Keynote speakers
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Benedict
Paten Associate Professor University of California, Santa Cruz, United States |
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Cole
Trapnell Associate Professor University of Washington, Seattle, United States |
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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 |
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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 A Draft Human Pangenome Reference |
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| 11:30 |
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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 |