A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes

[1]  J T Finch,et al.  Amyloid fibers are water-filled nanotubes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Mark Gerstein,et al.  A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. , 2002, Journal of molecular biology.

[3]  S. Karlin,et al.  Amino acid runs in eukaryotic proteomes and disease associations , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Ehud Gazit,et al.  A possible role for π‐stacking in the self‐assembly of amyloid fibrils , 2002, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[5]  Jonathan S Weissman,et al.  Multiple Gln/Asn-Rich Prion Domains Confer Susceptibility to Induction of the Yeast [PSI+] Prion , 2001, Cell.

[6]  S. Liebman,et al.  Prions Affect the Appearance of Other Prions The Story of [PIN+] , 2001, Cell.

[7]  M. F. Perutz,et al.  Cause of neural death in neurodegenerative diseases attributable to expansion of glutamine repeats , 2001, Nature.

[8]  R. Wickner,et al.  Prion Filament Networks in [Ure3] Cells of Saccharomyces cerevisiae , 2001, The Journal of cell biology.

[9]  S. Lindquist,et al.  The role of Sis1 in the maintenance of the [RNQ+] prion , 2001, The EMBO journal.

[10]  The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[11]  J. Weissman,et al.  A census of glutamine/asparagine-rich regions: implications for their conserved function and the prediction of novel prions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Chris Sander,et al.  CAST: an iterative algorithm for the complexity analysis of sequence tracts , 2000, Bioinform..

[13]  B. Roberts,et al.  Prions of yeast as heritable amyloidoses. , 2000, Journal of structural biology.

[14]  David P. Kreil,et al.  Asparagine repeats are rare in mammalian proteins. , 2000, Trends in biochemical sciences.

[15]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[16]  R. Wickner,et al.  Prions: Portable prion domains , 2000, Current Biology.

[17]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[18]  S. Lindquist,et al.  Protein-only inheritance in yeast: something to get [PSI+]-ched about. , 2000, Trends in cell biology.

[19]  J. Weissman,et al.  Molecular Basis of a Yeast Prion Species Barrier , 2000, Cell.

[20]  John M. Hancock,et al.  Amino Acid Reiterations in Yeast Are Overrepresented in Particular Classes of Proteins and Show Evidence of a Slippage-Like Mutational Process , 1999, Journal of Molecular Evolution.

[21]  M Singh,et al.  LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins , 1999, Journal of Molecular Biology.

[22]  F. Cohen,et al.  Thermodynamics of model prions and its implications for the problem of prion protein folding. , 1999, Journal of molecular biology.

[23]  Andrew Smith Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[24]  J. Weissman,et al.  A Critical Role for Amino-Terminal Glutamine/Asparagine Repeats in the Formation and Propagation of a Yeast Prion , 1998, Cell.

[25]  B. Berger,et al.  MultiCoil: A program for predicting two‐and three‐stranded coiled coils , 1997, Protein science : a publication of the Protein Society.

[26]  F E Cohen,et al.  The prion folding problem. , 1997, Current opinion in structural biology.

[27]  M. Sternberg,et al.  The disulphide beta-cross: from cystine geometry and clustering to classification of small disulphide-rich protein folds. , 1996, Journal of molecular biology.

[28]  G. Fink,et al.  Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. , 1996, Genetics.

[29]  M. Perutz,et al.  Polar zippers: Their role in human disease , 1994, Pharmaceutica acta Helvetiae.

[30]  S Karlin,et al.  Methods and algorithms for statistical analysis of protein sequences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[31]  D. Tautz,et al.  Cryptic simplicity in DNA is a major source of genetic variation , 1986, Nature.

[32]  W. Taylor,et al.  The classification of amino acid conservation. , 1986, Journal of theoretical biology.

[33]  E. Freyer Additional data , 1934 .

[34]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[35]  S. Lindquist,et al.  Rnq1: an epigenetic modifier of protein function in yeast. , 2000, Molecular cell.

[36]  M. Ashburner,et al.  The Gene Ontology Consortium , 2000 .

[37]  S. Lindquist,et al.  [PSI+]: an epigenetic modulator of translation termination efficiency. , 1999, Annual review of cell and developmental biology.

[38]  Kara Dolinski,et al.  Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure , 1999, Nucleic Acids Res..

[39]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[40]  J. Berg Genome sequence of the nematode C. elegans: a platform for investigating biology. , 1998, Science.

[41]  J. Wootton,et al.  Analysis of compositionally biased regions in sequence databases. , 1996, Methods in enzymology.