computational biology

Summary

Summary: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories applicable to MOLECULAR BIOLOGY and areas of computer-based techniques for solving biological problems including manipulation of models and datasets.

Top Publications

  1. pmc phyloXML: XML for evolutionary biology and comparative genomics
    Mira V Han
    School of Informatics, Indiana University, Bloomington, IN 47408, USA
    BMC Bioinformatics 10:356. 2009
  2. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
  3. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
  4. pmc A map of human genome variation from population-scale sequencing
    Richard M Durbin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Nature 467:1061-73. 2010
  5. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
  6. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
  7. ncbi MRBAYES: Bayesian inference of phylogenetic trees
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Bioinformatics 17:754-5. 2001
  8. pmc Jalview Version 2--a multiple sequence alignment editor and analysis workbench
    Andrew M Waterhouse
    School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Bioinformatics 25:1189-91. 2009
  9. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
  10. ncbi Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001

Detail Information

Publications260 found, 100 shown here

  1. pmc phyloXML: XML for evolutionary biology and comparative genomics
    Mira V Han
    School of Informatics, Indiana University, Bloomington, IN 47408, USA
    BMC Bioinformatics 10:356. 2009
    ..The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types...
  2. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
    ..This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process...
  3. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
    ..Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies...
  4. pmc A map of human genome variation from population-scale sequencing
    Richard M Durbin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Nature 467:1061-73. 2010
    ..These methods and public data will support the next phase of human genetic research...
  5. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics...
  6. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
    ..BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome...
  7. ncbi MRBAYES: Bayesian inference of phylogenetic trees
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Bioinformatics 17:754-5. 2001
    ..The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo...
  8. pmc Jalview Version 2--a multiple sequence alignment editor and analysis workbench
    Andrew M Waterhouse
    School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Bioinformatics 25:1189-91. 2009
    ..53 compliant sequence or annotation server...
  9. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
    ..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
  10. ncbi Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
    ..We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/...
  11. pmc The RAST Server: rapid annotations using subsystems technology
    Ramy K Aziz
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
    BMC Genomics 9:75. 2008
    ..The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them...
  12. pmc Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    Jeremy Goecks
    Department of Biology and Department of Mathematics and Computer Science, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
    Genome Biol 11:R86. 2010
    ..Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis...
  13. pmc OrthoMCL: identification of ortholog groups for eukaryotic genomes
    Li Li
    Department of Biology and Genetics, Center for Bioinformatics, and Genomics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 13:2178-89. 2003
    ..cbil.upenn.edu/gene-family). Analysis of clusters incorporating P. falciparum genes identifies numerous enzymes that were incompletely annotated in first-pass annotation of the parasite genome...
  14. pmc Cytoscape: a software environment for integrated models of biomolecular interaction networks
    Paul Shannon
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 13:2498-504. 2003
    ....
  15. pmc The Sequence Alignment/Map format and SAMtools
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Bioinformatics 25:2078-9. 2009
    ..SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments...
  16. ncbi SOAP2: an improved ultrafast tool for short read alignment
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen, 518083, China
    Bioinformatics 25:1966-7. 2009
    ..Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome...
  17. ncbi Combinatorial microRNA target predictions
    Azra Krek
    Center for Comparative Functional Genomics, Department of Biology, New York University, 100 Washington Square East, New York, New York 10003, USA
    Nat Genet 37:495-500. 2005
    ..In particular, we experimentally validate common regulation of Mtpn by miR-375, miR-124 and let-7b and thus provide evidence for coordinate microRNA control in mammals...
  18. pmc MUSCLE: a multiple sequence alignment method with reduced time and space complexity
    Robert C Edgar
    Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720 3102, USA
    BMC Bioinformatics 5:113. 2004
    ..We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles...
  19. ncbi Prediction of mammalian microRNA targets
    Benjamin P Lewis
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 115:787-98. 2003
    ..The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions...
  20. pmc ABySS: a parallel assembler for short read sequence data
    Jared T Simpson
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 19:1117-23. 2009
    ..Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes...
  21. pmc Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 37:1-13. 2009
    ....
  22. pmc The IntAct molecular interaction database in 2010
    B Aranda
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D525-31. 2010
    ..Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
  23. pmc The transcriptional landscape of the yeast genome defined by RNA sequencing
    Ugrappa Nagalakshmi
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 320:1344-9. 2008
    ..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated...
  24. pmc CHARMM: the biomolecular simulation program
    B R Brooks
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Comput Chem 30:1545-614. 2009
    ..This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983...
  25. pmc KAAS: an automatic genome annotation and pathway reconstruction server
    Yuki Moriya
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 35:W182-5. 2007
    ..The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database...
  26. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
    ..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
  27. ncbi The genetic landscape of a cell
    Michael Costanzo
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Science 327:425-31. 2010
    ..We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification...
