Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco - Andrian Yang, Abhinav Kishore, Benjamin Phipps, Joshua WK Ho

scDC: Single cell differential composition analysis - Yue Cao, Yingxin Lin, John T. Ormerod, Pengyi Yang, Jean Yang, Kitty K. Lo

FlowGrid: A python package for fast clustering for millions of single cell transcriptomic profiles - Xiunan Fang, Joshua W. K. Ho

Single-cell RNA-sequencing of Differentiating iPS Cells Reveals Dynamic Genetic Effects on Gene Expression - Anna SE Cuomo*, Daniel D Seaton*, Davis J. McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew Knights, Kedar Nath Natarajan, HipSci Consortium, Ludovic Vallier, John C Marioni, Mariya Chhatriwala, Oliver Stegle*

Discovery of Inflammatory Bowel Disease-associated miRNAs using a Novel Bipartite Clustering Approach - MD ALTAFUL AMIN, Mohammad Bozlul Karim, Pingzhao Hu, Naoaki ONO, Shigehiko Kanaya

Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces - Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Xiaoying Gao, Jinyan Li

Sierra: Discovery of differential transcript usage from polyA captured single-cell RNA-seq data - Ralph Patrick, David Humphreys, Joshua W. K. Ho, Alicia Oshlack, Richard Harvey, Kitty Lo

Janis: A Python framework for Portable Pipelines - Michael Franklin, Richard Lupat, Jiaan Yu, Evan Thomas, Daniel Park, Bernard Pope, Tony Papenfuss, Jason Li

DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. - Niraj Thapa, Meenal Chaudhari, Sean McManus, Kaushik Roy, Robert H Newman, Hiroto Saigo, Dukka KC

Toot-T: Discrimination of transport proteins from non-transport proteins - Munira Alballa, Gregory Butler

Predicting, exploring, and synthesising ancestral sequences using Graphical Representation of Ancestral Sequence Predictions (GRASP) - Gabriel Foley, Ariane Mora, Mikael Bodén

Integration of transcriptomics data in a genome-scale metabolic model to decipher the mechanisms of polymyxin resistance in Acinetobacter baumannii - Jinxin Zhao, Yan Zhu, Tony Velkov, Jian Li

Nanopore base-calling from a perspective of instance segmentation - Yao-zhong Zhang; Arda Akdemir; Georg Tremmel; Seiya Imoto; Satoru Miyano; Tetsuo Shibuya; Rui Yamaguchi

gencore: An Efficient Tool to Generate Consensus Reads for Error Suppressing and Duplicate Removing of NGS data - (Puxue Qiao as presenter), Shifu Chen, Yanqing Zhou, Yaru Chen, Tanxiao Huang, Wenting Liao, Yun Xu, Zhicheng Li, Jia Gu

Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data - Qing Wang, Vassiliki Kotoula, Pei-Chen Hsu, Kyriaki Papadopoulou, Joshua W.K. Ho, George Fountzilas, Eleni Giannoulatou

Enhanced prediction of the origin of genomic reads with logistic regression for circulating tumor cells (CTC) from patient-derived xenografts (PDX) - Goknur Giner, Delphine Merino, Jean Berthelet, Bhupinder Pal, Aaron T. L. Lun, Sepideh Foroutan, Melissa J. Davis, Jane E. Visvader, Gordon K. Smyth

Doing quantile normalization right - Yaxing Zhao, Limsoon Wong, Wilson Wen Bin Goh

Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation - Hao-Chun Chang, Hsuan-Cheng Huang, Hsueh-Fen Juan, Chia-Lang Hsu

Using tRNA-seq, RNA-seq, and proteomics data analysis to investigate the importance of tRNA modifications – A case study of tRNA Guanine and Inosine-N1-methyltransferase TRM5 in Arabidopsis thaliana. - Pei Qin (Sabrina) Ng, Qianqian Guo, Shanshan Shi, Diwen Fan, Jun Li, Jing Zhao, Hua Wang, Rakesh David, Parul Mittal, Trung Do, Ralph Bock, Ming Zhao, Wenbin Zhou, Iain R. Searle

A Bayesian hierarchical model for detecting differential gene expression distributions for RNA-seq data - Aedan G K Roberts, Daniel R Catchpoole, Paul J Kennedy

Rearrangement analysis of multiple bacterial genomes - Mehwish Noureen, Ipputa Tada, Takeshi Kawashima, Masanori Arita

SVEnsemble: an algorithm for ensemble structural variant calling using re-evaluated quality scores via probabilistic random forest - Ruining Dong, Justin Bedo, Anthony T Papenfuss

Methods for Transposable Element Insertion Detection - Adam Ewing

Unscrambling the tumor genome via integrated analysis of structural variation and copy number - Daniel L Cameron, Charles Shale, Jonathan Baber, Anthony T Papenfuss, Peter Priestly

PreNet: Predictive Network from ATAC-seq data - Nazmus Salehin, Patrick Tam and Pierre Osteil

Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast - Tzu-Hsien Yang

Efficient computation of stochastic cell-size transient dynamics - Cesar Augusto Nieto-Acuna, Cesar Augusto Vargas-Garcia, Abhyudai Singh, Juan Manuel Pedraza-Leal

3D-Cardiomics: A spatial transcriptional atlas of the mammalian heart - Monika Mohenska, Nathalia M. Tan, Alex Tokolyi, Milena B. Furtado, Mauro W. Costa, Andrew J. Perry, Jessica Hatwell-Humble, Jan M. Ruijter, Hieu T. Nim, Susan K. Nilsson, David R. Powell, Nadia A. Rosenthal, Fernando J. Rossello, Mirana Ramialison, Jose M. Polo

Hierarchical structural Component Model for Pathway analysis of Common Variants - Nan Jiang, Sungyoung Lee, Taesung Park

Sketch distance-based clustering of chromosomes for large genome database compression - Tao Tang, Yuansheng Liu, Buzhong Zhang, Benyue Su, Jinyan Li

SpliceFinder: ab initio prediction of splice sites using convolutional neural network - Ruohan WANG, Zishuai Wang, Jianping Wang, Shuaicheng Li

Estimating telomere length from long read sequencing data. - Pablo Galaviz, Michael Lee, Ted Wong, Martin Smith, Erdahl T. Teber, Hilda A. Pickett

DeepTRIAGE: Interpretable and Individualised Biomarker Scores using Attention Mechanism for the Classification of Breast Cancer Sub-types - Adham Beykikhoshk, Thomas P. Quinn, Samuel C. Lee, Truyen Tran, Svetha Venkatesh

Cancer Minority Report: Somatic changes in blood WGS predict future cancer - Mark Pinese, Paul Lacaze, Zoe McQuilten, Robyn Woods, John McNeil, David Thomas

Introme: Identifying atypical splice-altering mutations as drivers of high-risk paediatric cancer - Patricia Sullivan, Mark Pinese, Velimir Gayevskiy, Sarah Beecroft, Marie Wong, Chelsea Mayoh, Vanessa Tyrrell, Emily Oates, Mark Cowley

Genome-wide cell-free DNA fragmentation in patients with cancer - Stephen Cristiano, Alessandro Leal, Jillian Phallen, Jacob Fiksel, Vilmos Adleff, Daniel C. Bruhm, Sarah Østrup Jensen, Jamie E. Medina, Carolyn Hruban, James R. White, Doreen N. Palsgrove, Noushin Niknafs, Valsamo Anagnostou, Patrick Forde, Jarushka Naidoo, Kristen Marrone, Julie Brahmer, Brian D. Woodward, Hatim Husain, Karlijn L. van Rooijen, Mai-Britt Worm Ørntoft, Anders Husted Madsen, Cornelis J.H. van de Velde, Marcel Verheij, Annemieke Cats, Cornelis J.A. Punt, Geraldine R. Vink, Nicole C.T. van Grieken, Miriam Koopman, Remond J.A. Fijneman, Julia S. Johansen, Hans Jørgen Nielsen, Gerrit A. Meijer, Claus Lindbjerg Andersen, Robert B. Scharpf, Victor E. Velculescu

DeepMF: Deciphering the Latent Patterns in Omics Profiles with a Deep Learning Method - Lingxi Chen, Jiao Xu, Shuai Cheng Li

Dual Graph Convolutional Neural Network for Predicting Chemical Networks - Shonosuke Harada, Hirotaka Akita, Masashi Tsubaki, Yukino Baba, Ichigaku Takigawa, Yoshihiro Yamanishi, Hisashi Kashima

Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks - Rui Yin, Yu Zhang, Xinrui Zhou and Chee Keong Kwoh

ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning - Angel Ruiz-Rche, Akanksha Srivasava, Joel A. Ind, Ivan de la Rubi, Eduardo Eyras

Topological structure analysis of chromatin interaction networks - Juris Viksna, Gatis Melkus, Edgars Celms, Karlis Cerans, Karlis Freivalds, Paulis Kikusts, Lelde Lace, Martins Opmanis, Darta Rituma, Peteris Rucevskis

Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer - Chai-Jin Lee, Hongryul Ahn, Dabin Jeong, Minwoo Pak, Ji Hwan Moon, Sun Kim

Untangling chromatin structure from cell cycle in B cells with gene orientated Hi-C analysis - Hannah Coughlan, WingFuk Chan, Christine Keenan, Tim Johanson, Rhys Allan, Gordon Smyth

An epigenetic clock for human skeletal muscle - Sarah Voisin, Harvey NR, Haupt LM, Griffiths LR, Ashton KJ, Coffey VG, Doering TM, Thompson JM, Cedernaes J, Benedict C, Lindholm ME, Craig JM, Rowland DS, Sharples AP, Horvath S, Eynon N

Identifying miRNA synergism using multiple-intervention causal inference - Junpeng Zhang, Vu Viet Hoang Pham, Lin Liu, Taosheng Xu, Buu Truong, Jiuyong Li, Nini Rao, Thuc Duy Le

iPseU-NCP: Identifying RNA Pseudouridine sites using Random Forest and NCP-encoded features - Thanh-Hoang Nguyen-Vo, Quang Hong Nguyen, Trang Thi Thu Do, Thien-Ngan Nguyen, Susanto Rahardja, Binh Phu Nguyen

