Department of Information Engineering (DEI)
University of Padova
Via Giovanni Gradenigo 6
35131 Padova, Italy
Massively Parallel Sequencing
Proceedings and Overlay Track
Paper submission opens: December 9, 2019
Paper submission deadline: Extended to January 20, 2020
Paper acceptance decision: February 20, 2020
joint with RECOMB so refer to the main conference
Short talks and posters track
Abstract submission opens: January 22, 2020
Abstract submission deadline: March 23, 2020
Abstract acceptance decision: April 3, 2020
CALL FOR PAPERS
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 Tenth 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.
Topics of Interest (including 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
Consensus sequence construction
Discovery and genotyping of genomic variants, including SNPs, indels, and structural variants
Local and de novo sequence assembly Methods for analysis of RNA sequencing (RNA-seq) data, including RNA expression, novel transcript assembly and splicing
Methods for novel sequencing technologies such as single-cell sequencing, linked-read sequencing and Hi-C
Translational applications of sequencing data, including cancer genomics and infectious disease
Epigenetics and gene regulation, including ChIP-seq analysis, methylation profiling, and histone modification
Pan-genomics and genome graphs
We solicit contributions in four different categories as follows:
This track solicits manuscripts describing original work on computational aspects of genomic research involving massively parallel sequencing. All manuscripts in this track will be considered for publication in a special issue of the journal iScience. At the time of submission, and for the entire review period, the work should not be under review by any other conference or scientific journal. Authors of manuscripts that are selected for oral presentation at RECOMB-seq after review but are not deemed suitable for iScience (or if the authors do not select publication in iScience) will be required to host their manuscript on a public preprint server.
Manuscripts submitted to this track will be reviewed by the program committee and selected submissions will be invited for oral presentation. The manuscript should be hosted on a public preprint server (bioRxiv, arXiv or PeerJ) at the time of submission. There are no specific formatting or page length requirements, but the paper should generally be formatted in a way that emphasizes the methodological contributions. Manuscripts can be submitted elsewhere at the same time but should not be published or in press at the time of submission.
This track is for papers that have already been published or are in press. This track is joint with the main conference (deadline January 31, 2020). For instructions and more details, see the RECOMB 2020 website.
Abstracts for short talks or posters
Regular abstracts describing original work, including software applications. These will be considered for short oral presentations or posters. A 1-2 page abstract describing the methods and key results should be submitted via the EasyChair system.
PARTNERSHIP WITH iSCIENCE
All submissions to the proceedings track will be simultaneously considered for publication in a special issue of the journal iScience, if the authors agree. iScience is an open-access journal published by Cell Press for original research in the life, physical, and earth sciences.
In addition to the program committee of RECOMB-seq, editors of iScience will evaluate the papers for biological impact and suitability for publication. In particular, the following criteria will be used to evaluate the biological relevance:
- Can inputs be found through experiments?
- Can outputs be used directly in future experiment or analysis?
- Can outputs be obtained through well-established methodology for less cost?
- Is methodology proposed applicable in useful settings?
- Do biological data support the study?
- Is biological variability sufficiently accounted for?
Authors who do not wish their manuscript to be considered for iScience should use the overlay track for submission. Publication in iScience is subject to an Open Access charge of $3000.
Reduced Open Access charges for authors in developing countries and others in financial hardship are available.
PAPER AND ABSTRACT SUBMISSION PROCEDURES
Manuscripts for the "proceedings track" should not exceed 10 pages using at least 11 point font on U.S. standard 8 1/2 by 11 inch paper with no less than one inch margin all around. This excludes the cover page and references. The cover page should have the title and the corresponding author's email address. An optional short appendix, if absolutely necessary, can be included but will be considered at the discretion of the program committee. Manuscripts must be submitted electronically in PDF format via the EasyChair system.
The submission system will be open starting December 9th, 2019 and ending January 13th 2020.
Authors will be notified of acceptance or rejection by email on or before February 20th 2020.
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.
SPECIAL HANDLING OF PAPERS SUBMITTED TO RECOMB 2020
If you would like to consider submitting a paper rejected by RECOMB 2020 to the workshop, you may do so by the regular deadline of January 13th 2020.
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.
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.
Q&A ABOUT THE SUBMISSIONS
Question 1: I want to present a paper, which track should I use?
Answer: If you want it to be considered for publication in iScience, then submit to the proceedings track. If you want to publish elsewhere, then submit it to overlay. If it has been previously published or accepted for publication then it should be submitted as a highlight.
Question 2: Are my chances of being accepted for a talk different if I do different tracks?
Answer: No. Both overlay and proceedings will be peer-evaluated by the PC.
Question 3: Can my paper be rejected by iScience but still get a talk?
Answer: Yes. In this case it will be accepted to the overlay track.
Question 4: Can I submit to both RECOMB-seq and ISMB (or another conference)?
Answer: Yes, if you use the overlay track and post your preprint.
Question 5: What if I want to publish in RECOMB-Seq proceedings but not in iScience?
Answer: There are no RECOMB-Seq proceedings. The papers accepted through the overlay track will be posted as preprints but not published through RECOMB-Seq. The papers accepted through the proceedings track will be published in iScience.
Robert Patro, University of Maryland, PC Co-Chair
Leena Salmela, University of Helsinki, PC Co-Chair
Sharon Aviran, University of California
Davis Mohan Babu, University of Regina
Vikas Bansal, University of California San Diego
Mark Chaisson, University of Southern California
Dan DeBlasio, University of Texas at El Paso
Travis Gagie, Dalhousie University
Shilpa Garg, Harvard Medical School
Faraz Hach, University of British Columbia and Vancouver Prostate Centre
Farhad Hormozdiari, Harvard University
Andre Kahles, ETH Zurich
Antoine Limasset, Université de Lille
Wenxiu Ma, University of California Riverside
Serghei Mangul, University of California, Los Angeles
Camille Marchet, Université de Lille
Tobias Marshall, Max Planck Institute for Informatics
Niranjan Nagarajan, Genome Institute of Singapore
Prashant Pandey, Carnegie Mellon University
Sven Rahmann, University of Duisburg-Essen
Kristoffer Sahlin, Stockholm University
Alexander Schliep, Gothenburg University
Marcel Schulz, Goethe University
Jouni Sirén, University of California, Santa Cruz
Sharma V. Thankachan, University of Central Florida
Zhang Zhang, Beijing Institute of Genomics, Chinese Academy of Sciences