HiTSeq 2019

See the schedule in the official ISMB page here.


Keynote speakers


Christina Curtis
Christina Curtis
Assistant Professor of Medicine and Genetics
Stanford University School of Medicine
Co-Director, Molecular Tumor Board, Stanford Cancer Institute
Stanford University, United States
Andrew Adey
Andrew Adey

Assistant Professor
Molecular & Medical Genetics, School of Medicine
Member, Knight Cardiovascular Institute

Oregon Health and Sciences University, United States
Zamin Iqbal
Zamin Iqbal
Research Group Leader
European Bioinformatics Institute, United Kingdom


July 22, 2019

10:15
Welcome remarks
10:20

Keynote: Christina Curtis, Stanford University, United States
Quantifying the rates and routes of metastasis
11:20
   
Alignment-free Filtering for cfNA Fusion Fragments. Xiao Yang, Mohini Desai, Wenying Pan, Matthew Larson, Eric Scott, Pranav Singh, Hyunsung John Kim, Arjun Rao, Yasushi Saito, Earl Hubbell.
11:40

Descendant Cell Fraction: Copy-aware Inference of Clonal Composition and Evolution in Cancer. Simone Zaccaria, Ben Raphael, Mohammed El-Kebir.
12:00

Subpopulation detection and their comparative analysis across single cell experiments with PopCorn. Yijie Wang, Jan Hoinka, Teresa Przytycka.
12:20

Minnow: A principled framework for rapid simulation of dscRNA-seq data at the read level. Hirak Sarkar, Avi Srivastava, Robert Patro.



12:40

Lunch break



14:00

Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid Index. Ali Ghaffaari, Tobias Marschall.
14:20

Building Large Updatable Colored de Bruijn Graphs via Merging. Martin Muggli, Bahar Alipanahi, Christina Boucher.
14:40

Accurate determination of node and arc multiplicities in de Bruijn graphs using conditional random fields. Aranka Steyaert, Pieter Audenaert, Jan Fostier.
15:00

GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment. Mikko Rautiainen, Tobias Marschall.
15:20

cloudSPAdes: Assembly of Synthetic Long Reads Using de Bruijn graphs. Ivan Tolstoganov, Anton Bankevich, Pavel Pevzner.
15:40

Locality sensitive hashing for the edit distance. Guillaume Marçais, Dan DeBlasio, Prashant Pandey, Carl Kingsford.



16:00

Coffee break



16:40

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Yan Gao, Bo Liu, Yadong Wang, Yi Xing.
17:00

Keynote: Zamin Iqbal, European Bioinformatics Institute, United Kingdom
Bacterial pangenome graphs - an approximate solution to the correct problem


July 23, 2019


10:15
    
Keynote: Andrew Adey, Oregon Health and Sciences University, United States
Advances in single-cell epigenomics using combinatorial indexing
11:20

hicGAN infers super resolution Hi-C data with generative adversarial networks.
Qiao Liu, Hairong Lv, Rui Jiang.
11:40

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling. Mariano Gabitto, Anders Rasmussen, Richard Bonneau.
12:00

Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes. Vikas Bansal.
12:20

Haplotype threading: accurate polyploid phasing from long reads. Sven Schrinner, Rebecca Serra Mari, Jana Ebler, Gunnar W. Klau, Tobias Marschall.



12:40

Lunch break

   

14:00

Characterization of large-scale structural variants using Linked-Reads. Fatih Karaoglanoglu, Camir Ricketts, Ezgi Ebren, Marzieh Eslami Rasekh, Iman Hajirasouliha, Can Alkan.
14:20

Detection and assembly of novel sequence insertions using Linked-Reads. Dmitrii Meleshko, Patrick Marks, Stephen Williams, Iman Hajirasouliha.
14:40

Genotyping structural variations using long reads data. Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre.
15:00

Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives. Hyun-Hwan Jeong, Seon Young Kim, Maxime W.C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu.
15:20

Fast and accurate bisulfite alignment and methylation calling for mammalian genomes. Jonas Fischer, Marcel Schulz.
15:40

PipelineOlympics: benchmarking of processing workflows for bisulfite sequencing data. Toth Reka, Yassen Assenov, Philip Kensche, Renata Jurkowska, Christian Lawerenz, Ivo Buchhalter, Steve Hoffmann, Simon Heath, Marc Zapatka, Joern Walter, Matthias Schlesner, Christoph Plass, Karl Nordstroem, Lena Weiser, Gideon Zipprich, Angelika Merkel, Edahi Gonzalez-Avalos, Matthias Bieg, Stephen Kraemer, Murat Iskar, Helene Kretzmer, Lelia Wagner, Lilian Leiter, Giuseppe Petroccino, Anand Mayakonda, Kersten Breuer, Christoph Bock, Christoph Plass, Pavlo Lutsik.



16:00

Coffee break



16:25

Industry talk: AWS for Genomics in the Public Sector. Angus McAllister.
16:40

Flexible Experimental Designs for Valid Single-cell RNA-sequencing Experiments Allowing Batch Effects Correction. Yuanhua Huang, Davis McCarthy, Raghd Rostom, Sarah Teichmann, Oliver Stegle.
17:00

Bayesian deconvolution of somatic clones and pooled individuals with expressed variants in single-cell RNA-seq data. Yuanhua Huang, Davis McCarthy, Raghd Rostom, Sarah Teichmann, Oliver Stegle.
17:20

ImmunoPepper: generating neoepitopes from RNA-Seq data. Matthias Hüser, Jiayu Chen, Andre Kahles.
17:40

BANDITS: a Bayesian hierarchical model for differential splicing accounting for sample-to-sample variability and mapping uncertainty. Simone Tiberi, Mark D. Robinson.