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HiTSeq COSI Track Presentations

Attention Conference Presenters - please review the Speaker Information Page available here
Oliver Stegle: Computational methods for dissecting the transcriptome and epigenome diversity between single cells
Date: Monday, July 24
Time: 10:10 AM - 11:10 AM
Room: Forum Hall
    Tumor Phylogeny Inference Using Tree-Constrained Importance Sampling
    Date: Monday, July 24
    Time: 11:10 AM - 11:30 AM
    Room: Forum Hall
    • Benjamin Raphael, Princeton University, United States
    • Gryte Satas, Brown University, United States
    Integrating Diverse Transcriptomic Alterations to Identify Cancer-Relevant Genes and Signatures
    Date: Monday, July 24
    Time: 11:30 AM - 11:50 AM
    Room: Forum Hall
    • Andre Kahles, ETH Zurich, Switzerland
    • Claudia Calabrese, EMBL-EBI, United Kingdom
    • Angela Brooks, University of California, Santa Cruz, United States
    • Alvis Brazma, European Bioinformatics Institute, United Kingdom
    • Gunnar Rätsch, Memorial Sloan Kettering Center, United States
    • Jonathan Göke, Genome Institute of Singapore, Singapore
    • Kjong-Van Lehmann, ETH Zurich, Switzerland
    • Natalie Davidson, MSKCC, United States
    • Nuno A. Fonseca, EMBL-EBI, European Bioinformatics Institute, United Kingdom
    • Roland Schwarz, Max Delbrueck Center for Molecular Medicine, Germany
    • Zemin Zhang, Peking University, China
    Deconvolution of heterogeneous bulk tumor genomic data via structured mixed membership models
    Date: Monday, July 24
    Time: 11:50 AM - 12:10 PM
    Room: Forum Hall
    • Brenda Xiao, Carnegie Mellon University, United States
    • Russell Schwartz, Carnegie Mellon University, United States
    A Pan-cancer Analysis of Alternative Transcription Start Sites
    Date: Monday, July 24
    Time: 12:10 PM - 12:20 PM
    Room: Forum Hall
    • Andre Kahles, ETH Zurich, Switzerland
    • Engin Cukuroglu, Genome Institute of Singapore, Singapore
    • Deniz Demircioğlu, Genome Institute of Singapore, Singapore
    • Bin Tean Teh, National Cancer Centre Singapore, Singapore
    • Claudia Calabrese, EMBL-EBI, United Kingdom
    • Angela Brooks, University of California, United States
    • Alvis Brazma, European Bioinformatics Institute, United Kingdom
    • Gunnar Rätsch, ETH Zurich, Switzerland
    • Jonathan Göke, Genome Institute of Singapore, Singapore
    • Kjong Lehmann, ETH Zurich, Switzerland
    • Nuno A. Fonseca, EMBL-EBI, European Bioinformatics Institute, United Kingdom
    • Oliver Stegle, EMBL-European Bioinformatics Institute, United Kingdom
    • Patrick Tan, Genome Institute of Singapore, Duke-NUS Graduate Medical School, Singapore
    • Steve Rozen, Duke-NUS Graduate Medical School Singapore, Singapore
    • Tannistha Nandi, Genome Institute of Singapore, Singapore
    Modelling haplotypes with respect to reference cohort variation graphs
    Date: Monday, July 24
    Time: 2:00 PM - 2:20 PM
    Room: Forum Hall
    • Benedict Paten, UCSC, United States
    • Jordan Eizenga, University of California Santa Cruz, United States
    • Yohei Rosen, University of California, Santa Cruz, United States
    Quantitative assessment of genome integrity from whole genome sequencing data
    Date: Monday, July 24
    Time: 2:20 PM - 2:40 PM
    Room: Forum Hall
    • Anastasia Samsonova, Department of Oncology, University of Oxford, United Kingdom
    • Anas Rana, Department of Oncology, University of Oxford, United Kingdom
