HiTSeq 2017
See the schedule in the official ISMB page here.

July 24, 2017

10:00
Welcome remarks
10:10
Keynote: Oliver Stegle, EBI, United Kingdom
Computational methods for dissecting the transcriptome and epigenome diversity between single cells
11:10
Tumor phylogeny inference using tree-constrained importance sampling.
Gryte Satas and Benjamin J. Raphael
11:30
Integrating diverse transcriptomic alterations to identify cancer-relevant genes and signatures.
Natalie Davidson, Kjong-Van Lehmann, Andre Kahles, Alvis Brazma, Angela Brooks, Claudia Calabrese, Nuno A. Fonseca, Jonathan Göke, Roland Schwarz, Gunnar Rätsch and Zemin Zhang
11:50
Deconvolution of heterogeneous bulk tumor genomic data via structured mixed membership models.
Theodore Roman, Brenda Xiao and Russell Schwartz
12:10
A pan-cancer analysis of alternative transcription start sites.
Deniz Demircioğlu, Tannistha Nandi, Claudia Calabrese, Engin Cukuroglu, Nuno A. Fonseca, Andre Kahles, Kjong Lehmann, Steve Rozen, Bin Tean Teh, Oliver Stegle, Alvis Brazma, Angela Brooks, Gunnar Rätsch, Patrick Tan and Jonathan Göke


12:30
Lunch break


14:00 Modelling haplotypes with respect to reference cohort variation graphs.
Yohei Rosen, Jordan Eizenga and Benedict Paten
14:20 Quantitative assessment of genome integrity from whole genome sequencing data.
Anas Rana, Alexander Kanapin, Dimitris Vavoulis, Samantha Jl Knight, Anna Schuh and Anastasia Samsonova
14:40 Diversity in non-repetitive human sequences not found in the reference genome.
Birte Kehr, Anna Helgadóttir, Pall Melsted, Hákon Jónsson, Hannes Helgason, Adalbjörg Jonasdottir, Aslaug Jonasdottir, Asgeir Sigurdsson, Arnaldur Gylfason, Gisli H. Halldorsson, Snaedis Kristmundsdottir, Gudmundur Thorgeirsson, Isleifur Olafsson, Hilma Holm, Unnur Thorsteinsdottir, Patrick Sulem, Agnar Helgason, Daniel F. Gudbjartsson, Bjarni Halldorsson and Kári Stefánsson
15:00 Discovery and genotyping of novel sequence insertions in many sequenced individuals.
Pınar Kavak, Yen-Yi Lin, Ibrahim Numanagić, Hossein Asghari, Tunga Güngör, Can Alkan and Faraz Hach
15:20 Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding.
Xu Min, Wanwen Zeng, Ning Chen, Ting Chen and Rui Jiang
15:40 HopLand: Single-cell pseudotime recovery using continuous Hopfield network based modeling of Waddington’s epigenetic landscape.
Jing Guo and Jie Zheng
16:00 Coffee break
16:30 Reconstructing Reprogramming Dynamics Using High-throughput Single-cell Transcriptomes
Shan Sabri, Justin Langerman, Jason Ernst and Kathrin Plath
16:50 Keynote: Adam M. Phillippy, NIH, United States.
What’s old is new again: assembly and alignment algorithms for the long-read era.


July 25, 2017

08:30 Keynote: Veli Mäkinen, University of Helsinki, Finland.
Algorithmic aspects of sequence graph analysis.
09:30
Coffee break
10:00
DNA methylation dynamics of human hematopoietic stem cell differentiation.
Fabian Müller, Matthias Farlik, Florian Halbritter, Mattia Frontini, Thomas Lengauer and Christoph Bock
10:20
Profiling immunoglobulin repertoires across multiple human tissues by RNA sequencing.
Serghei Mangul, Igor Mandric, Harry Taegyun Yang, Nicolas Strauli, Dennis Montoya, Jeremy Rotman, Will Van Der Wey, Jiem R. Ronas, Benjamin Statz, Alex Zelikovsky, Roberto Spreafico, Sagiv Shifman, Noah Zaitlen, Maura Rossetti, K. Mark Ansel, Eleazar Eskin
10:40
SQANTI: extensive characterization of long read transcript sequences to remove artifacts in transcriptome identification and quantification.
Lorena de La Fuente Lorente, Manuel Tardaguila, Cristina Marti, Hector Del Risco, Cecile Pereira, Marissa Macchietto, Maravillas Mellado, Ali Mortazavi, Susana Rodriguez, Victoria Moreno and Ana Conesa
11:00
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.
Scott Norton, Jorge Vaquero-Garcia and Yoseph Barash
11:20
Improved data-driven likelihood factorizations for transcript abundance estimation.
Mohsen Zakeri, Avi Srivastava, Fatemehalsadat Almodaresi T S and Rob Patro
11:40
Tigmint: correct misassemblies using linked reads from large molecules.
Shaun D Jackman, Benjamin P Vandervalk, Rene L Warren, Hamid Mohamadi, Justin Chu, Sarah Yeo, Lauren Coombe, Joerg Bohlmann, Steven Jones and Inanc Birol
12:00
Computing optimal flow decompositions for assembly.
Kyle Kloster, Philipp Kuinke, Michael P. O'Brien, Felix Reidl, Andrew van der Poel, Fernando Sánchez Villaamil and Blair D. Sullivan


12:20
Lunch break


14:00
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.
Prashant Pandey, Michael A. Bender, Rob Johnson and Rob Patro
14:20
Abundance estimation and differential testing on strain level in metagenomics data.
Martina Fischer, Benjamin Strauch and Bernhard Y. Renard
14:40
Metagenome representation with scalable reference graphs.
Andre Kahles and Gunnar Rätsch
15:00
Rapid phylogenetic placement via ancestral reconstruction.
Benjamin Linard, Krister Swenson and Fabio Pardi
15:20
de novo assembly of viral quasispecies using overlap graphs.
Jasmijn Baaijens, Amal Zine El Aabidine, Eric Rivals and Alexander Schoenhuth
15:40
SeqOthello: a novel indexing structure to support accurate and scalable query over large scale sequencing reads.
Xinan Liu, Ye Yu, James N. MacLeod, Chen Qian and Jinze Liu
16:00
Improving the performance of minimizers and winnowing schemes.
Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir and Carl Kingsford
16:20 Closing remarks