Teresa M. Przytycka

117 papers A* 3A 2B 19C 5Misc 7Journal 60Unranked 13
YearRankTypeTitle / Venue / Authors
2025 B conf
A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data.
RECOMB
Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, John D. Bridgers, Eva Pérez-Guijarro, Kerrie Marie, Howard H. Yang, Charli Gruen, Chih Hao Wu, Welles Robinson, Huaitian Liu, Can Kizilkale, Michael C. Kelly, Cari Smith, Sung Chin, Jessica Ebersole, Sandra Burkett, Aydin Buluç, Maxwell P. Lee, Erin K. Molloy, Teresa M. Przytycka, Glenn Merlino, Chi-Ping Day, Salem Malikic, Funda Ergün, S. Cenk Sahinalp
2025 C conf
Improved Algorithms for Bi-Partition Function Computation.
WABI
John D. Bridgers, Jan Hoinka, S. Cenk Sahinalp, Salem Malikic, Teresa M. Przytycka, Funda Ergün
2025 C conf
Mutational Signature Refitting on Sparse Pan-Cancer Data.
WABI
Gal Gilad, Teresa M. Przytycka, Roded Sharan
2024 J jnl
Rosalind Franklin Society Proudly Announces the 2023 Award Recipient for
J. Comput. Biol.
Teresa M. Przytycka
2023 C conf
Algorithmic Approaches to Study Mutational Processes in Cancer (Invited Talk).
WABI
Teresa M. Przytycka
2023 J jnl
Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression.
PLoS Comput. Biol.
Bayarbaatar Amgalan, Chi-Ping Day, Teresa M. Przytycka
2023 J jnl
Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the
J. Comput. Biol.
Soumitra Pal, Brian Oliver, Teresa M. Przytycka
2021 J jnl
ISMB/ECCB 2021 proceedings.
Bioinform.
Christophe Dessimoz, Teresa M. Przytycka
2020 J jnl
AptaBlocks Online: A Web-Based Toolkit for the In Silico Design of Oligonucleotide Sticky Bridges.
J. Comput. Biol.
Jan Hoinka, Yijie Wang, Teresa M. Przytycka
2020 J jnl
Bioinformatics pipeline using JUDI: Just Do It!
Bioinform.
Soumitra Pal, Teresa M. Przytycka
2020 Misc conf
DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignatures.
PSB
Damian Wójtowicz, Mark D. M. Leiserson, Roded Sharan, Teresa M. Przytycka
2020 J jnl
Embedding gene sets in low-dimensional space.
Nat. Mach. Intell.
Jan Hoinka, Teresa M. Przytycka
2020 B conf
Reconstruction of Gene Regulatory Networks by Integrating Biological Model and a Recommendation System.
RECOMB
Yijie Wang, Justin M. Fear, Isabelle Berger, Hangnoh Lee, Brian Oliver, Teresa M. Przytycka
2020 Misc conf
Session Introduction.
PSB
Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan
2019 B conf
A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer.
RECOMB
Itay Sason, Damian Wójtowicz, Welles Robinson, Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan
2019 B conf
Accurate Sub-population Detection and Mapping Across Single Cell Experiments with PopCorn.
RECOMB
Yijie Wang, Jan Hoinka, Teresa M. Przytycka
2018 B conf
AptaBlocks: Accelerating the Design of RNA-Based Drug Delivery Systems.
RECOMB
Yijie Wang, Jan Hoinka, Piotr Swiderski, Teresa M. Przytycka
2018 J jnl
Detecting presence of mutational signatures in cancer with confidence.
Bioinform.
Xiaoqing Huang, Damian Wójtowicz, Teresa M. Przytycka
2017 B conf
BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract).
RECOMB
Phuong Dao, Yoo-Ah Kim, Sanna Madan, Roded Sharan, Teresa M. Przytycka
2017 J jnl
BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
PLoS Comput. Biol.
