Publications, Presentations, & Posters

• 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)
• 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)
• 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)

• 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.

• 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

• Restrained Molecular Dynamics
  CS 334, Computational Biology, Smith College, 21 October 2008.
  Restrained MD Tutorial (PDF)
  PDB Errors - Discussion (PDF)
• Molecular Dynamics
  CS 334, Computational Biology, Smith College, 16 October 2008.
  Lecture Slides (PDF)
  Molecular Dynamics Overview (PDF)
  GROMACS Tutorial (PDF)
• Building A Nano Robot
  CS 403, Robotics, University of Massachusetts, 27 March 2007.
  Slides (PDF)
  Class Handout (DPF)

• Looking for Little Green Men
  Computational Biology Laboratory Meeting, 01 October 2007
  Slides (PDF)
• A Developmental Genetics-Inspired Approach to Robot Control
  LPR Presentation, 29 June 2007.
  Slides (PDF)
• Articulated-Body Forward Dynamics, Adaptive Dynamics ... & Proteins
  Computational Biology Lab Meeting, 26 April 2007
  Slides (PDF)
• Pan troglodytes, Homo neanderthalensis, & Homo sapiens: DNA Sequencing and the Origin Of Modern Humans
  Computational Biology Lab Meeting, 28 November 2006
  Slides (PDF)

• 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)

• How Hydrogen Bond Redundancy Affects Protein Flexibility
  2009 Protein Society Annual Meeting, Boston, MA
  Poster (PDF)
• Using a Mechanistic Perspective to Simulate Protein Backbone Motion
  2007 Protein Society Annual Meeting, Boston, MA
  Poster (PDF)
• Robotics Inspired Proteomics
  USC CHARMM Summer Program, August 2006
  Poster (PDF)
• Computational Biology; Department of Computer Science at UMass Amherst
  2007 Protein Society Annual Meeting, Grad. Fair, Boston, MA
  Poster (PDF)