RECOMB 2018



Dates: 19-20 April, 2018

Scope

A wave of technologies transformed sequencing over a decade ago into the high-throughput era, demanding research in new computational methods to analyze this data. The applications of sequencing have continually expanded. The Eighth RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-Seq) brings together leading researchers in computational genomics and genomic biology to discuss emerging frontiers in algorithm development for massively parallel sequencing data. The emphasis of all contributed work will be on applying statistical and algorithmic approaches to improve sequence data management, analysis, and interpretation.

Invited Speakers

Alexis Battle
More…
Computational Biology & Medicine Group
Machine Learning & Data Intensive Computing Group
Department of Computer Science
Johns Hopkins, MD, USA

Olivier Jaillon
CEA – GENOSCOPE
France

Accepted regular talks

April 19, 10:30am session

Full-length de novo viral quasispecies assembly through variation graph construction
Jasmijn Baaijens, Bastiaan van der Roest, Johannes Koster, Leen Stougie and Alexander Schoenhuth

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

April 19, 3:00pm session

HALS: Fast and High Throughput Algorithm for PacBio Long Read Self-Correction [Conference version] [Updated journal version] [Updated website]
Ergude Bao, Fei Xie, Changjin Song and Dandan Song

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
Antoine Limasset, Jean-François Flot and Pierre Peterlongo

April 20, 9:30am session

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

Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index
Kiavash Kianfar, Christopher Pockrandt, Bahman Torkamandi, Haochen Luo and Knut Reinert

April 20, 3:00pm session

Resistome SNP Calling via Read Colored de Bruijn Graphs
Bahar Alipanahi, Martin Muggli, Musa Jundi, Noelle Noyes and Christina Boucher

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

Accepted short talks

April 19, 4:30pm session

Signal Enrichment of Metagenome Sequencing Reads using Topological Data Analysis
Aldo Guzman-Saenz, Niina Haiminen, Saugata Basu and Laxmi Parida

Identification of transcriptional signatures for cell types from single-cell RNA-Seq
Lynn Yi, Vasilis Ntranos, Pall Melsted and Lior Pachter

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

Fast expectation maximization source tracking
Liat Shenhav, Mike Thompson, Tyler Joseph, Ori Furman, David Bogumil, Itzik Mizrahi and Eran Halperin

GRASS-C – Graph-based RNA-Seq Analysis in Single cell level Subgraph Clustering
Harry Taegyun Yang

April 20, 10:50am session

Solving scaffolding problem with repeats
Igor Mandric and Alex Zelikovsky

Tigmint: Correct Assembly Errors Using Linked Reads 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

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

Fast and accurate bisulfite alignment and methylation calling for mammalian genomes
Jonas Fischer and Marcel Schulz

Accepted highlight talks

April 19, 11:20am session

BRIE: transcriptome-wide splicing quantification in single cells [slides]
Yuanhua Huang and Guido Sanguinetti

ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter
Shaun Jackman, Ben Vandervalk, Hamid Mohamadi, Sarah Yeo, Austin Hammond, Golnaz Jahesh, Hamza Khan, Lauren Coombe, Rene Warren and Inanc Birol

April 20, 11:30am session

Comprehensive analysis of RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues
Serghei Mangul

Detailed program with abstracts

Available

Schedule At-a-Glance

RECOMB main conference will take place April 21-24. A side-event, GATB programming training session, will take place on Wednesday, April 18.

Registration

Follow this “Registration link” (satellite registration is done through the same procedure as the main reconference)

Organizing Committee

Program Committee Chairs

• Rayan Chikhi, CNRS, University of Lille, France
• Mark Chaisson, University of Southern California, USA

Steering Committee

• Can Alkan, Bilkent University, Turkey
• Inanc Birol, Michael Smith Genome Sciences Centre, Canada
• Eran Halperin, UCLA, USA
• Paul Medvedev, Penn State, USA
• Ben Raphael, Princeton University, USA

Program Committee

• Can Alkan, Bilkent University, Department of Computer Engineering
• Lars Arvestad, Stockholm University
• Sharon Aviran, University of California, Davis
• Ken Chen, MD Anderson Cancer Center
• Faraz Hach, Simon Fraser University
• Iman Hajirasouliha, Weill Cornell Medicine of Cornell University
• Farhad Hormozdiari, Harvard University
• Carl Kingsford, Carnegie Mellon University
• Gunnar W. Klau, Heinrich Heine University Dusseldorf
• Wenxiu Ma, University of California Riverside
• Serghei Mangul, University of California, Los Angeles
• Tobias Marschall, Saarland University / Max Planck Institute for Informatics
• Paul Medvedev, The Pennsylvania State University
• Veli Mäkinen, University of Helsinki
• Niranjan Nagarajan, University of Maryland
• Rob Patro, Stony Brook University
• Teresa Przytycka, NIH
• Sven Rahmann, University of Duisburg-Essen
• Michael Schatz, Cold Spring Harbor Laboratory
• Alexander Schliep, Gothenburg University
• Russell Schwartz, Carnegie Mellon University
• Wing-Kin Sung, Nuational University of Singapore
• Fabio Vandin, University of Padova
• Jianyang Zeng, Tsinghua University

Key Dates

January 31: Abstract of full paper submission deadline
February 4 23h59 Paris Los Angeles time: Full paper submission deadline
February 5: Reviewers assigned
February 21: Reviews due & poster/highlight/short talk submission deadline
(2/3 update: all notifications have been sent except for highlights)
March 2: Program announced
April 19-20: Conference

Call for Contributions

We solicit contributions in three different categories as follows:

1. 1. Manuscripts describing original work on computational aspects of genomic research involving massively parallel sequencing.

