RECOMB-Seq 2018 Proceedings

Paris, France, April 19-20, 2018

PC Chairs: Mark Chaisson and Rayan Chikhi
Keynote Speakers: Alexis Battle and Olivier Jaillon

Full Papers

  • Full-length de novo viral quasispecies assembly through variation graph construction. Jasmijn Baaijens, Bastiaan van der Roest, Johannes Koster, Leen Stougie and Alexander Schoenhuth. Bioinformatics, 35 (24): 5086-5094, (2019)
  • Alignment-free clustering of barcode (UMI) tagged DNA molecules. Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Collin C. Collins, Cedric Chauve and Faraz Hach. Bioinformatics, 35 (11): 1829-1836, (2019)
  • Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Antoine Limasset, Jean-François Flot and Pierre Peterlongo. Bioinformatics, 36 (5): 1374-1381, (2020)
  • TNER: a novel background error suppression method for mutation detection in circulating tumor DNA. Shibing Deng, Maruja Lira, Donghui Huang, Kai Wang, Crystal Valdez, Jennifer Kinong, Paul Rejto, Jadwiga Bienkowska, James Hardwick and Tao Xie. BMC Bioinformatics, 18: 387, (2018)
  • Optimum search schemes for approximate string matching using bidirectional FM-Index. Kiavash Kianfar, Christopher Pockrandt, Bahman Torkamandi, Haochen Luo and Knut Reinert. bioRxiv 301085, (2018)
  • Resistome SNP calling via read colored de Bruijn graphs . Bahar Alipanahi, Martin Muggli, Musa Jundi, Noelle Noyes and Christina Boucher. Bioinformatics, 36 (22-23): 5275-5281, (2021)
  • Deconvoluting the diversity of within-host pathogen strains in a Multi-Locus Sequence Typing framework. Guo Liang Gan, Elijah Willie, Cedric Chauve and Leonid Chindelevitch. BMC Bioinformatics, 20: 637, (2019)

Short Talks Selected from Abstracts

  • Solving scaffolding problem with repeats. Igor Mandric and Alex Zelikovsky.
  • Signal enrichment of metagenome sequencing reads using topological data analysis. “Aldo Guzman-Saenz, Niina Haiminen, Saugata Basu and Laxmi.
  • Parida”. .
  • CliqueSNV: scalable reconstruction of intra-host viral populations from NGS reads. Sergey Knyazev, Viachaslau Tsyvina, Andrii Melnyk, Alexander Artyomenko, Tatiana Malygina, Yuri Porozov, Ellsworth Campbell, William Switzer, Pavel Skums and Alex Zelikovsky.
  • Interactive single cell RNA-Seq analysis with the Single Cell Toolkit (SCTK). David Jenkins, Tyler Faits, Emma Briars, Sebasitan Carrasco Pro, Steve Cunningham, Masanao Yajima and W. Evan Johnson.
  • GRASS-C - graph-based RNA-Seq analysis in single cell level subgraph clustering. Harry Taegyun Yang.
  • Tigmint: correct assembly errors using linked eeads from large molecules. Shaun D Jackman, Lauren Coombe, Justin Chu, Rene Warren,Ben Vandervalk, Sarah Yeo, Hamid Mohamadi, Joerg Bohlmann, Steven Jones and Inanc Birol.
  • Fast expectation maximization source tracking. Liat Shenhav, Mike Thompson, Tyler Joseph, Ori Furman, David Bogumil, Itzik Mizrahi and Eran Halperin.
  • Fast and accurate bisulfite alignment and methylation calling for mammalian genomes. Jonas Fischer and Marcel Schulz.
  • Identification of transcriptional signatures for cell types from single-cell RNA-Seq. Lynn Yi, Vasilis Ntranos, Pall Melsted and Lior Pachter.

Posters

  • mirLibSpark: a scalable NGS microRNA prediction pipeline with data aggregation. Chao-Jung Wu, Mohamed Amine Remita and Abdoulaye Baniré Diallo.
  • K-merator, an efficient design of highly specific k-mers for quantification of transcriptional signatures in large scale RNAseq cohorts.. Sébastien Riquier, Anne-Laure Bougé, Benoit Guibert, Jérôme Audoux, Daniel Gautheret, Thérèse Commes and Anthony Boureux.
  • Kevlar: Mapping-free approach for accurate discovery of de novo variants. Daniel Standage, C. Titus Brown and Fereydoun Hormozdiari.
  • Promoter and enhancer chromatin dynamics during pancreatic differentiation. Henriette Miko, Scott A. Lacadie and Uwe Ohler.
  • Ultrafast space-efficient k-mer indexing. Sven Rahmann.
  • ARKS: chromosome-scale human genome scaffolding with linked read kmers. Rene Warren, Lauren Coombe, Jessica Zhang, Ben Vandervalk, Justin Chu, Shaun Jackman and Inanc Birol.
  • Tigmint: correct assembly errors using linked reads from large molecules. Shaun Jackman, Lauren Coombe, Justin Chu, Rene Warren, Ben Vandervalk, Sarah Yeo, Zhuyi Xue, Hamid Mohamadi, Joerg Bohlmann, Steven Jones and Inanc Birol.
  • Multi-Index Bloom Filters: A probabilistic data structure for sensitive multi-reference sequence classification with multiple spaced seeds. Justin Chu, Emre Erhan, Hamid Mohamadi, Ben Vandervalk, Jeffrey Tse, Sarah Yeo, Shaun Jackman, Ka Ming Nip, Rene Warren and Inanc Birol.
  • De novo clustering of gene expressed variants in transcriptomic long reads data sets. Camille Marchet, Lolita Lecompte, Jean-Marc Aury, Corinne Da Silva, Corinne Cruaud, Jacques Nicolas and Pierre Peterlongo.
  • ONTig: contiguating genome assembly using oxford nanopore long reads. Hamid Mohamadi, Ben Vandervalk, Shaun Jackman, Lauren Coombe, Justin Chu, Rene Warren and Inanc Birol.
  • Rapid and precise analysis of human gut metagenomes using Oxford Nanopore sequencing technology. Hugo Roume, Mathieu Almeida, Florian Plaza Oñate and S. Dusko Ehrlich.
  • S3A: a scalable and accurate annotated assembly tool for targeted gene assembly. Laurent David, Hugues Richard, Riccardo Vicedomini and Alessandra Carbone.
  • Pan-genome structural analysis and visualisation. Paulina Dziadkiewicz, Jakub Tyrek and Norbert Dojer.
  • Reference-guided genome assembly in metagenomic samples. Cervin Guyomar, Wesley Delage, Fabrice Legeai, Christophe Mougel, Jean-Christophe Simon and Claire Lemaitre.
  • Nonparametric identification of epigenomic networks from large-scale ChIP-seq experiments. Gabriele Schweikert and Sanguinetti Guido.
  • Accelerating approximate pattern matching with processing-in-memory (PIM) and single-instruction multiple-data (SIMD) programming. Damla Senol Cali, Zulal Bingol, Jeremie Kim, Rachata Ausavarungnirun, Saugata Ghose, Can Alkan and Onur Mutlu.
  • Isoform assembly with quasi-lossless compression of quality scores in RNA-seq data. Ana Hernandez.
  • Map2Peak: from unmapped reads to CHIP-seq peaks in half the time. Krishna Reddy Gujjula and Kiavash Kianfar.