CS 260, Spring 2012: Seminar on Advanced Topics in Computational Biology
2:10 p.m. - 3:30 p.m. Sproul 1358
By appointment, please email me.
CS234 and/or CS238 and/or GEN240A/B
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
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