ANU Workshop on
Computational Genomics

Registration Deadline (August 13, 2023)

Register Program PDF
31 August, 2023
Workshop

Rationale

We invite researchers and students working in computational genomics or related fields to participate in a one-day hybrid workshop on the 31st August 2023 on ANU Campus.

The workshop will discuss latest advances and challenges in these interdisciplines at the interface between Computing, Biology, and Medical research, and other cognate disciplines. Topics may include (but not limited to) methods, models and applications of bioinformatics and computational biology for genomic data. We will bring together local and international students and researchers, in particular, those who worked with Dr. Yu Lin before. The idea of holding this workshop is inspired by the memory and intellectual legacy of Dr Yu Lin, whose seminal contributions and collaborative spirit are having a lasting influence in the research field and the ANU community.

The workshop will consist of long and short presentations in the morning, followed by break-out sessions and a panel dialogue on emerging trends and challenges in the afternoon.

 

 

In Memory of Yu Lin

Hansheng Xue, PhD Completion Talk

Wed 30 Aug 11 am, Hanna Neumann Room 3.41

(advised by Yu Lin, Vaibhav Rajan, Lexing Xie)

Meet The Speakers

Vaibhav Rajan

Natinoal University of Singapore

Program

Tony Hosking

Australian National University

Opening Statement

Chair: Liang Zheng

9:00am-9:10am

Vaibhav Rajan*

National University of Singapore

Keynote Speech

9:10am-9:45am

Session 1: Assembly and HiTseq

Chair: Eduardo Eyras

9:45am-10:45am

Pavel Pevzner*

University of California, San Diego

Yu Lin's Contribution to Genome Assembly

9:45am-10:00am

Kirat Alreja

Australian National University

Manual Curation Of Genome Assemblies For Australian Reptiles & Amphibians

10:00am-10:10am

Mingfu Shao*

Pennsylvania State University

Combinatorial And Learning Algorithms For Locality Sensitive Hashing Functions

10:10am-10:25am

Zixiong Zhuang

Australian National University

Discovering Population-Level Structural Variants In The Dieback Species Eucalyptus Viminalis With Long-Read Sequencing And HPC Read Mapping

10:25am-10:35am

Arthur Georges

University of Canberra

Resolving Sex Chromosome Assembly -- Brief History And Current Advances

10:35am-10:45am

Morning Tea

10:45am-11:15am

Session 2: Biology and Medical Applications

Chair: Robert Lanfear & Vijini Mallawaarachchi

11:15am-12:45pm

Justin Borevitz

Australian National University

Landscape Genomics For Climate Adaptation

11:15am-11:25am

Xiuwei Zhang*

Georgia Institute of Technology

Inference Of Cell Division Histories Using Lineage Tracing And Single Cell Data

11:25am-11:40am

Eduardo Eyras

Australian National University

Characterising The (Epi)Transcriptome At Single-Molecule Resolution With Long-Read Sequencing

11:40am-11:50am

Yanlin Zhang*

McGill University

Reference Panel Guided Topological Structure Annotation Of Hi-C Data

11:50am-12:00pm

Hardip Patel

Australian National University

National Centre For Indigenous Genomics Enabling Equitable Healthcare For All

12:00pm-12:10pm

Xiaowen Liu*

Tulane University

Complex Proteoform Identification By Top-Down Mass Spectrometry

12:10pm-12:20pm

Yuvaraj Ghodke

Australian National University

Omics Data In Clinical Trials

12:20pm-12:30pm

Liang Qiao*

Fudan University

Mass Spectrometry Methods In Microbe And Microbiome Characterization

12:30pm-12:45pm

Lunch Break

12:45pm-1:35pm

Session 3: Phylogenomics

Chair: Gavin Huttley

1:35pm-3:20pm

Minh Bui, Nhan Ly-Trong, Piyumal Demotte

Australian National University

Computational Phylogenomics At ANU

1:35pm-1:50pm

Rob Lanfear, Fred Jaya, Jeremias Ivan

Australian National University

Applied Phylogenomics at ANU: Models of Molecular Evolution for Bacteria; Choosing Sliding Window Size for Phylogenomic Analysis

1:50pm-2:05pm

Thomas Wong, Caitlin Cherryh

Australian National University

MAST: Phylogenetic Inference With Mixtures Across Sites And Trees And Applications To Metazoan Evolution

2:05pm-2:20pm

Robert McArthur

Australian National University

Spectral Cluster Supertree: Rapidly Merging Phylogenetic Trees With Thousands Of Taxa

