Teresa M Przytycka

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi Fold classification based on secondary structure--how much is gained by including loop topology?
    Jieun Jeong
    Department of Computer Science and Engineering, The Pennsylvania State University, University Park, USA
    BMC Struct Biol 6:3. 2006
  2. ncbi Scale-free networks versus evolutionary drift
    Teresa M Przytycka
    NCBI NLM NIH 8600 Rockville Pike, Bethesda, MD 20894, USA
    Comput Biol Chem 28:257-64. 2004
  3. ncbi Network integration meets network dynamics
    Teresa M Przytycka
    National Center of Biotechnology Information, NLM, NIH, Bethesda, MD 20814, USA
    BMC Biol 8:48. 2010
  4. ncbi Toward the dynamic interactome: it's about time
    Teresa M Przytycka
    National Center of Biotechnology Information, NLM, NIH, 8000 Rockville Pike, Bethesda MD 20814, USA
    Brief Bioinform 11:15-29. 2010
  5. ncbi Phenotypic variation meets systems biology
    Teresa M Przytycka
    National Institutes of Health, National Library of Medicine, National Center of Biotechnology Information, Bethesda, MD 20894, USA
    Genome Biol 10:313. 2009
  6. ncbi Differences in evolutionary pressure acting within highly conserved ortholog groups
    Teresa M Przytycka
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 8:208. 2008
  7. ncbi State of the art: refinement of multiple sequence alignments
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 7:499. 2006
  8. ncbi Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
    Raja Jothi
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
    Mol Syst Biol 5:294. 2009
  9. ncbi Interrogating domain-domain interactions with parsimony based approaches
    Katia S Guimarães
    National Center of Biotechnology, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 9:171. 2008
  10. ncbi Predicting protein domain interactions from coevolution of conserved regions
    Maricel G Kann
    Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 67:811-20. 2007

