection. Science Immunology. Vol. 2, Issue 16 (article featured on the cover), 2017.

PDF Project

. The Minimal Hitting Set Generation Problem: Algorithms and Computation. SIAM Journal on Discrete Mathematics. 2017; 31(1):63–100, 2017.

Preprint PDF Code Project AlgoRunContainer

. AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinformatics, Volume 32, Issue 15, 1 August 2016, Pages 2396–2398, 2016.

PDF Code AlgoRunWebsite

. QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PLoS Comput Biol. 2016 Jun 23;12(6):e1004809. PubMed PMID: 27336171; PubMed Central PMCID: PMC4919057, 2016.

PDF Code QuinWebServer

. An algebra-based method for inferring gene regulatory networks. BMC Syst Biol. 2014 Mar 26;8:37. PubMed PMID: 24669835 (chosen as Editor’s Picks), 2014.

PDF Code Project AlgoRunContainer

. OCSANA: optimal combinations of interventions from network analysis. Bioinformatics, Volume 29, Issue 12, 15 June 2013, Pages 1571–1573, 2013.

PDF Code Project Project

. Computational systems biology: Discrete models of gene regulation networks. Ledder G, Carpenter JP, Comar TD, editors. Washington: The Mathematical Association of America. Computational Systems Biology: Discrete Models of Gene Regulation Networks 189-200p, 2013.

Preprint PDF Materials