Phuong Dao, Yoo-Ah Kim, Damian Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka
2017 B conf
NetREX: Network Rewiring Using EXpression - Towards Context Specific Regulatory Networks.
RECOMB
Yijie Wang, Dong-Yeon Cho, Hangnoh Lee, Brian Oliver, Teresa M. Przytycka
2017 J jnl
WeSME: uncovering mutual exclusivity of cancer drivers and beyond.
Bioinform.
Yoo-Ah Kim, Sanna Madan, Teresa M. Przytycka
2016 B conf
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments.
RECOMB
Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka
2016 J jnl
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments.
CoRR
Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka
2016 J jnl
Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways.
BMC Syst. Biol.
Fan Zhang, Haoting Chen, Li Na Zhao, Hui Liu, Teresa M. Przytycka, Jie Zheng
2016 J jnl
ISMB 2016 Proceedings.
Bioinform.
Pierre Baldi, Teresa M. Przytycka
2016 — ch.
Maximum Agreement Subtree (of 3 or More Trees).
Encyclopedia of Algorithms
Teresa M. Przytycka
2016 J jnl
Preface.
J. Comput. Biol.
Teresa M. Przytycka
2016 J jnl
Understanding Genotype-Phenotype Effects in Cancer via Network Approaches.
PLoS Comput. Biol.
Yoo-Ah Kim, Dong-Yeon Cho, Teresa M. Przytycka
2016 J jnl
Ups and Downs of Poised RNA Polymerase II in B-Cells.
PLoS Comput. Biol.
Phuong Dao, Damian Wójtowicz, Steevenson Nelson, David Levens, Teresa M. Przytycka
2016 J jnl
WeSME: Uncovering Mutual Exclusivity of Cancer Drivers and Beyond.
CoRR
Yoo-Ah Kim, Sanna Madan, Teresa M. Przytycka
2016 — conf
WeSME: Uncovering Mutual Exclusivity of Cancer Mutations.
BCB
Yoo-Ah Kim, Sanna Madan, Teresa M. Przytycka
2015 J jnl
MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types.
Bioinform.
Yoo-Ah Kim, Dong-Yeon Cho, Phuong Dao, Teresa M. Przytycka
2015 B ed.
Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Warsaw, Poland, April 12-15, 2015, Proceedings
RECOMB
Teresa M. Przytycka
2014 B conf
AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application.
RECOMB
Jan Hoinka, Alexey Berezhnoy, Zuben E. Sauna, Eli Gilboa, Teresa M. Przytycka
2014 J jnl
LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.
BMC Bioinform.
Peng Yang, Min Wu, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng
2014 — ch.
When and How the Perfect Phylogeny Model Explains Evolution.
Discrete and Topological Models in Molecular Biology
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Riccardo Dondi, Teresa M. Przytycka
2013 B conf
Dissecting Cancer Heterogeneity with a Probabilistic Genotype-Phenotype Model.
RECOMB
Dong-Yeon Cho, Teresa M. Przytycka
2013 Misc conf
Modeling cell heterogeneity: from single-cell variations to mixed cells populations.
Pacific Symposium on Biocomputing
Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, Damian Wójtowicz
2013 Misc conf
Module Cover - A New Approach to Genotype-Phenotype Studies.
Pacific Symposium on Biocomputing
Yoo-Ah Kim, Raheleh Salari, Stefan Wuchty, Teresa M. Przytycka
2012 J jnl
Chapter 5: Network Biology Approach to Complex Diseases.
PLoS Comput. Biol.
Dong-Yeon Cho, Yoo-Ah Kim, Teresa M. Przytycka
2012 B conf
Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies.
RECOMB
Raheleh Salari, Chava Kimchi-Sarfaty, Michael M. Gottesman, Teresa M. Przytycka
2012 J jnl
Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers.
Bioinform.
Jan Hoinka, Elena Zotenko, Adam Friedman, Zuben E. Sauna, Teresa M. Przytycka
2012 — conf
Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse.
