Students wishing to do their internship with me should consider that not all of these projects are suitable for thesis, in particular some of them could be at an early stage and less likely to produce consistent results in the relatively short time of a batchelor/master project. Also, consider to set up your thesis with the tutor.
1. Scaffolding with SOLiD Mate Pairs
We recently finished to sequence the genome of a microalga (N. gaditana) with a hybrid approach 454 shotgun + SOLiD Mate Paired reads. I developed a custom program to exploit color space mate paired reads (at the time of the sequencing no program allowed this). I developed both a scaffolding lgorithmand a web-based interface for contig browsing.
I'm currently working to improve the user experience and the GUI.
2. Resequencing of three winegrape varieties
As part of the SERRES project, I am assemblying the genome of three grape varieties (originated by artificial breeding of different species). The idea is to use the genome of V. vinifera as a reference, yet to exploit Mate Paired reads to both identify structural variations, and moreover to de novo assembly peculiar regions not present in the reference.
3. SNP calling and validation
SOLiD color space is a useful tool to detect SNPs, and several pipelines can be used to perform this. I'm currently working on a web-based pipeline with integrated primer design for SNP validation.
4. User interaction with bioinformatics tools
Many powerful bioinformatics tools require a certain degree of confidence with Linux and its shell. When developers prepare a web version of their programs, it often lacks the power and flexibility of command line. The ability to identify user needs and prepare a simple GUI to allow them to perform the task is a pivotal demand for novel bioinformatics tools. An example of this could be the very common BLAST search tool: if optimized should return relevant information for the user like links to gene annotation if the match is within a gene, or a picture of the genomic browser...
- 2012: Novel method for telomere identification, used for N. gaditana
- 2011: N. gaditana genome scaffolding (to the chromosome level)
- 2009: 5'-RACE experiments on V. vinifera
- 2008: Investigating deep sea adaptation of P. profundum via RNA-Seq
- 2007: Combimatrix custom microarray desing and test