CSCI-4964/6964: Bioinformatics & Computational Biology, Spring 2013
Class: 10-11:50AM, MR, Low 3130
Instructor Office Hours: 12-1PM, MR
A tentative sequence of topics to be covered in the classes; changes are likely as the course progresses.
|Day: Date||Topic||Readings||Lecture Notes|
|M: Jan 21||NO CLASS (Martin Luther King Holiday)|
|R: Jan 24||Introduction||R1, R2||intro.ppt|
|M: Jan 28||Sequence Alignment||R3||Lecture1.pdf|
|R: Jan 31||Alignment & Scoring Matrices||R4, R5||Lecture2.pdf|
|M: Feb 4||More Scoring Matrices||Lecture3.pdf|
|R: Feb 7||Database Search and Significance||R6, R7||Lecture4.pdf|
|M: Feb 11||HMMs ( Guest Lecture: Prof. Chris Bystroff )||R8||HHM_1.pdf|
|R: Feb 14||Profile HMMs ( Guest Lecture: Prof. Chris Bystroff )||R9|
|T (Tuesday): Feb 19||Motif Discovery||R10||Lecture5.pdf|
|R: Feb 21||Motif Discovery||Lecture6.pdf|
|M: Feb 25||EXAM I|
|R: Feb 28||Suffix Trees, Genome Scale Alignment||R11, R12||Lecture7.pdf|
|M: Mar 4||Suffix Arrays, Phylogenetic Trees||R13, R14||Lecture8.pdf|
|R: Mar 7||Phylogenetic Trees||R15||Lecture9.pdf|
|M: Mar 11||NO CLASS (spring break)|
|R: Mar 14||NO CLASS (spring break)|
|M: Mar 18||Genome Rearrangements||R16, R17||Lecture10.pdf|
|R: Mar 21||Protein Structure Alignment||R18, R19, R20||Lecture11.pdf|
|M: Mar 25||Structure Alignment||R21||Lecture12.pdf|
|R: Mar 28||Protein Structure Prediction||R22||Lecture13.pdf|
|M: Apr 1||EXAM II|
|R: Apr 4||Protein Threading||Lecture14.pdf|
|M: Apr 8||Gene Expression Analysis||R23||Lecture15.pdf|
|R: Apr 11||Gene Expression Clustering||R24, R25||Lecture16.pdf|
|M: Apr 15||Biclustering Methods||Lecture17.pdf|
|R: Apr 18||Network Biology||R26, R27||Lecture18.pdf|
|M: Apr 22||Network Motifs||R28||Lecture19.pdf|
|R: Apr 25||Network Motifs||R29||Lecture20.pdf|
|M: Apr 29||Kernel Methods for Bioinfo||R30, R31||Lecture21.pdf|
|R: May 2||Kernel Methods for Bioinfo||Lecture22.pdf|
|M: May 6||EXAM III|
|R: May 9||NO CLASS (reading day)|
Computational Biology and Bioinformatics are essentially interchangeable terms, referring to the science of analyzing biological data. The goal of this course is to introduce the main topics and the frontiers of computational biology. The basic topics include sequence and protein structure analysis (alignment, evolution, search, motifs, and indexing). The emerging topics include next generation sequencing, gene expression analysis, network biology, and kernel data mining methods. The emphasis will be on the application of these methods to the various "omics" within computational systems biology, i.e., genomics, proteomics, interactomics, transcriptomics, and metabolomics.
After taking this course students will be
The pre-requisites for this course include data structures and algorithms, discrete mathematics, and probability & statistics. Knowledge of basic linear algebra will serve you well too. Assignments will require the use of Python, or R. Only these two scripting languages will be permitted for the assignments.
There is no required text for the course. Reading materials will be posted online.
Your grade will be a combination of the following items.
Attendance: Students are strongly encouraged to participate in the class, and should try to attend all classes.
Laptop Policy: No laptops or other electronic devices are permitted during lectures. You may however use these during exams to access course material online, or to use the calculator functions. Browsing the web for solutions, etc. is of course not permitted. Scripting (using python or R or other languages) is also not permitted to solve the exam questions, which are intended to be done by hand.
You may consult other members of the class on the homeworks, but this must be limited to the ideas only; you must submit your own implementation and work. Anytime you borrow material from the web or elsewhere, you must acknowledge the source.
The school takes cases of academic dishonesty very seriously, resulting in an automatic "F" grade for the course. Students should familiarize themselves with the relevant portion of the Rensselaer Handbook of Student Rights and Responsibilities on this topic.