BCB
Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng
2012 J jnl
Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression.
PLoS Comput. Biol.
Raheleh Salari, Damian Wójtowicz, Jie Zheng, David Levens, Yitzhak Pilpel, Teresa M. Przytycka
2011 C ed.
Algorithms in Bioinformatics - 11th International Workshop, WABI 2011, Saarbrücken, Germany, September 5-7, 2011. Proceedings
WABI
Teresa M. Przytycka, Marie-France Sagot
2011 J jnl
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mark Borodovsky, Teresa M. Przytycka, Sanguthevar Rajasekaran, Alexander Zelikovsky
2011 — ed.
IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, Orlando, FL, USA, February 3-5, 2011
ICCABS
Ion I. Mandoiu, Satoru Miyano, Teresa M. Przytycka, Sanguthevar Rajasekaran
2011 J jnl
Identifying Causal Genes and Dysregulated Pathways in Complex Diseases.
PLoS Comput. Biol.
Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka
2011 — conf
Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome.
BIBM
Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng
2010 — ed.
Bioinformatics Research and Applications, 6th International Symposium, ISBRA 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings
ISBRA
Mark Borodovsky, Johann Peter Gogarten, Teresa M. Przytycka, Sanguthevar Rajasekaran
2010 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Tanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh, Donna K. Slonim
2010 J jnl
SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks.
Bioinform.
Jie Zheng, David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala, Teresa M. Przytycka
2010 B conf
Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases.
RECOMB
Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka
2010 J jnl
State of the art: refinement of multiple sequence alignments.
BMC Bioinform.
Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant
2010 J jnl
Toward the dynamic interactome: it's about time.
Briefings Bioinform.
Teresa M. Przytycka, Mona Singh, Donna K. Slonim
2009 — ed.
Advances in Bioinformatics and Computational Biology, 4th Brazilian Symposium on Bioinformatics, BSB 2009, Porto Alegre, Brazil, July 29-31, 2009. Proceedings
BSB
Katia S. Guimarães, Anna R. Panchenko, Teresa M. Przytycka
2009 J jnl
Graph theoretical approach to study eQTL: a case study of
Bioinform.
Yang Huang, Stefan Wuchty, Michael T. Ferdig, Teresa M. Przytycka
2009 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Tanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh
2009 J jnl
The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis.
BMC Syst. Biol.
Rafal Zielinski, Pawel F. Przytycki, Jie Zheng, David Zhang, Teresa M. Przytycka, Jacek Capala
2008 J jnl
DOMINE: a database of protein domain interactions.
Nucleic Acids Res.
Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, Raja Jothi
2008 J jnl
Improving Strand Pairing Prediction through Exploring Folding Cooperativity.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka
2008 J jnl
Interrogating domain-domain interactions with parsimony based approaches.
BMC Bioinform.
Katia S. Guimarães, Teresa M. Przytycka
2008 — ch.
Maximum Agreement Subtree (of 3 or More Trees).
Encyclopedia of Algorithms
Teresa M. Przytycka
2008 — ch.
Protein Interaction Network Based Prediction of Domain-Domain and Domain-Peptide Interactions.
Protein-protein Interactions and Networks
Katia S. Guimarães, Teresa M. Przytycka
2008 — book
Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction
Protein-protein Interactions and Networks
Anna R. Panchenko, Teresa M. Przytycka
2008 J jnl
Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality.
PLoS Comput. Biol.
Elena Zotenko, Julián Mestre, Dianne P. O'Leary, Teresa M. Przytycka
2007 — conf
A Rigorous Analysis of the Pattern of Intron Conservation Supports the
RECOMB-CG
Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka
2007 C conf
Bringing Folding Pathways into Strand Pairing Prediction.
WABI
Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka
2007 J jnl
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment.
BMC Bioinform.
Raja Jothi, Teresa M. Przytycka, L. Aravind
2007 J jnl
Stability of Characters and Construction of Phylogenetic Trees.
