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 |
