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    www.fleabyte.org/morgue/020324-hlt/020324-hlt.txt - [Cached Version]
    Published on: 11/12/2001    Last Visited: 4/3/2006  

    Salah Ait-Mokhtar, Xerox Research Centre Europe (France) Alex Acero, Microsoft (USA) Tim Anderson, WPAFB (USA) Doug Appelt, SRI (USA) Breck Baldwin, Baldwin Language Technologies (USA) Srinivas Bangalore, AT&T Research (USA) Jerome Bellegarda, Apple Computer (USA) Ole Bernsen, NIS (Denmark) Christian Blaschke, CNB (National Center for Biotechnology) (Spain) Thorsten Brants, Xerox PARC (USA) Michael Brent, Washington University (USA) Eric Brill, Microsoft Research (USA) John Carroll, University of Sussex (UK) Khalid Choukri, ELRA/ELDA (Luxembourg and France) Renato de Mori, LIA (France) Gregor Erbach, Saarland University (Germany) Eric Fosler-Lussier, Bell Laboratories (USA) Horacio Franco, SRI International (USA) Jean-Luc Gauvain, LIMSI (France) Edouard Geoffrois, DGA (France) Bjorn Granstrom, CTT/KTH (Sweden) John Grieco, Air Force Research Lab (USA) David Grossman, Illinois Institute of Technology (USA) Sanda Harabagiu, University of Texas Dallas (USA) Ulf Hermjakob, ISI (USA) Julia

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    empoweringcaregivers.subportal.com/health/Diseases_and_ - [Cached Version]
    Published on: 8/24/2001    Last Visited: 6/8/2002  

    But lead researcher Michael Brent, an associate professor of computer science and genetics, believes otherwise.

    "Short utterances lay bare the structure of language," Brent says."Longer utterances may be helpful when the children are older and learning words faster," but in the infant stage, he says, a mother's use of isolated words forms a foundation for early vocabulary learning.

    He does, however, agree that, "although hearing words in isolation appears to be a factor, there are lots of other factors that correlate with a baby's ability to use a word."

    In the latest study, eight mothers of infants agreed to be recorded in their homes during a series of 14 visits while the babies were 9 months to 15 months old.Each taping lasted one to two hours.The tapes were transcribed and plugged into a computer program to analyze the times of each utterance, its beginning and end, within a twentieth of a second, allowing researchers to isolate single words.

    Checking periodically, the researchers found that the more frequently a mother used a word in isolation, the more likely her child was to know that word later.However, how frequently the mother used the word was not a predictor of whether the child would add it to his or her vocabulary.
    ...
    "What we found was that, while infants can segment speech, it seems to be relatively rare for young infants to learn words that are not spoken in isolation," Brent says.Of all utterances the mothers spoke to their children, 9 percent were isolated words, including nouns, verbs, adjectives and adverbs, the study says.Results were presented last week in San Francisco at a meeting of the American Association for the Advancement of Science.

    ...
    "If he's right," Bloom says of Brent, "learning language isn't as hard as we think."

    ...
    Brent admits one limitation of his study is that all the mothers involved had undergraduate or graduate degrees.He says his next step will be to work with mothers who are not as highly educated.

    ...
    So, how does Brent, a computer scientist, plan to use babytalk to create artificial intelligence?"By using computer models which can break down the language into sentences, symbols, letters and meaningful patterns," he says, "we can build a model that can pick out patterns and recover those patterns."

    The computer models he envisions would be able to "categorize nouns, verbs, find suffixes, learn word meanings and extract grammar," he says.

    The same type of programs that can break the code of patterns, and pattern recognition, Brent says, could help decipher the genomes of humans and other species.

    "We're trying to convince the world that linguists can contribute to genomics," he says.

    What To Do

    "Don't worry about what you say to your kids," Brent says."Instinctively, parents use this type of speech.It's just important to talk to your kids."

