David Haussler.
Published in Nature Biotechnology
David Haussler.
Information-theoretic dissection of pairwise contact potentials.
Published in Proteins Structure Function and Bioinformatics
Pairwise contact potentials have a long, successful history in protein structure prediction. They provide an easily-estimated representation of many attributes of protein structures, such as the hydrophobic effect. In order to improve on existing potentials, one should develop a clear understanding of precisely what information they convey. Here, u...
Genie—gene finding in Drosophila melanogaster.
Published in Genome Research
A hidden Markov model-based gene-finding system called Genie was applied to the genomic Adh region in Drosophila melanogaster as a part of the Genome Annotation Assessment Project (GASP). Predictions from three versions of the Genie gene-finding system were submitted, one based on statistical properties of coding genes, a second included EST alignm...
The fishes of Genome 10K.
Published in Marine Genomics
The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are be...
Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.
Published in Cancer Research
DNA sequencing offers a powerful tool in oncology based on the precise definition of structural rearrangements and copy number in tumor genomes. Here, we describe the development of methods to compute copy number and detect structural variants to locally reconstruct highly rearranged regions of the tumor genome with high precision from standard, sh...
Antiviral susceptibility of avian and swine influenza virus of the N1 neuraminidase subtype.
...Published in Journal of Virology
Influenza viruses of the N1 neuraminidase (NA) subtype affecting both animals and humans caused the 2009 pandemic. Anti-influenza virus NA inhibitors are crucial early in a pandemic, when specific influenza vaccines are unavailable. Thus, it is urgent to confirm the antiviral susceptibility of the avian viruses, a potential source of a pandemic vir...
The first living systems: a bioenergetic perspective.
Published in Microbiology and Molecular Biology Reviews
The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymer...
Solution of fatty acids from monolayers spread at the air-water interface: identification of phase transformations and t...
Published in The Journal of Lipid Research
The contraction or decrease in area of fatty acid monolayers maintained at a constant surface pressure of 16 dynes/cm was studied as a function of fatty acid chain length, unsaturation, temperature, and the hydrogen ion concentration in the subphase. The data were consistent with the hypothesis that fatty acid solution from the monolayer into the s...
Design, synthesis, and characterization of polyintercalating ligands.
Published in G Protein Coupled Receptors - Structure
Helicobacter pylori chemotaxis modulates inflammation and bacterium-gastric epithelium interactions in infected mice.
Published in Infection and Immunity
The ulcer-causing pathogen Helicobacter pylori uses directed motility, or chemotaxis, to both colonize the stomach and promote disease development. Previous work showed that mutants lacking the TlpB chemoreceptor, one of the receptors predicted to drive chemotaxis, led to less inflammation in the gerbil stomach than did the wild type. Here we expan...
