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Filip Jagodzinski 516 High Street, MS 9165 Department of Computer Science Western Washington University Bellingham, WA 98225 Phone (Office) : 360-650-3800 [email protected] http://facultyweb.cs.wwu.edu/~jagodzf Professional Experience Assistant Professor, Western Washington University Assistant Professor, Central Washington University Interim Director, Computational Science Masters Program – Central Washington Univ. Sr. Developer, Sales Activity Management, King of Prussia, PA Technician, Laser Confocal Scanning Microscopy, Tatton Lab, Mt. Sinai Medical Center 2015 - present 2012-2015 2014-2015 2003-2005 1999-2001 Education Ph.D., Computer Science – University of Massachusetts Amherst Advisor: Ileana Streinu M.S., Computer Science – Villanova University Advisor: Frank Klassner B.S., Biomedical Engineering, Imaging – Columbia University 2005-2012 2001-2003 1995-1999 Teaching (CS courses at CWU, CSCI at WWU) Introduction to Programming (CS110, CS111, CSCI141), Concurrent Programming (CSCI322), Networks (CS450), Bioinformatics (CSCI474), High Performance Computing (CS530, Graduate), Computer Architecture (CS312), Software Engineering Mobile Apps (CS498), Modeling (CS298). Research Interests Computational Structural Biology. Effects of mutations and point-substitutions on protein structure. Software engineering & web-technologies for scientific applications. Information and Intelligent Systems. Current and Past Graduate Students, Thesis Supervision/Committees Current (At WWU, Chair and Member are not used because there is no thesis option in CS) Role Advisor Past Role Chair Mem. Mem. Chair Student Name Project/Thesis E. Brooks Co-variance of biological traits Type M.S. M.S. M.S. M.S. Student Name G. Bolton E. Shah K. Boberg K. Moore Advisor F. Jagodzinski J. Anvik D. Klyve F. Jagodzinski Project/Thesis Computing Mountain Passes Neural Networks Directed Graph Cryptosystems Messier Marathon Scheduler Post graduation Boeing GM Docusign CWU,faculty Year 2014 2014 2014 2013 Refereed, Peer Reviewed Publications (* Student authors) 2016 – Present Michael Siderius* and Filip Jagodzinski. Identifying Amino Acids Sensitive to Mutations Using HighThroughput Rigidity Analysis. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016. 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. IEEE ICCABS 2016, Atlanta. 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, 6 Oct 2016. Joe Lemley*, Filip Jagodzinski, Razvan Andonie. Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-rectangles in High Dimensional Data. IEEE COMPSAC 2016, Atlanta. 2015 and Earlier Elizabeth Brooks*, Alison Scoville, Filip Jagodzinski. An extensible software infrastructure for testing the evolutionary consequences of developmental interactions. ACMBCB 2015, Atlanta. 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. Bahar Akbal-Delibas*, Filip Jagodzinski and Nurit Haspel. A Conservation and Rigidity Based Method for Detecting Critical Protein Residues. BMC Structural Biology 2013, 13(Suppl 1):S6. Brian Orndorff*, Filip Jagodzinski. A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes. 2013 International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, Washington D.C. Filip Jagodzinski, Akbal-Delibas, Nurit Haspel. An Evolutionary Conservation and Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues. 2013 International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, Washington D.C. Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu. Rigidity Analysis of Protein Biological Assemblies and Periodic Crystal Structures. BMC Bioinformatics 2013, 14(Suppl 18):S2. Emily Flynn, Filip Jagodzinski, Sharon Pamela Santana and Ileana Streinu. Rigidity and Flexibility of Protein-Nucleic Acid Complexes. 2013 IEEE International Conference on Computational Advances in Bio and Medical Sciences, New Orleans. Filip Jagodzinski and Ileana Streinu. Towards Biophysical Validation of Constraint Modeling for Rigidity Analysis of Proteins. 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Orlando. Naomi Fox, Filip Jagodzinski, Ileana Streinu. KINARI-Lib: a C++ library for pebble game rigidity analysis of mechanical models. Minisymposium on Publicly Available Geometric/Topological Software, Chapel Hill, NC, USA, Jun. 17-19, 2012 Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel. Towards a Hybrid Method for Detecting Critical Protein Residues. 