Affiliation: University of California
- Retrocopy contributions to the evolution of the human genomeRobert Baertsch
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
BMC Genomics 9:466. 2008..A subset of retroposed mRNAs (retrocopies) shows strong evidence of expression in primates, often yielding functional retrogenes...
- Aligning multiple genomic sequences with the threaded blockset alignerMathieu Blanchette
Howard Hughes Medical Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA
Genome Res 14:708-15. 2004..We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser...
- Forces shaping the fastest evolving regions in the human genomeKatherine S Pollard
Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
PLoS Genet 2:e168. 2006..A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome...
- Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomesW James Kent
Center for Biomolecular Science and Engineering and Howard Hughes Medical Institute, Department of Computer Science, University of California, Santa Cruz, CA 95064, USA
Proc Natl Acad Sci U S A 100:11484-9. 2003..To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments...
- Using native and syntenically mapped cDNA alignments to improve de novo gene findingMario Stanke
Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
Bioinformatics 24:637-44. 2008..For many eukaryotic genomes, expressed sequence tags (ESTs) are available as evidence for genes. Related genomes that have been sequenced, annotated, and aligned to the target genome provide evidence of existence and structure of genes...
- The structure of a rigorously conserved RNA element within the SARS virus genomeMichael P Robertson
The Center for the Molecular Biology of RNA, University of California, Santa Cruz, USA
PLoS Biol 3:e5. 2005....
- The UCSC Archaeal Genome BrowserKevin L Schneider
Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
Nucleic Acids Res 34:D407-10. 2006..We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the archaeal research community...
- A model for the proteolipid ring and bafilomycin/concanamycin-binding site in the vacuolar ATPase of Neurospora crassaBarry J Bowman
Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, USA
J Biol Chem 281:31885-93. 2006..crassa sequence to the E. hirae structure and the degree to which the structural model predicts the clustering of these residues suggest that the folding of the bacterial and eukaryotic polypeptides is very similar...