My research interests include bioinformatics, data visualization, server front end and back end tools, and algorithm development. For both ugrad and masters students, if you (a) are interested, (b) are motivated, (c) have passed the intro CS courses (CSCI141 and CSCI145), then please stop by and chat.

2023

• Changrui Li and Filip Jagodzinski. Identifying Impactful Pairs of Insertion Mutations in Proteins. 2023 Computational Structural Bioinformatics Workshop (CSBW) at ACM-BCB. ACM DL, PDF
• Sarah Coffland, Katie Christensen, Filip Jagodzinski and Brian Hutchinson. RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning. 2023 Computational Structural Bioinformatics Workshop (CSBW) at ACM-BCB. ACM DL, PDF

2022

• Alistair Turcan, Grant Chou, Lilu Martin, Theo Miller, Dylan Thompson, Filip Jagodzinski. Exhaustive In-Silico Simulation of Single Amino Acid Insertion and Deletion Mutations. 2022 IEEE International Conference on Bioinformatics and Biomedicein (BIBM), IEEE Explore.
• Muneeba Jilani, Alistair Turcan, Nurit Haspel, and Filip Jagodzinski. Elucidating the structural impacts of protein InDels. Biomolecules 12 (10, 1435), Open Access
• N Haspel, F. Jagodzinski, K Molloy. Algorithms and Methods in Structural Bioinformatics. Springer Nature
• Chris Daw, Brian Barragan Cruz, Nicholas Majeske, Filip Jagodzinski, Tanzima Islam, Brian Hutcinson. Low Rank Approximation Methods for Identifying Impactful Protein Mutations, in Algorithms and Methods In Structural Bioinfrmatics, Springer Nature 2022, pages 63-87.
• Muneeba Jilani, Nurit Haspel, Filip Jagodzinski. Detection and Analysis of Amino Acid Insertions and Deletions, in Algorithms and Methods In Structural Bioinfrmatics, Spring Nature 2022, pages 89-99.

2021

• Alistair Turcan, Anna Zivkovic, Dylan Thompson, Lorraine Wong, Lauren Johnson, and Filip Jagodzinski. CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins. Symmetry 2021, 13, 2401, MDPI Open Access.
• Muneeba Jilani, Alistair Turcan, Nurit Haspel, and Filip Jagodzinski. Assessing the Effects of Amino Acid Insertion and Deletion Mutations. Computation Structural Biology Workshop (CSBW), at IEEE BIBM 2021
• Matthew Lee, Bodi Van Roy, and Filip Jagodzinski. Characterizing the Behavior of Mutated Proteins with EMCAP: the Energy Minimization Curve Analysis Pipeline. Computation Structural Biology Workshop (CSBW), at IEEE BIBM 2021
• Haley A. Wofford, Josh Myers-Dean, Brandon A. Vogel, Kevin Alexander Estrada Alamo, Frederick A. Longshore-Neate, Filip Jagodzinski, and Jeanine F. Amacher. Domain Analysis and Motif Matcher (DAMM): A program to predict selectivity determinants in Monosiga brevicollis PDZ 3 domains using human PDZ data. Molecules, Vol. 26, Issue 19.
• Quentin Jensen, Filip Jagodzinski, Tanzima Islam. FILCIO: Application Agnostic I/O Aggregation to Scale Scientific Workflows. IEEE Compsac 2021, BDCAA. PDF
• David H. Smith IV, Qiang Hao, Christopher D. Hundhausen, Filip Jagodzinski, Josh Myers-Dean, Kira Jaeger. Towards Modeling Student Engagement with Interactive Computing Textbooks: An Empirical Study. ACM SIGCSE 2021. ACM DL, PDF

2020

• Edward Thompson, Tess Thackray, Cecilia Kalthoff, Ryan Rapoport and Filip Jagodzinski. Assessing Drug Resistance Due to Mutations via Energy Minimization Profiles. ACM-BCB, CSBW, 2020.
• Gideon Wolfe, Othmane Belhoussine, Anais Dawson, Maxwell Lisaius and Filip Jagodzinski. Impactful Mutations in Mpro of the SARS-CoV-2 Proteome. ACM-BCB, CSBW, 2020.
• Jack Stratton, Michael Albert, Quentin Jensen, Max Ismailov, Filip Jagodzinski, Tanzima Islam. Towards Aggregation based I/O Optimization for Scaling Bioinformatics Applications. IEEE COMPSAC 2020, BDCAA.
• Sam Herr, Josh Myers-Dean, Hunter Read, Filip Jagodzinski. PETRA: Drug engineering Via Rigidity Analysis. Molecules 2020, 25(6), pg 1304, PubMed
• Dylan Carpenter, Tess Thackray, Cecilia Kalthoff, Filip Jagodzinski. Assessing Protein-Drug Resistance Due to Mutations via a Rigidity Analysis in silico Approach. 12th International Conference on Bioinformatics and Computational Biology (BICOB) 2020. EasyChair EPiC , PDF