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, Philadelphia. Pamela Clark, Jessica Grant, Samantha Monastra, Filip Jagodzinski, Ileana Streinu. Periodic Rigidity of Protein Crystal Structures. 2012 IEEE International Conference on Computational Advances in Bio and Medical Sciences, Las Vegas. 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. Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu. KINARI-Web: A Server for Protein Rigidity Analysis. Nucleic Acids Research, 39 (Web Server Issue), 2011. Filip Jagodzinski, Jeanne Hardy, Ileana Streinu, Using Rigidity Analysis To Probe Mutation-Induced Structural Changes in Proteins. Workshop on Computational Structural Bioinformatics, IEEE Conference on Bioinformatics and Biomedicine, BIBM 2011, Atlanta, USA, November 2011. Filip Jagodzinski and Oliver Brock. Towards a Mechanistic View of Protein Motion. 46th IEEE Conference on Decision and Control, Special Session on Control and Optimization in Macro-molecular Folding and Association, New Orleans, USA, December 2007. Marcos André Gonçalves, Ganesh Panchanathan, Unnikrishnan Ravindranathan, Aaron Krowne, Edward A. Fox, Filip Jagodzinski and Lillian N. Cassel. The XML Log Standard for Digital Libraries: Analysis, Evolution, and Deployment. Third ACM/IEEE-CS Joint Conf. on Digital Libraries, JCDL, 2003. Tatton WG, Chalmers-Redman RM, Elstner M, Leesch W, Jagodzinski FB, Stupak DP, Sugrue MM, Tatton NA. Glyceraldehyde-3-phosphate dehydrogenase in neurodegeneration and apoptosis signaling. Journal of Neural Transmission, Supplementum, 2000;(60) White Papers, Conference Tutorial, Guest Lectures, Invited Talks, Outreach, Misc. 2016 – Present ModEvo: Modeling Evolutionary Dynamics. Filip Jagodzinski. Session Talk, ISCB Rocky 2016 Bioinformatics Conference, Snowmass, CO. Approximately 50% of abstracts were accepted for oral presentations. Identifying Amino Acids Sensitive to Mutations Using High-Throughput Rigidity Analysis. Filip Jagodzinski. Pacific Northwest National Laboratories (PNNL) Brown Bag Lunch 1hr presentation, 19 December 2016. 2015 and Earlier Two-Dimensional Rigidity Percolation : Not Your Regular Cup-O-Joe, Invited Section Talk, Pacific Northwest Mathematical Association of America Regional Meeting, Missoula, MT, June 2014. Katherine Moore, Filip Jagodzinski, Messier Marathon Scheduler: Improving Student Participation in Astronomy Outreach Events, 2013 Astronomical Society of the Pacific (ASP) Annual Meeting: Ensuring STEM Literacy, San Jose, CA. Ileana Streinu, Naomi Fox and Filip Jagodzinski, Analyzing Protein Flexibility: An Introduction to Combinatorial Rigidity Methods and Applications, 3-hour tutorial at IEEE Conference on Bioinformatics and Biomedicine, BIBM2011, Atlanta, USA, November 2011. KINARI-Mutagen : Using Rigidity Analysis to Infer Critical Regions in Mutant Proteins, Invited Department Colloquium, Computer Science, UMass Boston, February 2012 Filip Jagodzinski, Grid Rainfall Disaggregation Toward a Patch-Based Ensemble Kalman Filter for Soil Moisture Data Assimilation. White-paper, Goddard Earth Science and Technology Center (GSSP), NASA Goddard Space Flight Center, Summer 2003. Q. D. Wang, E. V. Gotthelf and C. C. Lang. A faint discrete source origin for the highly ionized iron emission from the Galactic Centre region. Nature 415, 148-150, 10 January 2002. Acknowledged for data calibration and analysis. Student Posters at Scientific Meetings (* Mentored Students, Mentored Student Conference Poster Winners) 2016 – Present Rainier Harvey*, ModEvo: A Web-Based Tool for Modeling Evolutionary Dynamics, ISCB Rocky 2016 Bioinformatics Conference, Snowmass, CO. Rebecca Hsieh*, Generating in silico Mutations to Infer the Effect of Multiple Amino Acid Substitutions on Protein Stability, Protein Society 30th Anniversary Symposium, Baltimore, MD. 2015 and Earlier Jennifer Thomas*, Happiness in Today’s Mobile World: How Your Phone Can Help, 2014 Sixteenth Annual Consortium for Computing Sciences, Northwest Regional Conference, Gonazaga U. Branndon Edwards*, Web-Tool Design for the Sciences, 2014 Sixteenth Annual Consortium for Computing Sciences in the Colleges, Northwest Regional Conference, Gonazaga U. Chris Walling*, Using Custom Scripts to Investigate Rigidity Properties of Proteins, 2014 Sixteenth Annual