August 27-28, 2021 (VIRTUAL)

RECOMB-Seq

Massively Parallel Sequencing

IMPORTANT

The RECOMB-SEQ Steering Committee and PC chairs decided to follow RECOMB’s decision to take place entirely virtually due to the COVID-19 situation. The previously announced dates of August 27-August 28, 2021 remain unchanged. 

The 11th RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-Seq 2021), will be held on August 27-28, 2021 just before the main RECOMB conference.

The workshop 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.

REGISTRATION

There are no registration fees to attend RECOMB-SEQ 2021  virtual satellite event  but registration is still required.

See registration page

PRELIMINARY PROGRAM

ALL TIMES ARE CEST 

Friday, August 27

14:30-14:40 WELCOME

14:40-15:40 SESSION 1 -  ALIGNMENT AND ASSEMBLY

Chair: Leena Salmela

14:40-15:00 Accurate spliced alignment of long RNA sequencing reads

Kristoffer Sahlin and Veli Mäkinen

 

15:00-15:20 Accel-Align: A Fast Sequence Mapper and Aligner Based on the Seed–Embed–Extend Method

Yiqing Yan, Nimisha Chaturvedi and Raja Appuswamy

 

15:20-15:40 Ariadne: Barcoded Linked-Read Deconvolution Using de Bruijn Graphs

Lauren Mak, Dmitry Meleshko, David C. Danko, Waris Barakzai, Natan Belchikov and Iman Hajirasouliha

15:40-15:50 BREAK

15:50-16:50 KEYNOTE LECTURE

Pan-genomic methods for fighting reference bias

Ben Langmead

16:50-18:00 LONG BREAK

18:00-19:00 SESSION 2 -  CANCER

Chair: Leonardo Pellegrina

 

18:00-18:20 BiTSC2: Bayesian inference of Tumor clonal Tree by joint analysis of Single-Cell SNV and CNA data

Ziwei Chen, Fuzhou Gong, Lin Wan and Liang Ma

 

18:20-18:40 HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery

Matthew Hayes, Angela Nguyen, Rahib Islam, Caryn Butler, Ethan Tran, Derrick Mullins and Chindo Hicks

 

18:40-19:00 A molecular taxonomy of tumors independent of tissue-of-origin

Peter Nguyen, Simon Coetzee, Daniel Lakeland and Dennis Hazelett

 

19:00-19:15 BREAK

 

19:15-20:15 SESSION 3 -  MIXED TOPICS

Chair: Dan DeBlasio

 

19:15-19:35 Automated strain separation in low-complexity metagenomes using long reads

Riccardo Vicedomini, Christopher Quince, Aaron Darling and Rayan Chikhi

 

19:35-19:55 CONSULT: Accurate contamination removal using locality-sensitive hashing

Eleonora Rachtman, Vineet Bafna and Siavash Mirarab

 

19:55-20:15 Population-scale detection of non-reference sequence variants using colored de Bruijn graphs

Thomas Krannich, W. Timothy J. White, Sebastian Niehus, Guillaume Holley, Bjarni V. Halldorsson and Birte Kehr

 

Saturday, August 28

14:30-15:30 SESSION 4 - SINGLE CELL

Chair: Faraz Hach

 

14:30-14:50  DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data

Jiaxing Chen, Chinwang Cheong, Liang Lan, Xin Zhou, Jiming Liu, Aiping Lyu, William K Cheung and Lu Zhang

 

14:50-15:10 A Reference-free Approach for Cell Type Classification with scRNA-seq

Qi Sun, Yifan Peng and Jinze Liu

 

15:10-15:30 ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational 

autoencoders

 A. Ali Heydari, Oscar Davalos, Lihong Zhao, Katrina Hoyer and Suzanne Sindi

 

15:30-15:45  BREAK

15:45-16:45  KEYNOTE LECTURE

ReadMapping on Pan-Genomes with Degenerate Texts

Nadia Pisanti

16:45-18:00  LONG BREAK

18:00-19:00 SESSION 5 - PANGENOMICS

Chair: Rayan Chikhi

 

Pan-genomic Matching Statistics for Targeted Nanopore Sequencing

Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael Schatz, Travis Gagie, Christina Boucher and Ben Langmead

 

Algorithms and Complexity on Indexing Founder Graphs

Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu and Veli Mäkinen

 

Linearization of genome sequence graphs revisited

Anna Lisiecka and Norbert Dojer

 

19:00-19:15  BREAK

19:15-20:15  SESSION 6 - MIXED TOPICS

Chair: Travis Gagie

 

19:15-19:35 Dynamic Partitioning of Search Patterns for Approximate Pattern Matching using Search Schemes

