Department of Computer Science, University of Pisa, Italy
Friday, October 21, 2011
This one-day workshop intends to bring together scientists interested in the design and analysis of efficient methods and algorithms for processing large-scale biological data. This includes primary biosequence data (DNA, RNA, proteins) as well as data on protein-DNA or protein-protein interaction, gene regulation, or all other kinds of ‘omics’-data obtained through modern high-throughput genomic technologies. The emphasis is on efficient algorithms and machine learning methods for processing, storing, mining and retrieving these data, based on sound formal models.
Workshop participants are invited to register through the registration page of the SPIRE 2011 conference; no traditional on-site registration service will be provided. There is no additional workshop participation fee for participants that have also registered / are also registering for the main SPIRE 2011 conference. A workshop-only registration fee is charged for those participants who are not registering for the main conference.
The workshop will take place in the Sala Seminari Ovest of the Department of Computer Science of the University of Pisa, Largo Pontecorvo 3, 56127 Pisa (see the SPIRE 2011 map for directions to this venue).
The final program of the workshop is as follows:
- 09:30 – 10:15: Kalle Karhu, Juho Mäkinen, Jussi Rautio, Hugh Salamon and Jorma Tarhio, GAST, a genomic alignment search tool
- 10:15 – 11:00: Norbert Dojer, Efficient sequencing read mapping
- 11:00 – 11:30: Coffee break
- 11:30 – 12:15: Scott Hazelhurst and Zsuzsanna Liptak, KABOOM! A new suffix-array based algorithm for clustering expression data
- 12:15 – 13:00: Marco Mina, Giovanni Ciriello, Pietro Hiram Guzzi and Concettina Guerra, PPI alignment algorithms uncover the modular organization of yeast complexes
- 13:00 – 14:30: Lunch
- 14:30 – 15:00: Maria Federico, Pierre Peterlongo, Nadia Pisanti and Marie-France Sagot, Long repetitions inference with indels
- 15:00 – 15:30: Gregory Kucherov, Tamar Pinhas and Michal Ziv-Ukelson, Regular Language Constrained Sequence Alignment Revisited
- 15:30 – 16:00: Roberto Grossi, Giulia Menconi, Nadia Pisanti and Marie-France Sagot, Structured motifs: don’t mind the gap!
- 16:00 – 16:30: Farewell coffee
- Gregory Kucherov (CNRS, Marne-la-Vallée, France), Chair
- Concettina Guerra (University of Padova, Italy / Georgia Institute of Technology, USA)
- Lucian Ilie (University of Western Ontario, Canada)
- Marco Pellegrini (IIT-CNR, Pisa Italy)
- Stéphane Vialette (CNRS, Marne-la-Vallée, France)