Filip Jagodzinski

46 papers A 1B 3Journal 9Unranked 33

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	PRIMRose: Insights into the Per-Residue Energy Metrics of Proteins with Double InDel Mutations using Deep Learning. BCB Companion Stella Brown, Nicolas Preisig, Autumn Davis, Brian Hutchinson, Filip Jagodzinski
2025	J	`jnl`	PRIMRose: Insights into the Per-Residue Energy Metrics of Proteins with Double InDel Mutations using Deep Learning. CoRR Stella Brown, Nicolas Preisig, Autumn Davis, Brian Hutchinson, Filip Jagodzinski
2025	—	`conf`	Protein-Protein Interface Angle Change (∆FA) as a Descriptor of Mutation-Induced Structural Perturbations. BCB Logan Nicholas Day, Filip Jagodzinski, James Tessmer, Bogdan Trigubov, Emelia Galante
2025	—	`conf`	Structural Impacts of Insertion Mutations on Protein-Protein Interfaces. BCB Companion James Tessmer, Logan Nicholas Day, Bogdan Trigubov, Emilia Galant, Filip Jagodzinski
2023	—	`conf`	Identifying Impactful Pairs of Insertion Mutations in Proteins. BCB Changrui Li, Filip Jagodzinski
2023	—	`conf`	RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning. BCB Sarah Coffland, Katie Christensen, Filip Jagodzinski, Brian Hutchinson
2023	J	`jnl`	RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning. CoRR Sarah Coffland, Katie Christensen, Filip Jagodzinski, Brian Hutchinson
2022	—	`conf`	Exhaustive In-silico Simulation of Single Amino Acid Insertion and Deletion Mutations. BIBM Alistair Turcan, Grant Chou, Lilu Martin, Theo Miller, Dylan Thompson, Filip Jagodzinski
2021	—	`conf`	Assessing the Effects of Amino Acid Insertion and Deletion Mutations. BIBM Muneeba Jilani, Alistair Turcan, Nurit Haspel, Filip Jagodzinski
2021	J	`jnl`	CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins. Symmetry Alistair Turcan, Anna Zivkovic, Dylan Thompson, Lorraine Wong, Lauren Johnson, Filip Jagodzinski
2021	—	`conf`	Characterizing the Behavior of Mutated Proteins with EMCAP: the Energy Minimization Curve Analysis Pipeline. BIBM Matthew Lee, Bodi Van Roy, Filip Jagodzinski
2021	B	`conf`	FILCIO: Application Agnostic I/O Aggregation to Scale Scientific Workflows. COMPSAC Quentin Jensen, Filip Jagodzinski, Tanzima Z. Islam
2021	A	`conf`	Towards Modeling Student Engagement with Interactive Computing Textbooks: An Empirical Study. SIGCSE David H. Smith IV, Qiang Hao, Christopher D. Hundhausen, Filip Jagodzinski, Josh Myers-Dean, Kira Jaeger
2020	B	`conf`	Towards Aggregation Based I/O Optimization for Scaling Bioinformatics Applications. COMPSAC Jack Stratton, Michael Albert, Quentin Jensen, Max Ismailov, Filip Jagodzinski, Tanzima Z. Islam
2019	—	`conf`	CONSEQUENCES: CONstrained SEQUENCE alignmentS With Multiple User Weights. BCB Elizabeth West, Kyle Daling, Courtney Miller, Wes Rosales, Sasa Vukovic, Filip Jagodzinski
2019	—	`conf`	PETRA: Protein-ligand Complex Engineering Through Rigidity Analysis. BCB Hunter Read, Dylan Carpenter, Sam Herr, Filip Jagodzinski
2019	—	`conf`	Quantifying the Effects of Prior Knowledge in Entry-Level Programming Courses. CompEd David H. Smith IV, Qiang Hao, Filip Jagodzinski, Yan Liu, Vishal Gupta
2018	J	`jnl`	A systematic exploration of ΔΔG cutoff ranges in machine learning models for protein mutation stability prediction. J. Bioinform. Comput. Biol. Richard Olney, Aaron Tuor, Filip Jagodzinski, Brian Hutchinson
2018	—	`conf`	ACM-BCB 2018 Computational Structural Bioinformatics Workshop (CSBW) Chairs' Welcome. BCB Filip Jagodzinski, Brian Y. Chen, Kevin Molloy
2018	—	`conf`	Elucidating Which Pairwise Mutations Affect Protein Stability: An Exhaustive Big Data Approach. COMPSAC (1) Nicholas Majeske, Filip Jagodzinski
2018	—	`conf`	Ensemble Voting Schemes that Improve Machine Learning Models for Predicting the Effects of Protein Mutations. BCB Sarah Gunderson, Filip Jagodzinski
