Isidore Rigoutsos

Summary

Affiliation: Thomas Jefferson University
Location: Philadelphia, USA
URL: http://computationalmedicinecenter.org
Summary:
non-coding RNA, process regulation, genomics, genetics, protein annotation, gene discovery, metagenomics

Publications

  1. pmc The Evi1, microRNA-143, K-Ras axis in colon cancer
    Jin Song Gao
    Division of Infectious Diseases, Department of Medicine, Miriam and Rhode Island Hospitals, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
    FEBS Lett 585:693-9. 2011
  2. pmc The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    Linda Z Holland
    Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093 0202, USA
    Genome Res 18:1100-11. 2008
  3. pmc Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs
    Aristotelis Tsirigos
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA
    Nucleic Acids Res 36:3484-93. 2008
  4. doi BLOSUM62 miscalculations improve search performance
    Mark P Styczynski
    Nat Biotechnol 26:274-5. 2008
  5. pmc The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1
    Wang Xia Wang
    Sanders Brown Center on Aging, University of Kentucky, Lexington, Kentucky 40536, USA
    J Neurosci 28:1213-23. 2008
  6. ncbi Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
    Falk Warnecke
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nature 450:560-5. 2007
  7. ncbi What's in the mix: phylogenetic classification of metagenome sequence samples
    Alice C McHardy
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA
    Curr Opin Microbiol 10:499-503. 2007
  8. ncbi MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1
    Yvonne M S Tay
    Stem Cell and Developmental Biology, Genome Institute of Singapore, 02 01 Genome, Singapore 138672
    Stem Cells 26:17-29. 2008
  9. ncbi Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
    Konstantinos Mavromatis
    Department of Energy Joint Genome Institute DOE JGI, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Methods 4:495-500. 2007
  10. ncbi Accurate phylogenetic classification of variable-length DNA fragments
    Alice Carolyn McHardy
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA
    Nat Methods 4:63-72. 2007