  28. pmc High-throughput functional annotation and data mining with the Blast2GO suite
    Stefan Götz
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Nucleic Acids Res 36:3420-35. 2008
    ..Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data...
  29. pmc BLAST+: architecture and applications
    Christiam Camacho
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    BMC Bioinformatics 10:421. 2009
    ..There are also some shortcomings in the user-interface of the current command-line applications...
  30. pmc EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J Vilella
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 19:327-35. 2009
    ..All data are made available in a number of formats and will be kept up to date with the Ensembl project...
  31. ncbi An improved general amino acid replacement matrix
    Si Quang Le
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS, Universite Montpellier II, Montpellier, France
    Mol Biol Evol 25:1307-20. 2008
    ..Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG...
  32. pmc Core signaling pathways in human pancreatic cancers revealed by global genomic analyses
    Sian Jones
    Sol Goldman Pancreatic Cancer Research Center, Ludwig Center and Howard Hughes Medical Institute at the Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
    Science 321:1801-6. 2008
    ..Dysregulation of these core pathways and processes through mutation can explain the major features of pancreatic tumorigenesis...
  33. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D5-16. 2010
    ..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  34. ncbi The consensus coding sequences of human breast and colorectal cancers
    Tobias Sjoblom
    Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
    Science 314:268-74. 2006
    ..These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention, and open fertile avenues for basic research in tumor biology...
  35. pmc MEGAN analysis of metagenomic data
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
    Genome Res 17:377-86. 2007
    ..Also, simulations that evaluate the performance of the approach for different read lengths are presented...
  36. pmc Fast and effective prediction of microRNA/target duplexes
    Marc Rehmsmeier
    Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research, Postfach 10 01 31, 33501 Bielefeld, Germany
    RNA 10:1507-17. 2004
    ..RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/)...
  37. pmc The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010
    ..Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/)...
  38. pmc BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources
    Chunlei Wu
    Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr, San Diego, CA 92121, USA
    Genome Biol 10:R130. 2009
    ..gnf.org, a centralized gene portal for aggregating distributed gene annotation resources. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform...
  39. pmc Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    James H Bullard
    Division of Biostatistics, University of California, Berkeley, Berkeley, CA, USA
    BMC Bioinformatics 11:94. 2010
    ..We provide a detailed evaluation of statistical methods for normalization and differential expression (DE) analysis of Illumina transcriptome sequencing (mRNA-Seq) data...
  40. pmc JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
    Elodie Portales-Casamar
    Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
    Nucleic Acids Res 38:D105-10. 2010
    ..Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches...
  41. pmc WoLF PSORT: protein localization predictor
    Paul Horton
    Computational Biology Research Center, AIST, Tokyo, Japan
    Nucleic Acids Res 35:W585-7. 2007
    ..Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org...
  42. pmc MicroRNA targets in Drosophila
    Anton J Enright
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Genome Biol 5:R1. 2003
    ..Application to the D. melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known miRNAs...
  43. pmc The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    Ross Overbeek
    Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA
    Nucleic Acids Res 33:5691-702. 2005
    ..The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms...
  44. pmc Predicting deleterious amino acid substitutions
    P C Ng
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genome Res 11:863-74. 2001
    ..may be used to identify plausible disease candidates among the SNPs that cause missense substitutions...
  45. pmc InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
    Gabriel Ostlund
    Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE 10691 Stockholm, Sweden
    Nucleic Acids Res 38:D196-203. 2010
    ..To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters...
  46. ncbi T-Coffee: A novel method for fast and accurate multiple sequence alignment
    C Notredame
    National Institute for Medical Research, The Ridgeway, London, NW7 1AA, UK
    J Mol Biol 302:205-17. 2000
    ..The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests...
  47. pmc Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    Mitchell Guttman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:503-10. 2010
    ..Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes...
  48. pdf DAVID: Database for Annotation, Visualization, and Integrated Discovery
    Glynn Dennis
    Science Applications International Corporation Frederick, Clinical Services Program, Laboratory of Immunopathogenesis and Bioinformatics, National Cancer Institute at Frederick, MD 21702, USA
    Genome Biol 4:P3. 2003
    ..A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information...
  49. ncbi Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    Adrian Alexa
    Max Planck Institute for Informatics Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
    Bioinformatics 22:1600-7. 2006
    ..g. based on Gene Ontology (GO). We develop methods that increase the explanatory power of this approach by integrating knowledge about relationships between the GO terms into the calculation of the statistical significance...
  50. pmc Integration of biological networks and gene expression data using Cytoscape
    Melissa S Cline
    Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
    Nat Protoc 2:2366-82. 2007
    ..These steps provide a broad sample of the types of analyses performed by Cytoscape...
  51. pmc SNP detection for massively parallel whole-genome resequencing
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Genome Res 19:1124-32. 2009
    ..Our analyses demonstrate that our method has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth...
