Computational Molecular Biology and Genomics Project Topics

Computational Molecular Biology and Genomics Project Topics - Fall 2006

[Bibliographic Resources] [Genomics] [Proteomic Technologies ] [Biological Networks]

General Bibliographic Resources

Genomics

Sequencing

Whole Genome Assembly
- Comparitive analysis of human genome assemblies reveals genome-level differences
  S. Li et al., Genomics 2002;80(2)
- On the sequencing of the human genome
  Waterston et al., PNAS 2002
- ARACHNE: a whole-genome shotgun assembler
  Batzoglouet al., Genome Research 2002
- Design of a compartmentalized shotgun assembler for the human genome
  Huson et al., Bioinformatics 2001
- A whole-genome assembly of Drosophila
  Myers et al., Science 2000

Genome analysis

Gene Prediction and Assessment
- Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
  T. Imanishi et al., 2004
- Computational Gene Recognition Bibliography
- A comparison of the Celera ensemble predicted gene sets reveals little overlap in novel genes
  J.B. Hogenesch et al., Cell 2002;106
- Computational prediction of eukaryotic protein-coding genes
  Zhang, Nat Rev Genetics 2002
- Human and mouse gene structure: comparative analysis and application to exon prediction
  Batzoglouet al., Genome Research 2000
- An assessment of gene prediction accuracy in large DNA sequences
  Guigo et al., Genome Research 2000
- Mining the human genome using microarrays of open reading frames
  S. Penn et al., Nature Genetics, 2000
Identifying regulatory motifs
- Sequencing and comparison of yeast species to identify genes and regulatory elements
  M. Kellis et al., Nature. 2003 May 15;423(6937):241-54
- Regulatory element detection using correlation with expression
  H. J. Bussemaker et al., Nature Genetics, 2001
- Discovery and modeling of transcriptional regulatory regions
  Fickett and Wasserman, Curr Opin Biotechnol 2000
- Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
  A. M. McGuire et al., Genome Research 2000; 10:744-757
- Human-mouse genome comparisons to locate regulatory sites
  W. Wasserman et al., Nature Genetics 2000;26
Alternative Splicing
- Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins
  from intron sequences
  F.A. Kondrashov & E.V. Koonin, Trends Genet. 2003 Mar;19(3):115-9
- Increase of functional diversity by alternative splicing
  E.V. Kriventseva et al., Trends Genet. 2003 Mar;19(3):124-8
- Alternative splicing: combinatorial output from the genome
  G.C. Roberts, C.W.J Smith, Current Opinion in Chemical Biology 2002;6
- Alternative splicing and genome complexity
  D. Brett et al., Nature Genetics 2002;30
- A genomic view of alternative splicing
  B. Modrek, C. Lee, Nature Genetics 2002;30

Human origins and genetic diversity

Single nucleotide polymorphisms, haplotype analysis
- Genealogical Trees, Coalescent Theory and the Analysis of Genetic Polymorphisms
  Rosenberg and Nordborg, Nature Reviews Genetics May 2002
- Linkage Disequilibrium, what history has to tell us
  Nordborg and Tavare, TIG 2002
- The HapMap Project
- Algorithms for Extracting Information from Human Genetic Variation
  Russell Schwartz, Departments of Biological Sciences and Computer Science, Carnegie Mellon University
- Human Genome Project SNP Fact Sheet
  See references to articles at the bottom of the page
- Using haplotype blocks to map human complex trait loci
  L.R. Cardon & G.R. Abecasis, Trends Genet. 2003 Mar;19(3):135-40
Human origins
- Patterns of human genetic diversity: Implications for human evolution and disease
  Sarah Tishkoff ,Department of Biology, University of Maryland
- The mosaic that is our genome.
  S Paabo, Nature. 2003 Jan 23;421(6921):409-12.
Human Health
- Genomic Medicine
  Science special issue, Vol. 32(5645), 24 Oct 2003
- Iceland's DeCODE genetics project:
  - Human Genetics: DeCODING Iceland's DNA
    UBC's Advanced Molecular Biology Laboratory
  - Icelandic database shelved as court judges privacy in peril
    Alison Abbott, Nature 429, 118 (13 May 2004)
- Pre-mRNA splicing and human disease
  Faustino and Cooper. Genes and Development 2003, 17:419-37
- The splicing machinery is a genetic modifier of disease severity.
  Nissim-Rafinia, M. and Kerem, B. 2005. Trends Genet. 21(9):480-3