J. Comput. Biol.
Teresa M. Przytycka
2006 B conf
An Important Connection Between Network Motifs and Parsimony Models.
RECOMB
Teresa M. Przytycka
2006 J jnl
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations.
Bioinform.
Raja Jothi, Elena Zotenko, Asba Tasneem, Teresa M. Przytycka
2006 Misc conf
Chordal Graphs in Computational Biology - New Insights and Applications.
International Conference on Computational Science (2)
Teresa M. Przytycka
2006 J jnl
Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations.
Algorithms Mol. Biol.
Elena Zotenko, Katia S. Guimarães, Raja Jothi, Teresa M. Przytycka
2006 J jnl
Graph Theoretical Insights into Evolution of Multidomain Proteins.
J. Comput. Biol.
Teresa M. Przytycka, George B. Davis, Nan Song, Dannie Durand
2006 J jnl
State of the art: refinement of multiple sequence alignments.
BMC Bioinform.
Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant
2005 — conf
Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations.
Systems Biology and Regulatory Genomics
Elena Zotenko, Katia S. Guimarães, Raja Jothi, Teresa M. Przytycka
2005 B conf
Graph Theoretical Insights into Evolution of Multidomain Proteins.
RECOMB
Teresa M. Przytycka, George B. Davis, Nan Song, Dannie Durand
2005 — conf
Predicting protein-protein interaction by searching evolutionary tree automorphism space.
ISMB (Supplement of Bioinformatics)
Raja Jothi, Maricel G. Kann, Teresa M. Przytycka
2004 J jnl
Scale-free networks versus evolutionary drift.
Comput. Biol. Chem.
Teresa M. Przytycka, Yi-Kuo Yu
2000 J jnl
An
SIAM J. Comput.
Richard Cole, Martin Farach-Colton, Ramesh Hariharan, Teresa M. Przytycka, Mikkel Thorup
1999 B conf
On an Optimal Split Tree Problem.
WADS
S. Rao Kosaraju, Teresa M. Przytycka, Ryan S. Borgstrom
1998 J jnl
Asymptotically Optimal Election on Weighted Rings.
SIAM J. Comput.
Lisa Higham, Teresa M. Przytycka
1998 J jnl
The Optimal Alphabetic Tree Problem Revisited.
J. Algorithms
Lawrence L. Larmore, Teresa M. Przytycka
1997 J jnl
A simple construction of high representativity triangulations.
Discret. Math.
Teresa M. Przytycka, Józef H. Przytycki
1997 A* conf
General Techniques for Comparing Unrooted Evolutionary Trees.
STOC
Ming-Yang Kao, Tak Wah Lam, Teresa M. Przytycka, Wing-Kin Sung, Hing-Fung Ting
1997 J jnl
Parallel Algorithms for the Hamiltonian Cycle and Hamiltonian Path Problems in Semicomplete Bipartite Digraphs.
Algorithmica
Jørgen Bang-Jensen, Mohamed El Haddad, Yannis Manoussakis, Teresa M. Przytycka
1996 J jnl
A Parallel Algorithm for Optimum Height-Limited Alphabetic Binary Trees.
J. Parallel Distributed Comput.
Lawrence L. Larmore, Teresa M. Przytycka
1996 J jnl
A Simple, Efficient Algorithm for Maximum Finding on Rings.
Inf. Process. Lett.
Lisa Higham, Teresa M. Przytycka
1996 A* conf
On the Complexity of String Folding.
ICALP
Mike Paterson, Teresa M. Przytycka
1996 J jnl
On the Complexity of String Folding.
Discret. Appl. Math.
Mike Paterson, Teresa M. Przytycka
1996 — conf
Optimal Cost-Sensitive Distributed Minimum Spanning Tree Algorithm.
SWAT
Teresa M. Przytycka, Lisa Higham
1996 J jnl
Parallel Construction of Binary Trees with Near Optimal Weighted Path Lengt.
