BNFO 602: Foundations of bioinformatics II
Spring 2018

Instructor:
Usman Roshan, GITC 4207
Ph: 973-596-2872
Office hours: M: 1 to 3pm, W: 11:30 to 2:30pm
Email: usman@njit.edu

Course overview: We will cover basic sequence alignment and mostly phylogenetics including phylogenies from whole genome data

Grading:

• Programming assignments and quizzes

Recommended texts:

• Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner
• Introduction to Bioinformatics by Arthur Lesk
• Biological Sequence Analysis by Durbin et. al.
• Algorithms on strings, trees, and sequences: computer science and computational biology by Dan Gusfield

Course plan:
   

Topic	Date	Lectures
Introduction	01/16/18	Basic bio background Python Python example 1 Python example 2 Python example 3 Python cheat sheet Pairwise sequence alignment Multiple sequence alignment Basic Unix command sheet Instructions for AFS login
Sequence alignment - Needleman-Wunsch in Python	01/23/18	Needleman Wunsch sequence alignment
Phylogenetics - maximum parsimony	01/30/18	Phylogenetics MP Tree data structure
Phylogenetics - small and big parsimony	02/06/18	Online phylogeny viewer
Small parsimony in Python	02/13/18	Code for small parsimony Assignment 1
Small parsimony in Python	02/20/18	Code for newick tree Code for random tree Code for nearest neighbor interchange Haemoglobin sequences (SWISSPROT species IDs) ClustalW webserver Haemoglobin aligned sequences Online phylogeny viewer
MP local search in Python with NNI local moves	02/27/18	Model tree (phylogram) Model tree (Newick text) Simulated data divergence .1 Simulated data divergence 1 Simulated data divergence 10 Simulated data divergence 100 Assignment 2 Sample input for assignment The optimal tree here has score 10. On the haemoglobin dataset you can expect a score of 112 after a 100 random restarts.
Phylogenetics - maximum likelihood	03/06/18	Basic statistics More basic statistics Applied statistics
Spring break	03/13/18
Phylogenetics - maximum likelihood	03/27/18	Phylogenetics ML
Phylogenetics - distance based methods	04/03/18	Distance based phylogenetics UPGMA implementation
Phylogenetics - UPGMA implementation	04/10/18
Phylogenetics - neighbor joining, bootstrapping, and MP vs. UPGMA on simulated data	04/17/18	UPGMA in Python NJ Assignment 3 NJ tree on haemoglobin aligned sequences
Phylogenetics - whole genome phylogeny, bootstrapping	04/24/18	Evolutionary distances BLAST-like alignment score E.coli K12 MG1655 genome Related proteobacteria genomes Bacterial phylogeny Assignment 4 Methods and studies Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions Use of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility The accuracy of phylogeny reconstruction on simulated whole genome sequences from Evolver Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment Whole genome prokaryotic phylogeny ALF genome evolution Mutation rates in mammalian genomes 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
Whole genome phylogenetics	05/01/18