Research Topics
| Michael BrentSummaryAffiliation: Washington University School of Medicine Country: USA Publications
Research Grants
| Collaborators
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Detail Information
Publications
Pairagon+N-SCAN_EST: a model-based gene annotation pipelineManimozhiyan 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..CONCLUSION: With sufficient mRNA/EST evidence, genome annotation without trans alignments can compete successfully with systems like ENSEMBL and ExoGean, which use trans alignments...- Using ESTs to improve the accuracy of de novo gene predictionChaochun 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... - Gene finding in the chicken genomeEduardo 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... - Eval: a software package for analysis of genome annotationsEvan Keibler
Department of Computer Science and Engineering, Washington University, St, Louis, MO 63130, USA
BMC Bioinformatics 4:50. 2003..AVAILABILITY: To obtain the module package with documentation, go to http://genes.cse.wustl.edu/ and follow links for Resources, then Software. Please contact brent@cse.wustl.edu.. 
Recent advances in gene structure predictionMichael 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....- Genome annotation past, present, and future: how to define an ORF at each locusMichael 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... - Steady progress and recent breakthroughs in the accuracy of automated genome annotationMichael 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... - 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 - The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMsEvan 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... 
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny mapPaul 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...- Begin at the beginning: predicting genes with 5' UTRsRandall H Brown
Laboratory for Computational Genomics, Washington University, St. Louis, MO 63130, USA
Genome Res 15:742-7. 2005.... - Gene prediction and verification in a compact genome with numerous small intronsAaron E Tenney
Laboratory for Computational Genomics and Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA
Genome Res 14:2330-5. 2004.... - Initial sequencing and comparative analysis of the mouse genomeRobert 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.... - Closing in on the C. elegans ORFeome by cloning TWINSCAN predictionsChaochun 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... - Pairagon: a highly accurate, HMM-based cDNA-to-genome alignerDavid 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... - Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequencesMarijke 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... - Iterative gene prediction and pseudogene removal improves genome annotationMarijke 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... - Using multiple alignments to improve gene predictionSamuel 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... - Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their nichesMarios 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... - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 432:695-716. 2004..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture... - The DNA sequence of human chromosome 7Ladeana 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... - A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splicesAaron 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... - Benchmarking regulatory network reconstruction with GRENDELBrian 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... - Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genesRoderic Guigo
Research Group in Biomedical Informatics, , 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... - Evolution of genes and genomes on the Drosophila phylogenyAndrew 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... - Targeted discovery of novel human exons by comparative genomicsAdam 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... - The genome sequence of Caenorhabditis briggsae: a platform for comparative genomicsLincoln 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... - Predicting full-length transcriptsMichael R Brent
Trends Biotechnol 20:273-5; discussion 275. 2002 - Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencingJia 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... - Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcriptsPaul 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... - Performance assessment of promoter predictions on ENCODE regions in the EGASP experimentVladimir 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... - The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformansBrendan 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... - Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mappingVanessa 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 Grants
- Predicting Gene Structure--Vertebrate Genome ComparisonMichael 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. ..
- INSTITUTIONAL TRAINING GRANT IN GENOMIC SCIENCEMichael Brent; Fiscal Year: 2006..abstract_text> ..
- Predicting Gene Structure: Vertebrate Genome ComparisonMichael 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. ..
- INSTITUTIONAL TRAINING GRANT IN GENOMIC SCIENCEMichael Brent; Fiscal Year: 2007..abstract_text> ..