RECOMB-Seq 2011 Proceedings

Vancouver, BC, Canada, March 26-27, 2011

PC Chair: Can Alkan University of Washington.
Keynote Speakers: Lior Pachter and David Jaffe

Full Papers

• Inferring viral spectrum from 454 pyrosequencing reads. Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion Mandoiu, Peter Balfe and Alex Zelikovsky. BMC Bioinformatics 12 (Suppl 6), S1 (2011).
• Genotyping common and rare variation using overlapping pool sequencing. Dan He, Noah Zaitlen, Bogdan Pasaniuc, Eleazar Eskin and Eran Halperin. BMC Bioinformatics 12 (Suppl 6), S2 (2011).
• Assembly of non-unique insertion content using next-generation sequencing. Nathaniel Parrish, Farhad Hormozdiari and Eleazar Eskin. BMC Bioinformatics 12 (Suppl 6), S3 (2011).
• A Hidden Markov Model for copy number variant prediction from whole genome resequencing data. Yufeng Shen, Yiwei Gu and Itsik Pe’Er. BMC Bioinformatics 12 (Suppl 6), S4 (2011).

Short Talks Selected from Abstracts

• A whole-genome probe design for massively parallel variant validation using selective circularization. Daniel Newburger, Georges Natsoulis, Hua Xu, Sue Grimes, John Bell and Hanlee Ji.
• Accurate estimation of gene expression levels from DGE sequencing data. Marius Nicolae and Ion Mandoiu.
• Constrained traversal of repeats with paired sequences. Sébastien Boisvert, Élénie Godzaridis, François Laviolette and Jacques Corbeil.
• Contig graph mining for duplication breakpoints. Jurgen F. Nijkamp, Jean-Marc Daran, Marcel J.T. Reinders and Dick De Ridder.
• Counting k-mers with a Bloom Filter. Pall Melsted and Jonathan Pritchard.
• Finding deletions with exact break points from noisy low coverage paired-end short sequence reads. Jin Zhang and Yufeng Wu.
• Improved variant discovery and allele frequency estimation from pooled dna resequencing with Bayesian latent class analysis and compositional bias models. Shom Paul and Aaron Mackey.
• Modeling and automation of sequencing-based determination of RNA structure. Sharon Aviran, Cole Trapnell, Julius Lucks, Stefanie Mortimer, Shujun Luo, Gary Schroth, Jennifer Doudna, Adam Arkin and Lior Pachter.
• mTiM: margin-based transcript mapping from RNA-seq. Georg Zeller, Nico Goernitz, Gunnar Raetsch, Jonas Behr, Andre Kahles, Soeren Sonnenburg and Pramod Mudrakarta.
• Separating metagenomic data into genomes via clustering. Olga Tanaseichuk and Tao Jiang.
• TavernaPBS: custom next-generation sequence analysis workflows using high-performance computing resources with Taverna and PBS. Mark Lawson, Paul Shuber and Aaron Mackey.

Posters

• Epigenetics of atherosclerosis. Lauren Mills, Brian Wamhoff, Brett Blackman, Aaron Mackey and Jessica Connelly.
• Genome-scale analysis of promoter melting in eukaryotic gene transcription. Fedor Kouzine, Damian Wójtowicz, Arito Yamane, Wolfgang Resch, Teresa M. Przytycka, David Levens and Rafael Casellas.
• Haplotype discovery based on unassembled sequences estimation. Serghei Mangul and Alex Zelikovsky.
• RGASP evaluation of RNA-seq read alignment algorithms. Andre Kahles, Regina Bohnert, Paolo Ribeca, Jonas Behr and Gunnar Raetsch.
• Screening for transposable element-induced adaptations in Drosophila melanogaster using next-gen sequencing data. Anna-Sophie Fiston-Lavier, Dmitri Petrov and Josefa Gonzalez.
• SeqMDD: symbolic data structures for accurate mapping. Marco Beccuti, Francesca Cordero, Susanna Donatelli and Raffaele Calogero.
• SlideSort: A fast and exact tool for finding all similar pairs from next-generation sequencing data. Kana Shimizu and Koji Tsuda.
• Smarti - A fast short read alignment algorithm. Florian Schatz, Sascha Möller and Manfred Schimmler.
• Toward assessing the quality of de novo assembly. Rasiah Loganantharaj.