Biography

I am an early career postdoctoral research fellow in Bioinformatics and Method Development. I am interested in exploring emerging technologies such as spatial transcriptomics, long-reads and single-cell to answer important biological questions. I have been in the field of Bioinformatics for more than 10 years. I thoroughly enjoy challenges I face as a Bioinformatics scientist and learning to solve problems in analysing high-throughput data in a collaborative environment. Other than research, I love participating in extra-curricular activities. Currently I am in the executive board of the Postdoctoral Association of Australian Regenerative Medicine Institute (ARMI) at Monash University. While I am not at work, I am a swimmer, a hiker, a daughter of two extraordinary parents, a loving (hopefully!) wife and a proud mother of a wonderful boy and a girl.

Selected Publications

• Amarasinghe, S., Su, S., Dong, X. et al. (2020) Opportunities and challenges in long-read sequencing data analysis. Genome Biol 21, 30 (2020). https://doi.org/10.1186/s13059-020-1935-5

• Amarasinghe S., Watson-Haigh N.S., Byrt C., James R., Qiu J., Berkowitz O., Whelan J., Roy, S.J., Gilliham M., Baumann U. (2019) Transcriptional variation is associated with differences in shoot sodium accumulation in distinct barley varieties. Environmental and Experimental Biology. DOI: 10.1016/j.envexpbot.2019.103812

• Amarasinghe S., Watson-Haigh N.S., Gilliham M., Roy, S.J., Baumann U. (2016) The evolutionary origin of CIPK16: A gene involved in enhanced salt tolerance, