HiTSeq 2019

Accepted Full papers

    • hicGAN infers super resolution Hi-C data with generative adversarial networks. Qiao Liu, Hairong Lv and Rui Jiang
    • Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes. Vikas Bansal
    • Alignment-free filtering for cfNA fusion fragments. Xiao Yang, Yasushi Saito, Arjun Rao, Hyunsung John Kim, Pranav Singh, Eric Scott, Matthew Larson, Wenying Pan, Mohini Desai and Earl Hubbell
    • TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Yan Gao, Bo Liu, Yadong Wang and Yi Xing
    • Fully-sensitive seed finding in sequence graphs using a hybrid index. Ali Ghaffaari and Tobias Marschall
    • Locality sensitive hashing for the edit distance. Guillaume Marçais, Dan DeBlasio, Prashant Pandey and Carl Kingsford
    • Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level. Hirak Sarkar, Avi Srivastava and Robert Patro
    • Building large updatable colored de Bruijn graphs via merging. Martin Muggli, Bahar Alipanahi and Christina Boucher
    • cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs. Ivan Tolstoganov, Anton Bankevich, Zhoutao Chen and Pavel Pevzner

Accepted Talks Selected from abstracts

  • Bspliced: a Bayesian hierarchical model for differential splicing accounting for sample-to-sample variability and mapping uncertainty. Simone Tiberi and Mark Robinson
  • Accurate determination of node and arc multiplicities in de Bruijn graphs using conditional random fields.  Aranka Steyaert, Pieter Audenaert and Jan Fostier
  • Flexible Experimental Designs for Valid Single-cell RNA-sequencing Experiments Allowing Batch Effects Correction. Fangda Song, Ga Ming Chan and Yingying Wei
  • 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 and Zhandong Liu
  • Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling. Mariano Gabitto, Anders Rasmussen and Richard Bonneau
  • Subpopulation detection and their comparative analysis across single cell experiments with PopCorn. Yijie Wang, Jan Hoinka and Teresa Przytycka
  • PipelineOlympics: benchmarking of processing workflows for bisulfite sequencing data. Toth Reka, Yassen Assenov, Karl Nordström, Angelika Merkel, Edahi Gonzalez-Avalos, Matthias Bieg, Stephen Kraemer, Murat Iskar, Helene Kretzmer, Lelia Wagner, Lilian Leiter, Giuseppe Petroccino, Anand Mayakonda, Kersten Breuer, Gideon Zipprich, Lena Weiser, Philip Kensche, Renata Jurkowska, Christian Lawerenz, Ivo Buchhalter, Steve Hoffmann, Simon Heath, Marc Zapatka, Joern Walter, Matthias Schlesner, Christoph Bock, Christoph Plass and Pavlo Lutsik
  • Characterization of large-scale structural variants using Linked-Reads. Fatih Karaoglanoglu, Camir Ricketts, Ezgi Ebren, Marzieh Eslami Rasekh, Iman Hajirasouliha and Can Alkan
  • 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 and Oliver Stegle
  • Genotyping structural variations using long reads data. Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier and Claire Lemaitre
  • GraphAligner: rapid and versatile sequence-to-graph alignment.  Mikko Rautiainen and Tobias Marschall
  • Descendant cell fraction: copy-aware inference of clonal composition and evolution in cancer. Mohammed El-Kebir, Simone Zaccaria and Ben Raphael
  • Fast and accurate bisulfite alignment and methylation calling for mammalian genomes. Jonas Fischer and Marcel Schulz
  • ImmunoPepper: generating neoepitopes from RNA-Seq data. Matthias Hüser, Jiayu Chen, Andre Kahles and Gunnar Rätsch
  • Haplotype threading: accurate polyploid phasing from long reads.  Sven Schrinner, Rebecca Serra Mari, Jana Ebler, Gunnar W. Klau and Tobias Marschall
  • Detection and assembly of novel sequence insertions using Linked-Reads. Dmitrii Meleshko, Patrick Marks, Stephen Williams and Iman Hajirasoulihay

Industry talk

  • AWS for Genomics in the Public Sector. Angus McAllister.

Proceedings of past hiTSeq Meetings

  • HiTSeq 2018: July 8-9, 2018. Chicago, IL, USA.
  • HiTSeq 2017: July 24-25, 2017. Prague, Czech Republic
  • HiTSeq 2016: July 8-9, 2016. Orlando, FL, USA
  • HiTSeq 2015: July 10-11, 2015. Dublin, Ireland
  • HiTSeq 2014: July 11-12, 2014. Boston,MA, USA