BNFO 615: Data analysis for bioinformatics
Fall 2015

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Wed 2:30-5:30
Email: usman@cs.njit.edu

Course Overview: Students will study and present bioinformatics papers and work on a bioinformatics project that makes extensive use of Python (or R). Students will work in teams of two and each member will make two separate presentations related to their project. Towards the end of the course students will make a class presentation of their project. Each student presentations counts for 20% of the grade (and both count for 40%) and the project work 60% of the grade. Without two paper presentations or completion of the project no grade will be assigned.

Course plan:

Topic	Date	Notes
Intro		Projects
Slides on R courtesy of Zhi Wei		Bio background Intro to R Probability Data exploration More R
Slides on Python	09/01/2015	Introduction to Python Needleman-Wunsch alignment Programming assignment Python programming assignment
Short read mapping and projects	09/15/2015	Projects2
Phylogeny reconstruction	09/22/2015	Phylogeny reconstruction
Papers	09/29/2015	Edward: Comparison of Family History and SNPs for Predicting Risk of Complex Disease Clarissa: Consistency of metagenomic assignment programs in simulated and real data E.coli genome Genome alignment Genome wide association studies
Papers	10/06/2015	Catherine: Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices Kathryn: Alignathon: A competitive assessment of whole genome alignment methods
Papers	10/13/2015	Shijie: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Ittehad: Risk estimation and risk prediction using machine-learning methods Genomic risk prediction of complex human disease and its clinical application
Papers and project updates	10/20/2015	Kayla: Alignment programs used in Alignathon study Kayla's talk
Papers	10/27/2015	Sruti: Variant detection sensitivity and biases in whole genome and exome sequencing Samantha: Whole genome prokaryotic phylogeny
Papers	11/03/2015	Clarissa: Kraken: ultrafast metagenomic sequence classification using exact alignments CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers Accurate read-based metagenome characterization using a hierarchical suite of unique signatures Ittehad: Risk estimation and risk prediction using machine-learning methods Genomic risk prediction of complex human disease and its clinical application Project data
Papers	11/10/2015	Catherine: Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences Kathryn: Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
Papers and project update	11/17/2015	Shijie: Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals Ittehad:
Papers	11/24/2015	Kayla: Scalable multi whole-genome alignment using recursive exact matching Edward: Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms
Papers	12/01/2015	Samantha: Automated reconstruction of whole genome phylogenies from short sequence reads Sruti:
Final project presentations	12/07/2015
Papers		Variant detection Variant detection sensitivity and biases in whole genome and exome sequencing A statistical method for the detection of variants from next-generation resequencing of DNA pools Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data GATK best practices Metagenomics Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics The PAMPA datasets: a metagenomic survey of microbial communities in Argentinean pampean soils A better sequence-read simulator program for metagenomics Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut Current opportunities and challenges in microbial metagenome analysisa bioinformatic perspective Consistency of metagenomic assignment programs in simulated and real data A comparative evaluation of sequence classification programs Whole genome alignment assessment Alignathon: A competitive assessment of whole genome alignment methods SVM sequence alignment Structural SVM for Protein Sequence Alignment Species tree from whole genome Whole genome prokaryotic phylogeny Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices Deep learning/Representation learning Representation Learning: A Review and New Perspectives Learning Feature Representations with K-means Analysis of single-layer networks in unsupervised feature learning Building high-level features using large-scale unsupervised learning Using deep learning to enhance cancer diagnosis and classification Deep learning of the tissue-regulated splicing code Gene expression The l1-l2 regularization framework unmasks the hypoxia signature hidden in the transcriptome of a set of heterogeneous neuroblastoma cell lines Detecting Stable Clusters Using Principal Component Analysis Gene selection for microarray data analysis using principal component analysis Techniques for clustering gene expression data Other Empirical performance of drug sensitivity prediction algorithms
Projects
Project resources
Project proposals