2:20pm-2:27pm

Matthew Macaulay

The University of Technology Sydney

Efficient Embeddings For Scalable Bayesian Phylogenetic Inference

2:27pm-2:35pm

Afternoon Tea

2:35pm-3:05pm

Session 4: Genomics and Algorithms

Chair: Justin Borevitz

3:05pm-4:15pm

Gavin Huttley

Australian National University

Graph Algorithms And Genomics

3:05pm-3:20pm

Vijini Mallawaarachchi

Flinders University

Metagenomic Binning Using Assembly Graphs

3:20pm-3:30pm

Anuradha Wickramarachchi

CSIRO

Metagenomics Binning For Long Reads

3:30pm-3:40pm

Hansheng Xue

Australian National University

Improving Metagenomic Contigs Binning By Encoding Assembled Fragments Graph With Heterophilous Constraints

3:40pm-3:50pm

Dongbo Bu*

Chinese Academic of Sciences

AIA --- AI-Aided Algorithm Design

3:50pm-4:00pm

Benjamin Schwessinger

Australian National University

Yu Lin And My Wonders

4:00pm-4:10pm

Minh Bui, Arthur Georges, Dan Andrews, Vijini Mallawaarachchi

Panel Dialogue: Emerging Trend and Collaboration Challenges that the Computing and Biology Researchers

Chair: Lexing Xie

4:15pm-4:45pm

Minh Bui

Australian National University

Final Reflection and Closing Remarks

4:45pm

Workshop Venue

The Shine Dome


Ian Wark Theatre
15 Gordon Street
Acton ACT 2601

Confirmed Participants

Kirat Alreja

Australian National University

 

James Bickerstaff

CSIRO

 

Justin Borevitz

Australian National University

 

Minh Bui

Australian National University

 

Carina Cai

Australian National University

 

Caitlin Cherryh

Australian National University

 

Piyumal Demotte

Australian National University

 

Haiqi Dong

Australian National University

 

Eduardo Eyras

Australian National University

 

Tadele Gashayie

Australian National University

 

Arthur Georges

University of Canberra

 

Yuvaraj Ghodke

Australian National University

 

Kosar Hooshmand

Australian National University

 

Lara Horvat

Australian National University

 

Gavin Huttley

Australian National University

 

Rob Lanfear

Australian National University

 

Jiajia Li

Australian National University

 

Sichao Li

Australian National University

 

Danyang Li

Australian National University

 

Jia Liu

Australian National University

 

Xiaowen Liu*

Tulane University

 

Matthew Macaulay

The University of Technology Sydney

 

Vijini Mallawaarachchi

Flinders University

 

Robert McArthur

Australian National University

 

Lachlan McGinness

Australian National University

 

Jinghua Mu

Australian National University

 

Ahad N. Zehmakan

Australian National University

 

Teresa Neeman

Australian National University

 

Siwanon Paphatmethin

Australian National University

 

Hardip Patel

Australian National University

 

Pavel Pevzner*

University of California, San Diego

 

Porntipa Poonpolsub

Australian National University

 

Zhangcheng Qiang

Australian National University

 

Liang Qiao*

Fudan University

 

Vaibhav Rajan*

National University of Singapore

 

Priya Rao

Australian National University

 

Huaiyan Ren

Australian National University

 

Benjamin Schwessinger

Australian National University

 

Aditya Sethi

Australian National University

 

Mingfu Shao*

Penn State University

 

Emi Tanaka

Australian National University

 

Nuren Tasneem

Australian National University

 

Putter Tiatragul

Australian National University

 

Jonathan Ting

Australian National University

 

Yuan-Sen Ting

Australian National University

 

Anuradha Wickramarachchi

CSIRO

 

Thomas Wong

Australian National University

 

Lexing Xie

Australian National University

 

Hansheng Xue

Australian National University

 

Wenjing Xue

Australian National University

 

Jiaxin Yuan

Australian National University

 

Xiaonan Zhang

University of Canberra

 

Xiuwei Zhang*

Georgia Institute of Technology

 

Yanlin Zhang*

McGill University

 

Liang Zheng

Australian National University

 

Ruibiao Zhu

Australian National University

 

Zixiong Zhuang

Australian National University

 

Photo Gallery

Meet The Organizers

Minh Bui

Australian National University

Quanling Deng

Australian National University

Yuan-Sen Ting

Australian National University

Lexing Xie

Australian National University

Hansheng Xue

Australian National University

Liang Zheng

Australian National University

Get In Touch

We want to hear from you.