Detail Information

Publications59

  1. pmc The Evi1, microRNA-143, K-Ras axis in colon cancer
    Jin Song Gao
    Division of Infectious Diseases, Department of Medicine, Miriam and Rhode Island Hospitals, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
    FEBS Lett 585:693-9. 2011
    ..We find an indirect relationship between miRNA-143 and Evi1 expression. A complex molecular axis linking Evi1, miRNA-143 is operational in human colon cancer...
  2. pmc The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    Linda Z Holland
    Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093 0202, USA
    Genome Res 18:1100-11. 2008
    ..Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates...
  3. pmc Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs
    Aristotelis Tsirigos
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA
    Nucleic Acids Res 36:3484-93. 2008
    ..We highlight the ramifications of this observation with a concrete example that involves the microsatellite instability gene MLH1...
  4. doi BLOSUM62 miscalculations improve search performance
    Mark P Styczynski
    Nat Biotechnol 26:274-5. 2008
  5. pmc The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1
    Wang Xia Wang
    Sanders Brown Center on Aging, University of Kentucky, Lexington, Kentucky 40536, USA
    J Neurosci 28:1213-23. 2008
    ....
  6. ncbi Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
    Falk Warnecke
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nature 450:560-5. 2007
    ..Our results underscore how complex even a 1-microl environment can be...
  7. ncbi What's in the mix: phylogenetic classification of metagenome sequence samples
    Alice C McHardy
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA
    Curr Opin Microbiol 10:499-503. 2007
    ..This step is essential for the reconstruction of the metabolic capabilities of individual organisms or phylogenetic clades of a community, and the study of their interactions...
  8. ncbi MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1
    Yvonne M S Tay
    Stem Cell and Developmental Biology, Genome Institute of Singapore, 02 01 Genome, Singapore 138672
    Stem Cells 26:17-29. 2008
    ....
  9. ncbi Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
    Konstantinos Mavromatis
    Department of Energy Joint Genome Institute DOE JGI, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Methods 4:495-500. 2007
    ..The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis...
  10. ncbi Accurate phylogenetic classification of variable-length DNA fragments
    Alice Carolyn McHardy
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA
    Nat Methods 4:63-72. 2007
    ..The method requires no more than 100 kb of training sequence for the creation of accurate models of sample-specific populations and can assign fragments >or=1 kb with high specificity...
  11. ncbi A linguistic model for the rational design of antimicrobial peptides
    Christopher Loose
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 443:867-9. 2006
    ..We used this set of grammars to create new, unnatural AmP sequences. Our peptides conform to the formal syntax of natural antimicrobial peptides but populate a previously unexplored region of protein sequence space...
  12. ncbi Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
    Hector Garcia Martin
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Biotechnol 24:1263-9. 2006
    ..The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems...
  13. ncbi A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
    Kevin C Miranda
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, P O Box 218, NY 10598, USA
    Cell 126:1203-17. 2006
    ..We also extended the method's key idea to a low-error microRNA-precursor-discovery scheme; our studies suggest that the number of microRNA precursors in mammalian genomes likely ranges in the tens of thousands...
  14. doi High-resolution metagenomics targets specific functional types in complex microbial communities
    Marina G Kalyuzhnaya
    Department of Microbiology, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, Washington 98105, USA
    Nat Biotechnol 26:1029-34. 2008
    ..This high-resolution, targeted metagenomics approach may be applicable to a wide variety of ecosystems...
  15. doi MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
    Yvonne Tay
    Stem Cell and Developmental Biology, Genome Institute of Singapore, Agency for Science Technology and Research, 08 01, Genome, 60 Biopolis Street, Singapore 138672, Singapore
    Nature 455:1124-8. 2008
    ....
  16. doi OMiR: Identification of associations between OMIM diseases and microRNAs
    Simona Rossi
    Dept of Experimental Therapeutics, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Genomics 97:71-6. 2011
    ..Our findings indicate that inclusion of miRNAs among the candidate genes to be considered could assist geneticists in their hunt for disease genes, particularly in the case of rare diseases...
  17. ncbi Gene-expression forum: Decoy for microRNAs
    Isidore Rigoutsos
    Nature 465:1016-7. 2010
  18. doi Short RNAs: how big is this iceberg?
    Isidore Rigoutsos
    Bioinformatics and Pattern Discovery Group, Computation Biology Center, IBM Thomas J Watson Research Center, PO Box 218, Yonktown Heights, NY 10598, USA
    Curr Biol 20:R110-3. 2010
    ..Studies of additional organisms support the new pathway's presence across animals...
  19. pmc Dynamic changes in the human methylome during differentiation
    Louise Laurent
    UCSD Medical Center, Department of Reproductive Medicine, San Diego, California 92103, USA
    Genome Res 20:320-31. 2010
    ..Our results highlight the value of high-resolution methylation maps, in conjunction with other systems-level analyses, for investigation of previously undetectable developmental regulatory mechanisms...
  20. pmc Atypical transcription of microRNA gene fragments
    Jin Song Gao
    Laboratory of Retrovirology, Division of Infectious Diseases, Rhode Island and Miriam Hospitals, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
    Nucleic Acids Res 38:2775-87. 2010
    ..Taken together, our findings suggest the existence of a previously unrecognized atypical transcription program for miRNA precursor sequences...
  21. doi Insights into the regulation of a common variant of HMGA2 associated with human height during embryonic development
    Yvonne Tay