Luca Renders, Kathleen Marchal and Jan Fostier

 

19:35-19:55 Real-Time, Direct Classification of Nanopore Signals with SquiggleNet

Yuwei Bao, Jack Wadden, John Erb-Downward, Piyush Ranjan, Robert Dickson, David Blaauw and Joshua Welch

 

19:55-20:15  Conditional resampling improves calibration and sensitivity in single-cell CRISPR screen analysis

Timothy Barry, Xuran Wang, Kathryn Roeder and Eugene Katsevich

20:15-20:30 CLOSING 

INVITED SPEAKERS

Ben Langmead, Johns Hopkins University

Nadia Pisanti, University of Pisa

ACCEPTED CONTRIBUTIONS 

See the list of RECOMB-Seq accepted contributions here.

PROGRAM COMMITTEE

Layla Oesper, PC Co-Chair
Cinzia Pizzi, PC Co-Chair

Sharon Aviran, University of California, Berkeley
Vikas Bansal, University of California San Diego
Dan DeBlasio, University of Texas at El Paso
Mark Chaisson, University of Washington
Rayan Chikhi, Institut Pasteur & CNRS

A. Ercüment Çiçek, Bilkent University
Fabio Cunial, Max Planck Institute of Molecular Cell Biology and Genetics

Barbara Di Camillo, University of Padova
Travis Gagie, Diego Portales University
Shilpa Garg, Harvard University
Faraz Hach, University of British Columbia and Vancouver Prostate Centre
Farhad Hormozdiari, Program in Genetic Epidemiology and Statistical
Genetics, Harvard University
Andre Kahles, ETH Zurich

Max Leiserson, University of Maryland
Antoine Limasset, CNRS
Wenxiu Ma, University of California Riverside
Serghei Mangul, University of California, Los Angeles
Tobias Marschall, Saarland University / Max Planck Institute for Informatics
Niranjan Nagarajan, Genome Institute of Singapore
Kristoffer Sahlin, Department of Mathematics, Stockholm University
Leena Salmela, University of Helsinki
Gryte Satas, Princeton University
Alexander Schliep, Gothenburg University
Marcel Schulz, Goethe University
Jouni Siren, University of California, Santa Cruz
Prashant Pandey, Berkeley Lab
Robert Patro, University of Maryland
Leonardo Pellegrina, University of Padova
Sven Rahmann, University of Duisburg-Essen
Simona E. Rombo, University of Palermo
Sharma V. Thankachan, University of Central Florida

Catie Welsh, University of North Carolina at Chapel Hill
Zhang Zhang, BIG Data Center, Beijing Institute of Genomics, Chinese Academy
of Sciences

STEERING COMMITTEE

Can Alkan

Eran Halperin

Paul Medvedev

Ben Raphael

Alexander Schoenhuth

PAPER SUBMISSION IS NOW CLOSED 

See the list of RECOMB-Seq accepted contributions here.

KEY DATES
Proceedings and Overlay Track
Paper submission opens: December 18, 2020 
Paper submission deadline: March 22, 2021 (NEW DATE!)  instead of January 18, 2021
Paper acceptance decision: April 27, 2021 (NEW DATE!) instead of February 15, 2021 



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 11th 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
Metagenomics
Pan-genomics and genome graphs
Optical mapping

CONTRIBUTIONS
We solicit contributions in four different categories as follows:

 

Proceedings track

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.
 

Overlay track
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.

Highlights Track
This track is for papers that have already been published or are in press. This track is joint with the main conference (deadline May 28, 2021 ). For instructions and more details, see the RECOMB 2021 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 Dec. 18, 2020 and ending March 22, 2021 (NEW DATE!) instead of January 18, 2021.

Authors will be notified of acceptance or rejection by email on or before April 27, 2021 (NEW DATE!) instead of February 15, 2021.
An author of each accepted paper is expected to attend the workshop (if held in person) and present the paper; otherwise, alternative arrangements should be made to have the paper presented.

SPECIAL HANDLING OF PAPERS SUBMITTED TO RECOMB 2021
If you would like to consider submitting a paper rejected by RECOMB 2021 to the workshop, you may do so by the regular deadline of March 22, 2021. 
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.

SPECIAL HANDLING OF PAPERS SUBMITTED TO ISMB-ECCB 2021

If you would like to consider submitting a paper rejected by ISMB-ECCB  2021 to the workshop, you may do so by the regular deadline of March 22, 2021.

In this case you have the choice to submit the paper as "fresh", or you can choose to include in your submission a Cover Letter with  the reviews received from ISMB-ECCB 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.