Consortium for Computing Sciences, Northwest Regional Conference, Gonazaga U. Paul Williams*, A Python, Bash-shell Script Approach for Quantifying the Bias of the Media's Many Voices, 2014 Sixteenth Annual Consortium for Computing Sciences in the Colleges, Northwest Regional Conference, Gonazaga U. Elizabeth Brooks*, Alison Scoville, Filip Jagodzinski, A Java Implementation of a Novel Quantitative Genetic Framework for the Evolution of Developmental Interactions, 2014 Symposium on University Research and Creative Expression (SOURCE), Central Washington University. Katherine Moore*, Filip Jagodzinski, Messier Marathon Scheduler: A Software Tool for Student Star- Gazers and Experienced Astronomers, 2013 Astronomical Society of the Pacific (ASP) Annual Meeting: Ensuring STEM Literacy, San Jose, CA. Garret Bolton*, Filip Jagodzinski, James Bisgard, A Mathematica Approach for Locating Mountain Pass Points on High Dimensional Surfaces, 2013 Symposium on University Research and Creative Expression (SOURCE), Central Washington University. Brian Orndorff*, Filip Jagodzinski, Rigidity Analysis of Protein-Ligand Conformations Generated by Molecular Dynamics, 2013 Symposium on University Research and Creative Expression (SOURCE), Central Washington University Katherine Moore*, Filip Jagodzinski, Messier Marathon Scheduler: A Software Tool for Novice StarGazers and Experienced Astronomers, 2013 Symposium on University Research and Creative Expression (SOURCE), Central Washington University Filip Jagodzinski, Naomi Fox, Diana Jaunzeikare, Ileana Streinu, A Software Tool for Surveying The Rigidity Properties of Protein Families, Biotechnology and Bioinformatics Symposium, October 9-10, 2009, Lincoln, Nebraska. Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu, A Web-Based Tool for Rigidity Analysis of Proteins, Biotechnology and Bioinformatics Symposium, October 9-10, 2009, Lincoln, Nebraska. Naomi Fox, Filip Jagodzinski, Jeanne Hardy, Ileana Streinu, How Hydrogen Bond Redundancy Affects Protein Flexibility, 23rd Symposium of the Protein Society, July 25-29, 2009, Boston, Massachusetts. Filip Jagodzinski and Oliver Brock, Using a Mechanistic Perspective to Simulate Protein Backbone Motion, 21st Annual Meeting of the Protein Society, July 21-25, 2007, Boston, Massachusetts. Filip Jagodzinski and Oliver Brock, Robotics Inspired Proteomics, University of Southern California CHARMM Summer Program, August 2006. Filip Jagodzinski, Lillian Cassel, Marcos A. Goncalves, Edward A. Fox, Digital Library Analysis: Advantages of Using the XML Log Standard Versus the Apache Server Logs, Third ACM/IEEE-CS Joint Conf. on Digital Libraries, JCDL, 2003, May 27-31, 2003, Houston, TX. Filip Jagodzinski and Lillian Cassel. Clickstream analysis using the new xml logging format. European Conference on Digital Libraries, ECDL, 2003, Trondheim, Norway. Service to the Department and University (dates 2015 and prior refer to CWU) Member Senator Member Member Member Member Chair Member Member Member Member Editor Advisor University Planning and Resource Council (UPRC) (university) Western Washington University, Faculty Senate (university) Graduate Committee (department) Outreach Committee (department) Student Centered Learning Committee (department, ad hoc) Academic Technology Advisor Council (university) Faculty 180 sub-council (university) Samuelsen STEM Planning Committee (university) Physics TT faculty search (university) EISC Lab Task Force (university) 2013, 2014 Computer Science Chair and faculty TT searches (department) CS Newsletter (department) Ada Lovelace Women in Computing Club (department) 2016-present 2016-present 2015-present 2016-present 2016-present 2012-2015 2013-2015 2014-2015 2013-2014 2013-2014 2013-2015 2012-2015 2012-2015 Service to Computer Science Program committee, IEEE Computers, Software and Applications (CompSAC), HSCS 2017 Tutorial Co-Chair, ACM-Bioinformatics and Computational Biology (ACMBCB) 2017 National Science Foundation Grant Panel 2015,2016 Program committee, ACM-Bioinformatics and Computational Biology (ACMBCB) 2014, 2016, 2017 Program committee, Bioinformatics and Computational Biology (BICoB) 2015, 2017 Program committee, Computational Structural Bioinformatics Workshop (CSBW) 2014-2016 Service to Community Grandparent Univ, 2-day introduction to programming course for grand-children and parents 2016