    To learn more about language acquisition, visit the ThinkQuest Web site.

    Read about the latest advances in computerized speech recognition and synthesis from the American Association for Artificial Intelligence

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    APS Observer | Members in the News - [Cached Version]
    Published on: 4/1/2001    Last Visited: 2/26/2002  

    Michael R. Brent, Washington University, Science News, February 22, 2001: Parents instinctive use of isolated words may help babies learn language

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    BIO.COM: Biotechnology Pharmaceutical Therapeutics,... - [Cached Version]
    Published on: 5/12/2005    Last Visited: 5/12/2005  

    Michael Brent, Ph.D., Washington University professor of computer science and engineering, used his unique software, TWINSCAN, on the genome of Caenorhabditis elegans (C. Elegans).The genome of another nematode C. briggsae, was also used to determine which parts of the sequence have changed since the nearest common ancestor of the two species.He found first of all that TWINSCAN predicted 60 percent of the genes in the C. Elegans genome exactly, right own to the last amino acid.

    "This (60 percent) is a new level of accuracy for a complex genome," Brent said.
    ...
    Brent and his colleagues say that the accuracy of WormBase can be improved with the use of TWINSCAN predictions.And Brent predicts that the age of the human genome annotator is passing -- the future belongs to computer-driven annotation.

    Crossing the tipping point

    "We've crossed the tipping point with gene prediction where it's becoming clear that machines can beat human annotators and analysts, on average," he said.

    Because of the increasing speed of computers, the TWINSCAN analysis of C. Elegans is able to use more accurate models of intron length than previous analyses.This is important for finding exons, which house the coding machinery of proteins.While getting intron length is helpful for gene annotation, the process is 15 times slower than the typical, less accurate methods.Being able to define intron length has implications for the human genome, which is much larger than C. Elegans and has an average intron length of about 4,000 base pairs, compared with an average intron length of a couple hundred base pairs in C. Elegans.

    Brent and colleagues from the Dana-Farber Cancer Institute and Harvard Medical School published their findings in the April, 2005 issue of Genome Research.Brent's graduate student, Chaochun Wei, is first author on the paper.The research was supported by grants from NIH, NSF, the National Cancer Institute, the National Human Genome Research Institute, and the National Institute of General Medical Sciences.

    Brent has brought his bioinformatics skills to many genomes, including those of mammals, other nematode species and most recently the fungus Cryptococcus neoformans.
    ...
    Brent said that some genome researchers have been reluctant to go towards an automated, hypothesis - driven approach because of a lingering sense that anything that's been looked at by a human will be more accurate than something produced by a machine.

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    Bio-IT Briefs April 1, 2005 - News - [Cached Version]
    Published on: 4/1/2005    Last Visited: 4/2/2005  

    Michael Brent, Washington University professor of computer science and engineering, used his bioinformatics software, TWINSCAN, on the genome of Caenorhabditis elegans (C. elegans).The genome of another nematode C. briggsae, was also used to determine which parts of the sequence have changed since the nearest common ancestor of the two species.TWINSCAN predicted 60 percent of the genes in the C. elegans genome exactly, down to the last amino acid.Brent and colleagues from the Dana-Farber Cancer Institute and Harvard Medical School published their findings in the April, 2005 issue of Genome Research.The manuscript will appear online at http://www.genome.org/cgi/doi/10.1101/gr.3329005 (sub. req.). (Wei, C., Lamesch, P., Arumugam, M., Rosenberg, J., Hu, P., Vidal, M., and Brent, M.R. 2005.

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    Bio.com -- Biotech, Biotechnology and Pharmaceutical... - [Cached Version]
    Published on: 10/9/2003    Last Visited: 5/14/2004  

    Michael R. Brent, Ph.D., associate professor of computer science, has applied software developed in his Washington University laboratory that sorts through the maze of genetic information and finds predicted sequences.
    ...
    "Normally, you get one 600 to 700 base pair sequence in a reaction, but under certain conditions, we've figured out how to get more than one sequence out of a single sequencing reaction," said Brent."In most cases, people would throw out a reaction with more than one sequence but we've developed software that allows us to sort out the mess and figure out the different sequences."

