Teresa Przytycka
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Computer Science Biology
Teresa Przytycka's Degrees
- PhD Computer Science University of Warsaw
- Masters Computer Science University of Warsaw
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Why Is Teresa Przytycka Influential?
(Suggest an Edit or Addition)According to Wikipedia, Teresa Maria Przytycka is a Polish-American computational biologist who works as a senior investigator in the Computational Biology Branch of the National Center for Biotechnology Information , where she heads the Algorithmic Methods in Computational and Systems Biology section. She started her research career in parallel algorithms; at the NCBI, her research takes a computational approach to problems in systems biology involving cancer, gene regulation, and the analysis of massive data.
Teresa Przytycka's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality (2008) (384)
- Chapter 5: Network Biology Approach to Complex Diseases (2012) (252)
- Transcription dependent dynamic supercoiling is a short-range genomic force (2013) (251)
- A Simple Parallel Tree Contraction Algorithm (1989) (249)
- Toward the dynamic interactome: it's about time (2010) (242)
- From hype to reality: data science enabling personalized medicine (2018) (203)
- Genome-wide Detection of DNase I Hypersensitive Sites in Single Cells and FFPE Samples (2015) (188)
- RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription (2016) (187)
- Identifying Causal Genes and Dysregulated Pathways in Complex Diseases (2011) (186)
- Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture (2009) (158)
- DOMINE: a database of protein domain interactions (2007) (144)
- Global Regulation of Promoter Melting in Naive Lymphocytes (2013) (139)
- Comparative validation of the D. melanogaster modENCODE transcriptome annotation (2014) (134)
- Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. (2017) (132)
- Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. (2006) (132)
- Predicting domain-domain interactions using a parsimony approach (2006) (130)
- An O(n log n) algorithm for the maximum agreement subtree problem for binary trees (1996) (118)
- On the Agreement of Many Trees (1995) (112)
- Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly (2022) (111)
- Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes. (2014) (109)
- A protein taxonomy based on secondary structure (1999) (108)
- Graph Theoretical Insights into Evolution of Multidomain Proteins (2005) (99)
- Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery (2015) (95)
- Crystal structures of the outer membrane domain of intimin and invasin from enterohemorrhagic E. coli and enteropathogenic Y. pseudotuberculosis. (2012) (89)
- Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment (2007) (87)
- DNA copy number evolution in Drosophila cell lines (2014) (85)
- Mediation of Drosophila autosomal dosage effects and compensation by network interactions (2012) (84)
- Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers (2012) (82)
- MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types (2015) (82)
- On an Optimal Split Tree Problem (1999) (80)
- Transcription factor networks in Drosophila melanogaster. (2014) (80)
- COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations (2006) (78)
- Predicting protein-protein interaction by searching evolutionary tree automorphism space (2005) (73)
- Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. (2007) (71)
- Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies (2012) (69)
- Detecting presence of mutational signatures in cancer with confidence (2017) (68)
- WeSME: uncovering mutual exclusivity of cancer drivers and beyond (2016) (63)
- AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application (2014) (63)
- Characterization of Coding Synonymous and Non-Synonymous Variants in ADAMTS13 Using Ex Vivo and In Silico Approaches (2012) (63)
- DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide (2014) (62)
- SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks (2009) (61)
- Interrogating domain-domain interactions with parsimony based approaches (2008) (61)
- Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment (2015) (60)
- Correlated evolution of interacting proteins: looking behind the mirrortree. (2009) (58)
- Aptamer-Drug Conjugates of Active Metabolites of Nucleoside Analogs and Cytotoxic Agents Inhibit Pancreatic Tumor Cell Growth (2016) (58)
- The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis (2009) (57)
- Understanding Genotype-Phenotype Effects in Cancer via Network Approaches (2016) (56)
- On the Complexity of String Folding (1996) (52)
- Predicting protein domain interactions from coevolution of conserved regions (2007) (51)
- Grid intersection graphs and boxicity (1993) (51)
- Endogenous factor VIII synthesis from the intron 22–inverted F8 locus may modulate the immunogenicity of replacement therapy for hemophilia A (2013) (50)
- Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations (2005) (50)