    • Dimitris Vavoulis, Department of Oncology, University of Oxford, United Kingdom
    • Anna Schuh, Department of Oncology, University of Oxford, United Kingdom
    • Alexander Kanapin, Department of Oncology, University of Oxford, United Kingdom
    • Samantha Jl Knight, NIHR Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
    Diversity in non-repetitive human sequences not found in the reference genome
    Date: Monday, July 24
    Time: 2:40 PM - 3:00 PM
    Room: Forum Hall
    • Daniel F. Gudbjartsson, deCODE Genetics/Amgen, Inc., Iceland
    • Bjarni Halldorsson, deCODE genetics and Reykjavik University, Iceland
    • Birte Kehr, Berlin Institute of Health, Germany
    • Aslaug Jonasdottir, deCODE Genetics/Amgen, Inc., Iceland
    • Asgeir Sigurdsson, deCODE Genetics/Amgen, Inc., Iceland
    • Arnaldur Gylfason, deCODE Genetics/Amgen, Inc., Iceland
    • Anna Helgadóttir, deCODE Genetics/Amgen, Inc., Iceland
    • Agnar Helgason, deCODE Genetics/Amgen, Inc., Iceland
    • Adalbjörg Jonasdottir, deCODE Genetics/Amgen, Inc., Iceland
    • Gisli H. Halldorsson, deCODE Genetics/Amgen, Inc., Iceland
    • Gudmundur Thorgeirsson, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland
    • Hákon Jónsson, deCODE Genetics/Amgen, Inc., Iceland
    • Hannes Helgason, deCODE Genetics/Amgen, Inc., Iceland
    • Hilma Holm, deCODE Genetics/Amgen, Inc., Iceland
    • Isleifur Olafsson, Department of Clinical Biochemistry, Landspitali–National University Hospital, Iceland
    • Kári Stefánsson, deCODE Genetics/Amgen, Inc., Iceland
    • Pall Melsted, University of Iceland, Iceland
    • Patrick Sulem, deCODE Genetics/Amgen, Inc., Iceland
    • Snaedis Kristmundsdottir, deCODE Genetics/Amgen, Inc., Iceland
    • Unnur Thorsteinsdottir, deCODE Genetics/Amgen, Inc., Iceland
    Discovery and genotyping of novel sequence insertions in many sequenced individuals.
    Date: Monday, July 24
    Time: 3:00 PM - 3:20 PM
    Room: Forum Hall
    • Pınar Kavak, Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey, Turkey
    • Yen-Yi Lin, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
    • Ibrahim Numanagić, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
    • Hossein Asghari, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
    • Tunga Güngör, Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey, Turkey
    • Can Alkan, Department of Computer Engineering, Bilkent University, Ankara, Turkey, Turkey
    • Faraz Hach, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
    Chromatin Accessibility Prediction via Convolutional Long Short-Term Memory Networks with k-mer Embedding
    Date: Monday, July 24
    Time: 3:20 PM - 3:40 PM
    Room: Forum Hall
    • Ning Chen, Tsinghua University, China
    • Rui Jiang, Tsinghua University, China
    • Ting Chen, Tsinghua University, China
    • Wanwen Zeng, Tsinghua University, China
    • Xu Min, Tsinghua University, China
    HopLand: Single-cell pseudotime recovery using continuous Hopfield network based modeling of Waddington’s epigenetic landscape
    Date: Monday, July 24
    Time: 3:40 PM - 4:00 PM
    Room: Forum Hall
    • Jie Zheng, Nanyang Technological University, Singapore
    • Jing Guo, Nanyang Technological University, Singapore
    Reconstructing Reprogramming Dynamics Using High-throughput Single-cell Transcriptomes
    Date: Monday, July 24
    Time: 4:30 PM - 4:50 PM
    Room: Forum Hall
    • Jason Ernst, UCLA, United States
    Adam M. Phillippy: What’s old is new again: assembly and alignment algorithms for the long-read era.
