HiTSeq 2019

Keynote speakers


Benedict Paten
Benedict Paten
Associate Professor
University of California, Santa Cruz, United States








Cole Trapnell
Cole Trapnell
Associate Professor
University of Washington, Seattle, United States








Yuzhen Ye
Yuzhen Ye
Professor
Indiana University, Bloomington, United States









July 12, 2022

10:30
Welcome remarks
10:35


Keynote: Yuzhen Ye, Indiana University
Utilizing multi-omics, networks and bacterial immune systems to understand microbiome
11:30



CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS. Hector Roux de  Bézieux, Leandro Lima, Fanny Perraudeau, Arnaud Mary, Sandrine Dudoit and Laurent Jacob
11:50


MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites. Xianglin Zhang and Xiaowo Wang
12:10


ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing. Jens-Uwe Ulrich, Ahmad Lutfi, Kilian Rutzen and Bernhard Renard



12:30
Lunch break



14:30


Rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing. Kerui Peng and Serghei Mangul
14:50




A unified somatic calling of next-generation sequencing data enhances the detection of clonal hematopoiesis of indeterminate potential. Shulan Tian, William Jenkinson, Alejandro Ferrer, Huihuang Yan, Saurabh Baheti, Terra Lasho, Joel Morales-Rosado, Mrinal Patnaik, Wei Ding, Konstantinos Lazaridis and Eric Klee
15:10


Mutational signatures of complex genomic rearrangements in human cancer. Lisui Bao, Xiaoming Zhong, Yang Yang and Lixing Yang



15:30
Coffee break



16:00
Keynote: Cole Trapnell, University of Washington
17:00



Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer. Haoyun Lei, Xianyan Guo, Yifeng Tao, Kai Ding, Xuecong Fu, Steffi Oesterreich, Adrian Lee and Russell Schwartz
17:20


  
Gene fusion detection and characterization in long-read cancer transcriptomes with FusionSeeker. Yu Chen, Yiqing Wang, Weisheng Chen, Yuwei Song, Yixin Zhang, Herbert Chen and Zechen Chong
17:40


Accurate assembly of multi-end RNA-seq data with Scallop2. Qimin Zhang, Qian Shi and Mingfu Shao



July 13, 2022


10:30

Keynote: Benedict Paten, University of California, Santa Cruz
11:30

  
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance. Yutong Qiu and Carl Kingsford
11:50

 
Stash: a data structure based on stochastic tile hashing. Armaghan Sarvar, Lauren Coombe, René Warren and Inanc Birol
12:10





GenASM: a high-performance, low-power approximate string matching acceleration framework for genome sequence analysis. Damla Senol Cali, Gurpreet Singh Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gómez Luna, Amiral Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose and Onur Mutlu



12:30

Lunch break



14:30


The minimizer Jaccard estimator is biased and inconsistent. Mahdi Belbasi, Antonio Blanca, Robert S. Harris, David Koslicki and Paul Medvedev
14:50

Sparse and skew hashing of k-mers. Giulio Ermanno Pibiri
15:10


Matchtigs: minimum plain text representation of kmer sets. Sebastian Schmidt, Shahbaz Khan, Jarno Alanko and Alexandru I. Tomescu



15:30

Coffee break



16:00


Markov chains improve the significance computation of overlapping genome annotations. Askar Gafurov, Broňa Brejová and Paul Medvedev
16:20


GoldRush-Path: a de novo assembler for long reads with linear time complexity. Johnathan Wong, Vladimir Nikolic, Lauren Coombe, Rene Warren and Inanc Birol
16:40



Quantification of complex genome editing events including large insertions and translocations using CRISPRlungo. Kendell Clement, Linda Lin, Daniel Bauer and Luca Pinello
17:00


Robust fingerprinting of genomic databases. Tianxi Ji, Erman Ayday, Emre Yilmaz and Pan Li
17:20


Clustering-independent estimation of dynamic cell abundance in bulk tissue using single-cell transcriptomic data. Rachael Aubin, Javier Montelongo and Pablo Camara
17:40


κ-velo improves single-cell RNA-velocity estimation. Valérie Marot-Lassauzaie, Brigitte Joanne Bouman, Fearghal Declan Donaghy and Laleh Haghverdi