(Irrelevant official name: Topics in Graph Theory)
Lectures: WF 10-11 in Sydney Smith (SS) 1084
Instructor: Michael Brudno
Office: Pratt (PT) 286C
Office Hours: Th 10-11am and by appointment
Presenter(s) | Title |
9-11am April 5 | |
Hertel, Hertel & Mirmohammadi | New Algorithms for Genome Assembly |
Hyndman & Germann | Motif Identification with Variable-length Random Projections |
Marcini & Samulowtiz | Approximate Alignment of Protein-Protein Interaction Networks |
Chung & Musso | Dynamic Markov Clustering |
Hu | Three Strategeies for multi-compartamental prediction of protein subcellular localizations |
Taylor | Detecting Interspecific REcombination in DNA Sequence Alignment with Phylogenetic Products of Experts |
9-11am April 7 | |
Jiang & Yan | Analysis of Single Nucleotide Patterns in Disease Genes |
Lan & Lee | The Relationship Between Sequence Similarity and Gene Function |
El Ayoubi & Juma | Maximum Parsimony Phylogeny using Integer Programming |
Diamantis & Sarkas | Fast Homology Search |
Sala | Protein Structural Alignment |
Snoek | Using Conditional Random Fields for Gene Prediction |
9-11am April 12 | |
Natarjan | A Discriminative Approach for Predicting Protein Backbone Structures using Dynamic Condiotional Random Fields |
Ray | Probabilistic Methods for Fast Integration of Multiple Sources of Biological Information |
Lang | Protein Constellations |
Abramson & Tilo | Substitution Models in Protein-protein Interaction prediction |
Dimitromanolakis & Papagelis | Dijkstra's Algorithm for Sequence Alignment |
Babak & Huang | Bayesian Learning of microRNA Regulatory Networks through prediction of Transcriptome Changes due to microRNA Regulation. |
Expected Background:
Students should be familiar with algorithms
(at least CSC 373 level), basic probability theory, and some machine learning.
Grading:
The basic requirements for the class will be a course project (50% of the
grade), four homework assignments (45% total), and class participation
(5%).
Administrative details:
This course is offered under the name "Topics in Graph Theory" due to a
lack of a more appropriate name/number. It will NOT concentrate on graph
theory (though we certainly will use graphs). Once a course with an
appropriate name/number is approved it will be possible to retroactively
change the transcripts of students to indicate the new course. The class
will satisfy the 2c breadth.