- Bridging the Gap between Genotype and Phenotype via Network Approaches (2013) (49)
- AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments. (2016) (48)
- The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli (2013) (47)
- Recursive domains in proteins (2002) (46)
- Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display. (2017) (45)
- Refining multiple sequence alignments with conserved core regions (2006) (40)
- Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage (2009) (39)
- Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation (2014) (38)
- AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments (2018) (37)
- Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly (2021) (36)
- A gene-specific method for predicting hemophilia-causing point mutations. (2013) (33)
- Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome (2010) (32)
- Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction (2008) (32)
- ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis (2015) (31)
- Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster (2016) (30)
- A Fast Algorithm for Optimum Height-Limited Alphabetic Binary Trees (1993) (30)
- BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions (2017) (30)
- eQTL Epistasis – Challenges and Computational Approaches (2013) (27)
- Network integration meets network dynamics (2010) (27)
- Constructing Huffman Trees in Parallel (1995) (27)
- Modeling information flow in biological networks (2011) (26)
- Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression (2012) (26)
- Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification (2006) (24)
- Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila (2018) (23)
- ISMB 2016 Proceedings (2016) (22)
- Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model (2013) (22)
- A 2′FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein (2018) (22)
- Module Cover - A New Approach to Genotype-Phenotype Studies (2012) (22)
- An Important Connection Between Network Motifs and Parsimony Models (2006) (22)
- Parallel construction of trees with optimal weighted path length (1991) (20)
- Computing the Agreement of Trees with Bounded Degrees (1995) (20)
- Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer (2018) (20)
- Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum (2009) (20)
- Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures. (2011) (20)
- A Simple, Efficient Algorithm for Maximum Finding on Rings (1992) (20)
- Scale-free networks versus evolutionary drift (2004) (19)
- Optimal Tree Ranking is in NC (1992) (18)
- General techniques for comparing unrooted evolutionary trees (1997) (18)
- Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer (2019) (17)
- Structural footprinting in protein structure comparison: the impact of structural fragments (2007) (17)
- AptaGUI—A Graphical User Interface for the Efficient Analysis of HT-SELEX Data (2015) (15)
- The Optimal Alphabetic Tree Problem Revisited (1994) (15)
- Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro (2018) (15)
- Phylogenetic Analysis of Mitochondrial Outer Membrane β-Barrel Channels (2011) (15)
- Analysis of F9 point mutations and their correlation to severity of haemophilia B disease (2012) (14)
- AptaPLEX - A dedicated, multithreaded demultiplexer for HT-SELEX data. (2016) (14)
- Improving Strand Pairing Prediction through Exploring Folding Cooperativity (2008) (13)
- Parallel construction of near optimal binary trees (1990) (13)
- Parallel construction of optimal alphabetic trees (1993) (12)
- Synthesis of FVIII in Hemophilia-A patients with the intron-22-inversion may modulate immunogenicity (2013) (12)
- Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases (2010) (12)
- Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots (2012) (11)
- Parallel Algorithms for Parity Graphs (1991) (11)
- Bringing Folding Pathways into Strand Pairing Prediction (2007) (11)
- Subpopulation Detection and Their Comparative Analysis across Single-Cell Experiments with scPopCorn. (2019) (11)
- When and How the Perfect Phylogeny Model Explains Evolution (2014) (11)
- Mutational Signatures: From Methods to Mechanisms. (2021) (11)
- Sparse dynamic programming for maximum agreement subtree problem (1996) (11)
- Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome (2011) (10)
- Parallel recognition of complement reducible graphs and cotree construction (1990) (10)
- Unique Cost Dynamics Elucidate the Role of Frameshifting Errors in Promoting Translational Robustness (2010) (10)
- State of the art: refinement of multiple sequence alignments (2006) (10)
- State of the art: refinement of multiple sequence alignments (2010) (9)
- In Vivo Chemical Probing for G-Quadruplex Formation. (2019) (8)
- An optimal parallel minimax tree algorithm (1990) (8)
- Direct, Competitive Comparison of Linear, Monocyclic, and Bicyclic Libraries Using mRNA Display (2020) (8)
- Fold classification based on secondary structure – how much is gained by including loop topology? (2006) (8)
- Computational Approaches to Predict Protein–Protein and Domain–Domain Interactions (2007) (8)
- LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms (2014) (8)
- LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data (2018) (8)
- Parallel Maximum Independent Set in Convex Bipartite Graphs (1996) (7)
- A Parallel Algorithm for Optimum Height-Limited Alphabetic Binary Trees (1996) (7)
- DNA REPAIR FOOTPRINT UNCOVERS CONTRIBUTION OF DNA REPAIR MECHANISM TO MUTATIONAL SIGNATURES (2019) (7)
- Significance of conformational biases in Monte Carlo simulations of protein folding: Lessons from Metropolis–Hastings approach (2004) (7)
- Physics approaches to protein interactions and gene regulation (2011) (7)
- Dosage-Dependent Expression Variation Suppressed on the Drosophila Male X Chromosome (2017) (6)
- Identifying Drug Sensitivity Subnetworks with NETPHIX (2019) (6)
- Mapping DNA Breaks by Next-Generation Sequencing. (2018) (6)
- AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems (2018) (6)
- Grid Intersection and Box Intersection Graphs on Surfaces (Extended Abstract) (1995) (6)
- Predicting DNA sequence motifs of recombination hotspots by integrative visualization and analysis (2012) (5)
- A Parallel Tree Contraction Algorithm (1987) (5)
- RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer (2020) (5)
- Comprar Protein-protein Interactions and Networks · Identification, Computer Analysis, and Prediction | Panchenko, Anna | 9781848001244 | Springer (2008) (5)
- Dynamics of biological networks: Session introduction (2008) (5)
- On a Lower Bound for Short Noncontractible Cycles in Embedded Graphs (1990) (5)
- Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies (2012) (5)
- Optimal Cost-Sensitive Distributed Minimum Spanning Tree Algorithm (1996) (5)
- A simple construction of high representativity triangulations (1993) (5)
- Differences in evolutionary pressure acting within highly conserved ortholog groups (2008) (4)
- Systems-biology dissection of eukaryotic cell growth (2010) (4)
- Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse (2012) (4)
- Dynamics of biological networks (2009) (4)
- A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer (2019) (4)
- Stability of Characters and Construction of Phylogenetic Trees (2007) (4)
- Bioinformatics Pipeline using JUDI: Just Do It. (2019) (4)
- BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract) (2017) (4)
- Algorithms in Bioinformatics - 11th International Workshop, WABI 2011, Saarbrücken, Germany, September 5-7, 2011. Proceedings (2011) (3)
- Shapely DNA attracts the right partner (2015) (3)
- Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes (2020) (3)
- Research in Computational Molecular Biology (2015) (3)
- Parallel construction of binary trees with near optimal weighted path length (1996) (3)
- Surface triangulations without short noncontractible cycles (1991) (3)
- Asymptotically Optimal Election on Weighted Rings (1994) (3)
- A Work-Time Trade-off in Parallel Computation of Huffman Trees and Concave Least Weight Subsequence Problem (1994) (2)
- Ups and Downs of Poised RNA Polymerase II in B-Cells (2016) (2)
- Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways (2016) (2)
- Mutational Signatures as Sensors of Environmental Exposures: Analysis of Smoking-Induced Lung Tissue Remodeling (2022) (2)
- Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots (2012) (2)
- Subexponentially computable truncations of Jones-types polynomials (1991) (2)
- Protein Interaction Network Based Prediction of Domain-Domain and Domain-Peptide Interactions (2008) (2)
- Efficient Construction of Binary Trees with Almost Optimal Weighted Path Length (1989) (2)
- Parallel techniques for construction of trees and related problems (1992) (2)
- RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer. (2021) (2)
- AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments (2016) (2)
- The language of a virus (2021) (2)
- DNA Aptamers for Early Detection of Ebolavirus (2021) (2)
- Reconstruction of Gene Regulatory Networks by integrating biological model and a recommendation system (2020) (2)
- Graph Theoretical Approaches to Delineate Dynamics of Biological Processes (2007) (2)
- Correlated rigid modes in protein families (2016) (1)
- Bioinformatics Pipeline using JUDI: Just Do It (2019) (1)
- Modeling cell heterogeneity: from single-cell variations to mixed cells populations (2012) (1)
- ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis (2015) (1)
- Transforming rooted agreement into unrooted agreement. (1998) (1)
- Symmetric Epistasis Estimation (SEE) and its application to dissecting interaction map of Plasmodium falciparum. (2012) (1)
- Advances in Bioinformatics and Computational Biology, 4th Brazilian Symposium on Bioinformatics, BSB 2009, Porto Alegre, Brazil, July 29-31, 2009. Proceedings (2009) (1)
- ISMB 2014 Proceedings Papers Committee (2014) (1)
- Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes (2023) (1)
- LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms (2014) (1)
- Discovery of Regulatory Mechanisms from Gene Expression Variation by eQTL Analysis (2009) (1)
- ISMB/ECCB 2021 proceedings (2021) (1)
