RECOMB-Seq 2015 Proceedings

Warsaw, Poland, April 10-11, 2015

PC Chairs: Niko Beerenwinkel and Jan Korbel
Keynote Speakers: Gerton Lunter and Jacek Błażewicz

Full Papers

  • PopIns: population-scale detection of novel sequence insertions. Birte Kehr, Pall Melsted and Bjarni Halldorsson. Bioinformatics, 32 (7): 961-967, (2016)
  • BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. Monica Golumbeanu, Pejman Mohammadi and Niko Beerenwinkel. Bioinformatics, 32 (7): 976-983, (2016)
  • SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. Daria Iakovishina, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Mireille Regnier and Valentina Boeva. Bioinformatics, 32 (7): 984-992, (2016)
  • Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics. Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Chuck Cannon and Fengzhu Sun. Bioinformatics, 32 (7): 993-1000, (2016)
  • Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Yuzhen Ye and Haixu Tang . Bioinformatics, 32 (7): 1001-1008, (2016)
  • OPTIMA: index-based map-to-sequence alignment in large eukaryotic genomes. Davide Verzotto, Audrey S.M. Teo, Axel Hillmer and Niranjan Nagarajan. GigaScience, 5 (1): s13742-016-0110-0, (2016)
  • Rank regularized RNA-seq. Nicolas Bray and Lior Pachter.

Short Talks Selected from Abstracts

  • Chromatin segmentation with a joint model for reads explains a larger portion of the epigenome. Alessandro Mammana and Ho-Ryun Chung.
  • Using csaw to detect differentially bound regions in ChIP-seq data. Aaron Lun and Gordon Smyth.
  • Computational detection of DNA double-stranded breaks and inferring mechanisms of their formation. Norbert Dojer, Abhishek Mitra, Yea-Lih Lin, Anna Kubicka, Magdalena Skrzypczak, Krzysztof Ginalski, Philippe Pasero and Maga Rowicka.
  • A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory. David Seifert, Francesca Di Giallonardo, Karin J. Metzner, Huldrych F. Günthard and Niko Beerenwinkel.
  • Genome-wide mapping and computational analysis of non-B DNA structures in vivo. Damian Wójtowicz, Fedor Kouzine, Arito Yamane, Craig J. Benham, Rafael C. Casellas, David Levens and Teresa M. Przytycka.

Posters

  • Deep sequencing characterization of Sus scrofa piRNA fraction shared between female and male gonads. Aleksandra Swiercz, Dorota Kowalczywiewicz, Luiza Handschuh, Katarzyna Lesniak, Marek Figlerowicz and Jan Wrzesinski.
  • GPU-accelerated whole genome assembly. Michał Kierzynka, Wojciech Frohmberg, Jacek Błażewicz, Piotr Żurkowski, Marta Kasprzak and Paweł Wojciechowski.
  • Scaling ABySS to longer reads using spaced k-mers and Bloom filters. Shaun Jackman, Karthika Raghavan, Benjamin Vandervalk, Daniel Paulino, Justin Chu, Hamid Mohamadi, Anthony Raymond, Rene Warren and Inanc Birol.
  • Conditional entropy in variation-adjusted windows detects positive selection signatures relevant to next Generation sequencing. Samuel K. Handelman, Michal Seweryn, Ryan M. Smith, Katherine Hartmann, Danxin Wang, Maciej Pietrzak, Andrew D. Johnson, Andrzej Kloczkowski, Wolfgang Sadee.