University of Wisconsin–Madison
Wisconsin Institute for Discovery
In August 2014, I completed my PhD in Computer Sciences (biomedical informatics and machine learning) with Mark Craven. In September I started a post-doc with Sushmita Roy.
During my PhD, I was a predoctoral trainee in the NLM-funded Computation and Informatics in Biology and Medicine Training Program. I did my undergraduate degree in computer science at beautiful Carleton College in Northfield, MN.
The central problem of my thesis research was to infer the relevant intracellular pathways involved in a biological response; for example, the host pathways that modulate the replication of a virus in a host cell, or the signaling pathways that regulate a yeast cell's transcriptional response to a stressful environment. We developed methods using integer linear programming and diffusion kernels to approach this problem.
During my postdoc, my work is focusing on developing methods to infer regulatory networks from multiple data types and study how networks change over time or between conditions.
Publications - Lead author
- PhD Thesis (August 2014) Improving the interpretability of integer linear programming methods for biological subnetwork inference. [pdf]
- Chasman D, Ho YH, Berry DB, Nemec CM, MacGilvray ME, Hose J, Merrill AE, Lee MV, Will JL, Coon JJ, Ansari AZ, Craven M, Gasch AP (2014) Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Mol Syst Biol 10(11):759. doi: 10.15252/msb.20145120 [link]
- Chasman D, Gancarz B, Hao L, Ferris M, Ahlquist P, Craven M (2014) Inferring host gene subnetworks involved in viral replication. PLoS Comput Biol 10(5): e1003626. doi:10.1371/journal.pcbi.1003626 [link]
- Chasman D, Gancarz B, Ahlquist P, Craven M (2009) Explaining effects of host gene knockouts on Brome Mosaic Virus replication. IJCAI'09 Workshop on Abductive and Inductive Knowledge Development [pdf]
Publications - Supporting role
- Larrainzar E, Riely BK, Kim SC, Carrasquilla-Garcia N, Yu HJ, Hwang HJ, Oh M, Kim GB, Surendrarao AK, Chasman D, Fotuhi Siahpirani A, Penmetsa RV, Lee GS, Kim N, Roy S, Mun JH, Cook DR (2015) Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals. Plant Physiol. 2015 Sep;169(1):233-65. doi: 10.1104/pp.15.00350. [link]
- Niu Z, Chasman D, Eisfeld AJ, Kawaoka Y Roy S. (2016) Multi-task Consensus Clustering of Genome-wide Transcriptomes from Related Biological Conditions. Bioinformatics. [link]
- Roy S, Fotuhi Siahpirani A, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan S. (2015) A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Research. 43(18): 8694-8712. doi: 10.1093/nar/gkv865 [link]
CV | Photographs
Contact me! chasman at cs.wisc.edu
Computer Science Department