Deborah ChasmanUniversity of Wisconsin–Madison |
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I have recently moved to the laboratory of Irene Ong at the University of Wisconsin-Madison Department of Obstetrics and Gynecology.
From Sept 2014--June 2018, I was postdoc in the laboratory of Sushmita Roy. My work focused on developing methods to infer regulatory networks from multiple data types and study how networks change over time or between conditions.
In August 2014, I completed my PhD in Computer Sciences (biomedical informatics and machine learning) with Mark Craven. 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.
I have been fortunate to have received pre- and post-doctoral traineeship support from 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.
Publications - Lead author
- Chasman D, Roy S (2017) Inference of cell type specific regulatory networks on mammalian lineages. Current Opinion in Systems Biology 2:129--138. [doi:10.1016/j.coisb.2017.04.001]
- Chasman D, Walters KB, Lopes TJS, Eisfeld AJ, Kawaoka Y, Roy S (2016) Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PLOS Computational Biology 12(7): e1005013. [link] In Top 10 recommended papers by RECOMB/ISCB Regulatory and Systems Genomics, 2015-2016
- Chasman D, Fotuhi Siahpirani A, Roy S (2016) Network-based approaches for analysis of complex biological systems. Current Opinion in Biotechnology 39:157--166. doi:10:1016/j.copbio.2016.04.007. [link]
- 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
- Azencott, CA, Aittokallio T, Roy S, DREAM Idea Challenge Consortium, Norman T, Friend S, Stolovitsky G, Goldenberg A. (2017) The inconvenience of data of convenience: computational research beyond post-mortem analyses. Nature Methods 14:937-938. (Member of consortium as a participant in one of the two winning submissions.)
- Garcia K, Chasman D, Roy S, Ané J (2017) Physiological responses and gene co-expression network of mycorrhizal roots under K+ deprivation. Plant Physiol. pp.01959.2016. [link]
- 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]
Conference presentations
- Deborah Chasman, Kevin Walters, Amie Eisfeld, Yoshihiro Kawaoka and Sushmita Roy. Integrative reconstruction of the regulatory network controlling host response to influenza infections. Great Lakes Bioinformatics Conference (GLBIO) 2015. Best Short Talk.
Contact me! chasman at cs.wisc.edu