Understanding the in vivo function of A-to-I RNA editing by ADARs - Xining Li, Alistair Chalk, Carl Walkley

Nascent transcriptome analysis to characterise mRNA export - Enid Yi Ni Lam, Ewa Michalaka, Ashley Anderson, Dean Tyler, Toby Williams, Kirsty Carey, Vicky Tan, Amber Rucinski, Vihandha Wickramasinghe, Marcus Bantscheff, Paola Grandi, Rab Prinjha, Sarah-Jane Dawson, Mark Dawson

Stably expressed genes in single-cell RNA-sequencing - Julie Deeke and Johann Gagnon-Bartsch

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis - Thomas Andrew Geddes, Taiyun Kim, Lihao Nan, James Geoffrey Burchfield, Jean Yee Hwa Yang, Dacheng Tao, Pengyi Yang

Supervised deconvolution of population heterogeneities in single cell RNA-seq via similarity-based embeddings - Soroor Hediyeh-zadeh, Yi Xie, Melissa J Davis

Sample size estimation and multiscale classification of cells using single and multiple references. - Yingxin Lin, Yue Cao, Hani Jieun Kim, Agus Salim, Terence P. Speed, David Lin, Pengyi Yang, Jean Yee Hwa Yang

schex avoids overplotting for large single cell RNA-sequencing datasets - Saskia Freytag, Ryan Lister

LEMON: A Method to Construct the Local Strains at Horizontal Gene Transfer Sites in Gut Metagenomics - Chen Li, Yiqi Jiang, ShuaiCheng Li

Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome - Vuong Le, Thomas P. Quinn, Truyen Tran, Svetha Venkatesh

Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer - Qing Wang, Jianzhong Ye, Daiqiong Fang, Longxian Lv, Wenrui Wu, Ding Shi, Yating Li, Liya Yang, Xiaoyuan Bian, Jingjing Wu, Xianwan Jiang, Kaicen Wang, Qiangqiang Wang, Mark P. Hodson, Loïc M. Thibaut, Joshua W.K. Ho, Eleni Giannoulatou, Lanjuan Li

Deep Analysis and Optimization of CARD Antibiotic Resistance Gene Discovery Models - Haobin Yao, Siu-Ming Yiu

Evaluation of experimental protocols for shotgun whole-genome metagenomic discovery of antibiotic resistant genes - Ken Hung-On Yu, Xiunan Fang, Haobin Yao, Bond Ng, Tak Kwan Leung, Ling-Ling Wang, Chi Ho Lin, Agnes Sze Wah Chan, Wai Keung Leung, Suet Yi Leung, Joshua W. K. Ho

Model-based cell clustering and population tracking for time-series flow cytometry data - Kodai Minoura, Ko Abe, Yuka Maeda, Hiroyoshi Nishikawa, Teppei Shimamura

Integrative subspace clustering by common and specific decomposition for cancer subtype identification - Yin Guo, Huiran Li, Menglan Cai, Limin Li

iProDNA-CapsNet: Predicting Protein-DNA Binding Residues using Capsule Neural Network - Binh Phu Nguyen, Quang Hong Nguyen, Giang-Nam Doan-Ngoc, Thanh-Hoang Nguyen-Vo, Susanto Rahardja

Venn-diaNet : Venn diagram based network propagation analysis framework for comparing multiple biological experiments - Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee, Sun Kim

Integrating multiplex immunohistochemistry with gene expression to study the immune microenvironment of prostate cancer - Anna S. Trigos, Anu Pasam, Patricia Banks, Simon Keam, Heather Thorne, Catherine Mitchell, David Clouston, Declan Murphy, Damien Bolton, Phil Darcy, Ygal Haupt, Scot Williams, David Goode, Paul Neeson, Shahneen Sandhu

wtest: an integrated R package for genetic epistasis testing - Rui Sun, Xiaoxuan Xia, Ka Chun Chong, Benny Chung-Ying Zee, William Ka Kei Wu, Maggie Haitian Wang

Fast and accurate microRNA search using CNN - Xubo Tang, Yanni Sun

Benchmarking state-of-the-art genome assembly methods for eukaryotic genomes - Dean C Southwood, Rahul V Rane, Siu F Lee, John G Oakeshott, Shoba Ranganathan

Optimal filtering of rare alleles enhances scores of intolerance to genetic variation - Loïc M. Thibaut, Eleni Giannoulatou

Integrative Approaches in Functional Genomics to Identify Genetic Dependencies in Paediatric Cancer - Claire Sun , Duncan Crombie , Caroline Drinkwater, Dhanya Sooraj , Gabrielle Bradshaw , Claire Shi , Sarah Parackal, Dasun Fernando, Naama Neeman, Bryan Williams, Daniel Gough, Peter Downie, Jason Cain, Ron Firestein