James E Galagan

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. 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
  2. pmc Short-term genome evolution of Listeria monocytogenes in a non-controlled environment
    Renato H Orsi
    Department of Food Science, Cornell University, Ithaca, NY, USA
    BMC Genomics 9:539. 2008
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  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. 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
  10. 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

Detail Information

Publications28

  1. 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...
  2. pmc Short-term genome evolution of Listeria monocytogenes in a non-controlled environment
    Renato H Orsi
    Department of Food Science, Cornell University, Ithaca, NY, USA
    BMC Genomics 9:539. 2008
    ..While a genome sequence for the 1988 food isolate has been reported, we sequenced the genomes of the 1988 human isolate as well as a human and a food isolate from the 2000 outbreak to allow for comparative genome analyses...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  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. 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...
  10. 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...
  11. 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...
  12. 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...
  13. 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. ..
  14. 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
    ....
  15. 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
    ....
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. 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/.]..
  21. pmc Dynamics of Pseudomonas aeruginosa genome evolution
    Kalai Mathee
    Department of Molecular Microbiology and Immunology, College of Medicine, School of Computing and Information Sciences, College of Engineering, Florida International University, Miami, FL 33199, USA
    Proc Natl Acad Sci U S A 105:3100-5. 2008
    ..Consequently, this organism can survive in a wide range of environmental reservoirs that can serve as sources of the infecting organisms...
  22. pmc Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum
    James K Hane
    Australian Centre for Necrotrophic Fungal Pathogens, Murdoch University, WA 6150, Australia
    Plant Cell 19:3347-68. 2007
    ..This suggests that the fungus is dependant on the degradation of wheat macromolecular constituents to provide the carbon skeletons and energy for the synthesis of proteins and other components destined for the developing pycnidiospores...
  23. ncbi request reprint Genome sequencing and analysis of Aspergillus oryzae
    Masayuki Machida
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Higashi 1 1 1, Tsukuba, Ibaraki 305 8566, Japan
    Nature 438:1157-61. 2005
    ..Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation...
  24. ncbi request reprint Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
    William C Nierman
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Nature 438:1151-6. 2005
    ..The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus...
  25. ncbi request reprint The genome sequence of the rice blast fungus Magnaporthe grisea
    Ralph A Dean
    Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nature 434:980-6. 2005
    ..The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation...
  26. pmc Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism
    Katherine A Borkovich
    Department of Plant Pathology, University of California, Riverside, California 92521, USA
    Microbiol Mol Biol Rev 68:1-108. 2004
    ..The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease...
  27. pmc Enabling a community to dissect an organism: overview of the Neurospora functional genomics project
    Jay C Dunlap
    Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
    Adv Genet 57:49-96. 2007
    ..In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes...
  28. 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...