*************************************************************************************************************************************************

Suggested papers for longer paper presentation

These papers can be good choices for paper presentation (around 40 minutes).

- There are many types of phylogenetic networks. Read this book and then
pick on particular type of phylogenetic network (by reading some
references cited in this paper). Then tell us something new. Note: this
book is more about concepts and not about particular techniques. You
should read the related literatures in order to know the technical
details. I think this is a large subject and more than one student can
choose this subject.

- DNA forensics is an interesting topic. I can suggest some papers if you are interested in this. (Pankaj)
- Metagenomics is an emerging field, where sequencing
plays an important role. There are papers using sequencing data
analysis for metagenomics and may be of interests to presnt. (Jin)

- A good topic to present is coalescent theory. The book by Tavare contains many interesting subjects. For example, I would like to hear some discussion about ABC (approximate Bayesian Computation), and how ABC is related to coalescent theory. There are also other aspects of coalescent theory that can be presented.
- There are emerging sequencing technologies. It will be
interesting if someone can survey these new technologies.

- Genome assembly is a fast evolving subject and there
are many related papers. Read seveeral of these papers (e.g.
the Velvet paper and the ALLPATHS
paper and other more recent papers using paired-end reads) and
present some more technical approaches in more details.

- It may be interesting to take a deeper look at the BWT.
Read this
paper and tell us something interesting about
it. This (and the compressed suffix array) paper can be a good choice
if you are interested in learning more algorithmic ideas.

- On compressed suffix array: Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching.

*************************************************************************************************************************************************

The following lists problems related to lectures. Each student should pick one problem and explain it to the class in 15-20 minutes. This is a great way to better understand the lecture topics. Note: you need to contact the instructor when picking a problem.

- [P8] Read this paper on DNA forensics, and tell us a little more about things not covered in the class. (Presented by Xin)
- [P7] Read section 3.5 of the book
by Tavare, and try to work out the detailed proof of Ewens sampling
formula (ESF) using the induction approach. And then tell us a little
more about ESF if you can.

- [P6] Read the chapter 2 of the book by Tavare, tell us something more about coalescent theory. For example, explain how variable population size is considered (Section 2.4). (Presented by Asa)
- [P5] There are more papers on short read assembly. For example, read this paper and tell us something interesting about it. (Presented by Tam)
- [P4] There are several papers for short read genome
assembly. Read one of these papers (e.g.
the Velvet paper and the ALLPATHS
paper) and tell us something interesting about it.

- [P3] There are also several other BWT-based reads mapping approach. Now, read the the Bowtie paper and tell us how it compares with the BWA paper I presented in class.
- [P2] There are many papers on short sequence reads
mapping. Now, read the
BFAST paper, and compare it with the MAQ paper we
discussed in class: what are the main differences? (Presented by Pankaj)

- [P1] This problem concerns the linear-time suffix array construction algorithm. The algorithm covered in class is from this paper. We note that there are two other papers (paper 2, paper 3) published around the same time. Now, read the two papers and compare them with the first paper. Then tell us what are the main difference of the three algorithms. Comment on these three algorithms about their pros and cons.