- NetREX: Network Rewiring using EXpression - Towards Context Specific Regulatory Networks (2017) (1)
- A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals (2007) (1)
- PLOS Computational Biology 2017 Reviewer and Editorial Board Thank You (2018) (1)
- Accurate sub-population detection and mapping across single cell experiments with PopCorn (2018) (1)
- Novel analysis of HT-SELEX data elucidates the role of DNA shape in transcription factor binding (2018) (1)
- Mediation of Drosophilaautosomal dosage effects and compensation by network interactions (2012) (1)
- Hidden Markov Models (2006) (1)
- Proceedings of the 11th international conference on Algorithms in bioinformatics (2011) (1)
- Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus (2022) (1)
- Correction to: DNA copy number evolution in Drosophila cell lines (2019) (1)
- NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks (2022) (1)
- Correction: Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression (2012) (0)
- C O M M E N TA R Y Open Access (2010) (0)
- Systemic approach to study the crosstalk between EGF, IGF, and Insulin Pathways - computational and experimental analysis (2008) (0)
- Towards uncovering phenotype / genotype relationships and systems level modeling of tumor heterogeneity (2013) (0)
- Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer (2020) (0)
- Mutational Signatures as Sensors of Environmental Exposures: Role of Smoking in COVID-19 Vulnerabilities (2021) (0)
- AptaBlocks: Accelerating the Design of RNA-based Drug Delivery Systems (2017) (0)
- LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data (2018) (0)
- AptaBlocks Online: A Web-Based Toolkit for the In Silico Design of Oligonucleotide Sticky Bridges (2020) (0)
- Influence network model uncovers relations between biological processes and mutational signatures (2021) (0)
- Methods for detecting contribution of mutational signatures in cancer genomes (2018) (0)
- Preface (2009) (0)
- Bioinformatics Research and Applications, 6th International Symposium, ISBRA 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings (2010) (0)
- Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer (2019) (0)
- A Simple Optimal Parallel List Ranking Algorithm (1987) (0)
- Maximum Agreement Subtree (of 3 or More Trees) (2016) (0)
- The Bioinformatics of Aptamers: HT-SELEX Analysis with AptaSUITE. (0)
- Genome-wide expression profiling Drosophila melanogaster deficiency heterozygotes reveals diverse genomic responses (2015) (0)
- A work-time trade-off in parallel computation of Huffman Tree and Concave Least Weight (1993) (0)
- I Is a Quantization. 4. If We Modify the Multiplication of Links in F I (0)
- Advances in Bioinformatics and Computational Biology (2009) (0)
- Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications (2011) (0)
- Author Correction: Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila (2019) (0)
- X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis (2012) (0)
- Embedding gene sets in low-dimensional space (2020) (0)
- Chordal Graphs in Computational Biology - New Insights and Applications (2006) (0)
- Correction to: DNA copy number evolution in Drosophila cell lines (2019) (0)
- Exploring tumor-normal cross-talk with TranNet: role of the environment in tumor progression (2023) (0)
- Zen and the Science of Pattern Identification: An Inquiry into Bayesian Skepticism (2013) (0)
- AptaBlocks Online - A web-based toolkit for the in-silico assembly of RNA complexes (2019) (0)
- Interplay between copy number, dosage compensation and expression noise in Drosophila (2016) (0)
- Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications (2007) (0)
- Genome analysis Bioinformatics pipeline using JUDI: Just Do It! (2020) (0)
- X-ray crystal structure of the transmembrane beta-domain from intimin from EHEC strain O157:H7 (2012) (0)
- Parallel algorithms for the hamiltonian cycle and hamiltonian path problems in semicomplete bipartite digraphs (1993) (0)
- WeSME: Uncovering Mutual Exclusivity of Cancer Mutations (2016) (0)
- Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology (2009) (0)
- Session Introduction (2019) (0)
- Phenotypic variation meets systems biology (2009) (0)
- Abstract 1166: APOBEC deaminases compete with tobacco smoking mutagenesis and affect age at onset of lung cancer (2023) (0)
- Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila (2018) (0)
- Integrative RNA Biology Special Interest Group Meeting (2015) (0)
- A 2′FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein (2018) (0)
- DNA copy number evolution in Drosophila cell lines (2014) (0)
- Proceedings of the 6th International Conference on Bioinformatics Research and Applications (2010) (0)
- Detection of Z-DNA Structures in Supercoiled Genome. (2023) (0)
- Cancer driver mutations: predictions and reality. (2023) (0)
- AptaTRACE Elucidates RNA Sequence-StructureMotifs from Selection Trends in HT-SELEX Experiments Graphical Abstract Highlights (2016) (0)
- Divergent Evolutionary Drift contradicts Power Law (2004) (0)
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