Teresa M Przytycka

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots
    Min Wu
    School of Computer Engineering, Nanyang Technological University, Singapore
    Proteome Sci 10:S11. 2012
  2. pmc Mediation of Drosophila autosomal dosage effects and compensation by network interactions
    John H Malone
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA
    Genome Biol 13:r28. 2012
  3. pmc 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
  4. pmc 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
  5. pmc Network integration meets network dynamics
    Teresa M Przytycka
    National Center of Biotechnology Information, NLM, NIH, Bethesda, MD 20814, USA
    BMC Biol 8:48. 2010
  6. pmc 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
  7. pmc 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
  8. pmc 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
  9. pmc 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
  10. pmc 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

Collaborators

Detail Information

Publications42

  1. pmc Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots
    Min Wu
    School of Computer Engineering, Nanyang Technological University, Singapore
    Proteome Sci 10:S11. 2012
    ..Using GO analysis we observed that the top genes are enriched with function of histone modification, highlighting the epigenetic regulatory mechanisms of recombination hotspots...
  2. pmc Mediation of Drosophila autosomal dosage effects and compensation by network interactions
    John H Malone
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA
    Genome Biol 13:r28. 2012
    ..While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering in expression networks...
  3. pmc 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...
  4. pmc 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...
  5. pmc 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...
  6. pmc 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...
  7. pmc 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...
  8. pmc 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)...
  9. pmc 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...
  10. pmc 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...
  11. pmc Symmetric Epistasis Estimation (SEE) and its application to dissecting interaction map of Plasmodium falciparum
    Yang Huang
    National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
    Mol Biosyst 8:1544-52. 2012
    ..falciparum, potentially reflecting host-pathogen interactions or drug-induced selection...
  12. ncbi request reprint 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...
  13. pmc 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...
  14. pmc 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...
  15. pmc 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
    ....
  16. pmc 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...
  17. pmc Predicting domain-domain interactions using a parsimony approach
    Katia S Guimarães
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 7:R104. 2006
    ..This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts...
  18. pmc 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
    ....
  19. pmc 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...
  20. pmc 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
    Xiangjun Du
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 41:5965-77. 2013
    ..Overall, the conspicuous enrichment of transition-susceptible sites in these specific regulatory regions suggests that non-B DNA structures may have roles in the transcriptional regulation of specific operons within the E. coli genome. ..
  21. pmc Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression
    Raheleh Salari
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    PLoS Comput Biol 8:e1002644. 2012
    ....
  22. pmc 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...
  23. ncbi request reprint 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...
  24. pmc 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...
  25. pmc 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..
  26. pmc Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies
    Raheleh Salari
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Nucleic Acids Res 41:44-53. 2013
    ..Subsequently, we applied remuRNA to determine which of the disease-associated non-coding SNPs are potentially related to RNA structural changes...
  27. pmc 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
    ....
  28. pmc 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?..
  29. pmc Transcription-dependent dynamic supercoiling is a short-range genomic force
    Fedor Kouzine
    Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, USA
    Nat Struct Mol Biol 20:396-403. 2013
    ..The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation...
  30. pmc Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers
    Jan Hoinka
    National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 28:i215-23. 2012
    ..At the same time, the combination of SELEX with novel sequencing technologies is beginning to provide the data that will allow the examination of a variety of properties of the selection process...
  31. pmc 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...
  32. ncbi request reprint 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...
  33. pmc 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
    ..Many of these methods are limited by the fact that they can handle only a small number of protein sequences. Also, details on evolutionary tree topology are missing as they use similarity matrices in lieu of the trees...
  34. pmc 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...
  35. pmc Global regulation of promoter melting in naive lymphocytes
    Fedor Kouzine
    Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 153:988-99. 2013
    ..Our studies identify promoter melting as a third key regulatory step and propose that this mechanism ensures a prompt lymphocyte response to invading pathogens...
  36. pmc eQTL Epistasis - Challenges and Computational Approaches
    Yang Huang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
    Front Genet 4:51. 2013
    ..This problem is aggravated, when epistatic effects between eQTLs are analyzed. In this review, we discuss recent algorithmic approaches for the detection of eQTL epistasis and highlight lessons that can be learned from current methods...
  37. pmc Crystal structures of the outer membrane domain of intimin and invasin from enterohemorrhagic E. coli and enteropathogenic Y. pseudotuberculosis
    James W Fairman
    National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Structure 20:1233-43. 2012
    ..We then use this set of sequences along with our structural data to find and map the evolutionarily constrained residues within the β domain...
  38. pmc 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
    ....
  39. pmc Chapter 5: Network biology approach to complex diseases
    Dong Yeon Cho
    National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland, United States of America
    PLoS Comput Biol 8:e1002820. 2012
    ..We hope that this chapter will give readers an appreciation for the wealth of algorithmic techniques that have been developed for the purpose of studying complex diseases as well as insight into their strengths and limitations...
  40. pmc Bridging the Gap between Genotype and Phenotype via Network Approaches
    Yoo Ah Kim
    National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine Bethesda, MD, USA
    Front Genet 3:227. 2012
    ....
  41. pmc 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
    ..Methods are limited in their ability to illuminate the full structure of the eQTL data. Most rely on an exhaustive, genome scale search that considers all possible locus-gene pairs and tests the linkage between each locus and gene...
  42. pmc 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...