CS 260, Spring 2012: Seminar on Advanced Topics in Computational Biology

Class Meeting

2:10 p.m. - 3:30 p.m. Sproul 1358

Office hours

By appointment, please email me.

Prerequisites

CS234 and/or CS238 and/or GEN240A/B

Slides

  • Slides [PDF Format 2slides/page] (Proposed Themes) -- updated
  • Proposed list of topics

  • Information Theory for Molecular Biology
  • Computational epigenetics (nucleosome positioning, histone code, DNA methylation)
  • Decoding the splicing code (isoform reconstruction from mRNA-seq, etc.)
  • Metagenomics
  • 3D structure of genomes
  • Structural variations in the human genome
  • Topics selected by the students

  • Information Theory for Molecular Biology
  • Computational epigenetics
  • Structural variations in the human genome
  • Course Format

    The course is structured it as a "journal club", where students alternate presenting papers and highlight and discuss possible new line of research.

    Calendar of Presentations

  • Apr   3: Course Organization, presentation of the six themes
  • Apr   5: presentation of the six themes
  • Apr 10: presentation of the six themes, vote
  • Apr 12: Stefano
  • Apr 17: Stefano
  • Apr 19: Stefano
  • Apr 24: Anton: "NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model", by A. Polishko, et al.
  • Apr 26: Amna: "Structural variation analysis with strobe reads" Bioinformatics, by A. Ritz, et al.
  • May   1: Scott: "A novel strategy of transcription regulation by intragenic nucleosome ordering", by C. Vaillan, et al.
  • May   3: Micheal: "The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes", NAR
  • May   8: Anton: "Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local", PLoS Comp Bio
  • May 10: Hind: "Fast and accurate long-read alignment with Burrows-Wheeler transform", Bioinformatics
  • May 15: Sean: "Detecting structural variations in the human genome using next generation sequencing" by Ruibin Xi, Tae-Min Kim and Peter J. Park
  • May 17: Amna: "A geometric approach for classification and comparison of structural variants" by Suzanne Sindi et al.
  • May 22: Scott: "The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups", Curtis et al.
  • May 24: Denise: "Efficient de novo assembly of large genomes using compressed data structures" by J. Simpson and R. Durbin
  • May 29: Sean: "Nucleosome deposition and DNA methylation at coding region boundaries", by Choi et al.
  • May 31: Denise: "DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis", by Elrich et al.
  • Jun   5: Michael: "Sensitive and accurate detection of copy number variants using read depth of coverage", by Yoon et al.
  • Jun   7: Hind: "Genome-wide genetic marker discovery and genotyping usingnext-generation sequencing", by Davey et al.
  • Some papers on Information Theory for Molecular Biology (BWT, wavelet trees, and other compressed data structures; pooling design (group testing), compressed sensing and connections to error-correcting codes; bar-coding design; compression-based sequence similary metric)

  • REVIEW: Textual data compression in computational biology: a synopsis, Bioinformatics

  • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology
  • Space-Efficient Whole Genome Comparisons with Burrows-Wheeler Transforms, JCB
  • Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics
  • Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics
  • Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree, IEEE TCBB
  • Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment, BMC Bioinformatics
  • Efficient de novo assembly of large genomes using compressed data structures, Genome Research
  • Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex, Nature Methods
  • A new pooling strategy for high-throughput screening: the Shifted Transversal Design, BMC Bioinformatics
  • Shifted Transversal Design smart-pooling for high coverage interactome mapping, Genome Research
  • Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping, Nature Methods
  • DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis, Genome Research
  • Bacterial Community Reconstruction Using Compressed Sensing, JCB
  • Identification of rare alleles and their carriers using compressed se(que)nsing, NAR
  • Compressed Genotyping, IEEE TIT
  • Some papers on computational epigenetics (nucleosomes; DNA methylation; histone modifications)

  • REVIEW: Epigenetics in Alternative Pre-mRNA Splicing, Cell
  • REVIEW: Computational epigenetics, Bioinformatics
  • REVIEW: Nucleosome positioning and gene regulation: advances through genomics, Nature Review Genetics
  • REVIEW: What controls nucleosome positions?, Trend Genetics

  • Nucleosome positioning as a determinant of exon recognition, Nature SM&B
  • A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning, Genome Research
  • Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens, PLoS Comp Bio
  • Relationship between nucleosome positioning and DNA methylation, Nature
  • High-throughput sequencing reveals a simple model of nucleosome energetics, PNAS
  • The organization of nucleosomes around splice sites, NAR
  • A novel strategy of transcription regulation by intragenic nucleosome ordering, Genome Research
  • Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local, PLoS Comp Bio
  • Predicting nucleosome positioning using a duration Hidden Markov ModelBMC Bioinfo
  • The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes, NAR
  • Nucleosome deposition and DNA methylation at coding region boundaries, BMC Genome Biology
  • Incorporating nucleosomes into thermodynamic models of transcription regulation, Genome Research
  • Nucleosome organization in the Drosophila genome, Nature
  • A genomic code for nucleosome positioning, Nature
  • A three-dimensional model of the yeast genome, Nature
  • Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature
  • BS Seeker: precise mapping for bisulfite sequencing, BMC Bioinfo
  • Some papers on structural variations (detecting SNPs; mapping paired-end reads to detect structural variations; copy number variations)

  • REVIEW: Genome structural variation discovery and genotyping, Nature Review Gen
  • REVIEW: Mechanisms of change in gene copy number, Nature Reviews Genetics
  • REVIEW: Analysis of next-generation genomic data in cancer: accomplishments and challenges, Human Mol Gen

  • Detection and characterization of novel sequence insertions using paired-end next-generation sequencing, Bioinformatics
  • A robust framework for detecting structural variations in a genome, Bioinformatics
  • Detecting copy number variation with mated short reads, Genome Research
  • Detecting structural variations in the human genome using next generation sequencing, Functional Genomics
  • Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes, Genome Research
  • CNAseg-a novel framework for identification of copy number changes in cancer from second-generation sequencing data, Bioinformatics
  • Sensitive and accurate detection of copy number variants using read depth of coverage, Genome Research
  • Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm, NAR
  • Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome, Genome Research
  • BreakDancer: an algorithm for high-resolution mapping of genomic structural variation, Nature Methods
  • Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants, PLoS Comp Bio
  • Structural variation analysis with strobe reads, Bioinformatics
  • A geometric approach for classification and comparison of structural variants, Bioinformatics