RECOMB-Seq 2012 Proceedings

Barcelona, Spain, April 19-20, 2012

PC Chairs: Paul Medvedev and Eleazar Eskin
Keynote Speakers: Alex Zelikovsky and Pavel Pevzner

Full Papers

• Exploiting sparseness in de novo genome assembly. Chengxi Ye, Zhanshan Sam Ma, Charles H Cannon, Mihai Pop and Douglas W Yu. BMC Bioinformatics 13 (Suppl 6), S1 (2012).
• MGMR: leveraging RNA-Seq population data to optimize expression estimation. Roye Rozov, Eran Halperin and Ron Shamir. BMC Bioinformatics 13 (Suppl 6), S2 (2012).
• Haplotype reconstruction using perfect phylogeny and sequence data. Anatoly Efros and Eran Halperin. BMC Bioinformatics 13 (Suppl 6), S3 (2012).
• Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. Ekaterina E Khrameeva and Mikhail S Gelfand. BMC Bioinformatics 13 (Suppl 6), S4 (2012).
• KIS SPLICE: de-novo calling alternative splicing events from RNA-seq data. Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix. BMC Bioinformatics 13 (Suppl 6), S5 (2012).
• An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. Jin Zhang, Jiayin Wang and Yufeng Wu. BMC Bioinformatics 13 (Suppl 6), S6 (2012).
• PAIR: polymorphic Alu insertion recognition. Jón Ingi Sveinbjörnsson and Bjarni V Halldórsson. BMC Bioinformatics 13 (Suppl 6), S7 (2012).
• High-resolution genetic mapping with pooled sequencing. Matthew D Edwards and David K Gifford. BMC Bioinformatics 13 (Suppl 6), S8 (2012).
• A context-based approach to identify the most likely mapping for RNA-seq experiments. Thomas Bonfert, Gergely Csaba, Ralf Zimmer and Caroline C Friedel. BMC Bioinformatics 13 (Suppl 6), S9 (2012).
• Reconstructing cancer genomes from paired-end sequencing data. Layla Oesper, Anna Ritz, Sarah J Aerni, Ryan Drebin and Benjamin J Raphael. BMC Bioinformatics 13 (Suppl 6), S10 (2012).
• Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. Boyko Kakaradov, Hui Yuan Xiong, Leo J Lee, Nebojsa Jojic and Brendan J Frey. BMC Bioinformatics 13 (Suppl 6), S11 (2012).

Posters

• Detection of chromosomal inversions with paired-end sequencing. José Ignacio Lucas Lledó and Mario Cáceres.
• A context-based approach to identify the most likely mapping for RNA-seq experiments. Thomas Bonfert, Gergely Csaba, Ralf Zimmer and Caroline C. Friedel.
• Understanding the nucleation of the microRNA-mRNA pairing by using CLIP-Seq and RNA folding data. Ray Marin and Jiri Vanicek.
• Calling inversions from next-generation sequencing paired-end mapping data with GRIAL. Sònia Casillas, Can Alkan, Evan E Eichler and Mario Cáceres.
• Empirical evaluation of different modern reference panels for imputation and their implication for Genome Wide Association Studies.. Sílvia Bonàs, Josep M. Mercader and David Torrents.
• Filtering duplicate reads from 454 pyrosequencing data. Susanne Balzer, Ketil Malde, Inge Jonassen and Markus A. Grohme.
• Improving loss of heterozygosity identification by tumor purity estimation. Eva König, Lars Feuerbach, Barbara Hutter, Matthias Schlesner, Qi Wang, Benedikt Brors and Thomas Lengauer.
• A probabilistic method for structural variant prediction from strobe sequencing data. Anna Ritz, Suzanne Sindi, Ali Bashir and Benjamin Raphael.
• Integrative de novo transcriptome assembly in fruit fly. Nathan Boley.
• The devil is in the detail: mining and annotating genomic variants in the Tasmanian Devil facial tumour genome. Ole Schulz-Trieglaff, Elizabeth Murchison, Zemin Ning and Anthony Cox.
• Automated workflow for RNA-Seq analysis: application and testing with various types of RNA-Seq protocols. Irina Khrebtukova, Ryan Kelley, Shujun Luo, Tim Hill, Patrick Lau, Jennifer Chiniquy, Kathryn Stephens, Semyon Kruglyak and Gary P Schroth.
• The de novo Genome Assembly Assessment Server. André Corvelo and Tyler Alioto.
• Improving RNA sequencing interpretation: a case study on breast cancer cell lines. Kirstine Belling, David Flores, Daniel Elias, Jan Stenvang, Jun Wang, Nils Brünner, Henrik Ditzel and Ramneek Gupta.
• Coalescing discordant read mapping signatures for structural variant breakpoint detection. Ryan M. Layer, Aaron R. Quinlan and Ira M. Hall.
• Analysis of pandemic (H1N1) 2009 Influenza A virus circulating in Mexico during the 2011-2012 season by ultra-deep sequencing. Joanna Ortiz Alcantara, Elizabeth González Durán, Araceli Rodriguez Castillo, Fabiola Garcés Ayala, José Miguel Segura Candelas, Claudia Wong Arámbula, Patricia Alcántara Pérez, Abril Rodríguez, Brisia Rodríguez, Juan Carlos Del Mazo, Susana Serrano, Gisela Barrera Badillo, Irma López Martínez, Lucía Hernández Rivas, Hugo López-Gatell, Celia Alpuche Aranda and José Ernesto Ramírez González.
• YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Gregory Faust and Ira Hall.
• Efficient and error-tolerant sequencing read mapping. Norbert Dojer and Piotr Jaroszyński.
• Identifying genomic copy number alteration and loss of heterozygosity in next-generation sequence data. John R. McPherson, Yingting Wu, Patrick Tan and Steve Rozen.
• Algorithms to find mutated pathways in cancer. Fabio Vandin, Hsin-Ta Wu, Eli Upfal and Ben Raphael.
• Torrent Variant Caller: it’s all about speed, accuracy, and long indels. Dumitru Brinza, Zheng Zhang, Eric Tsung, Charles Scafe, Onur Sakarya, Alexander Joyner, Sowmi Utiramerur, Guy Del Mistro, Fiona Hyland and Ellen Beasley.
• The GEM toolkit: world-class short read mapping, and more. Santiago Marco Sola and Paolo Ribeca.
• Strategies for sequencing and analysis of low-diversity samples. Maga Rowicka and Abhishek Mitra.
• Instant-Seq:- an integrated tool with web interface for fast analysis of ChIP-Seq data. Abhishek Mitra and Maga Rowicka.
• Quasispecies spectrum reconstruction using multi-commodity flows. Nicholas Mancuso, Bassam Tork, Pavel Skums, Ion Mandoiu and Alex Zelikovsky.
• On the comparison of sets of alternative transcripts. Aida Ouangraoua, Krister Swenson and Anne Bergeron.
• CNVeM: Copy number variation detection using uncertainty of read mapping. Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin.
• GRAPE RNAseq analysis pipeline environment. David Gonzalez-Knowles, Maik Roder, Angelika Merkel and Roderic Guigo.