James E Galagan

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM
    Jonathan M Dreyfuss
    Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 9:e1003126. 2013
  2. pmc Inferring carbon sources from gene expression profiles using metabolic flux models
    Aaron Brandes
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS ONE 7:e36947. 2012
  3. pmc Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region
    Brian Weiner
    The Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS ONE 7:e26038. 2012
  4. pmc The Mycobacterium tuberculosis regulatory network and hypoxia
    James E Galagan
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Nature 499:178-83. 2013
  5. pmc Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis
    Abigail Manson McGuire
    Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
    BMC Genomics 13:120. 2012
  6. ncbi request reprint TB database 2010: overview and update
    James E Galagan
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Tuberculosis (Edinb) 90:225-35. 2010
  7. pmc Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production
    Caroline Colijn
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 5:e1000489. 2009
  8. pmc Cross-kingdom patterns of alternative splicing and splice recognition
    Abigail M McGuire
    The Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 9:R50. 2008
  9. ncbi request reprint Dual modes of natural selection on upstream open reading frames
    Daniel E Neafsey
    Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Mol Biol Evol 24:1744-51. 2007
  10. ncbi request reprint Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    James E Galagan
    The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
    Nature 438:1105-15. 2005

Detail Information

Publications25

  1. pmc Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM
    Jonathan M Dreyfuss
    Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 9:e1003126. 2013
    ....
  2. pmc Inferring carbon sources from gene expression profiles using metabolic flux models
    Aaron Brandes
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS ONE 7:e36947. 2012
    ..Our method prioritizes a list of candidate carbon sources for their compatibility with a gene expression profile using the framework of flux balance analysis to model the organism's metabolic network...
  3. pmc Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region
    Brian Weiner
    The Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS ONE 7:e26038. 2012
    ..The identified duplications suggest that large-scale gene duplication may be more common in M. tuberculosis than previously considered...
  4. pmc The Mycobacterium tuberculosis regulatory network and hypoxia
    James E Galagan
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Nature 499:178-83. 2013
    ..The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub. ..
  5. pmc Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis
    Abigail Manson McGuire
    Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
    BMC Genomics 13:120. 2012
    ..bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum...
  6. ncbi request reprint TB database 2010: overview and update
    James E Galagan
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Tuberculosis (Edinb) 90:225-35. 2010
    ..By integrating a wide range of genomic data with tools for their use, TBDB is a unique platform for both basic science research in TB, as well as research into the discovery and development of TB drugs, vaccines and biomarkers...
  7. pmc Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production
    Caroline Colijn
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 5:e1000489. 2009
    ..Our method also predicts a number of additional potential modulators of TB mycolic acid biosynthesis. E-Flux thus provides a promising new approach for algorithmically predicting metabolic state from gene expression data...
  8. pmc Cross-kingdom patterns of alternative splicing and splice recognition
    Abigail M McGuire
    The Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 9:R50. 2008
    ..We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized...
  9. ncbi request reprint Dual modes of natural selection on upstream open reading frames
    Daniel E Neafsey
    Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Mol Biol Evol 24:1744-51. 2007
    ..Our analysis suggests that uORFs are an important and underappreciated mechanism of post-transcriptional gene regulation in eukaryotes...
  10. ncbi request reprint Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    James E Galagan
    The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
    Nature 438:1105-15. 2005
    ..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...
  11. pmc Large-scale identification of genetic design strategies using local search
    Desmond S Lun
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Syst Biol 5:296. 2009
    ....
  12. pmc Conserved secondary structures in Aspergillus
    Abigail Manson McGuire
    The Broad Institute of M I T and Harvard, Cambridge, Massachusetts, United States of America
    PLoS ONE 3:e2812. 2008
    ..Little is known about the RNAs present in this set of fungi, and this diverse set of genomes has an optimal level of sequence conservation for observing the correlated evolution of base-pairs seen in RNAs...
  13. ncbi request reprint Genomics of the fungal kingdom: insights into eukaryotic biology
    James E Galagan
    The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141, USA
    Genome Res 15:1620-31. 2005
    ..We also discuss insights into the fundamental cellular biology shared between fungi and other eukaryotic organisms...
  14. pmc Conrad: gene prediction using conditional random fields
    David DeCaprio
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 17:1389-98. 2007
    ..Conrad's implementation of SMCRFs advances the state of the art in gene prediction in fungi and provides a robust platform for both current application and future research...
  15. ncbi request reprint Combo: a whole genome comparative browser
    Reinhard Engels
    The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02142, USA
    Bioinformatics 22:1782-3. 2006
    ..They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats...
  16. ncbi request reprint Genomic insights into tuberculosis
    James E Galagan
    Department of Biomedical Engineering, Bioinformatics program and National Emerging Infectious Diseases Laboratory, Boston University, 34 Cummington Mall 1002, Boston, Massachusetts 02215 and Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Rev Genet 15:307-20. 2014
    ..tuberculosis, as well as the molecular basis for its pathogenicity. These have important implications for our perspective of the disease, development of new drugs and vaccines, and treatment of patients using existing therapeutics. ..
  17. ncbi request reprint Improving genome annotations using phylogenetic profile anomaly detection
    Tarjei S Mikkelsen
    The Eli and Edythe L Broad Institute, Massachusetts Institute of Technology and Harvard University 320 Charles Street, Cambridge, MA 02141, USA
    Bioinformatics 21:464-70. 2005
    ..We have sought to develop a method for improving new annotations that can automatically synthesize and use the information available in a database of other annotated genomes...
  18. pmc Patterns of intron gain and loss in fungi
    Cydney B Nielsen
    Department of Biology, Massachusetts Institute of Technology Cambridge, Massachusetts, USA
    PLoS Biol 2:e422. 2004
    ..Contrary to standard models, we find no increased frequency of intron loss toward the 3' ends of genes. Thus, recent intron dynamics do not support a model whereby 5' intron positional bias is generated solely by 3'-biased intron loss...
  19. pmc Positive selection for unpreferred codon usage in eukaryotic genomes
    Daniel E Neafsey
    Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    BMC Evol Biol 7:119. 2007
    ....
  20. ncbi request reprint RIP: the evolutionary cost of genome defense
    James E Galagan
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 04124, USA
    Trends Genet 20:417-23. 2004
    ..Most if not all paralogs in N. crassa duplicated and diverged before the emergence of RIP. Thus, RIP illustrates the extraordinary extent to which genomes will go to defend themselves against mobile genetic elements...
  21. ncbi request reprint The genome sequence of the filamentous fungus Neurospora crassa
    James E Galagan
    Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 422:859-68. 2003
    ..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes...
  22. pmc Assembly of polymorphic genomes: algorithms and application to Ciona savignyi
    Jade P Vinson
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141 2023, USA
    Genome Res 15:1127-35. 2005
    ..Our method represented loci in a single copy more reliably and achieved greater contiguity than a conventional whole-genome assembly method...
  23. pmc How accurate can genetic predictions be?
    Jonathan M Dreyfuss
    Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA
    BMC Genomics 13:340. 2012
    ....
  24. ncbi request reprint A genome-wide map of diversity in Plasmodium falciparum
    Sarah K Volkman
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Nat Genet 39:113-9. 2007
    ..We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite...
  25. pmc The genome of M. acetivorans reveals extensive metabolic and physiological diversity
    James E Galagan
    Whitehead Institute Center for Genome Research, Cambridge, Massachusetts 02141, USA
    Genome Res 12:532-42. 2002
    ..acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.]..