  52. pmc Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
    Sharon R Browning
    Department of Statistics, The University of Auckland, Auckland, New Zealand
    Am J Hum Genet 81:1084-97. 2007
    ..1 days of computing time, with 99% of masked alleles imputed correctly. Our method is implemented in the Beagle software package, which is freely available...
  53. ncbi Generating samples under a Wright-Fisher neutral model of genetic variation
    Richard R Hudson
    Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA
    Bioinformatics 18:337-8. 2002
    ..The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models...
  54. pmc Biopython: freely available Python tools for computational molecular biology and bioinformatics
    Peter J A Cock
    Plant Pathology, SCRI, Invergowrie, Dundee, UK
    Bioinformatics 25:1422-3. 2009
    ....
  55. ncbi Switching from repression to activation: microRNAs can up-regulate translation
    Shobha Vasudevan
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
    Science 318:1931-4. 2007
    ..Thus, activation is a common function of microRNPs on cell cycle arrest. We propose that translation regulation by microRNPs oscillates between repression and activation during the cell cycle...
  56. pmc Criteria for annotation of plant MicroRNAs
    Blake C Meyers
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Plant Cell 20:3186-90. 2008
    ..Herein, we update the specific criteria required for the annotation of plant miRNAs, including experimental and computational data, as well as refinements to standard nomenclature...
  57. pmc PROSITE, a protein domain database for functional characterization and annotation
    Christian J A Sigrist
    Structural Biology and Bioinformatics Department, University of Geneva, Swiss Institute of Bioinformatics, Centre Medical Universitaire, CH 1211 Geneva 4, Switzerland
    Nucleic Acids Res 38:D161-6. 2010
    ..The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/...
  58. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004
    ..The expression of miR395, the sulfurylase-targeting miRNA, increases upon sulfate starvation, showing that miRNAs can be induced by environmental stress...
  59. ncbi Computational methods for transcriptome annotation and quantification using RNA-seq
    Manuel Garber
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 8:469-77. 2011
    ..Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications...
  60. ncbi A review of feature selection techniques in bioinformatics
    Yvan Saeys
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    Bioinformatics 23:2507-17. 2007
    ....
  61. pmc WormBase: a comprehensive resource for nematode research
    Todd W Harris
    Ontario Institute for Cancer Research, Toronto, ON, Canada
    Nucleic Acids Res 38:D463-7. 2010
    ..Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base...
  62. pmc PANTHER: a library of protein families and subfamilies indexed by function
    Paul D Thomas
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2129-41. 2003
    ..Third, we use the family HMMs to rank missense single nucleotide polymorphisms (SNPs), on a database-wide scale, according to their likelihood of affecting protein function...
  63. pmc BioMart--biological queries made easy
    Damian Smedley
    Ontario Institute for Cancer Research, MaRS Centre, 101 College Street, Toronto, Ontario, Canada
    BMC Genomics 10:22. 2009
    ..This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution...
  64. ncbi Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 23:127-8. 2007
    ..Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. AVAILABILITY: iTOL is available at http://itol.embl.de..
  65. pmc MINT, the molecular interaction database: 2009 update
    Arnaud Ceol
    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome
    Nucleic Acids Res 38:D532-9. 2010
    ..MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium...
  66. pmc ChIP-seq: advantages and challenges of a maturing technology
    Peter J Park
    Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
    Nat Rev Genet 10:669-80. 2009
    ..ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms...
  67. pmc ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    Markus Wiederstein
    Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
    Nucleic Acids Res 35:W407-10. 2007
    ..ProSA-web is accessible at https://prosa.services.came.sbg.ac.at...
  68. pmc AmiGO: online access to ontology and annotation data
    Seth Carbon
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioinformatics 25:288-9. 2009
    ..AmiGO is free open source software developed and maintained by the GO Consortium...
  69. 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...
  70. ncbi The structure of haplotype blocks in the human genome
    Stacey B Gabriel
    Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
    Science 296:2225-9. 2002
    ..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
  71. ncbi UniRef: comprehensive and non-redundant UniProt reference clusters
    Baris E Suzek
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Bioinformatics 23:1282-8. 2007
    ..Clustering of protein sequence space based on sequence similarity helps organize all sequences into manageable datasets and reduces sampling bias and overrepresentation of sequences...
  72. ncbi The protein kinase complement of the human genome
    G Manning
    SUGEN Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
    Science 298:1912-34. 2002
    ..We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons...
  73. pmc Quantifying similarity between motifs
    Shobhit Gupta
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA
    Genome Biol 8:R24. 2007
    ..Experimental simulations demonstrate the accuracy of Tomtom's E values and its effectiveness in finding similar motifs...
  74. pmc Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
    Eli Meyer
    University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    BMC Genomics 10:219. 2009
    ..We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora...
  75. pmc WGCNA: an R package for weighted correlation network analysis
    Peter Langfelder
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Bioinformatics 9:559. 2008
    ..While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial...
