Michael Brent

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. pmc Pairagon+N-SCAN_EST: a model-based gene annotation pipeline
    Manimozhiyan Arumugam
    Laboratory for Computational Genomics and Department of Computer Science, Washington University, One Brookings Drive, St, Louis, MO 63130, USA
    Genome Biol 7:S5.1-10. 2006
  2. pmc Using ESTs to improve the accuracy of de novo gene prediction
    Chaochun Wei
    Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, One Brookings Drive, St, Louis, MO 63130, USA
    BMC Bioinformatics 7:327. 2006
  3. pmc Gene finding in the chicken genome
    Eduardo Eyras
    Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 6:131. 2005
  4. pmc Eval: a software package for analysis of genome annotations
    Evan Keibler
    Department of Computer Science and Engineering, Washington University, St, Louis, MO 63130, USA
    BMC Bioinformatics 4:50. 2003
  5. ncbi request reprint Recent advances in gene structure prediction
    Michael R Brent
    Laboratory for Computational Genomics, Campus Box 1045, Washington University, One Brookings Drive, St Louis, Missouri 63130, USA
    Curr Opin Struct Biol 14:264-72. 2004
  6. ncbi request reprint Genome annotation past, present, and future: how to define an ORF at each locus
    Michael R Brent
    Laboratory for Computational Genomics and Department of Computer Science, Washington University, St Louis, Missouri 63130, USA
    Genome Res 15:1777-86. 2005
  7. ncbi request reprint Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    Michael R Brent
    Center for Genome Sciences, Campus Box 8510, Washington University, 4444 Forest Park Blvd, Saint Louis, Missouri 63108, USA
    Nat Rev Genet 9:62-73. 2008
  8. ncbi request reprint How does eukaryotic gene prediction work?
    Michael R Brent
    Center for Genome Sciences, Campus Box 1045, Washington University, One Brookings Drive, Saint Louis, Missouri 63130, USA
    Nat Biotechnol 25:883-5. 2007
  9. ncbi request reprint The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs
    Evan Keibler
    Laboratory for Computational Genomics, Campus Box 1045, Washington University, St Louis, MO 63130, USA
    Bioinformatics 23:545-54. 2007
  10. pmc Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map
    Paul Flicek
    Department of Computer Science and Engineering, Washington University, St Louis, Missouri 63130, USA
    Genome Res 13:46-54. 2003

