Filip Jagodzinski

Orcid: 0000-0001-7783-2241

According to our database1, Filip Jagodzinski authored at least 39 papers between 2003 and 2023.

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Bibliography

2023
Identifying Impactful Pairs of Insertion Mutations in Proteins.
Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning.
Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022
Exhaustive In-silico Simulation of Single Amino Acid Insertion and Deletion Mutations.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021
CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins.
Symmetry, 2021

Towards Modeling Student Engagement with Interactive Computing Textbooks: An Empirical Study.
Proceedings of the SIGCSE '21: The 52nd ACM Technical Symposium on Computer Science Education, 2021

FILCIO: Application Agnostic I/O Aggregation to Scale Scientific Workflows.
Proceedings of the IEEE 45th Annual Computers, Software, and Applications Conference, 2021

Characterizing the Behavior of Mutated Proteins with EMCAP: the Energy Minimization Curve Analysis Pipeline.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

Assessing the Effects of Amino Acid Insertion and Deletion Mutations.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020
Towards Aggregation Based I/O Optimization for Scaling Bioinformatics Applications.
Proceedings of the 44th IEEE Annual Computers, Software, and Applications Conference, 2020

2019
Quantifying the Effects of Prior Knowledge in Entry-Level Programming Courses.
Proceedings of the ACM Conference on Global Computing Education, 2019

CONSEQUENCES: CONstrained SEQUENCE alignmentS With Multiple User Weights.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

PETRA: Protein-ligand Complex Engineering Through Rigidity Analysis.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018
Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach.
J. Comput. Biol., 2018

A systematic exploration of ΔΔG cutoff ranges in machine learning models for protein mutation stability prediction.
J. Bioinform. Comput. Biol., 2018

Elucidating Which Pairwise Mutations Affect Protein Stability: An Exhaustive Big Data Approach.
Proceedings of the 2018 IEEE 42nd Annual Computer Software and Applications Conference, 2018

Low Rank Smoothed Sampling Methods for Identifying Impactful Pairwise Mutations.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

ACM-BCB 2018 Computational Structural Bioinformatics Workshop (CSBW) Chairs' Welcome.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

Ensemble Voting Schemes that Improve Machine Learning Models for Predicting the Effects of Protein Mutations.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017
ModEDI: An extendable software architecture for examining the effects of developmental interactions on evolutionary trajectories.
Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2017

Investigating Rigidity Properties of Protein Cavities.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

Predicting the Effect of Point Mutations on Protein Structural Stability.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

ProMuteHT: A High Throughput Compute Pipeline for Generating Protein Mutants <i>in silico</i>.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016
Assessing how multiple mutations affect protein stability using rigid cluster size distributions.
Proceedings of the 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2016

Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-Rectangles in High Dimensional Data.
Proceedings of the 40th IEEE Annual Computer Software and Applications Conference, 2016

Identifying amino acids sensitive to mutations using high-throughput rigidity analysis.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
An extensible software infrastructure for testing the evolutionary consequences of developmental interactions.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2013
Rigidity analysis of protein biological assemblies and periodic crystal structures.
BMC Bioinform., 2013

Rigidity and flexibility of protein-nucleic acid complexes.
Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013

A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes.
Proceedings of the ACM Conference on Bioinformatics, 2013

An Evolutionary Conservation & Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
Using Rigidity Analysis to Probe Mutation-induced Structural Changes in proteins.
J. Bioinform. Comput. Biol., 2012

Periodic rigidity of protein crystal structures.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

Combining conservation and rigidity methods to detect critical residues in proteins.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

Towards a hybrid method for detecting critical protein residues.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

Towards biophysical validation of constraint modeling for rigidity analysis of proteins.
Proceedings of the ACM International Conference on Bioinformatics, 2012

Towards sequence-based DNA flexibility analysis.
Proceedings of the ACM International Conference on Bioinformatics, 2012

2011
KINARI-Web: a server for protein rigidity analysis.
Nucleic Acids Res., 2011

2007
Towards a mechanistic view of protein motion.
Proceedings of the 46th IEEE Conference on Decision and Control, 2007

2003
The XML Log Standard for Digital Libraries: Analysis, Evolution, and Deployment.
Proceedings of the ACM/IEEE 2003 Joint Conference on Digital Libraries (JCDL 2003), 2003


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