  76. pmc KEGG for representation and analysis of molecular networks involving diseases and drugs
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 38:D355-60. 2010
    ..The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets...
  77. pmc ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    Adam A Margolin
    Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
    BMC Bioinformatics 7:S7. 2006
    ..This method uses an information theoretic approach to eliminate the majority of indirect interactions inferred by co-expression methods...
  78. pmc CD-HIT Suite: a web server for clustering and comparing biological sequences
    Ying Huang
    California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
    Bioinformatics 26:680-2. 2010
    ..Users can now interactively explore the clusters within web browsers. We also provide downloadable clusters for several public databases (NCBI NR, Swissprot and PDB) at different identity levels...
  79. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 38:D473-9. 2010
    ..The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism...
  80. pmc Predicting new molecular targets for known drugs
    Michael J Keiser
    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94143 2550, USA
    Nature 462:175-81. 2009
    ..The chemical similarity approach is systematic and comprehensive, and may suggest side-effects and new indications for many drugs...
  81. ncbi Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
    Vitantonio Pantaleo
    Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino, Italy
    Plant J 62:960-76. 2010
    ..Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs...
  82. pmc Tablet--next generation sequence assembly visualization
    Iain Milne
    Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK
    Bioinformatics 26:401-2. 2010
    ..Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine...
  83. pmc An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Hongkai Ji
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Biotechnol 26:1293-300. 2008
    ....
  84. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
  85. ncbi Locating proteins in the cell using TargetP, SignalP and related tools
    Olof Emanuelsson
    Stockholm Bioinformatics Center, AlbaNova, Stockholm University, SE 10691 Stockholm, Sweden
    Nat Protoc 2:953-71. 2007
    ..In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular...
  86. pmc Global reconstruction of the human metabolic network based on genomic and bibliomic data
    Natalie C Duarte
    Bioengineering Department, University of California at San Diego, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 104:1777-82. 2007
    ..These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology...
  87. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
    ..This service is available free to all users at http://molprobity.biochem.duke.edu...
  88. pmc RNA-Seq gene expression estimation with read mapping uncertainty
    Bo Li
    Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA
    Bioinformatics 26:493-500. 2010
    ..Previous computational methods either discard reads that map to multiple locations or allocate them to genes heuristically...
  89. pmc RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    Karin Lagesen
    Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, NO 0027 Oslo, Norway
    Nucleic Acids Res 35:3100-8. 2007
    ..Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server...
  90. pmc JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
    Jan Christian Bryne
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N 5008 Bergen, Norway
    Nucleic Acids Res 36:D102-6. 2008
    ..JASPAR is available at http://jaspar.genereg.net...
  91. ncbi Multiple alignment of DNA sequences with MAFFT
    Kazutaka Katoh
    Digital Medicine Initiative, Kyushu University, Fukuoka, Japan
    Methods Mol Biol 537:39-64. 2009
    ..For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE...
  92. ncbi Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
    ....
  93. pmc Differential expression analysis for sequence count data
    Simon Anders
    European Molecular Biology Laboratory, Mayerhofstraße 1, 69117 Heidelberg, Germany
    Genome Biol 11:R106. 2010
    ..We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package...
  94. ncbi Genesis: cluster analysis of microarray data
    Alexander Sturn
    Institute of Biomedical Engineering, Graz University of Technology, Krenngasse 37, 8010 Graz, Austria
    Bioinformatics 18:207-8. 2002
    ..Additionally, mapping of gene expression data onto chromosomal sequences was implemented to enhance promoter analysis and investigation of transcriptional control mechanisms...
  95. ncbi GenABEL: an R library for genome-wide association analysis
    Yurii S Aulchenko
    Department of Epidemiology and Biostatistics, Erasmus MC Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands
    Bioinformatics 23:1294-6. 2007
    ..We evaluated GenABEL using one simulated and two real data sets. We conclude that GenABEL enables the analysis of GWA data on desktop computers...
  96. ncbi A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    Marc Sultan
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Science 321:956-60. 2008
    ..A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing...
  97. ncbi The genomic landscapes of human breast and colorectal cancers
    Laura D Wood
    Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
    Science 318:1108-13. 2007
    ..These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy...
  98. ncbi Lost in translation: an assessment and perspective for computational microRNA target identification
    Panagiotis Alexiou
    Institute of Molecular Oncology, Biomedical Sciences Research Center Alexander Fleming, 166 72 Varkiza, Greece
    Bioinformatics 25:3049-55. 2009
    ..The review includes an assessment of the prediction quality of these programs and their combinations...
  99. pmc ELM: the status of the 2010 eukaryotic linear motif resource
    Cathryn M Gould
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D167-80. 2010
    ..Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation...
