Filip Jagodzinski

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 27

Top Topics

Sampling Methods

Protein Structural

Machine Learning

Top Venues

Publications

Sarah Coffland, Katie Christensen, Filip Jagodzinski, Brian Hutchinson
RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning. CoRR (2023)
Changrui Li, Filip Jagodzinski
Identifying Impactful Pairs of Insertion Mutations in Proteins. BCB (2023)
Sarah Coffland, Katie Christensen, Filip Jagodzinski, Brian Hutchinson
RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning. BCB (2023)
Alistair Turcan, Grant Chou, Lilu Martin, Theo Miller, Dylan Thompson, Filip Jagodzinski
Exhaustive In-silico Simulation of Single Amino Acid Insertion and Deletion Mutations. BIBM (2022)
Alistair Turcan, Anna Zivkovic, Dylan Thompson, Lorraine Wong, Lauren Johnson, Filip Jagodzinski
CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins. Symmetry 13 (12) (2021)
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. SIGCSE (2021)
Muneeba Jilani, Alistair Turcan, Nurit Haspel, Filip Jagodzinski
Assessing the Effects of Amino Acid Insertion and Deletion Mutations. BIBM (2021)
Quentin Jensen, Filip Jagodzinski, Tanzima Z. Islam
FILCIO: Application Agnostic I/O Aggregation to Scale Scientific Workflows. COMPSAC (2021)
Matthew Lee, Bodi Van Roy, Filip Jagodzinski
Characterizing the Behavior of Mutated Proteins with EMCAP: the Energy Minimization Curve Analysis Pipeline. BIBM (2021)
Jack Stratton, Michael Albert, Quentin Jensen, Max Ismailov, Filip Jagodzinski, Tanzima Z. Islam
Towards Aggregation Based I/O Optimization for Scaling Bioinformatics Applications. COMPSAC (2020)
David H. Smith IV, Qiang Hao, Filip Jagodzinski, Yan Liu, Vishal Gupta
Quantifying the Effects of Prior Knowledge in Entry-Level Programming Courses. CompEd (2019)
Elizabeth West, Kyle Daling, Courtney Miller, Wes Rosales, Sasa Vukovic, Filip Jagodzinski
CONSEQUENCES: CONstrained SEQUENCE alignmentS With Multiple User Weights. BCB (2019)
Hunter Read, Dylan Carpenter, Sam Herr, Filip Jagodzinski
PETRA: Protein-ligand Complex Engineering Through Rigidity Analysis. BCB (2019)
Nicholas Majeske, Filip Jagodzinski, Brian Hutchinson, Tanzima Z. Islam
Low Rank Smoothed Sampling Methods for Identifying Impactful Pairwise Mutations. BCB (2018)
Filip Jagodzinski, Brian Y. Chen, Kevin Molloy
ACM-BCB 2018 Computational Structural Bioinformatics Workshop (CSBW) Chairs' Welcome. BCB (2018)
Nicholas Majeske, Filip Jagodzinski
Elucidating Which Pairwise Mutations Affect Protein Stability: An Exhaustive Big Data Approach. COMPSAC (1) (2018)
Michael Siderius, Filip Jagodzinski
Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach. J. Comput. Biol. 25 (1) (2018)
Sarah Gunderson, Filip Jagodzinski
Ensemble Voting Schemes that Improve Machine Learning Models for Predicting the Effects of Protein Mutations. BCB (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. J. Bioinform. Comput. Biol. 16 (5) (2018)
Erik Andersson, Filip Jagodzinski
. BCB (2017)
Joseph Lemley, Filip Jagodzinski, Razvan Andonie
Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-rectangles in High Dimensional Data. CoRR (2017)
Roshanak Farhoodi, Max Shelbourne, Rebecca Hsieh, Nurit Haspel, Brian Hutchinson, Filip Jagodzinski
Predicting the Effect of Point Mutations on Protein Structural Stability. BCB (2017)
Stephanie Mason, Tim Woods, Brian Y. Chen, Filip Jagodzinski
Investigating Rigidity Properties of Protein Cavities. BCB (2017)
Elizabeth Brooks, Graham Roberts, Alison Scoville, Filip Jagodzinski
ModEDI: An extendable software architecture for examining the effects of developmental interactions on evolutionary trajectories. ICCABS (2017)
Joseph Lemley, Filip Jagodzinski, Razvan Andonie
Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-Rectangles in High Dimensional Data. COMPSAC (2016)
Erik Andersson, Rebecca Hsieh, Howard Szeto, Roshanak Farhoodi, Nurit Haspel, Filip Jagodzinski
Assessing how multiple mutations affect protein stability using rigid cluster size distributions. ICCABS (2016)
Michael Siderius, Filip Jagodzinski
Identifying amino acids sensitive to mutations using high-throughput rigidity analysis. BIBM (2016)
Elizabeth Brooks, Alison Scoville, Filip Jagodzinski
An extensible software infrastructure for testing the evolutionary consequences of developmental interactions. BCB (2015)
Brian Orndorff, Filip Jagodzinski
A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes. BCB (2013)
Filip Jagodzinski, Bahar Akbal-Delibas, Nurit Haspel
An Evolutionary Conservation & Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues. BCB (2013)
Emily Flynn, Filip Jagodzinski, Sharon Pamela Santana, Ileana Streinu
Rigidity and flexibility of protein-nucleic acid complexes. ICCABS (2013)
Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu
Rigidity analysis of protein biological assemblies and periodic crystal structures. BMC Bioinform. 14 (S-18) (2013)
Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel
Combining conservation and rigidity methods to detect critical residues in proteins. BIBM Workshops (2012)
Filip Jagodzinski, Jeanne Hardy, Ileana Streinu
Using Rigidity Analysis to Probe Mutation-induced Structural Changes in proteins. J. Bioinform. Comput. Biol. 10 (3) (2012)
Pamela Clark, Jessica Grant, Samantha Monastra, Filip Jagodzinski, Ileana Streinu
Periodic rigidity of protein crystal structures. ICCABS (2012)
Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel
Towards a hybrid method for detecting critical protein residues. BIBM Workshops (2012)
Emily Flynn, Filip Jagodzinski, Ileana Streinu
Towards sequence-based DNA flexibility analysis. BCB (2012)
Filip Jagodzinski, Ileana Streinu
Towards biophysical validation of constraint modeling for rigidity analysis of proteins. BCB (2012)
Filip Jagodzinski, Jeanne Hardy, Ileana Streinu
Using rigidity analysis to probe mutation-induced structural changes in proteins. BIBM Workshops (2011)
Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu
KINARI-Web: a server for protein rigidity analysis. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Filip Jagodzinski, Oliver Brock
Towards a mechanistic view of protein motion. CDC (2007)
Marcos André Gonçalves, Ganesh Panchanathan, Unnikrishnan Ravindranathan, Aaron Krowne, Edward A. Fox, Filip Jagodzinski, Lillian N. Cassel
The XML Log Standard for Digital Libraries: Analysis, Evolution, and Deployment. JCDL (2003)