Download Filip Jagodzinski - WWU Computer Science Faculty Web Pages

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