HiTSeq 2018
See the schedule in the official ISMB page here.

Keynote speakers


S. Cenk Şahinalp
Professor of Computer Science
Co-Director, Center for Genomics and Bioinformatics
Indiana University, Bloomington, IN, United States



Ekta Khurana
Assistant Professor of Computational Genomics
Weill Cornell Medical College, New York, NY, United States



Nancy J. Cox
Director of Vanderbilt Genetics Institute
Director of Division of Genetic Medicine
Mary Phillips Edmonds Gray Professor of Genetics
Vanderbilt University, Nashville, TN, United States


July 8, 2018

10:15
Welcome remarks
10:20
Keynote: Nancy J. Cox, Vanderbilt University, United States
Using Biobanks to swim upstream: phenome risk scores as a way to start with function and move to phenotype
11:20
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes. Ibrahim Numanagić, Salem Malikić, Michael Ford, Xiang Qin, Lorraine Toji, Milan Radovich, Todd Skaar, Victoria Pratt, Bonnie Berger, Steve Scherer, S. Cenk Sahinalp.
11:40
Realignment of short reads around short tandem repeats significantly improves accuracy of genomic variants detection. Daniel Tello, Juanita Gil, Jorge Duitama.
12:00
Jointly aligning a group of DNA reads improves accuracy of identifying large deletions. Anish Man Singh Shrestha, Martin C Frith, Kiyoshi Asai, Hugues Richard.
12:20
Convolutional filtering for mutation signature detection. Christopher Yau, Yun Feng.


12:40
Lunch Break


14:00
Novo &Stitch: accurate reconciliation of genome assemblies via optical maps. Weihua Pan, Steve Wanamaker, Audrey Ah-Fong, Howard Judelson, Stefano Lonardi.
14:20
A graph-based approach to diploid genome assembly. Shilpa Garg, Mikko Rautiainen, Adam Novak, Erik Garrison, Richard Durbin, Tobias Marschall.
14:40
Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. Maryam Ghareghani, David Porubsky, Ashley Sanders, Sascha Meiers, Evan Eichler, Jan Korbel, Tobias Marschall.
15:00
A space and time-efficient index for the compacted colored de Bruijn graph.  Fatemeh Almodaresi, Hirak Sarkar,  Avi Srivastava, Robert Patro.
15:20
Integrating Hi-C links with assembly graphs for chromosome-scale assembly. Jay Ghurye, Arang Rhie, Brian Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam Phillippy, Sergey Koren.
15:40
Bridging linear to graph-based alignment with whole genome population reference graphs. Mohamed Gunady, Stephen Mount, Hector Corrada Bravo, Sangtae Kim.


16:00
Coffee Break


16:40
Hercules: a profile HMM-based hybrid error correction algorithm for long reads. Can Firtina, Ziv Bar-Joseph, Can Alkan, A. Ercument Cicek.
17:00
Keynote: Ekta Khurana, Weill Cornell Medical College, United States
Non-coding genetic variation in cancer


July 9, 2018

10:15
Keynote: S. Cenk Sahinalp, Indiana University, United States
Coordinated evolution of tumor phylogeny inference methods and sequencing technologies
11:20
Haplotype phasing in single-cell DNA sequencing data. Gryte Satas, Ben Raphael.
11:40
HiVA: a web platform for haplotyping and copy number analysis of single-cell genomes and mosaicism detection in bulk DNA. Amin Ardeshirdavani, Masoud Zamani Esteki, Daniel Alcaide, Heleen Masset, Alejandro Sifrim, Parveen Kumar, Nathalie Brison, Niels Van der Aa, Eftychia Dimitriadou, Koen Theunis, Hilde Peeters, Jan Aerts, Joris Vermeesch, Thierry Voet, Yves Moreau.
12:00
Probabilistic inference of clonal gene expression through integration of RNA & DNA-seq at single-cell resolution. Kieran Campbell, Alexandre Bouchard-Cote, Sohrab Shah.
12:20
De novo single-cell transcript sequence reconstruction with Bloom filters. Ka Ming Nip, Readman Chiu, Justin Chu, Inanc Birol.


12:40
Lunch break


14:00
ABySS-LR: de novo assembly pipeline for Linked-Reads. Benjamin Vandervalk, Justin Chu, Shaun Jackman, Lauren Coombe, Jeffrey Tse, Hamid Mohamadi, Yee Fay Lim, Rene Warren, Inanc Birol.
14:20
Kourami: graph-guided assembly for novel HLA allele discovery. Heewook Lee, Carl Kingsford.
14:40
Versatile genome assembly evaluation with QUAST-LG. Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich.
15:00
AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. Kendell Clement, Rick Farouni, Daniel Bauer, Luca Pinello.
15:20
A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. Nima Nouri, Steven H. Kleinstein.
15:40
IsoCon: deciphering highly similar multigene family transcripts from Iso-Seq data. Kristoffer Sahlin, Marta Tomaszkiewicz, Kateryna Makova, Paul Medvedev.


16:00
Coffee break


16:40
Asymptotically optimal minimizers schemes. Guillaume Marçais, Dan DeBlasio, Carl Kingsford.
17:00
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Martin Steinegger, Johannes Soeding.
17:20
Quantification of private information leakage and privacy-preserving file formats for functional genomics data. Gamze Gursoy, Molly Green, Arif Harmanci, Mark Gerstein.
17:40
CliqueSNV: scalable reconstruction of intra-host viral populations from NGS reads. Sergey Knyazev, Viachaslau Tsyvina, Andrew Melnyk, Alexander Artyomenko, Tatyana Malygina, Yuri Porozov, Ellsworth Campbell, William Switzer, Pavel Skums, Alex Zelikovsky.


18:00
Closing remarks and awards.