Keynote speakers
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S.
Cenk Şahinalp Professor of Computer Science Co-Director, Center for Genomics and Bioinformatics Indiana University, Bloomington, IN, United States |
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Ekta Khurana Assistant Professor of Computational Genomics Weill Cornell Medical College, New York, NY, United States |
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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. |