GIW/ ABACBS 2019 30TH INTERNATIONAL CONFERENCE ON GENOME INFORMATICS & AUSTRALIAN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY SOCIETY ANNUAL CONFERENCE WELCOME WELCOME 2019 marks a very special time in the history of the analysis, precision medicine, single-cell analytics, Australasian Bioinformatics and Computational Biology non-human, agricultural, environmental and microbial Society (ABACBS). This is the first time that the annual genomics, proteomics and metabolomics and finally, ABACBS conference has partnered the International methods development and reproducibility research. Conference on Genome Informatics (GIW). This year, We have eight international and four national keynote these two conferences will join forces to bring together presenters, in addition to 36 presentations from GIW, members from all over Australia, the Asia-Pacific region selected from peer-reviewed full paper submissions and and the world to enjoy the opportunity to interact and 32 presentations from ABACBS selected from peer- hear fantastic stories about genomics, bioinformatics reviewed abstracts. We look forward to 12 exciting and computational biology research with an emphasis fast forward talks and two dynamic posters sessions on how advances in computational with 170 posters. and statistical techniques are applied ABACBS to solve important biological and ABACBS was founded in We wish to sincerely thank our biomedical problems. 2014 and represents over local organising committee, program 850 bioinformaticians committee chairs and representatives To keep pace with the growing and computational from the ABACBS and GIW communities biologists from across bioinformatics community, the who gave so much of their time to make Australia. Our members ABACBS conference is launching are a mix of students, this conference a reality. We are very parallel sessions as well as live academics, researchers, and grateful to all of our sponsors for their streaming of presentations. In addition professionals. The annual generous support of this conference, in to subsidising childcare at this year’s conference is one of the particular our gold sponsors, the NSW highlights for the society and conference, live streaming reflects our Department of Industry and Amazon scientific community for continued commitment to maximise face-to-face interactions. Web Services. opportunities for researchers in our vibrant community to attend our GIW On behalf of the local organising annual conference. The Genome Informatics committee, we look forward to Workshop (GIW) was first welcoming you to the beautiful campus held in Tokyo in 1990 and We would like to thank the continued annual workshops of Sydney University, on the traditional ABACBS and GIW program committee in Japan until 2000. Since lands of the Gadigal people of the Eora co-chairs who have organised an 2001, it has been renamed nation. We hope that you enjoy the outstanding program covering the as the international GIW conference, the social events and the conference, providing unique themes of genomics and integrative many wonders that Sydney has to offer. opportunities that bridge bioinformatics theory and experiments, academia and industry, and East and West. Prof Tony Papenfuss A/Prof Mark Cowley Prof Jean Yang Prof Shoba Prof Jinyan Li Peter MacCallum Children’s Cancer University of Ragnanathan University of Cancer Centre and Institute, ABACBS Sydney, ABACBS Macquarie University, Technology Walter Eliza Hall co-convenor co-convenor GIW co-convenor Sydney, Australia, Institute, ABACBS GIW co-convenor Conference Chair 1 GIW/ ABACBS 2019 SYDNEY AUSTRALIA ORGANISING COMMITTEE CONFERENCE CHAIR PROF. TONY PAPENFUSS CONFERENCE C0-CHAIRS PROF. JEAN YANG A/PROF. MARK COWLEY PROF. SHOBA RANGANATHAN PROF. JINYAN LI LOCAL ORGANISING COMMITTEE PROF. AARON DARLING DR. KITTY LO YINGXIN LIN DR. IGNATIUS PANG KATARINA STUART DR. NATALIE TWINE DR. SEBASTIAN KURSCHEID PROGRAM COMMITTEE DR. ELENI GIANNOULATOU DR. PENGYI YANG A/PROF. JOSHUA W. K. HO (CHAIR) A/PROF. KYUNG-AH SOHN A/PROF. JIANGNING SONG PROF. TATSUYA AKUTSU 2 GIW/ ABACBS 2019 SYDNEY AUSTRALIA MEMBERS OF THE FULL-LENGTH PAPERS PROGRAM COMMITTEE (PC) BINH NGUYEN LING-YUN WU JOSHUA W. K. HO KWANGSIK NHO WEI WU KYU-BAEK HWANG EUNOK PAEK JIANMIN WU WATARU IWASAKI LAXMI PARIDA JINBO XU JESPER JANSSON TAESUNG PARK YOSHIHIRO YAMANISHI ASIF JAVED DAECHAN PARK JINN-MOON YANG HYUN-HWAN JEONG REBECCA POULOS PENGYI YANG JE-GUN JOUNG GAJENDRA PAL SINGH WANG YANG SHIMIZU KANA RAGHAVA SUNGROH YOON SUN KIM SHOBA RANGANATHAN AIDONG ZHANG DOKYOON KIM MARIE-FRANCE SAGOT LOUXIN ZHANG SARAH KUMMERFELD HIROTO SAIGO SHUQIN ZHANG THUC DUY LE JEAN-MARC SCHWARTZ JINGHUI ZHANG DOHEON LEE TETSUO SHIBUYA ZIDING ZHANG EUNJUNG ALICE LEE HYUNJUNG SHIN YAOQI ZHOU