Genome Content and Organization

Protein Families and Domains
- Survey of current protein family databases and their application in comparative,
  structural and functional genomics
  Redfern, et al.J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Feb 5;815(1-2):97-107
- Protein families and their evolution-a structural perspective
  Orengo CA, Thornton JM. Annu Rev Biochem. 2005;74:867-900
- Classification schemes for protein structure and function
  Ouzounis, et al.Nat Rev Genet. 2003 Jul;4(7):508-19
- Towards a covering set of protein family profiles
  A. Heger, Lisa Holm, Progress in Biophysics & Molecular Biology 2000;73
- Methodologies for target selection in structural genomics
  M. Linial, G. Yona, Progress in Biophysics & Molecular Biology 2000;73
- The origin of multicellular eukaryotes-insights from proteome comparisons
  L.Aravind, G. Subramanian, Current Opinion in Genetics & Development 1999;9
Gene order
- Evolutionary origin and maintenance of coexpressed gene clusters in mammals
  M. Semon and L. Duret, Mol Biol Evol. 2006 Sep;23(9):1715-23
- The evolutionary dynamics of eukaryotic gene order
  Hurst LD, Pal C, Lercher MJ. Nat Rev Genet. 2004 Apr;5(4):299-310. Review
- Shared strategies in gene organization among prokaryotes and eukaryotes
  J.G. Lawrence, Cell. 2002 Aug 23;110(4):407-13
- Clustering of housekeeping genes provides a unified model of gene order in the human genome
  Lercher et al.,Nat Genet. 2002 Jun;31(2):180-3.
- Evidence for co-evolution of gene order and recombination rate
  Pal and Hurst,Nat Genet. 2003 Mar;33(3):392-5
Genome Context and Operon Prediction
- Exploiting the co-evolution of interacting proteins to discover interaction specificity
  A.K. Ramani & E.M. Marcotte, J Mol Biol. 2003 Mar 14;327(1):273-84
- Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
  S.V. Date & E.M. Marcotte, Nat Biotechnol. 2003 Sep;21(9):1055-62
- Localizing proteins in the cell from their phylogenetic profiles
  E.M. Marcotte et al., PNAS 2000;97(22)
- Computational methods for protein function analysis
  M. Pellegrini, Current Opinion in Chem Bio 2001;5
- Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
  M. Pellegrini et al., PNAS 1999;96
- Detecting Protein Function and Protein-Protein Interactions from Genome Sequences
  E.M. Marcotte et al., Science 1999;28
- The use of gene clusters to infer functional coupling
  R. Overbeek et al., PNAS 1999;96

Genome Evolution

RNA world
- The antiquity of RNA-based evolution
  Joyce, GF, Nature. 2002 Jul 11;418(6894):214-21.
- The chemical repertoire of natural ribozymes
  Doudna JA, Cech TR, Nature. 2002 Jul 11;418(6894):222-8
Whole Genome Trees and Phylogenomics
- Genome trees from conservation profiles
  Tekaia F, Yeramian E. PLoS Comput Biol. 2005 Dec;1(7)
- Functional classification using phylogenomic inference
  Brown and Sjolander, PLoS Comput Biol. 2006 Jun 30;2(6):e77
- Phylogeny determined by protein domain content
  Yang S, Doolittle RF, Bourne PE. Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):373-8
- Genome trees and the tree of life
  Wolf et al., Trends in Genetics 2002
- Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis
  J.A. Eisen, Genome Research 1998;8
- A phylogenomic study of DNA repair genes, protiens and processes
  J.A. Eisen, P.C Hanawalt, Mutation Research 1999;435
- A phylogenomic study of the MutS family of proteins
  J.A. Eisen, Nucleic Acids Research 1998;26(18)
Genome duplication
- Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
  Bowers JE et al., Nature. 2003 Mar 27;422(6930):433-8
- A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome
  Blanc G, et al., Genome Research Feb 2003 13(2):137-144
- Vertebrate evolution: doubling and shuffling with a full deck
  Durand D, Trends Genet. 2003 Jan;19(1):2-5
Genome rearrangement
- Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
  W.J. Murphy et al., Science. 2005 Jul 22;309(5734):613-7
- Genome rearrangements in mammalian evolution: lessons from human and mouse genomes
  Pevzner P, Tesler G., Genome Res. 2003 Jan;13(1):37-45
- Mammalian phylogenomics comes of age
  Murphy WJ, Pevzner PA, O'Brien SJ. Trends Genet. 2004 Dec;20(12):631-9
- Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
  Pevzner P, Tesler G. Proc Natl Acad Sci USA. 2003 Jun 24;100(13):7672-7
- Chromosomal breakpoint re-use in the inference of genome sequence rearrangement
  David Sankoff, Phil Trinh. RECOMB 2004. Pages: 30 - 35
- Genome rearrangements in mammalian evolution: lessons from human and mouse genomes
  Pevzner P, Tesler G., Genome Res. 2003 Jan;13(1):37-45
Horizontal gene transfer
- Prokaryotic evolution in light of gene transfer
  Gogarten, JP, Doolittle, WF, Lawrence, JG, Mol Biol Evol. 2002 Dec;19(12):2226-38
Genome-scale sequence evolution/Molecular clocks
- Genomic clocks and evolutionary timescales
  S.B. Hedges & S. Kumar, Trends Genet. 2003 Apr;19(4):200-6