    Date: Monday, July 24
    Time: 4:50 PM - 6:00 PM
    Room: Forum Hall
      Veli Mäkinen: Algorithmic aspects of sequence graph analysis
      Date: Tuesday, July 25
      Time: 8:30 AM - 9:30 AM
      Room: Forum Hall
        DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation
        Date: Tuesday, July 25
        Time: 10:00 AM - 10:20 AM
        Room: Forum Hall
        • Fabian Müller, Max Planck Institute for Informatics, Germany
        • Christoph Bock, CeMM Research Center for Molecular Medicine, Austria
        • Florian Halbritter, CeMM Research Center for Molecular Medicine, Austria
        • Matthias Farlik, CeMM Research Center for Molecular Medicine, Austria
        • Mattia Frontini, University of Cambridge, United Kingdom
        • Thomas Lengauer, Max Planck Institute for Informatics, Germany
        Profiling immunoglobulin repertoires across multiple human tissues by RNA Sequencing
        Date: Tuesday, July 25
        Time: 10:20 AM - 10:40 AM
        Room: Forum Hall
        • Serghei Mangul, UCLA, United States
        • Igor Mandric
        • Harry Taegyun Yang
        • Nicolas Strauli
        • Dennis Montoya
        • Jeremy Rotman
        • Wi1l Van Der Wey
        • Jiem R. Ronas
        • Benjamin Statz
        • Alex Zelikovsky
        • Roberto Spreafico
        • Sagiv Shifman
        • Noah Zaitlen
        • Maura Rossetti
        • K. Mark Ansel
        • Eleazar Eskin
        SQANTI: extensive characterization of long read transcript sequences to remove artifacts in transcriptome identification and quantification
        Date: Tuesday, July 25
        Time: 10:40 AM - 11:00 AM
        Room: Forum Hall
        • Cristina Marti, CIPF, Spain
        • Cecile Pereira, University of Florida - Dr. Conesa's Lab, United States
        • Ana Conesa, Genomics of Gene Expression Lab, Spain
        • Ali Mortazavi, University of California, Irvine, United States
        • Hector Del Risco, University of Florida - Dr. Conesa's Lab, United States
        • Lorena de La Fuente Lorente, Centro de Investigación Príncipe Felipe (CIPF), Spain
        • Manuel Tardaguila, UNIVERSITY OF FLORIDA, United States
        • Maravillas Mellado, Centro de Investigación Príncipe Felipe, Spain
        • Marissa Macchietto, University of California Irvine, United States
        • Susana Rodriguez, Centro de Investigación Príncipe Felipe, Spain
        • Victoria Moreno, CENTRO DE INVESTIGACION PRINCIPE FELIPE, Spain
        Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
        Date: Tuesday, July 25
        Time: 11:00 AM - 11:20 AM
        Room: Forum Hall
        • Jorge Vaquero-Garcia, University of Pennsylvania, United States
        • Scott Norton, University of Pennsylvania, United States
        • Yoseph Barash, University of Pennsylvania, United States
        Improved Data-Driven Likelihood Factorizations for Transcript Abundance Estimation
        Date: Tuesday, July 25
        Time: 11:20 AM - 11:40 AM
        Room: Forum Hall
        • Avi Srivastava, Stony Brook University, United States
        • Fatemehalsadat Almodaresi T S, Stony Brook University, United States
        • Mohsen Zakeri, Stony Brook University, United States
        • Rob Patro, Stony Brook University, United States
        Tigmint: Correct Misassemblies Using Linked Reads From Large Molecules
        Date: Tuesday, July 25
        Time: 11:40 AM - 12:00 PM
        Room: Forum Hall
        • Benjamin P Vandervalk, BC Cancer Agency Genome Sciences Centre, Canada
        • Hamid Mohamadi, BC Cancer Agency Genome Sciences Centre, Canada
        • Inanc Birol, BC Cancer Agency Genome Sciences Centre, Canada
        • Joerg Bohlmann, Department of Forest and Conservation Sciences, University of British Columbia, Canada