    Neural Stem Cells, Institute of Medical Biology, Agency for Science Technology and Research A STAR, 8A Biomedical Grove, 06 06 Immunos, Singapore 138648, Singapore
    Stem Cell Rev 5:328-33. 2009
    ..We briefly discuss this result in the context of other known functions for miR-196b during vertebrate development...
  22. pmc Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes
    Aristotelis Tsirigos
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
    PLoS Comput Biol 5:e1000610. 2009
    ....
  23. pmc MicroRNA 125a and its regulation of the p53 tumor suppressor gene
    Yingjie Zhang
    Division of Infectious Diseases, Department of Medicine, Laboratory of Retrovirology, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
    FEBS Lett 583:3725-30. 2009
    ..The basis of this activity is the high degree of sequence homology between the seed sequence of miR-125a and the 3'-UTR of p53. Our findings add miRNA-125a to the growing list of miRNA with oncogenic targets...
  24. doi miR-34a contributes to megakaryocytic differentiation of K562 cells independently of p53
    Francisco Navarro
    Immune Disease Institute and Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Blood 114:2181-92. 2009
    ..However, in p53-null K562 cells, phorbol esters induce miR-34a expression independently of p53 by activating an alternative phorbol ester-responsive promoter to produce a longer pri-miR-34a transcript...
  25. pmc Pattern-based phylogenetic distance estimation and tree reconstruction
    Michael Hohl
    Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
    Evol Bioinform Online 2:359-75. 2006
    ..The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances...
  26. pmc Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability
    Yohei Kirino
    Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Nat Cell Biol 11:652-8. 2009
    ..Our findings underscore the significance of sDMA modification of Piwi proteins in the germline and suggest an interacting pathway of genes that are required for piRNA function and PGC specification...
  27. doi New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites
    Isidore Rigoutsos
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York 10598, USA
    Cancer Res 69:3245-8. 2009
    ..Recent work has shown that miRNAs can target extensively the amino acid coding region of animal mRNAs and can do so at locations that are not necessarily conserved across organisms...
  28. pmc Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes
    Isidore Rigoutsos
    IBM Thomas J Watson Research Center, P O Box 218, Yorktown Heights, NY 10598, USA
    Proc Natl Acad Sci U S A 103:6605-10. 2006
    ..These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome...
  29. ncbi Data mining and clinical data repositories: Insights from a 667,000 patient data set
    Irene M Mullins
    Department of Public Health Sciences, University of Virginia Health System, Charlottesville, VA, USA
    Comput Biol Med 36:1351-77. 2006
    ..The initial results from this study suggest that these approaches have the potential to expand research capabilities through identification of potentially novel clinical disease associations...
  30. ncbi A generic motif discovery algorithm for sequential data
    Kyle L Jensen
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Bioinformatics 22:21-8. 2006
    ..However, previous methods have been unable to combine exhaustive search with complex motif representations and are each typically only applicable to a certain class of problems...
  31. ncbi The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins
    Paramvir Dehal
    U S Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Science 298:2157-67. 2002
    ..The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi...
  32. pmc Dictionary-driven protein annotation
    Isidore Rigoutsos
    Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, Yorktown Heights, NY 10598, USA
    Nucleic Acids Res 30:3901-16. 2002
    ..Finally, we have computed the annotations of more than 70 complete genomes and made them available on the World Wide Web at http://cbcsrv.watson.ibm.com/Annotations/...
  33. pmc Dictionary-driven prokaryotic gene finding
    Tetsuo Shibuya
    Exploratory Technology, IBM Tokyo Research Laboratory, 1623 14 Shimotsuruma, Yamato shi, Kanagawa 242 8502, Japan
    Nucleic Acids Res 30:2710-25. 2002
    ..Examples of previously unreported genes are also shown and discussed in detail...
  34. ncbi In silico structural and functional analysis of the human cytomegalovirus (HHV5) genome
    J Novotny
    Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
    J Mol Biol 310:1151-66. 2001
    ....
  35. ncbi Non-alpha-helical elements modulate polytopic membrane protein architecture
    R P Riek
    Molecular Cardiology Unit Victor Chang Cardiac Research Institute, St Vincent's Hospital, Darlinghurst, New South Wales, 2010, Australia
    J Mol Biol 306:349-62. 2001
    ..Deconvolution of these non-canonical features into their composite elements is essential for understanding the pleiotropy of polytopic protein structure and function, and must be considered in developing valid macromolecular models...
  36. ncbi The emergence of pattern discovery techniques in computational biology
    I Rigoutsos
    Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, Yorktown Heights, New York 10598, USA
    Metab Eng 2:159-77. 2000
    ..In this presentation, and after defining the problem in its generality, we review some of the algorithms that have appeared in the literature and describe several applications of pattern discovery to problems from computational biology...
  37. ncbi Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes
    I Rigoutsos
    Computational Biology Center, IBM TJ Watson Research Center, Yorktown Heights, NY 10598, USA
    Proc Int Conf Intell Syst Mol Biol . 1999
    ....
  38. ncbi Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins
    I Rigoutsos
    Computational Biology Center, Thomas J Watson Research Center, Yorktown Heights, New York 10598, USA
    Proteins 37:264-77. 1999
    ....
  39. ncbi Molecular moment similarity between clozapine and substituted [(4-phenylpiperazinyl)-methyl] benzamides: selective dopamine D4 agonists
    B D Silverman
    IBM Thomas J Watson Research Center, Yorktown Heights, NY 10598, USA
    J Comput Aided Mol Des 12:525-32. 1998
    ..The proximity of the dopamine D4 antagonist clozapine to the molecules of this series is also examined in the moment space...