Proteomic Technologies

Nucleic acid expression arrays
- Spot your Genes: An Overview of the MicroArray
  BioTeach, UBC's Advanced Molecular Biology Laboratory
- Fundamentals of experimental design for cDNA microarrays
  Gary Churchill, Nat. Genetics 32 supplement pp490 - 495
- Comprehensive Identification of Cell Cycle–regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization
  P. Spellman et al., Molecular Biology of the Cell 1998;9
- Nature Genome Gateway - Profiling Microarrays
- Micro-array background
  Nature Genetics, volume 21, Supplement (1999)
Proteomics (Protein expression, protein chips)
- Proteomics: Where's Waldo in yeast?
  Wohlschlegel and Yates, 2003; Nature 425, 671 - 672
- Investigating the cellular machinery: Protein identification
  BioTeach, UBC's Advanced Molecular Biology Laboratory
- Nature Insight Proteomics
- Science magazine: News Focus on Proteomics
  Dec 7, 2001
- Nature genome gateway - Proteomics in Action
  Especially the articles from the Jan 10, 2002 issue.
Protein-protein interactions
- Yeast Two Hybrid Data
  - The Yeast Two-Hybrid Assay An Exercise in Experimental Eloquence
    BioTeach, UBC's Advanced Molecular Biology Laboratory
  - Toward a protein–protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
    T. Ito et al., PNAS 2000;97(3)
  - A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
    P. Uetz et al., Nature 2000;403, pp. 623 - 627
- Protein Complex Data (Tandem Affinity Purification)
  - Playing tag with the yeast proteome
    B. J. Andrews et al., Nature Biotechnology 2003 Volume 21 Number 11 pp 1297 - 1299
  - A generic protein purification method for protein complex characterization and proteome exploration
    G. Rigaut et al., Nature Biotechnology 1999;17
  - Functional organization of the yeast proteome by systematic analysis of protein complexes
    A. Gavin et al., Nature 2002;415
  - Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    Y. Ho et al., Nature 2002;415
Protein-DNA interactions
- Transcriptional regulatory code of a eukaryotic genome
  C.T. Harbison et al., Nature. 2004 Sep 2;431(7004):99-104
- An improved map of conserved regulatory sites for Saccharomyces cerevisiae
  K.D. MacIsaac et al, BMC Bioinformatics. 2006 Mar 7;7:113
- Chromatin ImmunoPrecipitation (ChIP)
  - Transcriptional regulatory networks in Saccharomyces cerevisiae
    Lee et al., Science. 2002 Oct 25;298(5594):799-804
High throughput functional screens
- The RNAi revolution
  Novina & Sharp, Nature 2004
- RNA Interference
  G.J. Hannon, Nature 2002;418
- Analysis of yeast protein kinases using protein chips
  H. Zhu et al., Nature Genetics, 2000
- A Balancing Act
  J. Rossant, Nature 2003;425, p. 29-32.
- Functional genetic analysis of mouse chromosome 11
  B. T. Kile et al., Nature 2003;425.
- Functional profiling of the Saccharomyces cerevisiae genome
  G. Giaever et al., Nature 2002;418(6896):387-91
- Human genetics: An expression of interest
  N. J. Cox. Nature 2004; 430, 733-734
- Genetic analysis of genome-wide variation in human gene expression
  Morley et al., Nature 2004; 430, 743-747.
Structural Genomics and Structure Prediction
- Structural genomics: computational methods for structure analysis
  Goldsmith-Fischman S, Honig B. Protein Sci. 2003 Sep;12(9):1813-21
- A Tour of Structural Genomics
  S. E. Brenner, Nat Rev 2001;2, p. 801-809
- Structural genomics: an overview
  T.L. Blundell, K. Mizuguchi, Progress in Biophysics & Molecular Biology 2000;73
- Protein structure prediction
  B. Al-Lazikani et al., Current Opinion in Chem Bio 2001;5
- Protein structure prediction and structural genomics
  Baker and Sali et al., Science 2001
- Global efforts in structural genomics
  Stevens et al., Science 2001
- Special supplement on structural genomics
  Nature Structural Biology, 2000
- Methodologies for target selection in structural genomics
  M. Linial, G. Yona, Progress in Biophysics & Molecular Biology 2000;73

