CS 260, Spring 2011: Seminar on Advanced Topics in Computational Biology
Class Meeting
2:10 p.m. - 3:30 p.m. SPTH 1307
Office hours
By appointment, please email me.
Prerequisites
CS234 and/or CS238.
Slides
Slides [PDF Format 2slides/page] (Proposed Themes) -- updated
Initial list of topics
Cloud computing for computational biology Decoding the epigenetics code (nucleosome positioning, histone code, DNA methylation) Decoding the splicing code (isoform reconstruction from mRNA-seq, etc.) Metagenomics 3D structure of genomes Copy number variations in the human genome
Topics selected by the students
Computational epigenetics (nucleosome positioning, histone code, DNA methylation) Unraveling transcription (splicing, isoform reconstruction from mRNA-seq, etc.) Structural variations (SNPs, copy number variations, genome-wide association studies) in the human genome
Some papers on 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 transcription/splicing (splicing code, RNA-seq mapping, sioform reconstruction)
REVIEW: Epigenetics in Alternative Pre-mRNA Splicing, Cell REVIEW: Alternative splicing and evolution: diversification, exon definition and function, Nature Review Genetics REVIEW: Splicing in disease: disruption of the splicing code and the decoding machinery, Nature Review Genetics REVIEW: Alternative Splicing: New Insights from Global Analyses, Cell
Nascent transcript sequencing visualizes transcription at nucleotide resolution, Nature Deciphering the splicing code, Nature A network of conserved co-occurring motifs for the regulation of alternative splicing, NAR Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq, NAR Model-based detection of alternative splicing signals, Bioinformatics Alternative isoform regulation in human tissue transcriptomes, Nature Discovery and Analysis of Evolutionarily Conserved Intronic Splicing Regulatory Elements, PLoS Genetics Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing, Nature HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data, PLoS One A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq, PLoS One A General Definition and Nomenclature for Alternative Splicing Events, PLoS Comp Bio TopHat: discovering splice junctions with RNA-Seq, Bioinformatics Inference of Isoforms from Short Sequence Reads, JCB Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments, NAR Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs, Nature Biotech Analysis and design of RNA sequencing experiments for identifying isoform regulation, Nature Meth Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotech
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
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
Mar 29: Course Organization, presentation of the six themes Mar 31: presentation of the six themes Apr 5: New themes, vote on three, Stefano: Computational Challenges of the Barley Genome project Apr 7: Stefano: Computational Challenges of the Barley Genome project Apr 12: Wei: Transcriptome Assembly from RNA-Seq Data--Objectives, Algorithms and Challenges Apr 14: Mohammad: A network of conserved co-occurring motifs for the regulation of alternative splicing Apr 19: Elena: A geometric approach for classification and comparison of structural variants Apr 21: Katya: Detection and characterization of novel sequence insertions using paired-end next-generation sequencing Apr 26: Hamid: Alternative isoform regulation in human tissue transcriptomes Apr 28: Moses: A robust framework for detecting structural variations in a genome May 3: Mo: The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes May 5: Alex: Deciphering the splicing code May 10: Mohammad: BreakDancer: an algorithm for high-resolution mapping of genomic structural variation May 12: Elena: Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants May 17: Mo: Incorporating nucleosomes into thermodynamic models of transcription regulation May 19: Alex: CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data May 24: Katya: Structural variation analysis with strobe reads May 26: Moses: A three-dimensional model of the yeast genome May 31: Wei: Splice site strength–dependent activity and genetic buffering by poly-G runs Jun 2: Hamid: Detecting structural variations in the human genome using next generation sequencing