CIS 700: Machine Learning for Bioinformatics

Schedule

• 10 Overview
• 12 regulatory networks
  • Local graph alignment and motif search in biological networks [pdf]
  • weeder [pdf]
  • alignACE [pdf]
  • Finding signals that regulate alternative splicing in the post-genomic era [pdf]
  • Systematic Identification and Analysis of Exonic Splicing Silencers [pdf]
• 17 (network alignments)
  • Berg et al. Structure and evolution of protein interaction networks [pdf]
  • Karp. Pathway databases: a case study in computational symbolic theories [pdf]
  • Melnik et al. Similarity flooding: a versatile graph matching algorithm and its application to schema matching [pdf]
  • Skim Emes et al. Evolution and comparative genomics of odorant and pheromone-associated genes in rodents [pdf]
  • Skim Grant. Synapse signalling complexes and networks: machines underlying cognition [pdf]
• 19 Alternative splicing -- reviews
  • Lareau et al. (2004). The evolving roles of alternative splicing [pdf]
  • Modrek and Lee. (2002). A genomic view of alternative splicing [pdf]
  • Stamm et al. (2005). Function of alternative splicing [pdf]
• 24 (networks)
  • Wagner and Wright (2004) Compactness and Cycles in Signal Transduction and Transcriptional Regulation Networks: A Signature of Natural Selection? [pdf]
  • Wagner (2003) How the global structure of protein interaction networks evolves [pdf]
  • Dutilh et al. (2006) A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. [pdf]
  • This pertains to our discussion last week: Baudot et al. A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. [pdf]
• 26 Nutrigenomics
  • Kitajka et al.(2004) Effects of dietary omega-3 polyunsaturated fatty acids on brain gene expression. [pdf]
  • Guarente and Picard (2005) Review: Calorie Restriction-- the SIR2 Connection. [pdf]
  • Kaeberlein et al. (2005) Regulation of Yeast Replicative Life Span by TOR and Sch9 in Response to Nutrients. [pdf]
• 31 (notes)
  • Inferring protein domain interactions from databases of interacting proteins [pdf]
  • The natural history of protein domains [link]

• 2 Stress response pathway (notes)
  • Two-dimensional Transcriptome Analysis in Chemostat Cultures -- combinatorial effects of oxygen availability and macronutrient limitation in saccharomyces cerevisiae [pdf]
  • Differential network expression during drug and stress response [pdf]
• 7 Protein domains and phylogeny
  • Phylogeny determined by protein domain content [pdf]
  • Tree pattern matching in phylogenetic trees [pdf]
• 9 Pathway databases and methods (notes)
  • Expansion of the BioCyc collection of pathway/genome databases to 160 genomes [pdf]
  • From genomics to chemical genomics: new developments in KEGG [pdf]
  • Genomic analysis of regulatory network dynamics reveals large topological changes [pdf]
  • A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles [pdf]
• 14
  • This is pretty much a proof-of-concept paper..... Evolution of protein topologies through multistep gene rearrangements [pdf]
• 16 ChiP-chip data--review (notes)
  • Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays [link]
  • Genomic approaches that aid in the identification of transcription factor target genes [link]
• 21
• 23 meta server
  • Meta-DP: domain prediction meta-server [link]
  • Structure prediction meta server [link]
  • Pcons: A neural-network based consensus predictor that improves fold recognition [link]
• 28

• 2
• 7 Spring break
• 9 Spring break
• 14
• 16
• 21
• 23
• 28 Everyone at this point you should
  • have your data downloaded
  • have algorithm refined (please update your web site)
  • have major software selected
  • contribution clearly specified (please add to web site) We will do XXX. This differs from the other leading brand YYY in that we ZZZ. This is important because it will give better WWW.
• 30

• 4
• 6
• 11
• 13
• 18
• 20
• 25 READING DAYS
• 27 READING DAYS