HYUNJU LEE SHIRLEY SIU SHANDAR AHMAD YOUNGHEE LEE KYUNG-AH SOHN TATSUYA AKUTSU SAEL LEE JIANGNING SONG ROLF BACKOFEN MING LI YANNI SUN NOURI BEN ZAKOUR WEI LI WING-KIN SUNG MIKAEL BODEN TINGTING LI CLARA TANG HONGMIN CAI FUYI LI SONIKA TYAGI EVA CHAN JINYAN LI FATEMEH VAFAEE PHOEBE CHEN HEE WOONG LIM ALFONSO VALENCIA LUONAN CHEN BING LIU MAGGIE WANG WAI-KI CHING TAO LIU RUI-SHENG WANG YANG DAI RUIBANG LUO YINGYING WEI NADIA DAVIDSON JESSICA MAR ROHAN WILLIAMS MELISSA DAVIS HIDEO MATSUDA HONG-HEE WON SANAZ FIROUZI YOUNG JI NA EMILY WONG MATTHIAS FUTSCHIK JOSE NACHER KOON HO WONG SHILA GHAZANFAR KA-LOK NG LIMSOON WONG MICHAEL GROMIHA 3 GIW/ ABACBS 2019 SYDNEY AUSTRALIA INTERNATIONAL SPEAKERS RAFAEL IRIZARRY - JOINT PLENARY Professor Irizarry’s work has focused on applications in Genomics. In particular, he has worked on the analysis and signal processing of high-throughput data. He has distinguished himself by disseminating his statistical methodology as open source software shared through the Bioconductor Project, a leading open source and open development software project for the analysis of high-throughput genomic data. His widely downloaded software tools have helped him become one of the most highly cited scientists in his field. Although Professor Irizarry’s focus has been in genomics, he is an applied statistician generally interested in read-world problems. During his career he as co-authored papers on a variety of topics including musical sound, infectious diseases, circadian patterns in health, fetal health monitoring, and estimating the effects of Hurricane María in Puerto Rico. MONA SINGH Prof. Mona Singh’s research is in computational molecular biology, as well as its interface with machine learning and algorithms. Her group is particularly interested in predicting specificity in protein interactions and uncovering how molecular interactions and networks vary across context, organisms and individuals. Mona leverages high-throughput biological datasets in order to develop data-driven algorithms for predicting protein interactions and specificity; foruncovering protein functions via sequences and structures, and for analysing biological networks in order to uncover cellular organization, function, and pathways. JÜRGEN COX Jürgen Cox is a research group leader at the Max Planck Institute for Biochemistry in Martinsried where he heads the Lab for Computational Systems Biochemistry. He received his PhD in physics at the Massachusetts Institute of Technology and has since developed MaxQuant, a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. Dr. Cox is the author of numerous peer reviewed publications in the field of data analysis in mass spectrometry and quantitative proteomics. JOHN MARIONI Dr John Marioni’s group use computational approaches to understand the molecular mechanisms that underlie cell fate decisions. Since cell fate decisions are ultimately made at the single-cell level, this requires assaying molecular characteristics of individual cells. The field of single-cell biology has revolutionised our ability to make such measurements, especially in the area of single-cell transcriptomics. John’s group has developed cutting-edge computational methods in this domain and has applied them, with outstanding collaborators, to study cell fate decisions in a variety of contexts, focussing especially on early mammalian development. 4 GIW/ ABACBS 2019 SYDNEY AUSTRALIA INTERNATIONAL SPEAKERS ELANA FERTIG Dr. Fertig runs a hybrid computational and experimental lab in the systems biology of cancer and therapeutic response. Her wet lab develops time course models of therapeutic resistance and performs single cell technology development. Her computational methods blend mathematical modeling and artificial intelligence to determine the biomarkers and molecular mechanisms of therapeutic resistance from multi-platform genomics data. These techniques have broad applicability beyond her resistance models, including notably to the analysis of clinical biospecimens, developmental biology, and neuroscience. JASON WONG Dr Jason Wong is an Associate Professor at the University of Hong Kong. He obtained is B.Sc from the University of Sydney and D.Phil from the University of Oxford. His research is in the field of cancer genomics. He has a particular interest in the study of mutational processes in cancer with a focus on understanding the interactions between DNA damage, repair and epigenetic mechanisms in the human genome. His research leverages large cancer genomics datasets making use of computational and statistical methods to uncover novel mutational processes in cancer. He is also interested in the study of the impact of somatic mutations in the non-coding regions of cancer genomes such as the role