||4/25: Student presentation
X. Wang: Phylogenetic network
Yu Wu: compressed suffix array
4/23: Student presentation
A. Thibodeau: RNA-seq
N. Tran: Genome assembly
paper on phylogenetic network based on clusters.
The paper on compressed suffix array: Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
||4/19: Student presentation
T. Xu: Genome assembly
A. Al-OKaily: phylogenetic networks
4/17: Student presentation
J. Lindsay: scaffolding for genome assembly
K. Marinelli: I/O issues in computing
assembly using GPU.
A book on phylogenetic network
A scaffolding paper (from RECOMB 2011).
Notes by Kevin on I/O issues.
||4/12: No class.
4/10: Student presentaiton
Sequencing applications in metagenomics (J. Zhang)
Topics in DNA forensics (P. .Ghimire)
A paper on metagenomic assembly.
The paper presented in class about match probability in forensics DNA.
||4/5: Phylogenetic networks.
Notes by A. Thibodeau
4/3: Subtree prune and regraft algorithms.
|This is my
own paper about phylogenetic networks.
Read this book for more background and related types of phylogenetic networks.
This is the paper for the fixed parameter tractable algorithm for SPR.
||3/29: Subtree prune and
Notes by A. Thibodeau
3/27: Algorithms for building ARGs. Introduction to subtree prune and regraft.
my own paper about subtree prune and regraft.
This is the paper about tree-based ARG construction.
||3/22: Algorithms for
building ancestral recombination graph.
Notes by K. Marinelli
3/20: Ancestral recombination graph. The history bound.
Notes by N. Tran.
by Gusfield on ancestral recombination graph.
This is the paper that first develop the history bound.
||3/8: Lower bound on
3/6: Recombination: coalescent view and lower bound.
|The haplotype bound
paper talked about in class.
Notes by Gusfield on recombinaiton lower bounds and ancestral recombination graphs.
Here is a paper on coalescent ancestral configurations in recombination analysis.
||3/1: Perfect phylogeny.
Introduction to recombination.
2/28: A little more about DNA forensics. Perfect phylogeny problem.
Notes by X. Wang.
|Here is a chapter
written by Gusfield about recombination. This provides some more
accessible introduction to recombination to non-biologists
The paper on perfect phylogeny linear time construction by Gusfield.
||2/23: More probability
computation on coalescent theory. A little about DNA forensics.
2/21: Probability computation with coalescent theory
|Much of what is discussed
in class is Tavare's
Paper by Griffiths and Lessard on Ewens' sampling formula.
Some info about DNA forensics.
An article on DNA forensics, which mentions a problem discussed in class.
||2/16: coalescent theory
Notes by J. Zhang
2/14: Genome assembly with paired reads. Introduction to probability theory
|See Wakeley's book for
(very accessible) introduction to coalescent theory.
Anothere good reference to coalescent theory (although a little harder to read) is Tavare's writing.
Two papers (paper 1 and paper 2) on genome assembly with paired reads.
||2/9: Genome assembly (cont.)
2/7: Genome assembly: introduction
Notes on genome assembly (by T. Xu).
|Pevzner, et al's paper
using Eulerian path.
Large part of genome assembly introduction comes from Gusfield's book.
||2/2: More BWT-based reads
mapping. Calling genetic variants with sequence reads.
1/31: Short reads mapping (cont.)
Notes on reads mapping (by Yu Wu).
calling paper discussed in class.
The BWT-based reads mapping: the BWA paper
Compressed suffix array: Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
Another paper on compressed suffix array:
||1/26: Short sequence reads
1/24: Pattern matching with BWT
Notes (by P. Ghimire) on BWT.
|The short reads mapping
paper is: the MAQ
The main paper covered on BWT pattern matching is: Opportunistic data structures with applications (FOCS 2000)
1/18: Introduction to string matching.
Notes (by Y. Wu) on string algorithm introduction
many online reference on BWT. There are also books on BWT (e.g. link).
Some more notes on suffix tree and array:
An introduction to suffix tree by Dan Gusfield (PDF). A simple introduction to suffix array link.
If you want, you can also read the original paper on linear-time suffix array algorithm (PDF).