  100. ncbi Bio2RDF: towards a mashup to build bioinformatics knowledge systems
    François Belleau
    Centre de Recherche du CHUL, Universite Laval, 2705 Boulevard Laurier, Que, Canada G1V4G2
    J Biomed Inform 41:706-16. 2008
    ..The Bio2RDF repository can be queried at http://bio2rdf.org...

Research Grants68

  1. Multi-dimensional Bio-informatics for Genomic Data
    MUNTHER DAHLEH; Fiscal Year: 2004
    ..Finally, we will prototype the technology and make the tool available for pilot testing. ..
  2. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
  3. Novel TIRF microscopy analyzing trafficking & signaling at the cell cortex
    Derek Toomre; Fiscal Year: 2009
    ..Consistent with the recovery act's goal, this funding will provide full-time summer employment for 4 undergraduate students and accelerate scientific achievement of the parent DP2 award...
  4. NIH Director's Pioneer Award
    ERICH JARVIS; Fiscal Year: 2009
    ..Repairing the pathway in vocal learners, when damaged, would have profound impact for correcting neurological disorders of speech. ..
  5. VACCINE INDUCED IMMUNITY IN THE YOUNG AND AGED
    Rafi Ahmed; Fiscal Year: 2013
    ..Core (Ahmed/Ansari), a Clinical Research Core (Mulligan/Chokephaibulkit/Yu) and a Genomics &Computational Biology Core (Haining/Lee)...
  6. Mechanisms of Neutralizing Antibody Resistance in Chronic HCV and HIV Infection
    JUSTIN RICHARD BAILEY; Fiscal Year: 2013
    ..at Johns Hopkins Hospital and an internationally- recognized expert in HCV virology, humoral immunity, and computational biology and Dr. James E. Crowe, Jr...
  7. Non-coding RNA engineers antibody diversity
    Uttiya Basu; Fiscal Year: 2011
    ..Here, we use a combination of modern computational biology, proteomics, high-throughput genomics and mouse genetics to identify and functionally characterize ncRNA ..
  8. PRE- AND POSTGRADUATE TRAINING IN MOLECULAR HEMATOLOGY
    J Evan Sadler; Fiscal Year: 2013
    ..and Oncology, as well as extensive institutional resources for genome sequencing, crystallography, computational biology, animal studies, and patient-oriented clinical research...
  9. Insights from Comparative Genomics for the Treatment of Pneumococcal Infections
    Natalia Luisa Hiller; Fiscal Year: 2011
    ..animal models, with a state-of-the-art facilities for DNA sequencing, comparative genomic hybridization, computational biology, and confocal laser scanning microscopy...
  10. Insights from Comparative Genomics for the Treatment of Pneumococcal Infections
    Natalia Luisa Hiller; Fiscal Year: 2013
    ..animal models, with a state-of-the-art facilities for DNA sequencing, comparative genomic hybridization, computational biology, and confocal laser scanning microscopy...
  11. DNA Methylation Control Hematopoietic Stem Cell Lineage Differentiation
    GRANT ANTHONY CHALLEN; Fiscal Year: 2013
    ..three first-author papers in high-impact journals, learning research techniques in epigenetics and computational biology and completing the career development activities to enhance my scientific background...
  12. Transposons in Female Reproductive Health and Disease
    Zev Williams; Fiscal Year: 2013
    ..the course of this award period he will expand his proficiency in genomics, RNA biology, assay design and computational biology with the overarching goal of elucidating the effect of transposons on oocytes and fertility...
  13. SMOOTH MUSCLE MYOSIN PHOSPHATASE SUBUNIT ISOFORMS
    Steven A Fisher; Fiscal Year: 2013
    ..These studies will provide novel insights regarding the role of Tra2b, and novel links between transcriptional and splicing controls, in the generation and modulation of vascular smooth muscle contractile phenotypic diversity. ..
  14. Translating human PPARy binding regions to gene regulation and metabolic disease
    RAYMOND EDWARD SOCCIO; Fiscal Year: 2013
    ..The career development plan includes training in genomics, bioinformatics, and computational biology, since a thorough understanding of these burgeoning fields will be essential to the cutting-edge studies ..
  15. Regulation of Host Nitrogen Balance by the Gut Microbiome
    Gary D Wu; Fiscal Year: 2012
    ..the expertise of senior investigators with experience in metabolic diseases, deep genomic sequencing, and computational biology assembled for a recently funded NIH pathway initiative grant known as the Human Microbiome Project...
  16. A Validated Resource of Thyroid Cancer Cell Lines for Pathway Discovery
    JEFFREY ALLEN KNAUF; Fiscal Year: 2010
    ..we are collaborating with nationally recognized bioinformatics and computational experts to apply novel computational biology strategies to identify important signaling pathways that will better define disease pathogenesis...
  17. Genomic profiling of yeast resistance to AFB1, a P450-activated carcinogen
    MICHAEL THOMAS FASULLO; Fiscal Year: 2013
    ..The project will be a valuable training tool in systems and computational biology.