2018	—	`conf`	Low Rank Smoothed Sampling Methods for Identifying Impactful Pairwise Mutations. BCB Nicholas Majeske, Filip Jagodzinski, Brian Hutchinson, Tanzima Z. Islam
2018	J	`jnl`	Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach. J. Comput. Biol. Michael Siderius, Filip Jagodzinski
2017	J	`jnl`	Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-rectangles in High Dimensional Data. CoRR Joseph Lemley, Filip Jagodzinski, Razvan Andonie
2017	—	`conf`	Investigating Rigidity Properties of Protein Cavities. BCB Stephanie Mason, Tim Woods, Brian Y. Chen, Filip Jagodzinski
2017	—	`conf`	ModEDI: An extendable software architecture for examining the effects of developmental interactions on evolutionary trajectories. ICCABS Elizabeth Brooks, Graham Roberts, Alison Scoville, Filip Jagodzinski
2017	—	`conf`	Predicting the Effect of Point Mutations on Protein Structural Stability. BCB Roshanak Farhoodi, Max Shelbourne, Rebecca Hsieh, Nurit Haspel, Brian Hutchinson, Filip Jagodzinski
2017	—	`conf`	ProMuteHT: A High Throughput Compute Pipeline for Generating Protein Mutants BCB Erik Andersson, Filip Jagodzinski
2016	—	`conf`	Assessing how multiple mutations affect protein stability using rigid cluster size distributions. ICCABS Erik Andersson, Rebecca Hsieh, Howard Szeto, Roshanak Farhoodi, Nurit Haspel, Filip Jagodzinski
2016	B	`conf`	Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-Rectangles in High Dimensional Data. COMPSAC Joseph Lemley, Filip Jagodzinski, Razvan Andonie
2016	—	`conf`	Identifying amino acids sensitive to mutations using high-throughput rigidity analysis. BIBM Michael Siderius, Filip Jagodzinski
2015	—	`conf`	An extensible software infrastructure for testing the evolutionary consequences of developmental interactions. BCB Elizabeth Brooks, Alison Scoville, Filip Jagodzinski
2013	—	`conf`	A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes. BCB Brian Orndorff, Filip Jagodzinski
2013	—	`conf`	An Evolutionary Conservation & Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues. BCB Filip Jagodzinski, Bahar Akbal-Delibas, Nurit Haspel
2013	J	`jnl`	Rigidity analysis of protein biological assemblies and periodic crystal structures. BMC Bioinform. Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu
2013	—	`conf`	Rigidity and flexibility of protein-nucleic acid complexes. ICCABS Emily Flynn, Filip Jagodzinski, Sharon Pamela Santana, Ileana Streinu
2012	—	`conf`	Combining conservation and rigidity methods to detect critical residues in proteins. BIBM Workshops Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel
2012	—	`conf`	Periodic rigidity of protein crystal structures. ICCABS Pamela Clark, Jessica Grant, Samantha Monastra, Filip Jagodzinski, Ileana Streinu
2012	—	`conf`	Towards a hybrid method for detecting critical protein residues. BIBM Workshops Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel
2012	—	`conf`	Towards biophysical validation of constraint modeling for rigidity analysis of proteins. BCB Filip Jagodzinski, Ileana Streinu
2012	—	`conf`	Towards sequence-based DNA flexibility analysis. BCB Emily Flynn, Filip Jagodzinski, Ileana Streinu
2012	J	`jnl`	Using Rigidity Analysis to Probe Mutation-induced Structural Changes in proteins. J. Bioinform. Comput. Biol. Filip Jagodzinski, Jeanne Hardy, Ileana Streinu
2011	J	`jnl`	KINARI-Web: a server for protein rigidity analysis. Nucleic Acids Res. Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu
2011	—	`conf`	Using rigidity analysis to probe mutation-induced structural changes in proteins. BIBM Workshops Filip Jagodzinski, Jeanne Hardy, Ileana Streinu
2007	—	`conf`	Towards a mechanistic view of protein motion. CDC Filip Jagodzinski, Oliver Brock
2003	—	`conf`	The XML Log Standard for Digital Libraries: Analysis, Evolution, and Deployment. JCDL Marcos André Gonçalves, Ganesh Panchanathan, Unnikrishnan Ravindranathan, Aaron Krowne, Edward A. Fox, Filip Jagodzinski, Lillian N. Cassel