Research Topics
Genomes and Genes | James E GalaganSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
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Publications
Patterns of intron gain and loss in fungiCydney 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...
Short-term genome evolution of Listeria monocytogenes in a non-controlled environmentRenato 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...
Genomics of the fungal kingdom: insights into eukaryotic biologyJames 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...- The genome sequence of the filamentous fungus Neurospora crassaJames 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... - RIP: the evolutionary cost of genome defenseJames 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... - Inferring carbon sources from gene expression profiles using metabolic flux modelsAaron 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... - Cross-kingdom patterns of alternative splicing and splice recognitionAbigail 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... - Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid productionCaroline 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... - Dual modes of natural selection on upstream open reading framesDaniel 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... - Conrad: gene prediction using conditional random fieldsDavid 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... - Positive selection for unpreferred codon usage in eukaryotic genomesDaniel E Neafsey
Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
BMC Evol Biol 7:119. 2007.... - Combo: a whole genome comparative browserReinhard Engels
The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02142, USA
Bioinformatics 22:1782-3. 2006..Argo is written in Java, runs on multiple platforms and is freely available for download at http://www.broad.mit.edu/annotation/argo/... - Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzaeJames 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... - Large-scale identification of genetic design strategies using local searchDesmond S Lun
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Mol Syst Biol 5:296. 2009.... 
TB database 2010: overview and updateJames 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...- Conserved secondary structures in AspergillusAbigail 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... - Improving genome annotations using phylogenetic profile anomaly detectionTarjei 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... - The genome of M. acetivorans reveals extensive metabolic and physiological diversityJames 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/.].. - Assembly of polymorphic genomes: algorithms and application to Ciona savignyiJade 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... - Enabling a community to dissect an organism: overview of the Neurospora functional genomics projectJay 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... - Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organismKatherine 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... - The genome sequence of the rice blast fungus Magnaporthe griseaRalph 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... - Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatusWilliam 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... - Genome sequencing and analysis of Aspergillus oryzaeMasayuki 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... - Dynamics of Pseudomonas aeruginosa genome evolutionKalai 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... - Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorumJames 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... - A genome-wide map of diversity in Plasmodium falciparumSarah 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...