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Filip Jagodzinski
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2020 – today
- 2023
- [c34]Changrui Li
, Filip Jagodzinski
Identifying Impactful Pairs of Insertion Mutations in Proteins. BCB 2023: 99:1-99:8 - [c33]Sarah Coffland
RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning. BCB 2023: 107:1-107:9 - [i2]Sarah Coffland, Katie Christensen, Filip Jagodzinski, Brian Hutchinson:
RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning. CoRR abs/2310.13806 (2023) - 2022
- [c32]Alistair Turcan, Grant Chou
Exhaustive In-silico Simulation of Single Amino Acid Insertion and Deletion Mutations. BIBM 2022: 3498-3503 - 2021
- [j6]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): 2401 (2021) - [c31]Muneeba Jilani, Alistair Turcan, Nurit Haspel, Filip Jagodzinski:
Assessing the Effects of Amino Acid Insertion and Deletion Mutations. BIBM 2021: 2511-2518 - [c30]Matthew Lee, Bodi Van Roy, Filip Jagodzinski:
Characterizing the Behavior of Mutated Proteins with EMCAP: the Energy Minimization Curve Analysis Pipeline. BIBM 2021: 2527-2532 - [c29]Quentin Jensen, Filip Jagodzinski, Tanzima Z. Islam:
FILCIO: Application Agnostic I/O Aggregation to Scale Scientific Workflows. COMPSAC 2021: 1587-1592 - [c28]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: 914-920 - 2020
- [c27]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: 1250-1255
2010 – 2019
- 2019
- [c26]Hunter Read, Dylan Carpenter, Sam Herr, Filip Jagodzinski:
PETRA: Protein-ligand Complex Engineering Through Rigidity Analysis. BCB 2019: 568-573 - [c25]Elizabeth West, Kyle Daling, Courtney Miller, Wes Rosales, Sasa Vukovic, Filip Jagodzinski:
CONSEQUENCES: CONstrained SEQUENCE alignmentS With Multiple User Weights. BCB 2019: 574-579 - [c24]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: 30-36 - 2018
- [j5]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): 1840022:1-1840022:19 (2018) - [j4]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): 89-102 (2018) - [c23]Sarah Gunderson, Filip Jagodzinski:
Ensemble Voting Schemes that Improve Machine Learning Models for Predicting the Effects of Protein Mutations. BCB 2018: 211-219 - [c22]Filip Jagodzinski, Brian Y. Chen, Kevin Molloy:
ACM-BCB 2018 Computational Structural Bioinformatics Workshop (CSBW) Chairs' Welcome. BCB 2018: 613-614 - [c21]Nicholas Majeske, Filip Jagodzinski, Brian Hutchinson
Low Rank Smoothed Sampling Methods for Identifying Impactful Pairwise Mutations. BCB 2018: 681-686 - [c20]Nicholas Majeske, Filip Jagodzinski:
Elucidating Which Pairwise Mutations Affect Protein Stability: An Exhaustive Big Data Approach. COMPSAC (1) 2018: 508-515 - 2017
- [c19]Roshanak Farhoodi, Max Shelbourne, Rebecca Hsieh, Nurit Haspel, Brian Hutchinson
Predicting the Effect of Point Mutations on Protein Structural Stability. BCB 2017: 247-252 - [c18]Erik Andersson, Filip Jagodzinski:
ProMuteHT: A High Throughput Compute Pipeline for Generating Protein Mutants in silico. BCB 2017: 655-660 - [c17]Stephanie Mason, Tim Woods, Brian Y. Chen, Filip Jagodzinski:
Investigating Rigidity Properties of Protein Cavities. BCB 2017: 698-703 - [c16]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: 1-6 - [i1]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 abs/1704.00683 (2017) - 2016
- [c15]Michael Siderius, Filip Jagodzinski:
Identifying amino acids sensitive to mutations using high-throughput rigidity analysis. BIBM 2016: 1732-1738 - [c14]Joseph Lemley
Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-Rectangles in High Dimensional Data. COMPSAC 2016: 563-571 - [c13]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: 1-6 - 2015
- [c12]Elizabeth Brooks, Alison Scoville
An extensible software infrastructure for testing the evolutionary consequences of developmental interactions. BCB 2015: 557-558 - 2013
- [j3]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): S2 (2013) - [c11]Filip Jagodzinski, Bahar Akbal-Delibas, Nurit Haspel:
An Evolutionary Conservation & Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues. BCB 2013: 779 - [c10]Brian Orndorff, Filip Jagodzinski:
A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes. BCB 2013: 793 - [c9]Emily Flynn, Filip Jagodzinski, Sharon Pamela Santana, Ileana Streinu:
Rigidity and flexibility of protein-nucleic acid complexes. ICCABS 2013: 1-6 - 2012
- [j2]Filip Jagodzinski, Jeanne Hardy, Ileana Streinu:
Using Rigidity Analysis to Probe Mutation-induced Structural Changes in proteins. J. Bioinform. Comput. Biol. 10(3) (2012) - [c8]Filip Jagodzinski, Ileana Streinu:
Towards biophysical validation of constraint modeling for rigidity analysis of proteins. BCB 2012: 408-413 - [c7]Emily Flynn, Filip Jagodzinski, Ileana Streinu:
Towards sequence-based DNA flexibility analysis. BCB 2012: 607-609 - [c6]Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel:
Towards a hybrid method for detecting critical protein residues. BIBM Workshops 2012: 82-85 - [c5]Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel:
Combining conservation and rigidity methods to detect critical residues in proteins. BIBM Workshops 2012: 940 - [c4]Pamela Clark, Jessica Grant, Samantha Monastra, Filip Jagodzinski, Ileana Streinu:
Periodic rigidity of protein crystal structures. ICCABS 2012: 1-6 - 2011
- [j1]Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu:
KINARI-Web: a server for protein rigidity analysis. Nucleic Acids Res. 39(Web-Server-Issue): 177-183 (2011) - [c3]Filip Jagodzinski, Jeanne Hardy, Ileana Streinu:
Using rigidity analysis to probe mutation-induced structural changes in proteins. BIBM Workshops 2011: 432-437
2000 – 2009
- 2007
- [c2]Filip Jagodzinski, Oliver Brock:
Towards a mechanistic view of protein motion. CDC 2007: 4557-4562 - 2003
- [c1]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: 312-314
Coauthor Index
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