RECOMB-CG 2021 Program



        — All Times US Eastern Time;
        — The meeting starts at 7am in New York (USA), 1pm in Paris (France), and 7pm in Singapore
        — Virtual platform Instructions

        — Agenda on Day 1, Day 2 and Day 3; Schedule Download

        — R/H: Regular or highlight 20-min talks; Others are 10-min talks
        — Posters and Abstracts



        Day 1: Tuesday, September 21, 2021
6:30am – 7:00am WELCOME REMARKS
7:00am – 7:50am KEYNOTE TALK (Chair: Louxin Zhang)
Learning Tumor Phylogenies from Single-cell Sequencing Data
Niko Beerenwinkel
SHORT BREAK
8:00am – 8:40am Session 1: TALKS (Chair: Katharina Jahn)
(R) The Potential of Family-free Rearrangements Towards Gene Orthology Inference
Diego P. Rubert, Daniel Doerr and Marilia Braga
Peripheral Structures in Unlabelled Trees and Inference About Autopolyploids
Fatemeh Pouryahya and David Sankoff
Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis
Shu-Ting Cho, Hung-Jui Kung, Weijie Huang, Saskia Hogenhout and Chih-Horng Kuo
8:40am – 9:00am COFFEE CONNECT (via gather.town)
9:00am – 9:50am KEYNOTE TALK (Chair: Rohan Williams)
Exploring Archaic Introgression in Island Southeast Asia and New Guinea Using Introgressed Haplotypes
Guy Jacobs
SHORT BREAK
10:00am – 10:40am Session 2: TALKS (Chair: Vaibhav Rajan)
(H) Bacteriophage Classification for Assembled Contigs Using Graph Convolutional Network
Jiayu Shang, Jingzhe Jiang, Yanni Sun
Novel Adversarial Autoencoders to Simulate Human Genomic Data for Clinical Research
Callum Burnard, William Ritchie and Alban Mancheron
Comparative Genomics of Priestia Bacteria Isolated from the Air
Sam Spence, Stephan Schuster and Hie Lim Kim
10:40am – 11:00am COFFEE CONNECT (via gather.town)
11:00am – 11:40am Session 3: TALKS (Chair: Siavash Mirarab)
(R) Colorful Orthology Clustering In Bounded-Degree Similarity Graphs
Alitzel López Sánchez and Manuel Lafond
(R) Comparing the Topology of Phylogenetic Network Generators
Remie Janssen and Pengyu Liu




        Day 2: Wednesday, September 22, 2021
7:00am – 7:50am KEYNOTE TALK (Chair: Marilia Braga)
A Symmetry-inclusive Algebraic Approach to Genome Rearrangement
Venta Terauds
SHORT BREAK
8:00am – 8:40am Session 4: TALKS (Chair: Hie Lim Kim)
(R) Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using M. tuberculosis Isolates
Afif Elghraoui, Siavash Mirarab, Krister Swenson and Faramarz Valafar
The Role of Potential Mobile Units in Phytoplasma Genome Evolution
Ching-Ting Huang, Shu-Ting Cho, Choon-Meng Tan, J.-R. Li, Y.-Y. Chien, Y.-C. Chiu, J.-Y. Yang and C.-H. Kuo
Accuracy of RACCROCHE in Reconstructing Chromosomal Gene Order of Early Plant Ancestors
Qiaoji Xu, James H. Leebens-Mack, Lingling Jin and David Sankoff
8:40am – 9:00am COFFEE CONNECT (via gather.town)
9:00am – 9:40am Session 5: TALKS (Chair: Manuel Lafond)
(R) Small Parsimony for Natural Genomes in the DCJ-Indel Model
Daniel Doerr and Cedric Chauve
Where Do Lost Genes Go?
Zhe Yu, David Sankoff and Chunfang Zheng
Trees Versus Traits for Ancestral Genome Reconstruction
Yuting Xiao, Maureen Stolzer and Dannie Durand
SHORT BREAK
9:50am – 10:40am KEYNOTE TALK (Chair: Dannie Durand)
Real-time Tracking of SARS-CoV-2 Spread and Evolution
Richard Neher
10:40am – 11:00am COFFEE CONNECT (via gather.town)
11:00am – 11:50am Session 6: TALKS (Chair: Mukul Bansal)
(R) BOPAL 2.0 and A Study of tRNA and rRNA Gene Evolution in Clostridium
Meghan Chua, Anthony Tan and Olivier Tremblay-Savard
Markov chain Monte Carlo Simulation of Domain Architecture Evolution
Maureen Stolzer, Alejandro Garces and Dannie Durand
Structural Variant Identification with Various Types of Genomic Data
Clarence Malcolm Todd, Kevin Koh, David Sankoff, Isobel Parkin and Lingling Jin
Multiple Spliced Alignment for Transcript Evolution Estimation and Gene Models Prediction
Safa Jammali, Abigaïl Djossou, Aïda Ouangraoua




        Day 3: Thursday, September 23, 2021
7:00am – 7:50am KEYNOTE TALK (Chair: Swaine Chen)
The Developmental Origin and Evolution of A Novel Complex Trait: Butterfly Eyespots
Antonia Monteiro
SHORT BREAK
8:00am – 8:40am Session 7: TALKS (Chair: Giltae Song)
(R) Population-specific Adaptation to Malaria Infection in Endemic Regions of Asia
Elena S Gusareva, Paolo A. Lorenzini, Nurul A. B. Ramli, Amit Gourav Ghosh and Hie Lim Kim
Detecting Transposable Elements in Plant Genomes
Shivani Sehrawat and Lingling Jin
Branch Mutation Rates and Selection Give Insights on Gene Family Trees: N-methyltransferases, FAD2 Enzymes and Terpenes
Daniella Santos Munoz and David Sankoff
8:40am – 9:00am COFFEE CONNECT (via gather.town)
9:00am – 9:50am Session 8: TALKS (Chair: Aida Ouangraoua)
(R) Involving Repetitive Regions in Scaffolding Improvement
Quentin Delorme, Remy Costa, Yasmine Mansour, Anna-Sophie Fiston-Lavier and Annie Chateau
(R) Evidence for Exon Shuffling is Sensitive to Model Choice
Xiaoyue Cui, Maureen Stolzer and Dannie Durand
Recovery of Metagenome-assembled Genomes from Long Read Metagenome Data Using Compositional Analysis of
Contig K-mer Frequencies
Rohan Williams, Krithika Arumugam, Peerada Prommeenate, M. Haryono, I. Bessarab, Y. Ipsen,
B. Suraraksa and V. Kongduan
SHORT BREAK
10:00am – 11:10am Session 9: TALKS (Chair: Annie Chateau)
(R) The Monoploid Chromosome Complement of Reconstructed Ancestral Genomes in A Phylogeny
Qiaoji Xu, Xiomeng Zhang, Yue Zhang, Chunfang Zheng, Jim Leebens-Mack, Lingling Jin and David Sankoff
(R) DNN-BOOST: Somatic Mutation Identification of Tumor-only Whole-exome Sequencing Data Using Deep Neural
Network and Xgboost
Firda Aminy Maruf, Rian Pratama and Giltae Song
(R) Incorporating Intergenic Regions into Reversal and Transposition Distances with Indels
Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias and Zanoni Dias
Evolutionarily Conserved Regions of THAP9 Transposase Reveal New Motifs for Subcellular Localization and
Post-translational Modification
Richa Rashmi, Chandan Nandi and Sharmishtha Majumdar
11:10am – 11:15am CLOSING REMARKS












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