        • Justin Chu, BC Cancer Agency Genome Sciences Centre, Canada
        • Lauren Coombe, BC Cancer Agency Genome Sciences Centre, Canada
        • Rene L Warren, BC Cancer Agency Genome Sciences Centre, Canada
        • Sarah Yeo, BC Cancer Agency Genome Sciences Centre, Canada
        • Shaun D Jackman, BC Cancer Agency Genome Sciences Centre, Canada
        • Steven Jm Jones, BC Cancer Agency Genome Sciences Centre, Canada
        Computing Optimal Flow Decompositions for Assembly
        Date: Tuesday, July 25
        Time: 12:00 PM - 12:20 PM
        Room: Forum Hall
        • Blair D. Sullivan, NC State University, United States
        • Andrew van der Poel, North Carolina State University, United States
        • Felix Reidl, RWTH Aachen, Germany
        • Fernando Sánchez Villaamil, RWTH Aachen, Germany
        • Kyle Kloster, North Carolina State University, United States
        • Michael P. O'Brien, North Carolina State University, United States
        • Philipp Kuinke, RWTH Aachen, Germany
        deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph
        Date: Tuesday, July 25
        Time: 2:00 PM - 2:20 PM
        Room: Forum Hall
        • Michael A. Bender, Stony Brook University, United States
        • Prashant Pandey, Stony Brook University, United States
        • Rob Johnson, Stony Brook University, United States
        • Rob Patro, Stony Brook University, United States
        Abundance estimation and differential testing on strain level in metagenomics data
        Date: Tuesday, July 25
        Time: 2:20 PM - 2:40 PM
        Room: Forum Hall
        • Benjamin Strauch, Robert Koch Institute, Germany
        • Bernhard Y. Renard, Robert Koch Institute, Germany
        • Martina Fischer, Robert Koch Institute, Germany
        Metagenome representation with Scalable Reference Graphs
        Date: Tuesday, July 25
        Time: 2:40 PM - 3:00 PM
        Room: Forum Hall
        • Andre Kahles, ETH Zurich, Switzerland
        • Gunnar Rätsch, ETH Zurich, Switzerland
        Rapid phylogenetic placement via ancestral reconstruction
        Date: Tuesday, July 25
        Time: 3:00 PM - 3:20 PM
        Room: Forum Hall
        • Benjamin Linard, LIRMM - CNRS, France
        • Fabio Pardi, LIRMM - CNRS, France
        • Krister Swenson, LIRMM - CNRS, France
        De novo assembly of viral quasispecies using overlap graphs
        Date: Tuesday, July 25
        Time: 3:20 PM - 3:40 PM
        Room: Forum Hall
        • Eric Rivals, University of Montpellier, France
        • Amal Zine El Aabidine, University of Montpellier, France
        • Alexander Schoenhuth, Centrum Wiskunde & Informatica, Netherlands
        • Jasmijn Baaijens, Centrum Wiskunde & Informatica, Netherlands
        SeqOthello: A Novel Indexing Structure to Support Accurate and Scalable Query over Large Scale Sequencing Reads
        Date: Tuesday, July 25
        Time: 3:40 PM - 4:00 PM
        Room: Forum Hall
        • Chen Qian, University of California Santa Cruz, United States
        • James N. MacLeod, University of Kentucky, United States
        • Jinze Liu, UKY, United States
        • Xinan Liu, University of Kentucky, United States
        • Ye Yu, University of Kentucky, United States
        Improving the performance of minimizers and winnowing schemes
        Date: Tuesday, July 25
        Time: 4:00 PM - 4:20 PM
        Room: Forum Hall
        • Guillaume Marçais, Carnegie Mellon University, United States
        • David Pellow, Tel Aviv University, Israel
        • Daniel Bork, University of Pittsburgh, United States
        • Yaron Orenstein, MIT, United States
        • Ron Shamir, School of Computer Science, Tel Aviv University, Israel
        • Carl Kingsford, Carnegie Mellon University, United States