  18. Transport ATPases: From Molecules to Maladies
    Rajini Rao; Fiscal Year: 2010
    ..together approximately 150 investigators from diverse scientific disciplines, including structural and computational biology, genetics and medicine, cell biology, biochemistry and pharmacology, to discuss exciting new developments ..
  19. Bioconductor: an open computing resource for genomics
    Martin Morgan; Fiscal Year: 2010
    ..project provides an open resource for the development and distribution of innovative reliable software for computational biology and bioinformatics...
  20. Structural Biology of the Apical Bile Acid Transporter.
    Peter W Swaan; Fiscal Year: 2012
    ..Using a novel approach that combines molecular and computational biology our long-term goal is to delineate the three-dimensional structure, ligand-binding domains, and cellular ..
  21. Tissue compartmentalization of human lymphocytes
    Donna L Farber; Fiscal Year: 2013
    ..We have assembled an outstanding team of top immunologists together with experts in bioinformatics and computational biology to use this unique tissue resource in conjunction with tissues from transplant recipients and employ ..
  22. ImmGen: gene expression and regulation in immune cells
    Christophe O Benoist; Fiscal Year: 2013
    The Immunological Genome Project (ImmGen) is a collaborative group of immunology and computational biology laboratories who have performed in current grant period using a rigorous data generation and QC pipeline, a thorough dissection of ..
  23. Epigenomics of the regenerating and aging beta-cell
    Klaus H Kaestner; Fiscal Year: 2013
    ..In summary, we will utilize genome-wide approaches and computational biology tools to transform our knowledge of how the epigenome reflects the aging of the (-cell and its loss of ..
  24. Predictors of Progression from Barrett's Esophagus to esophageal adenocarcinoma
    Brian J Reid; Fiscal Year: 2010
    ..team encompasses expertise in clinical research, genomics, evolutionary biology, molecular biology, computational biology, epidemiology and biostatistics, including the analysis of complex datasets...
  25. Gene Expression and Regulatory Networks in Human Leukocytes
    Diane J Mathis; Fiscal Year: 2010
    ..Using a combination of high-throughput genomic techniques and computational biology, we will perform a broad exploration of gene expression in human blood cells across groups of African-..
  26. Analysis of novel in vivo derived Plasmodium falciparum transcriptional profiles
    JOHANNA PATRICIA DAILY; Fiscal Year: 2012
    ..Furthermore we have developed team of leaders in clinical malaria, computational biology and molecular biology to combine their skills to further our understanding of disease...
  27. The Use of Whole-Exome Sequencing to Guide the Care of Cancer Patients
    Pasi A Janne; Fiscal Year: 2013
    ..team consists of world leaders in translational oncology, cancer genomics, clinical cancer genetics, computational biology, outcomes research, and research ethics...
  28. Using Transport to Map the Brain
    Elaine L Bearer; Fiscal Year: 2010
    ..Brown University), in small animal 5MRI imaging (Caltech), and in computational analysis (Center for Computational Biology (CCB) at UCLA, one of the centers of the National Centers for Biological Computing), are brought together ..
  29. ANESTHETIC-INDUCED CARDIAC PRECONDITIONING
    Zeljko J Bosnjak; Fiscal Year: 2012
    ..existing infrastructure and programmatic experience in physiology, biophysics, genomics, proteomics, and computational biology to advance our understanding of the cellular and subcellular effects of anesthetics in organ protection...
  30. CRCNS: PKMzeta-Dependent Protein Synthesis Maintains Synaptic Plasticity
    HAREL ZEEV SHOUVAL; Fiscal Year: 2013
    ..The proposed stochastic simulations of translation-dependent bi-stability are also novel in computational biology. Broader Impact: As the first demonstrated molecular mechanism of experience-dependent, long-term ..
  31. Methods for modeling air pollution effects on exhaled biomarkers
    SANDRAH PROCTOR ECKEL; Fiscal Year: 2013
    ..Duncan C. Thomas), biomedical engineering (Dr. David D'Argenio), and computational biology (Dr. Paul Marjoram)...
  32. Carbohydrate Antigenic Biomarkers for Epithelial Cancers
    Minoru Fukuda; Fiscal Year: 2013
    ..and technical capabilities in carbohydrates, immunobiology, cancer cell biology, oncology, proteomics, and computational biology, as well as unique and well-annotated clinical specimens...
  33. Role of Helix Formation in Mediating Protein-Protein Interactions
    George I Makhatadze; Fiscal Year: 2010
    ..Rules that affect specificity and affinity in this type of interaction will be crucial in computational biology and bioinformatics to better predict target sequences that can interact with ubiquitin...
  34. Nanomedicine Center for Nucleoprotein Machines
    Gang Bao; Fiscal Year: 2013
    ..nanostructured probes, cryo-electron microscopy, signal-cell imaging, quantitative image analysis and computational biology, and light microscopy instrumentation...