Algorithmica
David G. Kirkpatrick, Teresa M. Przytycka
1996 J jnl
Parallel Maximum Independent Set in Convex Bipartite Graphs.
Inf. Process. Lett.
Artur Czumaj, Krzysztof Diks, Teresa M. Przytycka
1996 — conf
Sparse dynamic programming for maximum agreement subtree problem.
Mathematical Hierarchies and Biology
Teresa M. Przytycka
1995 A conf
Computing the Agreement of Trees with Bounded Degrees.
ESA
Martin Farach, Teresa M. Przytycka, Mikkel Thorup
1995 J jnl
Constructing Huffman Trees in Parallel.
SIAM J. Comput.
Lawrence L. Larmore, Teresa M. Przytycka
1995 A conf
Grid Intersection and Box Intersection Graphs on Surfaces (Extended Abstract).
GD
Jan Kratochvíl, Teresa M. Przytycka
1995 J jnl
On the Agreement of Many Trees.
Inf. Process. Lett.
Martin Farach, Teresa M. Przytycka, Mikkel Thorup
1994 J jnl
A Fast Algorithm for Optimum Height-Limited Alphabetic Binary Trees.
SIAM J. Comput.
Lawrence L. Larmore, Teresa M. Przytycka
1994 J jnl
A Work-Time Trade-off in Parallel Computation of Huffman Trees and Concave Least Weight Subsequence Problem.
Parallel Process. Lett.
Christos Levcopoulos, Teresa M. Przytycka
1994 — conf
Asymptotically Optimal Election on Weighted Rings.
SWAT
Lisa Higham, Teresa M. Przytycka
1994 A* conf
The Optimal Alphabetic Tree Problem Revisited.
ICALP
Teresa M. Przytycka, Lawrence L. Larmore
1993 — conf
A Simple, Efficient Algorithm for Maximum Finding on Rings.
WDAG
Lisa Higham, Teresa M. Przytycka
1993 J jnl
Grid intersection graphs and boxicity.
Discret. Math.
S. Bellantoni, Irith Ben-Arroyo Hartman, Teresa M. Przytycka, Sue Whitesides
1993 B conf
Parallel Construction of Optimal Alphabetic Trees.
SPAA
Lawrence L. Larmore, Teresa M. Przytycka, Wojciech Rytter
1992 J jnl
Optimal Tree Ranking is in NC.
Parallel Process. Lett.
Pilar de la Torre, Raymond Greenlaw, Teresa M. Przytycka
1991 J jnl
Parallel Algorithms for Parity Graphs.
J. Algorithms
Teresa M. Przytycka, Derek G. Corneil
1991 B conf
Parallel Construction of Trees with Optimal Weighted Path Length.
SPAA
Lawrence L. Larmore, Teresa M. Przytycka
1991 — conf
Subexponentially computable truncations of Jones-types polynomials.
Graph Structure Theory
Teresa M. Przytycka, Józef H. Przytycki
1991 — conf
Surface triangulations without short noncontractible cycles.
Graph Structure Theory
Teresa M. Przytycka, Józef H. Przytycki
1990 — conf
An optimal parallel minimax tree algorithm.
SPDP
David G. Kirkpatrick, Teresa M. Przytycka
1990 J jnl
On a Lower Bound for Short Noncontractible Cycles in Embedded Graphs.
SIAM J. Discret. Math.
Teresa M. Przytycka, Józef H. Przytycki
1990 B conf
Parallel Construction of near Optimal binary Trees.
SPAA
David G. Kirkpatrick, Teresa M. Przytycka
1990 J jnl
Parallel recognition of complement reducible graphs and cotree construction.
Discret. Appl. Math.
David G. Kirkpatrick, Teresa M. Przytycka
1989 J jnl
A Simple Parallel Tree Contraction Algorithm.
J. Algorithms
Karl R. Abrahamson, Norm Dadoun, David G. Kirkpatrick, Teresa M. Przytycka