CSC 570: Special Topics in Computer Science: Bioinformatics
Fall 2011

Instructor: Alexander Dekhtyar,, 14-215

Office Hours:
Who Where
Tuesday 11:00 - 12:00pm Alex 14-215
Wednsday 9:00am - 11:00am Alex 14-215
Thursday 11:00 - 12:00pm Alex 14-215

Additional appoinments: send email.

Final Exam Date: Tuesday, December 6, 2011, 7:10--10:00pm

(note: there is no final exam, but we will do project presentations in that time)

News and Notes

Old News and Notes

Course Materials

Syllabus Postscript PDF
Project Teams HTML
Photographic Evidence HTML


Project A SuperGene Predictor Anya Goodman Description [doc] [September 28, 2011]
Project B Bacterial Strain Identification and Maintenance Chris Kitts Description [doc] [September 28, 2011]
Project C Pyroprint Simulation Michael Black Description [doc] [September 28, 2011]
Project B Background/CPLOP DB [doc] [September 28, 2011]


Assignment 1 Research presentation Due: November 15/December 1 Postscript PDF [October 5, 2011]
Assignment 2 Project Deliverables Due: December 6 Postscript PDF [November 22, 2011]

Lecture Notes Template

LaTeX template LaTeX Postscript PDF
Sample figurexfig .fig Encapsulated Postscript

Presentation Schedule

DatePresentation 1Presentation 2Presentation 3
November 15, Tuesday Michael Hilton
Tyler Yero
Cailin Cushing
Diana Shealy
Connor Lange
Clovas Hansen
Jim Langlois
Bob Somers
Ryan Schmitt
November 17, Thursday Ryan Hnarkis
Allen Dunlea
James Penton
Arlo White
DJ Mitchell
Michael Black
Anya Goodman
Chris Kitts
November 22, Tuesday Massimo Becker
Darrin Weng
Russel Fritch
Steven Tartakovsky
Ryan Verdon
Jan Lorenz Soliman
November 29, Tuesday Matt Carson
Dirk Cummings
Chris Hoover
Jason Banich
Eriq Augustine
Aldrin Montana
Scott Kuroda

Lecture Notes

Lecture 0 September 22 Bioinformatics in a nutshell Postscript PDF [September 19, 2011]
Lecture 1 September 27 String Matching Postscript PDF [September 27, 2011]
Lecture 2 October 4-6 Suffix Trees Postscript PDF [October 4, 2011]
Lecture 3 October 6 Repeated Sequence/Palindrome Detection Postscript PDF [October 19, 2011]
Lecture 4 October 11 Restriction Mapping Postscript PDF [October 19, 2011]
Lecture 5 October 13 Motif Finding Postscript PDF [October 19, 2011]
Lecture 6 October 18 Genome Rearrangement/Greedy Algorithms Postscript PDF [October 19, 2011]


Exact String Matching

Approximate String Matching

Suffix Trees

Repeat/Palindrome Detection

Parallel and Distributed Programming for Bioinformatics

Student Presentations

Topic Students Date acquired
Approximate String Matching Jim Langlois, Bob Somers, Ryan Schmitt September 27
Algorithms on Suffix Trees Michael Hilton, Tyler Yero, Cailin Cushing October 4
Advanced Palindrome Detection Techniques Diana Shealy, Connor Lange, Clovas Hansen October 6
Parallel and Multicore Processing for Bioinformatics Massimo Becker, Darrin Weng, Russel Fritch, Steven Tartakovsky October 11
Biometrics Ryan Hnarkis, Allen Dunlea, James Penton October 13
Species Divergence in Evolutionary Tree Arlo White, DJ Mitchell October 13
Advanced Genome Rearrangement Matt Carson, Dirk Cummings October 18
NoSQL Databases and Map-Reduce for Bioinformatics Ryan Verdon, Jan Soliman October 20
Systems Biology Eriq Augustine, Aldrin Montana, Scott Kuroda October 20
PAM and BLOSUM Chris Hoover, Jason Banich October 25

September 19, 2011, dekhtyar at