  35. High Performance Validation and Classification of Metagenomic Ribosomal-RNA Seque
    Daniel Frank; Fiscal Year: 2011
    ..research team will use their extensive backgrounds in RNA structural biology, molecular-evolution, and computational biology to build and validate software tools that extend the basic feature set of INFERNAL, with special emphasis ..
  36. ER mitochondrial signaling and alcoholic tissue injury
    Joannes B Hoek; Fiscal Year: 2010
    ..structures in intact tissues, high resolution electron tomography, sophisticated molecular biology and computational biology to address a fundamental question of how a deregulation of local interactions between organelles can ..
  37. Analysis of the Molecular Machinery of microRNA-processing pathways
    Daniel Cifuentes; Fiscal Year: 2013
    ..Career Development Award to fulfill his short-term goal of acquiring specific training in the areas of i) computational biology and ii) mass- spectrometry...
  38. Individualization of nifedipine dosing for preterm labor
    Sara K Quinney; Fiscal Year: 2013
    ..Quinney. The Center for Computational Biology and Bioinformatics (CCBB) provides access to computational resources needed for the completion of the ..
  39. AD Gene Discovery: Exome Chip, New Endophenotypes &Functional Studies in CHARGE
    Sudha Seshadri; Fiscal Year: 2013
    ..We seek modest analytic resources to leverage existing phenotypic and genotypic data worth millions, to discover new AD genes and potentially novel prevention and treatment approaches for AD. ..
  40. Role of the transcriptional coregulator, TRIP Br2, in adipocyte metabolism
    Chong Wee Liew; Fiscal Year: 2011
    ..Aim 2 proposed during the K99 phase will provide me with the training in analysis of complex datasets with computational biology necessary to independently to complete Aim 2 during the R00 phase...
  41. Beagle: A Supercomputer for Computational Biology, Simulation, and Data Analysis
    Ian Foster; Fiscal Year: 2010
    ..substantial support from the University of Chicago for operations and application support, and an extremely experienced technical staff allows us to propose a system with capabilities unprecedented in academic biomedicine. ..
  42. Dissecting expression divergence in developmental networks across Drosophilids
    ZEBA BATOOL WUNDERLICH; Fiscal Year: 2013
    ..The PI for this project, Dr. Wunderlich, aims to combine her graduate training in computational biology with her postdoctoral training in experimental Drosophila systems biology to lay the foundation for an ..
  43. FASEB SRC on Mitosis: Spindle Assembly and Function
    Claire E Walczak; Fiscal Year: 2012
    ..In fact, the field of mitosis amalgamates molecular cell biology, biochemistry, biophysics, computational biology, and functional genomics...
  44. In vivo systems level analysis of gene-environment interactions
    Robert L Tanguay; Fiscal Year: 2010
    ..of diseases through the use of DNA sequencing, microarray technology, new imaging modalities, and computational biology. Thematic Area #2, Translating Basic Science Discoveries into New and Better Treatments, challenges the ..
  45. Design and Interpretation of SNP Association Studies of Addiction
    FRANK SCOTT SACCONE; Fiscal Year: 2013
    ..his education in psychopharmacology and the biochemical basis of addiction, and also in molecular and computational biology. This will be done with a superb set of mentors, consultants, and coursework...
  46. Prevention and Risk Identification of SUDEP Mortality - the PRISM Project
    Samden Lhatoo; Fiscal Year: 2013
    ..Such an approach is the most likely to produce effective SUDEP prevention strategies. ..
  47. Origins and Biological Consequences of Human Infertility
    Linda C Giudice; Fiscal Year: 2013
    ..pregnancy outcomes These projects are supported by Core A for administration (Linda Giudice), Core B for computational biology research (Jun Song), and Core C for education and community outreach (Synthia Mellon)...
  48. Core Facilities for Neurobiology at Brandeis
    Michael Rosbash; Fiscal Year: 2013
    ..Finally, we will establish a new Computational Core Facility to support large scale neural simulations and computational biology projects as part of a large high-performance computing cluster...
  49. Novel antivirals targeting the RNase H activity of HIV reverse transcriptase
    Zhengqiang Wang; Fiscal Year: 2013
    ..for this we will use a multidisciplinary approach based on our extensive expertise in structural biology, computational biology, medicinal chemistry, enzymology, biochemistry and virology...
  50. Training Program in Pharmaceutical Sciences
    Robert S Kass; Fiscal Year: 2012
    ..broadly with neurobiology, cardiovascular biology, immunology, cancer, genetics, chemistry, biochemistry, computational biology, and molecular biophysics...
  51. Small-molecule Inhibition of the Interactions of the Urokinase Receptor: A Targe
    Samy Meroueh; Fiscal Year: 2012
    ..To that end, a multidisciplinary research program involving computational biology, synthetic chemistry, biophysical chemistry, structural biology, and cell biology will be followed...