  40. ncbi Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm
    I Rigoutsos
    Computational Biology Center, IBM Thomas J Watson Research Center, York Town Heights, NY 10598, USA
    Bioinformatics 14:55-67. 1998
    ..Finally, experimental analysis indicates that the algorithm is output sensitive, i.e. its running time is quasi-linear to the size of the generated output...
  41. ncbi FLASH: a fast look-up algorithm for string homology
    A Califano
    IBM T J Watson Research Center, Yorktown Heights, NY 10598, USA
    Proc Int Conf Intell Syst Mol Biol 1:56-64. 1993
    ..It contains the full Swiss-Prot database rel 25 (10 MR) and the genome of E. Coli (2 MR). The system is currently being expanded to include the complete Genbank database.(ABSTRACT TRUNCATED AT 250 WORDS)..
  42. pmc In silico pattern-based analysis of the human cytomegalovirus genome
    Isidore Rigoutsos
    Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, Yorktown Heights, New York 10598, USA
    J Virol 77:4326-44. 2003
    ..All of the results of the present study can be found and interactively explored online (http://cbcsrv.watson.ibm.com/virus/)...
  43. ncbi Evaluation of annotation strategies using an entire genome sequence
    Ioannis Iliopoulos
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 19:717-26. 2003
    ..In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner...
  44. pmc The web server of IBM's Bioinformatics and Pattern Discovery group
    Tien Huynh
    Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA
    Nucleic Acids Res 31:3645-50. 2003
    ..The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/...
  45. ncbi Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families
    Nikos Darzentas
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, UK
    Proteins 61:926-37. 2005
    ..Our analysis suggests that pattern discovery methods can be substantially more sensitive in detecting remote protein relationships while at the same time guaranteeing high specificity...
  46. pmc A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes
    Aristotelis Tsirigos
    New York University, Computer Science, New York, NY 10021, USA
    Nucleic Acids Res 33:3699-707. 2005
    ..Atypical region predictions for many eukaryotic viruses, including the alpha-, beta- and gamma-herpesvirinae, and 123 archaeal and bacterial genomes, have been made available online at http://cbcsrv.watson.ibm.com/HGT_SVM/...
  47. pmc Evolution of distinct EGF domains with specific functions
    Merridee A Wouters
    Computational Biology and Bioinformatics Program, Victor Chang Cardiac Research Institute, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
    Protein Sci 14:1091-103. 2005
    ....
  48. pmc A new computational method for the detection of horizontal gene transfer events
    Aristotelis Tsirigos
    New York University, Computer Science New York, NY 10021, USA
    Nucleic Acids Res 33:922-33. 2005
    ..Our method's horizontal gene transfer predictions for 123 microbial genomes are available online at http://cbcsrv.watson.ibm.com/HGT/...
  49. ncbi An extension and novel solution to the (l,d)-motif challenge problem
    Mark P Styczynski
    Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Genome Inform 15:63-71. 2004
    ..We demonstrate the performance of the algorithm on publicly available datasets and show that the algorithm deterministically enumerates the optimal motifs...
  50. pmc The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update
    Tien Huynh
    Bioinformatics and Pattern Discovery Group, IBM T J Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA
    Nucleic Acids Res 32:W10-5. 2004
    ..The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/...
  51. pmc Transcriptional organization of the Clostridium acetobutylicum genome
    Carlos J Paredes
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
    Nucleic Acids Res 32:1973-81. 2004
    ..Based on the set of known C.acetobutylicum TUs, the presented TU map offers an 88% prediction accuracy...
  52. ncbi Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks
    Matthew S Wong
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Physiol Genomics 16:247-55. 2004
    ..In conclusion, this model may be useful as a prototype physiological regulatory network where gene expression profiles are analyzed in concert with changes in cell function...
  53. pmc Reevaluation of human cytomegalovirus coding potential
    Eain Murphy
    Department of Molecular Biology, Princeton University, Princeton, NJ 80544, USA
    Proc Natl Acad Sci U S A 100:13585-90. 2003
    ..Support for several of the predictions of our in silico analysis was obtained by sequencing several domains within a clinical isolate of human cytomegalovirus...
  54. ncbi Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: "waiting for Godot"
    Kaoru Azumi
    Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
    Immunogenetics 55:570-81. 2003
    ..However, there are key V regions, the essential feature of an immunoglobulin superfamily VC1-like core, and possible proto-MHC regions scattered throughout the genome waiting for Godot...
  55. ncbi Global secondary structure packing angle bias in proteins
    Daniel E Platt
    Bioinformatics and Pattern Discovery, IBM T J Watson Research Center, Yorktown Heights, New York, USA
    Proteins 53:252-61. 2003
    ..Selection for interactive segment triplets shows results consistent with prior studies...
  56. pmc Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors
    Isidore Rigoutsos
    Bioinformatics and Pattern Discovery Research Group, IBM Thomas J Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA
    Nucleic Acids Res 31:4625-31. 2003
    ..The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html...
  57. pmc The complex transcriptional landscape of the anucleate human platelet
    Paul F Bray
    Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA
    BMC Genomics 14:1. 2013
    ..The goal of this effort was to deep-sequence RNA from leukocyte-depleted platelets to capture the complex profile of all expressed transcripts...
  58. doi The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome
    Eric R Londin
    Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Biol Direct 9:3. 2014
    ..We profiled the platelet transcriptome of 10 healthy young males (5 white and 5 black) with no notable clinical history using RNA sequencing and by Affymetrix microarray...