Paper List (In Progress)

Cancer

Reviews

  • Genome Sequencing Technology and Algorithms [Ch. 11]
  • Chromsome Aberrations in Solid Tumors
  • The Cancer Genome Atlas (pp. 22-29)
  • Chromsome Aberrations in Solid Tumors
  • The Cancer Genome Atlas (pp. 22-29)
  • Comparative Genomic Hybridization
  • Cancer as an evolutionary and ecological process.
  • Oncogenetic Trees

    • Genetics and GWAS

    Reviews

    Many of these are from Nature Genetics review focus on GWAS.

  • Genome-wide association studies: progress and potential for drug discovery and development
  • The Haplotyping Problem: An Overview of Computational Models and Solutions, Chapter 10 [pp. 151-154] of Genome Sequencing Technology and Algorithms. [Online version available from Brown]
  • Genome-wide association studies for complex traits: consensus, uncertainty and challenges
  • Statistical analysis strategies for association studies involving rare variants
  • The pursuit of genome-wide association studies: where are we now?
  • Genome-wide Association Studies: Theoretical and Practical Concerns
  • Genome-wide Association Studies and Human Disease
  • Bayesian statistical methods for genetic association studies

    • Research

    Gene Combinations in Genetics

    Reviews

  • Pathway-Based Approaches for Analysis of Genomewide Association Studies
  • Analysing biological pathways in genome-wide association studies

  • Research

  • RAPID detection of gene–gene interactions in genome-wide association studies

    • Gene Combinations in Cancer

    Reviews

    Research

    Epigenetics

    Reviews

  • Nature Reviews Genetics Focus on Epigenetics
  • High-Throughput Assessments of Epigenomics in Human Disease, Chapter 12 of Genome Sequencing Technology and Algorithms. [Online version available from Brown]

    • Research

    Genome Assembly

    Reviews

  • Fragment Assembly Algorithms, Chapter 7 of Genome Sequencing Technology and Algorithms. [Online version available from Brown]

    • Research

  • Maximum Likelihood Genome Assembly. P. Mendevev and M. Brudno
  • HapCUT: an efficient and accurate algorithm for the haplotype assembly problem V. Bansal and V. Bafna
    • Myers EW. The fragment assembly string graph.
  • EULER assembler
  • Euler-DB
    • Genovo: De Novo Assembly for Metagenomes

    Resequencing and Strutural Variation

    Research

  • Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. F. Hormozdiari C. Alkan E. E. Eichler and S. C. Sahinalp.
  • Structural variation analysis with strobe reads
  • HapCUT: an efficient and accurate algorithm for the haplotype assembly problem
  • Background reading: An MCMC algorithm for haplotype assembly from whole-genome sequence data

    • Other

    Reviews

    Analysis and Principles of Biological Networks

    Research

  • Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.Elena Nabieva , Kam Jim , Amit Agarwal1 , Bernard Chazelle, and Mona Singh
  • Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. Mathieu Lavallée-Adam, Benoit Coulombe and Mathieu Blanchette
  • Detecting disease-specific disregulated pathways via analysis of clinical expression profiles. I. Ulitsky, R.M. Karp and R. Shamir
  • Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles
  • Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways
  • An integrative approach for causal gene identification and gene regulatory pathway inference
  • eQED: an efficient method for interpreting eQTL associations using protein networks
    • Network comparison
  • SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
    • Bayesian Rose Trees
  • Inference of Population Structure Using Multilocus Genotype Data [Read up to "Applications to data" p.949. Appendix is alow useful to understand model.]
  • MMG: a probabilistic tool to identify submodules of metabolic pathways