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Filip Jagodzinski
Professional Preparation
Columbia University
Villanova University
University of Massachusetts
New York City, NY Biomedical Engineering
Villanova, PA
Computer Science
Amherst, MA
Computer Science
BS, 1999
MS, 2002
PhD, 2012
Appointments
Assistant Professor, Western Washington University
Assistant Professor, Central Washington University
2015 - present
2012-2015
Publications (*student authors)
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Michael Siderius* and Filip Jagodzinski. Identifying amino acids sensitive to
mutations using high-throughput rigidity analysis. 2016 IEEE International
Conference on Bioinformatics and Biomedicine (BIBM), 2016.
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Erik Andersson*, Rebecca Hsieh*, Howard Szeto*, Roshanak Farhoodi*, Nurit Haspel
and Filip Jagodzinski. Assessing How Multiple Mutations Affect Protein Stability
Using Rigid Cluster Size Distributions. 6th IEEE International Conference on
Computational Advances in Bio and Medical Sciences (ICCABS), October 2016,
Atlanta.
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Nurit Haspel, Filip Jagodzinski. Methods for Detecting Critical Residues in
Proteins. Springer Protocols, In Vitro Mutagenesis, Volume 1498, Methods in Molecular
Biology Series, pp 227-242, o6 Oct 2016
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Joe Lemley, Filip Jagodzinski, Razvan Andonie. Big Holes in Big Data: A Monte Carlo
Algorithm for Detecting Large Hyper-rectangles in High Dimensional Data.
Proceedings, IEEE COMPSAC 2016, Atlanta.
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Filip Jagodzinski, Akbal-Delibas, Nurit Haspel. An Evolutionary Conservation and
Rigidity Analysis Machine Learning Approach for Detecting Critical Protein
Residues. Proceedings, CSBW Workshop at ACM-BCB 2013, Washington D.C.
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Filip Jagodzinski, Jeanne Hardy, Ileana Streinu. Using Rigidity Analysis to Probe
Mutation-Induced Structural Changes in Proteins. Journal of Bioinformatics and
Computational Biology, 10(3), 2012.
Synergistic Activities
Curricular Development : developed undergraduate tutorial for Molecular Dynamics
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https://facultyweb.cs.wwu.edu/~jagodzf/pdfs/md_restrainedMD_21Oct_2008_smith.pdf
https://facultyweb.cs.wwu.edu/~jagodzf/pdfs/MDEquations.pdf
https://facultyweb.cs.wwu.edu/~jagodzf/pdfs/MD_gromacs_tutorial.pdf
Curricular Materials : Co-author of tutorial at BIBM2012 Conference
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https://facultyweb.cs.wwu.edu/~jagodzf/pdfs/bibm2011AnalyzingProteinFlexibility.pdf
Broadening the participation of groups under-represented in computer science
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Currently co-advise (with Ali Scoville, Biology professor at Central Washington
University) graduate student Elizabeth Brooks in developing tools for variability analysis
of genetic data
Current advise undergraduate students Rebeca Hsieh and Stephanie Hagstrom in
developing tools for analyzing effects of mutations on protein structures.
Undergraduate student mentoring
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Supervising Michael Vinning and Sasa Vukovic in developing a front-end/back-end turn
key server rMutant for in silico generating mutations and inferring their effects
Supervising Rebecca Hsier and Erik Andersson in developing a mutation engine
capable of generating single and multiple mutations in a PDB file
Supervising Michael Siderius in developing a high-throughput analysis computation
pipeline for exhaustively in silico generating all mutations in a biomolecular structure.
Student Success (CWU = Central Washington University)
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Elizabeth Brooks, McNair scholar, honors thesis, 2015 Harvard REU participant
Jennifer Thomas, 3rd place poster winner, Consortium for Computing NW 2014
Brian Orndorff, CWU SOURCE best poster award, 2013
Chris Walling, CWU SOURCE best oral presentation 2015
Service to CS outside of the immediate organization
Tutorial Co-Chair, ACM-Bioinformatics and Computational Biology (ACMBCB)
2017
Program committee, IEEE Computers, Software & Applications (CompSAC), HSCS
2017
Program committee, ACM-Bioinformatics and Computational Biology (ACMBCB) 2014, 2016
Program committee, Bioinformatics and Computational Biology (BICoB)
2015
Program committee, Computational Structural Bioinformatics Workshop (CSBW) 2014-2016