Detail Information

Publications29

  1. ncbi Fold classification based on secondary structure--how much is gained by including loop topology?
    Jieun Jeong
    Department of Computer Science and Engineering, The Pennsylvania State University, University Park, USA
    BMC Struct Biol 6:3. 2006
    ..Second, how to properly measure the effect of new information in a large data sample. We investigate alternative ways of computing and presenting this information...
  2. ncbi Scale-free networks versus evolutionary drift
    Teresa M Przytycka
    NCBI NLM NIH 8600 Rockville Pike, Bethesda, MD 20894, USA
    Comput Biol Chem 28:257-64. 2004
    ..Instead they adhere quite closely to the Yule distribution. This finding indicates that the direct applicability of scale-free models in understanding the evolution of biological network may not be as wide as it has been hoped for...
  3. ncbi Network integration meets network dynamics
    Teresa M Przytycka
    National Center of Biotechnology Information, NLM, NIH, Bethesda, MD 20814, USA
    BMC Biol 8:48. 2010
    ..However, combining various types of networks into one coherent large-scale dynamic model remains a formidable challenge. A recent paper in BMC Systems Biology describes a promising step in this direction...
  4. ncbi Toward the dynamic interactome: it's about time
    Teresa M Przytycka
    National Center of Biotechnology Information, NLM, NIH, 8000 Rockville Pike, Bethesda MD 20814, USA
    Brief Bioinform 11:15-29. 2010
    ..This burgeoning research area, which entails a shift from static to dynamic network analysis, promises to be a major step forward in our ability to model and reason about cellular function and behavior...
  5. ncbi Phenotypic variation meets systems biology
    Teresa M Przytycka
    National Institutes of Health, National Library of Medicine, National Center of Biotechnology Information, Bethesda, MD 20894, USA
    Genome Biol 10:313. 2009
    ..A report of the 18th Annual Growth Factor and Signal Transduction Symposium, Ames, USA, 11-14 June 2009...
  6. ncbi Differences in evolutionary pressure acting within highly conserved ortholog groups
    Teresa M Przytycka
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 8:208. 2008
    ..g. Proteobacteria or Firmicutes)...
  7. ncbi State of the art: refinement of multiple sequence alignments
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 7:499. 2006
    ..Refinement of existing alignment can prove to be an intelligent choice considering the increasing importance of high quality alignments in large scale high-throughput analysis...
  8. ncbi Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
    Raja Jothi
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
    Mol Syst Biol 5:294. 2009
    ..We propose that the interplay between network organization and TF dynamics could permit differential utilization of the same underlying network by distinct members of a clonal cell population...
  9. ncbi Interrogating domain-domain interactions with parsimony based approaches
    Katia S Guimarães
    National Center of Biotechnology, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 9:171. 2008
    ..Understanding the power and the limitations of these methods is key to the development of improved approaches and better understanding of the nature of these interactions...
  10. ncbi Predicting protein domain interactions from coevolution of conserved regions
    Maricel G Kann
    Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 67:811-20. 2007
    ..We provide a theoretical validation of our results leading to new insights into the interplay between coevolution and speciation of interacting proteins...
  11. ncbi Modeling information flow in biological networks
    Yoo Ah Kim
    National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Phys Biol 8:035012. 2011
    ....
  12. ncbi The crosstalk between EGF, IGF, and Insulin cell signaling pathways--computational and experimental analysis
    Rafal Zielinski
    National Center for Biotechnology Information, National Library of Medicine National Institutes of Health Bethesda, MD, USA
    BMC Syst Biol 3:88. 2009
    ..Furthermore, absence of the reaction coefficients necessary for detailed modeling of signal propagation raises the question whether simple parameter-free models could provide useful information about such pathways...
  13. ncbi Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 362:861-75. 2006
    ....
  14. ncbi COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 22:779-88. 2006
    ..These methods do not attempt to preserve the non-transitivity and hierarchic nature of the orthology relation...
  15. ncbi Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 8:173. 2007
    ..Here, proteins with similar profiles are inferred to be functionally related under the assumption that proteins involved in the same metabolic pathway or cellular system are likely to have been co-inherited during evolution...
  16. ncbi Identifying causal genes and dysregulated pathways in complex diseases
    Yoo Ah Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Comput Biol 7:e1001095. 2011
    ..While copy number alterations and gene expression data of glioblastoma patients provided opportunities to test our approach, our method can be applied to any disease system where genetic variations play a fundamental causal role...
  17. ncbi State of the art: refinement of multiple sequence alignments
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 11:3. 2010
    ..ABSTRACT: Correction to Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA and Bryant SH: State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 2006, 7:499...
  18. ncbi SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks
    Jie Zheng
    National Center for Biotechnology Information, NLM NIH, Bethesda, MD, USA
    Bioinformatics 26:141-2. 2010
    ..AVAILABILITY: SimBoolNet package (with manual) is freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/SimBoolNet..
  19. ncbi Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage
    Yang Huang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:6799-810. 2009
    ..Collectively, the results fit the concept of selection against mistranslation-induced protein misfolding being one of the factors shaping the evolution of both coding and non-coding sequences...
  20. ncbi Structural footprinting in protein structure comparison: the impact of structural fragments
    Elena Zotenko
    Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    BMC Struct Biol 7:53. 2007
    ..How do these choices affect the ability of the method to detect various types of structural similarity?..
  21. ncbi Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
    Elena Zotenko
    Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    BMC Struct Biol 6:12. 2006
    ....
  22. ncbi Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome
    Jie Zheng
    Computational Biology Branch, NCBI, NLM, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Genome Biol 11:R103. 2010
    ..At the same time, recombination hotspots are heritable. Previous studies showed instances where differences in recombination rate could be associated with sequence polymorphisms...
  23. ncbi Refining multiple sequence alignments with conserved core regions
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:2598-606. 2006
    ..A standalone version of the program is available by ftp distribution (ftp://ftp.ncbi.nih.gov/pub/REFINER) and will be incorporated into the next release of the Cn3D structure/alignment viewer...
  24. ncbi Predicting protein-protein interaction by searching evolutionary tree automorphism space
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:i241-50. 2005
    ..When compared with related computational approaches, our method reduces the search space by approximately 3 x 10(5)-fold and at the same time increases the accuracy of predicting correct binding partners...
  25. ncbi Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation
    Jie Zheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 24:2583-92. 2007
    ..The developed procedure for the identification and analysis of conserved introns and other characters with minimal or no homoplasy is expected to be useful for resolving many hard phylogenetic problems...
  26. ncbi Systems-biology dissection of eukaryotic cell growth
    Teresa M Przytycka
    National Center for Biotechnology Information, NLM, NIH, 8000 Rockville Pike, Bethesda, MD 20814, USA
    BMC Biol 8:62. 2010
    ....
  27. ncbi Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum
    Yang Huang
    National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20894, USA
    Bioinformatics 25:i15-20. 2009
    ..Furthermore, GeD allows us to uncover additional eQTLs with lower FDR, providing an important complement to traditional eQTL analysis methods...
  28. ncbi DOMINE: a database of protein domain interactions
    Balaji Raghavachari
    Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083, USA
    Nucleic Acids Res 36:D656-61. 2008
    ..DOMINE is freely available at http://domine.utdallas.edu...