Research Topics
Genomes and Genes | Isidore RigoutsosSummaryAffiliation: Thomas Jefferson University Location: Philadelphia, USA URL: http://computationalmedicinecenter.org Summary: non-coding RNA, process regulation, genomics, genetics, protein annotation, gene discovery, metagenomics Publications
| Collaborators
|
Detail Information
Publications
The Evi1, microRNA-143, K-Ras axis in colon cancerJin 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...- The amphioxus genome illuminates vertebrate origins and cephalochordate biologyLinda 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... - Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifsAristotelis 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... - BLOSUM62 miscalculations improve search performanceMark P Styczynski
Nat Biotechnol 26:274-5. 2008 - 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 1Wang Xia Wang
Sanders Brown Center on Aging, University of Kentucky, Lexington, Kentucky 40536, USA
J Neurosci 28:1213-23. 2008.... - Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termiteFalk 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... - What's in the mix: phylogenetic classification of metagenome sequence samplesAlice 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... - MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1Yvonne M S Tay
Stem Cell and Developmental Biology, Genome Institute of Singapore, 02 01 Genome, Singapore 138672
Stem Cells 26:17-29. 2008.... - Use of simulated data sets to evaluate the fidelity of metagenomic processing methodsKonstantinos 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... - Accurate phylogenetic classification of variable-length DNA fragmentsAlice 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... - A linguistic model for the rational design of antimicrobial peptidesChristopher 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... - A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexesKevin 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... - High-resolution metagenomics targets specific functional types in complex microbial communitiesMarina 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... - MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiationYvonne 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.... - OMiR: Identification of associations between OMIM diseases and microRNAsSimona 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... - Gene-expression forum: Decoy for microRNAsIsidore Rigoutsos
Nature 465:1016-7. 2010 - 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... - Dynamic changes in the human methylome during differentiationLouise 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... - Atypical transcription of microRNA gene fragmentsJin 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... - Insights into the regulation of a common variant of HMGA2 associated with human height during embryonic developmentYvonne 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... - Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classesAristotelis Tsirigos
Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
PLoS Comput Biol 5:e1000610. 2009.... - MicroRNA 125a and its regulation of the p53 tumor suppressor geneYingjie 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... - miR-34a contributes to megakaryocytic differentiation of K562 cells independently of p53Francisco 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... - Pattern-based phylogenetic distance estimation and tree reconstructionMichael 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... - Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stabilityYohei 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... - New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sitesIsidore 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... - Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processesIsidore 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... - Data mining and clinical data repositories: Insights from a 667,000 patient data setIrene 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... - A generic motif discovery algorithm for sequential dataKyle L Jensen
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Bioinformatics 22:21-8. 2006..AVAILABILITY: Gemoda is freely available at http://web.mit.edu/bamel/gemoda.. - In silico pattern-based analysis of the human cytomegalovirus genomeIsidore 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/)... - The draft genome of Ciona intestinalis: insights into chordate and vertebrate originsParamvir 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... - Dictionary-driven protein annotationIsidore 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/... - Dictionary-driven prokaryotic gene findingTetsuo 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... - In silico structural and functional analysis of the human cytomegalovirus (HHV5) genomeJ Novotny
Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
J Mol Biol 310:1151-66. 2001.... - Non-alpha-helical elements modulate polytopic membrane protein architectureR 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... - The emergence of pattern discovery techniques in computational biologyI 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... - Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomesI Rigoutsos
Computational Biology Center, IBM TJ Watson Research Center, Yorktown Heights, NY 10598, USA
Proc Int Conf Intell Syst Mol Biol . 1999.... - Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteinsI Rigoutsos
Computational Biology Center, Thomas J Watson Research Center, Yorktown Heights, New York 10598, USA
Proteins 37:264-77. 1999.... - Molecular moment similarity between clozapine and substituted [(4-phenylpiperazinyl)-methyl] benzamides: selective dopamine D4 agonistsB 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... - Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithmI 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... - Evaluation of annotation strategies using an entire genome sequenceIoannis Iliopoulos
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 19:717-26. 2003..The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences... - The web server of IBM's Bioinformatics and Pattern Discovery groupTien 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/... - Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein familiesNikos 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... - A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomesAristotelis 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/... - Evolution of distinct EGF domains with specific functionsMerridee 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.... - A new computational method for the detection of horizontal gene transfer eventsAristotelis 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/... - An extension and novel solution to the (l,d)-motif challenge problemMark 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... - The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 updateTien 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/... - Transcriptional organization of the Clostridium acetobutylicum genomeCarlos 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... - Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networksMatthew 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... - Reevaluation of human cytomegalovirus coding potentialEain 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... - 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... - Global secondary structure packing angle bias in proteinsDaniel 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... - Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptorsIsidore 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... - FLASH: a fast look-up algorithm for string homologyA 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)..