2019

• Valgardson J, Cosbey R, Houser P, Rupp M, Van Bronkhorst R, Lee M, Jagodzinski F, Amacher JF. MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity. Protein Science Dec. 2019, 25, pp 2127-2143, PubMed
• Elizabeth West, Kyle Daling, Courtney Miller, Wes Rosales, Sasa Vukovic, Filp Jagodzinski. CONSEQUENCES : CONstrained SEQUENCE alignmentS With Multiple User Weights. CSBW at ACMBCB 2019, Niagara Falls, NY. ACM Digital Library
• David H. Smith IV, Qiang Hao, Filip Jagodzinski, Yan Liu, Vishal Gupta. Quantifying the Effects of Prior Knowledge in Entry-Level Programming Courses. ACM CompEd 2019, Chengdu, China. PDF at ACM Digital Library
• Hunter Read, Dylan Carpenter, Sam Herr, Filip Jagodzinsski. PEtRA: Protein-ligand Complex Engineering Through Rigidity Analysis. BCB '19, Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Bioloyg and Health Informatics, Niagara Falls, NY. PDF at ACM Digital Library

2018

• Richard Olney, Aaron Tuor, Filip Jagodzinski, Brian Hutchinson. A systematic exploration of ΔΔG cutoff ranges in machine learning models for protein mutation stability prediction. Journal of Bioinformatics and Computational Biology, Vol. 16, No. 5, 2018.
• Nicholas Majeske, Brian Hutchinson, Filip Jagodzinski, Tanzima Islam. Low Rank Smoothed Sampling Methods for Identifying Impactful Pair-wise Mutations. Computational Structural Bioinformatics Workshop at ACMBCB 2018, Washington D.C. PDF
• Sarah Gunderson, Filip Jagodzinski. Ensemble Voting Schemes that Improve Machine Learning Models for Predicting the Effects of Protein Mutations. 2018 ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Washington D.C. (~30% acceptance rate). PDF at ACM Digital Library
• Nicholas Majeske, Filip Jagodzinski. Elucidating Which Pairwise Mutations Affect Protein Stability : an Exhaustive Big Data Approach. 2018 IEEE International Conference on Computers, Software & Applications (COMPSAC), Tokyo (23% acceptance rate). PDF
• Stephanie Mason, Brian Chen, Filip Jagodzinski. Exploring Protein Cavities through Rigidity Analysis. Molecules, 2018, Jan, 23(2). PubMed
• Evan Ricks, Ramin Dehghanpoor, Katie Hursh, Sarah Gunderson, Roshanak Farhoodi, Nurit Haspel, Brian Hutchinson, Filip Jagodzinski. Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability. Molecules, 2018, Jan 27:23(2). PubMed
• Michael Siderius, Filip Jagodzinski. Mutation Sensitivity Maps : Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis in silico Mutation Approach. Journal of Computational Biology, Jan. 2018, 25(1):89-102, https://doi.org/10.1089/cmb.2017.0165.
• Hunter Read, Kyle Daling, Connor Freitas and Filip Jagodzinski. cMutant : A Web Server and Compute Pipeline for Exploring the Effects of Amino Acid Substitutions via Rigidity Mutation Maps. 10th International Conference on Bioinformatics and Computational Biology. PDF
• Richard Olney, Aaron Tuor, Filip Jagodzinski and Brian Hutchinson. Protein Mutation Stability Ternary Classification using Neural Networks and Rigidity Analysis. 10th International Conference on Bioinformatics and Computational Biology. Best Paper Finalist. PDF

2017

• Elizabeth Brooks, Graham Roberts, Ali Scoville, Filip Jagodzinski. ModEDI: An Extendable Software Architecture for Examining the Effects of Nonlinear Developmental Interactions on Evolutionary Trajectories. 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS, (preprint, IEEE Xplore)
• Roshanak Farhoodi, Max Shelbourne, Rebecca Hsieh, Nurit Haspel, Brian Hutchinson, and Filip Jagodzinski. Predicting the Effect of Point Mutations on Protein Structural Stability. ACM-BCB'17: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM Digital Library, preprint).
• Erik Andersson and Filip Jagodzinski. ProMuteHT : A High Throughput Compute Pipeline for Generating Protein Mutants in Silico. CSBW (Computational Structural Biology Workshop) at ACM-BCB'17: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM Digital Library, preprint).
• Stephanie Mason, Tim Woods, Brian Chen, and Filip Jagodzinski Investigating Rigidity Properties of Protein Cavities. CSBW (Computational Structural Biology Workshop) at ACM-BCB'17: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM Digital Library, preprint).

2016

• Michael Siderius and Filip Jagodzinski. Identifying amino acids sensitive to mutations using high-throughput rigidity analysis Proceedings, IEEE 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. Proceedings, IEEE ICCABS, 2016
• 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
• 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

2015

• Elizabeth Brooks, Alison Scoville, Filip Jagodzinski. An extensible software infrastructure for testing the evolutionary consequences of developmental interactions. Proceedings, ACMBCB 2015.

2013

• 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.
• Brian Orndorff, Filip Jagodzinski. A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes. Proceedings, CSBW Workshop at ACM-BCB 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, 14(Suppl 18):S2, 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.
• 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 (Abstract).
• 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. PDF, 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. IEEE Explorer Entry

2011 and Earlier

• 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)

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, NASA, Summer Internship, 2003.
• 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

• 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
• 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

• 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.
• 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.
  
• 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)

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)