    Writing in the April issue of Genome Research, Brent and collaborators at Baylor College of Medicine, led by Richard A. Gibbs, Ph.D., director of Baylor's Human Genome Sequencing Center, discuss related techniques in genome analysis, while noting that the recent publication of a third mammalian genome, the brown rat, suggests a new approach to genome annotation is needed.
    ...
    Brent and his collaborators tested 444 TWINSCAN-predicted rat genes that showed significant homology, or correspondence, to known human genes implicated in disease.Ensembl and other techniques that use protein-to-genome mapping missed these genes.

    Brent and his collaborators verified the existence of 59 percent of their predicted genes.

    "We showed that we can do this efficiently with a reasonable fraction of the genes that TWINSCAN predicts and that you can actually produce a gene structure with the method," Brent said.
    ...
    "Currently, experimental sequencing of both genomes and gene products is followed by computational analysis of the resulting sequences," said Brent."It's a one way street.

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    Bio.com -- Biotech, Biotechnology and Pharmaceutical... - [Cached Version]
    Published on: 3/31/2004    Last Visited: 3/31/2004  

    Michael R. Brent, Ph.D., associate professor of computer science and engineering at Washington University in St. Louis, contributed to the analysis of the gene set.According to Brent, results from the study show that the change from the last common ancestor of rodents and humans has occurred much faster along the rodent branch than change along the human branch.Also, the study finds that approximately one-fourth of the human genome is shared with both rats and mice.

    That's approximately 700 megabases of DNA shared by all three animals.

    "It's surprising that the amount of shared DNA is so small," Brent said.

    Relative to their last common ancestor, the rodent lineage has mutated more than the human lineage, Brent pointed out, while analysis of the human genome reveals significantly more segmental duplication - a biological process whereby a large piece of the genome is copied in small numbers.Segmental duplications are one of the key things that differentiate the human genome from that of chimpanzees, and may contribute to the physical and behavioral difference between the two species.

    Rodent mutation is due to various different factors, an obvious one being generation time - they reproduce faster than humans.The results of the analysis show that the rat has mutated slightly more frequently than the mouse from the last common ancestor.

    "It's not clear how to explain that because they both have the same generation time," Brent said.

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    BioMed Central | BMC Bioinformatics - [Cached Version]
    Published on: 6/22/2005    Last Visited: 6/22/2005  

    Michael R BrentWashington University, St. Louis, USA

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    Biochemist e-volution: Biochemistry news - [Cached Version]
    Published on: 5/19/2005    Last Visited: 6/5/2005  

    Its genome was thought to have been completed but Michael Brent, Washington University professor of computer science and engineering, used his own software, TWINSCAN.The program has also predicted the existence of 1,119 additional genes.

    The genome of another nematode C. briggsae, was also used to determine which parts of the sequence have changed since the nearest common ancestor of the two species.He found that TWINSCAN predicted 60 percent of the genes in the C. elegans genome exactly, to the last amino acid.

    "This is a new level of accuracy for a complex genome," Brent said.
    ...
    Brent and colleagues from the Dana-Farber Cancer Institute and Harvard Medical School published their findings in the April issue of Genome Research.

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    Bioscience Technology - [Cached Version]
    Published on: 4/4/2005    Last Visited: 4/5/2005  

    To improve the completeness and accuracy of the current C. elegans gene set, Michael Brent, PhD, professor of computer science and engineering, Washington University, St. Louis, and colleagues from the Dana-Farber Cancer Institute and Harvard Medical School, Boston, adapted and extended the TWINSCAN gene-prediction algorithm, originally developed for the annotation of the human genome, for C. elegans and C. briggsae.

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