Biological Networks

Network biology: understanding the cell's functional organization
Barabasi AL, Oltvai ZN, Nat Rev Genet. 2004 Feb;5(2):101-13
Biological Networks
Alm and Arkin, Curr. Op. Struct. Biol. 2003;13
Metabolomics and systems biology: making sense of the soup
D.B. Kell, Cur Opin in Microb 2004, 7:296–307
Regulatory networks
- Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling
  Gardner et al., Science, Vol 301, Issue 5629, 102-105 , 4 July 2003
- Computational discovery of gene modules and regulatory networks
  Bar-Joseph et al., Nat Biotechnol. 2003 Nov;21(11):1337-42.
- The evolution of genetic regulatory systems in bacteria
  McAdams HH, Srinivasan B, Arkin AP. Rev Genet. 2004 Mar;5(3):169-78
- Transcriptional regulatory networks in Saccharomyces cerevisiae
  Lee et al., Science. 2002 Oct 25;298(5594):799-804
- A genomic regulatory network for development
  Davidson et al., Science. 2002 Mar 1;295(5560):1669-78
Protein-protein interaction networks
- Inferring network mechanisms: the Drosophila melanogaster protein interaction network
  Middendorf M, Ziv E, Wiggins CH, Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3173-4
- A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules
  Tong et al., Science. 2002 Jan 11;295(5553):321-4. Epub 2001 Dec 13
- Protein domain networking
  Legrain, Pierre, Nat Biotechnol. 2002 Feb;20(2):128-9
Metabolic Networks
- The effect of oxygen on biochemical networks and the evolution of complex life
  J. Raymond and D. Segre, Science. 2006 Mar 24;311(5768):1764-7
- The regulatory software of cellular metabolism
  D. Segre, Trends Biotechnol. 2004 Jun;22(6):261-5
- Metabolomics and systems biology: making sense of the soup
  Kell, Current Opinion in Microbiology 2004, 7:296-397
- Metabolic network structure determines key aspects of functionality and regulation
  Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Nature. 2002 Nov 14;420(6912):190-3
- A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
  Schuster S, Fell DA, Dandekar T. Nat Biotechnol. 2000 Mar;18(3):326-32
- Two approaches for metabolic pathway analysis?
  Klamt S, Stelling J. Trends Biotechnol. 2003 Feb;21(2):64-9
- Metabolic pathways in the post-genome era
  Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. Trends Biochem Sci. 2003 May;28(5):250-8
- The small world of metabolism
  Fell DA, Wagner A. Nat Biotechnol. 2000 Nov;18(11):1121-2
- Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast
  Papp B, Pal C, Hurst LD. Nature. 2004 Jun 10;429(6992):661-4
Scale-free networks
- Emergence of scaling in random networks
  Barabasi and Albert, Science, 1999
- The large-scale organization of metabolic networks
  Jeong et al., Nature, 407, 2000
  The structure of the protein universe and genome evolution
  Koonin et al., Nature, 420, 2002
- Expanding protein universe and its origin from the biological Big Bang
  Dokholyan et al., PNAS, 99(22), 2002
Network motifs and network comparison
- Modeling cellular machinery through biological network comparison
  R. Sharan, T. Ideker, Nat Biotechnol. 2006 Apr;24(4):427-33
- Pairwise Alignment of Protein Interaction Networks
  Koyutürk, et al., JCB. Mar 2006, Vol. 13, No. 2: 182-199
- Lasting impressions: motifs in protein-protein maps may provide footprints of evolutionary events
  Rice et al., Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3173-4
- Network motifs: simple building blocks of complex networks
  Milo et al., Science. 2002 Oct 25;298(5594):824-7
- Network motifs in the transcriptional regulation network of Escherichia coli
  Shen-Orr et al., Nat Genet. 2002 May;31(1):64-8
Genetic Interaction Networks
- Systematic interpretation of genetic interactions using protein networks
  R. Kelley and T. Ideker, Nat Biotechnol. 2005 May;23(5):561-6
- Modular epistasis in yeast metabolism
  D. Segre et al., Nat Genet. 2005 Jan;37(1):77-83. Epub 2004 Dec 12

Last modified: Sept 25, 2006.
Maintained by Dannie Durand (durand@cs.cmu.edu) and Annette McLeod (welsch+@cs.cmu.edu).