The XML Log Standard for Digital Libraries: Analysis, Evolution, and Deployment. - Marcos André Gonçalves; Ganesh Panchanathan; Unnikrishnan Ravindranathan; Aaron Krowne; Edward A. Fox; Filip Jagodzinski; Lillian N. Cassel (JCDL, 2003)

Towards a mechanistic view of protein motion. - Filip Jagodzinski; Oliver Brock (CDC, 2007)

KINARI-Web: a server for protein rigidity analysis. - Naomi Fox; Filip Jagodzinski; Yang Li 104; Ileana Streinu (Nucleic Acids Res., 2011)

Towards sequence-based DNA flexibility analysis. - Emily Flynn; Filip Jagodzinski; Ileana Streinu (BCB, 2012)

Towards biophysical validation of constraint modeling for rigidity analysis of proteins. - Filip Jagodzinski; Ileana Streinu (BCB, 2012)

Towards a hybrid method for detecting critical protein residues. - Bahar Akbal-Delibas; Filip Jagodzinski; Nurit Haspel (BIBM Workshops, 2012)

Combining conservation and rigidity methods to detect critical residues in proteins. - Bahar Akbal-Delibas; Filip Jagodzinski; Nurit Haspel (BIBM Workshops, 2012)

Periodic rigidity of protein crystal structures. - Pamela Clark; Jessica Grant; Samantha Monastra; Filip Jagodzinski; Ileana Streinu (ICCABS, 2012)

Using Rigidity Analysis to Probe Mutation-induced Structural Changes in proteins. - Filip Jagodzinski; Jeanne Hardy; Ileana Streinu (J. Bioinform. Comput. Biol., 2012)

An Evolutionary Conservation & Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues. - Filip Jagodzinski; Bahar Akbal-Delibas; Nurit Haspel (BCB, 2013)

A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes. - Brian Orndorff; Filip Jagodzinski (BCB, 2013)

Rigidity and flexibility of protein-nucleic acid complexes. - Emily Flynn; Filip Jagodzinski; Sharon Pamela Santana; Ileana Streinu (ICCABS, 2013)

Rigidity analysis of protein biological assemblies and periodic crystal structures. - Filip Jagodzinski; Pamela Clark; Jessica Grant; Tiffany Liu; Samantha Monastra; Ileana Streinu (BMC Bioinform., 2013)

An extensible software infrastructure for testing the evolutionary consequences of developmental interactions. - Elizabeth Brooks; Alison Scoville; Filip Jagodzinski (BCB, 2015)

Identifying amino acids sensitive to mutations using high-throughput rigidity analysis. - Michael Siderius; Filip Jagodzinski (BIBM, 2016)

Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-Rectangles in High Dimensional Data. - Joseph Lemley; Filip Jagodzinski; Razvan Andonie (COMPSAC, 2016)

Assessing how multiple mutations affect protein stability using rigid cluster size distributions. - Erik Andersson; Rebecca Hsieh; Howard Szeto; Roshanak Farhoodi; Nurit Haspel; Filip Jagodzinski (ICCABS, 2016)

ProMuteHT: A High Throughput Compute Pipeline for Generating Protein Mutants in silico. - Erik Andersson; Filip Jagodzinski (BCB, 2017)

Predicting the Effect of Point Mutations on Protein Structural Stability. - Roshanak Farhoodi; Max Shelbourne; Rebecca Hsieh; Nurit Haspel; Brian Hutchinson; Filip Jagodzinski (BCB, 2017)

Investigating Rigidity Properties of Protein Cavities. - Stephanie Mason; Tim Woods; Brian Y. Chen; Filip Jagodzinski (BCB, 2017)

ModEDI: An extendable software architecture for examining the effects of developmental interactions on evolutionary trajectories. - Elizabeth Brooks; Graham Roberts; Alison Scoville; Filip Jagodzinski (ICCABS, 2017)

Ensemble Voting Schemes that Improve Machine Learning Models for Predicting the Effects of Protein Mutations. - Sarah Gunderson; Filip Jagodzinski (BCB, 2018)

ACM-BCB 2018 Computational Structural Bioinformatics Workshop (CSBW) Chairs' Welcome. - Filip Jagodzinski; Brian Y. Chen; Kevin Molloy (BCB, 2018)

Low Rank Smoothed Sampling Methods for Identifying Impactful Pairwise Mutations. - Nicholas Majeske; Filip Jagodzinski; Brian Hutchinson; Tanzima Z. Islam (BCB, 2018)

Elucidating Which Pairwise Mutations Affect Protein Stability: An Exhaustive Big Data Approach. - Nicholas Majeske; Filip Jagodzinski (COMPSAC (1), 2018)

A systematic exploration of ΔΔG cutoff ranges in machine learning models for protein mutation stability prediction. - Richard Olney; Aaron Tuor; Filip Jagodzinski; Brian Hutchinson (J. Bioinform. Comput. Biol., 2018)

Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach. - Michael Siderius; Filip Jagodzinski (J. Comput. Biol., 2018)

PETRA: Protein-ligand Complex Engineering Through Rigidity Analysis. - Hunter Read; Dylan Carpenter; Sam Herr; Filip Jagodzinski (BCB, 2019)

CONSEQUENCES: CONstrained SEQUENCE alignmentS With Multiple User Weights. - Elizabeth West; Kyle Daling; Courtney Miller; Wes Rosales; Sasa Vukovic; Filip Jagodzinski (BCB, 2019)

Quantifying the Effects of Prior Knowledge in Entry-Level Programming Courses. - David H. Smith IV; Qiang Hao; Filip Jagodzinski; Yan Liu; Vishal Gupta (CompEd, 2019)

Towards Aggregation Based I/O Optimization for Scaling Bioinformatics Applications. - Jack Stratton; Michael Albert 006; Quentin Jensen; Max Ismailov; Filip Jagodzinski; Tanzima Z. Islam (COMPSAC, 2020)

Assessing the Effects of Amino Acid Insertion and Deletion Mutations. - Muneeba Jilani; Alistair Turcan; Nurit Haspel; Filip Jagodzinski (BIBM, 2021)

Characterizing the Behavior of Mutated Proteins with EMCAP: the Energy Minimization Curve Analysis Pipeline. - Matthew Lee 014; Bodi Van Roy; Filip Jagodzinski (BIBM, 2021)

FILCIO: Application Agnostic I/O Aggregation to Scale Scientific Workflows. - Quentin Jensen; Filip Jagodzinski; Tanzima Z. Islam (COMPSAC, 2021)

Towards Modeling Student Engagement with Interactive Computing Textbooks: An Empirical Study. - David H. Smith IV; Qiang Hao; Christopher D. Hundhausen; Filip Jagodzinski; Josh Myers-Dean; Kira Jaeger (SIGCSE, 2021)

CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins. - Alistair Turcan; Anna Zivkovic; Dylan Thompson; Lorraine Wong; Lauren Johnson; Filip Jagodzinski (Symmetry, 2021)

Exhaustive In-silico Simulation of Single Amino Acid Insertion and Deletion Mutations. - Alistair Turcan; Grant Chou; Lilu Martin; Theo Miller; Dylan Thompson; Filip Jagodzinski (BIBM, 2022)

RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning. - Sarah Coffland; Katie Christensen; Filip Jagodzinski; Brian Hutchinson (BCB, 2023)

Identifying Impactful Pairs of Insertion Mutations in Proteins. - Changrui Li; Filip Jagodzinski (BCB, 2023)