1. Highlights Track abstracts. 1-2 pages describing computational aspects of work that has been published in a journal after December 1, 2016, or papers that are in press at the time of submission and are already linked on the journal website.
2. Short talks / Posters / Lightning poster talks. Regular abstracts or 1-2 pages describing original work, including software applications. These will be considered for short presentations as well as for posters. Lightning poster talks will be encouraged to acquaint the audience with work presented in a poster.

Topics

(include but not limited to)

• Read mapping for second and third generation sequencing technologies.
• Techniques for managing (e.g., data compression) and visualizing massive amount of sequencing data.
• Discovery and genotyping of genomic variants, including SNPs, indels, and structural variants.
• Local and de novo sequence assembly.
• RNA sequencing (RNAseq) methods, including the analysis of RNA expression and novel transcript assembly.
• Methods for emerging sequencing technologies, such as single-cell or single molecule real time sequencing.
• Translational applications of sequencing data, including cancer genomics and infectious disease diagnostics and surveillance.
• Epigenetics and gene regulation, including ChIP-seq analysis, methylation profiling, and histone modification.
• Metagenomics.

Paper Submission Procedures

Manuscripts should be no more than 10 single-spaced US letter or A4 pages with at most a 6.5×9″ text area in at least 11 point font. Title and authors, corresponding author’s email address, 100-250 word abstract, references, figures, and tables all included. An optional short appendix may contain details or additional data to be consulted at the discretion of the program committee. The Bioinformatics journal manuscript template may be used but then the number of pages must be under 7, with default font size (note: previous instructions were to use 11pt font, but it is not straightforward to modify font size in the Bioinformatics latex template). Manuscripts must be submitted electronically in PDF format via the EasyChair system.

Manuscripts submitted for review should represent original, previously unpublished work. At the time of submission to the workshop, and for the entire review period, the work should not be under review by any other conference or scientific journal.

The submission system will be open starting January 2nd, 2018 and ending February 4th, 2018, 23h59 Paris Los Angeles time. It is required to submit an abstract for your paper before January 31st, 2018. Authors will be notified of acceptance or rejection by email on or before February 21th, 2018. An author of each accepted paper is expected to attend the workshop and present the paper; otherwise, alternative arrangements should be made to have the paper presented.

Guidelines for submitting the full paper abstract (before January 31st): please submit a 100-250 word abstract that is as close to the abstract of the final submission as possible. It is not required to send any (PDF) file in the Easychair ‘Uploads’ form. For the full article, please update the same submission as the abstract. Note that a different track will soon be added for posters/ short talks / highlights.

Bioinformatics Journal Partners with RECOMB-Seq Satellite Workshop

The Eighth RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-Seq) is continuing its successful partnership with Bioinformatics. Selected papers accepted for the workshop will be considered for a special track publication in the journal Bioinformatics.

Bioinformatics is a biweekly peer-reviewed scientific journal covering research and software in computational biology. The journal was established as Computer Applications in the Biosciences (CABIOS) in 1985. In 1998, the journal obtained its current name. Bioinformatics is published by Oxford University Press, and as of 2016, the editors-in-chief are Alfonso Valencia and Janet Kelso.

Special Handling of Papers Submitted to RECOMB 2018

If you would like to consider submitting a paper rejected by RECOMB 2018 to the satellite workshop, you may do so by the regular deadline of February 4th and also submit the abstract by January 31. You must include in your submission a Cover Letter that includes the reviews received from RECOMB together with a rebuttal addressing the concerns raised by the reviewers. If there is no additional file upload field in Easychair, please just concatenate the cover letter to the paper in a single PDF file. The submitted manuscript should also be modified according to the reviews, or provide an explanation of why modifications are unnecessary. All reviews will be treated confidentially and will only be visible to the PC members evaluating your paper.

Posters, Short talks and Highlights submission

The submission Easychair website for those tracks is open until February 21. For Posters/Short talks, please send a 100-250 word abstract (or a 1-2 page description of the work) to the “Sequencing Satellite Posters” track. This track is joint for both short talks and posters. Authors of abstracts that are selected for short talks will be notified shortly after the submission deadline. For Highlights, please send a 1-2 page description of the computational aspects of the work to the “Sequencing Satellite Highlights” track.