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Publications, Presentations, & Posters

Conference Proceedings and Peer-Reviewed Journal Publications
  • 2013
  • Filip Jagodzinski, Akbal-Delibas, Nurit Haspel. An Evolutionary Conservation and Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues. CSBW Workshop at ACM-BCB 2013, to appear, September 2013
  • Brian Orndorff, Filip Jagodzinski. A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes. CSBW Workshop at ACM-BCB 2013, to appear, September 2013
  • 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
  • Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra1, Ileana Streinu. Rigidity analysis of protein biological assemblies and periodic crystal structures. BMC Structural Biology, to appear, 2013
  • Emily Flynn, Filip Jagodzinski, Sharon Pamela Santana and Ileana Streinu. Rigidity and Flexibility of Protein-Nucleic Acid Complexes. 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, (ICCABS 2013), New Orleans, June 2013.

  • 2012
  • Filip Jagodzinski and Ileana Streinu. Towards Biophysical Validation of Constraint Modeling for Rigidity Analysis of Proteins. ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2012 (ACM-BCB 2012), Orlando, October 2012.
  • Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel. Towards a Hybrid Method for Detecting Critical Protein Residues, Computational Structural Bioinformatics Workshop (CSBW) at 2012 IEEE International Conference on Bioinformatics and Biomedicie (BIBM), Philadelphia, October 2012.
  • Filip Jagodzinski. Towards Large-Scale Validation of Protein Flexibility Using Rigidity Analysis, Ph.D. Dissertation, University of Massachusetts Amherst, 2012.
  • 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. (publisher's site)
  • Pamela Clark, Jessica Grant, Samantha Monastra, Filip Jagodzinski, Ileana Streinu. Periodic Rigidity of Protein Crystal Structures. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2012), Las Vegas, February 2012. (link to IEEE Explorer)

  • 2011
  • Filip Jagodzinski, Jeanne Hardy, Ileana Streinu. Using Rigidity Analysis to Probe Mutation-Induced Structural Changes in Proteins. Proceedings, Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference (BIBM), Atlanta, USA, 2011; 432-437.
  • Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu. KINARI-Web: A Server for Protein Rigidity Analysis, Nucleic Acids Research, 39 (Web Server Issue), 2011. (open access article)

  • Prior to 2011
  • Filip Jagodzinski and Oliver Brock. Towards a Mechanistic View of Protein Motion. Proceedings, 46th IEEE Conference on Decision and Control, Special Session on Control and Optimization in Macro-molecular Folding and Assocation, New Orleans, USA, December 2007; 4557-4562. (link to IEEE Explorer)
  • 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 Conference on Digital Libraries, JCDL, 2003: 312-314. PDF
  • 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 Transmissions Supplemental 2000;(60):77-100. (link to NCBI)
White Papers, Master's Thesis
  • Filip Jagodzinski, Grid Rainfall Disaggregation Toward a Patch-Based Ensemble Kalman Filter for Soil Moisture Data Assimilation.Goddard Earth Science and Technology Center (GSSP) Summer Project. (Goddard Space Flight Center, Summer Internship, 2003) PDF
  • Filip Jagodzinski, The Analysis of Autonomous Planners and Their Scalability Onto Spacecraft With Limited Energy and Computational Resources, Master's Thesis, Villanova University, 2003.
Acknowledged in publications
  • 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. (reference to help in data calibration and analysis in the Acknowledgement section) PDF

Posters/Student Presentations - at Scientific Meetings
  • 2013
  • Katherine Moore, Filip Jagodzinski, Messier Marathon Scheduler: A Software Tool for Student Star-Gazers and Experienced Astronomers (poster); 2013 Astronomical Society of the Pacific (ASP) Annual Meeting: Ensuring STEM Literacy, San Jose, CA.
  • Katherine Moore, Filip Jagodzinski, Messier Marathon Scheduler: Improving Student Participation in Astronomy Outreach Events (presentation); 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 (poster); 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 (poster); 2013 Symposium on University Research and Creative Expression (SOURCE), Central Washington University
  • Katherine Moore, Filip Jagodzinski, Messier Marathon Scheduler: A Software Tool for Novice Star-Gazers and Experienced Astronomers (presentation); 2013 Symposium on University Research and Creative Expression (SOURCE), Central Washington University

  • Prior to 2013
  • How Hydrogen Bond Redundancy Affects Protein Flexibility (poster); 2009 Protein Society Annual Meeting, Boston, MA, Poster (PDF)
  • Using a Mechanistic Perspective to Simulate Protein Backbone Motion (poster); 2007 Protein Society Annual Meeting, Boston, MA, Poster (PDF)
  • Robotics Inspired Proteomics (poster): USC CHARMM Summer Program, August 2006, Poster (PDF)

Tutorials / Misc. Lectures & Presentations Tutorials
  • Analyzing protein flexibility: an introduction to combinatorial rigidity methods and applications
    With Ileana Streinu and Naomi Fox; BIBM 2011, 14 November 2011
    Slides (PDF) Announcement (PDF)
  • Modeling Biological Systems; Opportunities for Computer Scientists
    RBO Tutorial Series; 25 June 2007
    Slides (PDF)