  52. Dissecting sarcoma complexity via innovative microRNA and informatics approaches
    Dimitrios Spentzos; Fiscal Year: 2012
    ..methods will be used, based on the candidate's exceptional training on medical applications of computational biology. Also, based on solid preliminary feasibility data, paraffin sarcoma tissue will be used for this study in ..
  53. Training Program in Lung Biology and Translational Medicine
    Victor J Thannickal; Fiscal Year: 2013
    ..Translational research in statistical genetics, computational biology, biomarker discovery, and drug discovery/development and clinical trials (group 3) will facilitate the ..
  54. Genetics of struvite formation
    Leticia Reyes; Fiscal Year: 2010
    ..the genetics of susceptibility to disease, I will need to gain expertise in genomics, bioinformatics, and computational biology. I have assembled a core interdisciplinary group of mentors chosen for their approaches in infectious ..
  55. Post-transcriptional regulation of gene expression in major TDP43 diseases
    NEIL MACDONALD RENWICK; Fiscal Year: 2013
    ..in pathobiology and assay design and will expand his scientific skills in genetics, biochemistry, and computational biology, and knowledge of neurodegenerative diseases over the course of the award period...
  56. Small RNAs at the placental maternal communication interface
    Yoel Sadovsky; Fiscal Year: 2013
    ..We have assembled a trans-disciplinary team that spans expertise in development, computational biology, and pathology, sharing the common goal of elucidating the role of microRNAs and small RNAs in the cross ..
  57. ENHANCER-MEDIATED MECHANISMS OF PATTERN FORMATION
    Stephen J Small; Fiscal Year: 2013
    ..They will also provide a framework for studying how changes in patterning mechanisms might control body plan diversification during evolution. ..
  58. Technical Information Research Resources for Cancer Preventive Agent Development
    Caroline Sigman; Fiscal Year: 2010
    ..Thus, the primary purpose of this project shall be to provide research, technical support, and analysis to assist in evaluating ongoing and proposed activities. ..
  59. Role of the transcriptional coregulator, TRIP Br2, in adipocyte metabolism
    Chong Wee Liew; Fiscal Year: 2013
    ..Aim 2 proposed during the K99 phase will provide me with the training in analysis of complex datasets with computational biology necessary to independently to complete Aim 2 during the R00 phase...
  60. Alterations in Lung Microbiome in Acute and Chronic HIV infection
    Andrew P Fontenot; Fiscal Year: 2013
    ..Utilizing the tremendous expertise in the fields of HIV-1 pathogenesis, lung immunology, computational biology and bioinformatics present at the University of Colorado, we hypothesize that the immunodeficiency ..
  61. High-performance compute cluster for biomedical computing
    Andrea Califano; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): The Center for Computational Biology and Bioinformatics (C2B2) was established in 2003, with the mission of providing the biomedical research community with Structural and Systems Biology algorithms ..
  62. Statistical Genomics and Systems Biology Workshop
    JEANETTE CHRISTINE PAPP; Fiscal Year: 2013
    ..and biomedical research, interdisciplinary and translational sciences, bioinformatics, statistics, computational biology, computer science, applied mathematics, physics, and social science...
  63. Novel Pathogen Associated Cancers (PQ12)
    David Wang; Fiscal Year: 2013
    ..of investigators with complementary expertise in cancer biology, infectious diseases, virus discovery, computational biology and epidemiology, which will have access to unique tumor specimens originating from individuals with HIV ..
  64. Mechanisms of Dinitroaniline Action, Selectivity and Resistance
    Naomi S Morrissette; Fiscal Year: 2010
    ..Our previous studies used a combination of genetic analysis and computational biology to conclude that the dinitroanilines have a novel mechanism of action: they bind to a-tubulin and disrupt ..
  65. Emerging Helminthiases in China: Genetic Diversity,
    Zheng Feng; Fiscal Year: 2006
    ..Specific point-by-point responses to the Study Section comments and recommendations are detailed at the beginning of the three relevant project applications (projects 4, 5, and 7). ..
  66. FASEB Summer Research Conference on Retinal Neurobiology and Visual Processing
    Maureen A McCall; Fiscal Year: 2010
    ..The primary goal of the meeting is to bring together participants from diverse areas of neurobiology, computational biology and vision research to discuss state-of-the-art techniques and apply creative scientific thinking to ..
  67. Workshop on Methods for Macromolecular Modeling
    Tamar Schlick; Fiscal Year: 2004
    ..conference goals and themes resonate well with many activities at the NIGMS Center for Bioinformatics and Computational Biology as well as several additional NIH roadmap themes/groups, including structural biology and ..
  68. Angiogenesis in hyperoxic lung fibrosis
    Ivor Douglas; Fiscal Year: 2007
    ..To advance his knowledge in computational biology he will attend courses in applied statistics. Steven Greenberg M.D...