CS 260, Spring 2015: Seminar on Advanced Topics in Computational Biology

Class Meeting

Monday, Wednesday, 2:10pm - 3:30pm, MSE 113

Office hours

By appointment, please email me.

Prerequisites

CS234 and/or CS238 and/or GEN240A/B

Slides

  • Slides/1 [PDF Format 2slides/page] (Proposed Themes)
  • Slides/2 [PDF Format 2slides/page] (Proposed Themes)
  • Proposed list of topics

  • DNA/RNA methylation
  • Metagenomics
  • 3D structure of genomes
  • Genome Editing (CRISPR/Cas9)
  • Structural variations in the human genome
  • Topics selected by the students

  • Metagenomics
  • 3D structure of genomes
  • DNA/RNA methylation
  • 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

  • March 30: Stefano: Course Organization, Presentation of the six themes
  • Apr  1: Stefano: Presentation of the six themes
  • Apr  6: Stefano: Presentation of the six themes
  • Apr  8: Stefano: Presentation of the six themes, vote
  • Apr 13: Hind: "Accurate viral population assembly from ultra-deep sequencing data", Bioinformatics, 2014
                 Xing: "A novel abundance-based algorithm for binning metagenomic sequences", JCB 2011, Slides
  • Apr 15: Abbas: "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome", Science, 2009, Slides
                 Abid: "Scaling metagenome sequence assembly with probabilistic de Bruijn graphs", PNAS, 2012, Slides
  • Apr 20: Shikhar: "CompostBin : A DNA Composition- Based Algorithm for Binning Environment Shotgun Reads", RECOMB 2008
                 Ashraful: "Meta-IDBA: a de Novo assembler for metagenomic data", Bioinformatics, 2011, Slides
  • Apr 22: Patel: "Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data", PLoS ONE, 2014
                 Suhas: "Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing", NAR, 2013, Slides
  • Apr 27: Feroz: "Detection of allele-specific methylation through a generalized heterogeneous epigenome model", Bioinformatics, 2012, Slides
                 Sonu: Identifying biologically relevant differences between metagenomic communitites, Bioinformatics, 2010
  • Apr 29: Andrew: "BS Seeker: precise mapping for bisulfite sequencing", BMC Bioinfo, 2010
                 Albert: CpG Island Mapping by Epigenome Prediction, PLoS Comp Bio, 2007, Slides
  • May  4: Weihua: "GDNorm: An Improved Poisson Regression Model for Reducing Biases in Hi-C Data", WABI, 2014, Slides
                 Anthony: "Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome", Cell, 2012
  • May  6: Yang: "Detection of significantly differentially methylated regions in targeted bisulfite sequencing data", Bioinformatics, 2013
                 Leo: The human genome: a multifractal analysis, BMC Genomics, 2011
  • May 11: Chunying: "Filling annotation gaps in yeast genomes using genome-wide contact maps", Bioinformatics, 2014
                 Abid: "An optimized algorithm for detecting and annotating regional differential methylation", BMC Bioinformatics, 2013
  • May 13: Feroz: "A statistical approach for inferring the 3D structure of the genome", Bioinformatics, 2014
                 Ashraful: "Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data", Bioinformatics, 2012
  • May 18: Xing: "A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data", Bioinformatics, 2013
  •              Albert: Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nature Genetics, 2011
  • May 20: Yang: "Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes", Nature Biotech, 2014
                 Sonu: "A three dimensional model of the yeast genome", Nature, 2010
  • May 25: Holiday
  • May 27: Suhas: "Genomic landscape of human allele-specific DNA methylation", PNAS, 2012
                 Leo: "Two-dimensional segmentation for analyzing Hi-C data", Bioinformatics, 2014
  • June 1: Andrew: "Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications", Bioinformatics, 2011
                 Weihua: "3D genome reconstruction from chromosomal contacts", Nature Methods, 2014
  • June 3: Patel: "Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions", NAR, 2013
                 Abbas: "Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data", NAR, 2013
  • Papers on Metagenomics (taken)

  • "Accurate viral population assembly from ultra-deep sequencing data", Bioinformatics, 2014
  • "A novel abundance-based algorithm for binning metagenomic sequences", JCB 2011
  • "Scaling metagenome sequence assembly with probabilistic de Bruijn graphs", PNAS, 2012
  • "CompostBin : A DNA Composition- Based Algorithm for Binning Environment Shotgun Reads", RECOMB 2008
  • "Meta-IDBA: a de Novo assembler for metagenomic data", Bioinformatics, 2011
  • "Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data", PLoS ONE, 2014
  • Identifying biologically relevant differences between metagenomic communitites, Bioinformatics, 2010
  • "Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data", Bioinformatics, 2012
  • "Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes", Nature Biotech, 2014
  • Papers on Metagenomics (not taken)

  • Genovo: De Novo Assembly for Metagenomes, JCB, 2011
  • Papers on 3D structure of genomes (taken)

  • "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome", Science, 2009
  • "GDNorm: An Improved Poisson Regression Model for Reducing Biases in Hi-C Data", WABI, 2014
  • "Filling annotation gaps in yeast genomes using genome-wide contact maps", Bioinformatics, 2014
  • "A statistical approach for inferring the 3D structure of the genome", Bioinformatics, 2014
  • "3D genome reconstruction from chromosomal contacts", Nature Methods, 2014
  • "Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome", Cell, 2012
  • Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nature Genetics, 2011
  • "Two-dimensional segmentation for analyzing Hi-C data", Bioinformatics, 2014
  • Papers on 3D structure of genomes (not taken)

  • "Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts", Genome Research, 2014
  • "Single-cell Hi-C reveals cell-to-cell variability in chromosome structure", Nature, 2013
  • "A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping", Cell, 2014
  • "Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data", NAR, 2013
  • TBD
  • Papers on DNA/RNA methylation (taken)

  • "Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing", NAR, 2013
  • "Detection of allele-specific methylation through a generalized heterogeneous epigenome model", Bioinformatics, 2012
  • "Detection of significantly differentially methylated regions in targeted bisulfite sequencing data", Bioinformatics, 2013
  • "Genomic landscape of human allele-specific DNA methylation", PNAS, 2012
  • "Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions", NAR, 2013
  • "BS Seeker: precise mapping for bisulfite sequencing, BMC Bioinfo, 2010"
  • "Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications", Bioinformatics, 2011
  • "A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data", Bioinformatics, 2013
  • Papers on DNA/RNA methylation (not taken)

  • "Modeling DNA methylation dynamics with approaches from phylogenetics", Bioinformatics, 2014
  • TBD