Research Grants

Detail Information

Publications33

  1. pmc Pairagon+N-SCAN_EST: a model-based gene annotation pipeline
    Manimozhiyan Arumugam
    Laboratory for Computational Genomics and Department of Computer Science, Washington University, One Brookings Drive, St, Louis, MO 63130, USA
    Genome Biol 7:S5.1-10. 2006
    ..Because they are based on probability models, both Pairagon and N-SCAN_EST can be trained automatically for new genomes and data sets...
  2. pmc Using ESTs to improve the accuracy of de novo gene prediction
    Chaochun Wei
    Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, One Brookings Drive, St, Louis, MO 63130, USA
    BMC Bioinformatics 7:327. 2006
    ..TWINSCAN is the most accurate de novo gene finder available for nematodes and N-SCAN is the most accurate for mammals, as measured by exact CDS gene prediction and exact exon prediction...
  3. pmc Gene finding in the chicken genome
    Eduardo Eyras
    Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 6:131. 2005
    ..We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method...
  4. pmc Eval: a software package for analysis of genome annotations
    Evan Keibler
    Department of Computer Science and Engineering, Washington University, St, Louis, MO 63130, USA
    BMC Bioinformatics 4:50. 2003
    ..Input is in the standard Gene Transfer Format (GTF). Eval can be run interactively or via the command line, in which case output options include easily parsable tab-delimited files...
  5. ncbi request reprint Recent advances in gene structure prediction
    Michael R Brent
    Laboratory for Computational Genomics, Campus Box 1045, Washington University, One Brookings Drive, St Louis, Missouri 63130, USA
    Curr Opin Struct Biol 14:264-72. 2004
    ....
  6. ncbi request reprint Genome annotation past, present, and future: how to define an ORF at each locus
    Michael R Brent
    Laboratory for Computational Genomics and Department of Computer Science, Washington University, St Louis, Missouri 63130, USA
    Genome Res 15:1777-86. 2005
    ..0...
  7. ncbi request reprint Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    Michael R Brent
    Center for Genome Sciences, Campus Box 8510, Washington University, 4444 Forest Park Blvd, Saint Louis, Missouri 63108, USA
    Nat Rev Genet 9:62-73. 2008
    ..By combining several computational and experimental methods, we are now closer to producing complete and accurate gene catalogues than ever before...
  8. ncbi request reprint How does eukaryotic gene prediction work?
    Michael R Brent
    Center for Genome Sciences, Campus Box 1045, Washington University, One Brookings Drive, Saint Louis, Missouri 63130, USA
    Nat Biotechnol 25:883-5. 2007
  9. ncbi request reprint The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs
    Evan Keibler
    Laboratory for Computational Genomics, Campus Box 1045, Washington University, St Louis, MO 63130, USA
    Bioinformatics 23:545-54. 2007
    ..Existing approaches to reducing memory usage either sacrifice optimality or trade increased running time for reduced memory...
  10. pmc Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map
    Paul Flicek
    Department of Computer Science and Engineering, Washington University, St Louis, Missouri 63130, USA
    Genome Res 13:46-54. 2003
    ..Our human annotation using the mouse assembly is conservative, predicting only 25,622 genes, and appears to be one of the best de novo annotations of the human genome to date...
  11. pmc Begin at the beginning: predicting genes with 5' UTRs
    Randall H Brown
    Laboratory for Computational Genomics, Washington University, St Louis, MO 63130, USA
    Genome Res 15:742-7. 2005
    ....
  12. pmc Gene prediction and verification in a compact genome with numerous small introns
    Aaron E Tenney
    Laboratory for Computational Genomics and Department of Computer Science, Washington University, St Louis, Missouri 63130, USA
    Genome Res 14:2330-5. 2004
    ....
  13. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  14. pmc Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
    Chaochun Wei
    Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, St Louis, Missouri 63130, USA
    Genome Res 15:577-82. 2005
    ..The results also suggest that this technology can significantly improve our knowledge of the "parts list" for even the best-studied model organisms...
  15. pmc Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner
    David V Lu
    Department of Computer Science and Center for Genome Sciences, Washington University, St Louis, MO 63130, USA
    Bioinformatics 25:1587-93. 2009
    ..Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics...
  16. ncbi request reprint Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences
    Marijke J van Baren
    Washington University, St Louis, Missouri, USA
    Curr Protoc Bioinformatics . 2007
    ..Detailed discussion about the appropriate parameter settings, input-sequence processing, and choice of genome for comparison are included...
  17. pmc Iterative gene prediction and pseudogene removal improves genome annotation
    Marijke J van Baren
    Laboratory for Computational Genomics, Department of Computer Science Washington University, Saint Louis, Missouri 63130, USA
    Genome Res 16:678-85. 2006
    ..This allows us to run the gene prediction/PPFINDER procedure on newly sequenced genomes for which few genes are known...
  18. ncbi request reprint Using multiple alignments to improve gene prediction
    Samuel S Gross
    Department of Computer Science and Engineering, Washington University, St Louis, MO 63130, USA
    J Comput Biol 13:379-93. 2006
    ..Analyses of the predictions reveal that N-SCAN's accuracy in both human and fly exceeds that of all previously published whole-genome de novo gene predictors...
  19. ncbi request reprint Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches
    Marios Giannakis
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    J Biol Chem 281:11292-300. 2006
    ..The results reveal shared as well as distinctive features of adult gut stem cells when compared with other stem cell populations...
  20. ncbi request reprint The DNA sequence of human chromosome 7
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 424:157-64. 2003
    ..Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame...
  21. pmc A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
    Aaron E Tenney
    Laboratory for Computational Genomics and Department of Computer Science, Washington University, St Louis, Missouri 63130, USA
    Genome Res 17:212-8. 2007
    ..We also present a method for mapping double-insertion events in a random insertional-mutagenesis library...
  22. pmc Benchmarking regulatory network reconstruction with GRENDEL
    Brian C Haynes
    Center for Genome Sciences and Department of Computer Science, Washington University, St Louis, MO, USA
    Bioinformatics 25:801-7. 2009
    ..The rate at which new network inference methods are being proposed far outpaces our ability to objectively evaluate and compare them. This is largely due to a lack of fully understood biological networks to use as gold standards...
  23. pmc Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
    Roderic Guigo
    Research Group in Biomedical Informatics, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra Centre de Regulació Genòmica, E08003 Barcelona, Catalonia, Spain
    Proc Natl Acad Sci U S A 100:1140-5. 2003
    ..This is likely to constitute a significant fraction of the previously unknown, multiexon mammalian genes...
  24. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  25. pmc Targeted discovery of novel human exons by comparative genomics
    Adam Siepel
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 17:1763-73. 2007
    ..However, they suggest that hundreds-not thousands-of protein-coding genes are completely missing from the current gene catalogs...
  26. pmc The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Biol 1:E45. 2003
    ..elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes...
  27. ncbi request reprint Predicting full-length transcripts
    Michael R Brent
    Trends Biotechnol 20:273-5; discussion 275. 2002
  28. pmc Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing
    Jia Qian Wu
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:665-71. 2004
    ..Spliced sequences were amplified in 46 cases (34%). We conclude that this procedure for elucidating gene structures with native cDNA sequences is cost-effective and will become even more so as it is further optimized...
  29. pmc Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Genome Biol 7:S8.1-9. 2006
    ..MARS is able to use an arbitrary number of informant sequences and predicts a number of alternative transcripts at each gene locus...
  30. pmc Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
    Vladimir B Bajic
    South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
    Genome Biol 7:S3.1-13. 2006
    ..The systems analyzed operate on various principles and we assessed the effectiveness of different conceptual strategies used to correlate produced promoter predictions with the manually annotated 5' gene ends...
  31. pmc The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    Brendan J Loftus
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:1321-4. 2005
    ..neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes...
  32. ncbi request reprint Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
    Vanessa Vermeirssen
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Nat Methods 4:659-64. 2007
    ..Both strategies outperform library screens in terms of coverage, confidence and throughput. These versatile strategies can be adapted both to TFs in other systems and, likely, to other biomolecules and assays as well...

Research Grants9

  1. Predicting Gene Structure--Vertebrate Genome Comparison
    Michael Brent; Fiscal Year: 2004
    ..Potential biomedical applications include: (1) Identifying novel protein families that could serve as drug targets, and (2) Accelerating positional cloning projects for the identification of disease related genes. ..
  2. INSTITUTIONAL TRAINING GRANT IN GENOMIC SCIENCE
    Michael Brent; Fiscal Year: 2006
    ..abstract_text> ..
  3. Predicting Gene Structure: Vertebrate Genome Comparison
    Michael Brent; Fiscal Year: 2007
    ..This project will result in open source software that predicts exon-intron structures in vertebrate genomes more accurately than any current system. It will also increase the sensitivity and specificity of gene verification by RT-PCR. ..
  4. INSTITUTIONAL TRAINING GRANT IN GENOMIC SCIENCE
    Michael Brent; Fiscal Year: 2007
    ..abstract_text> ..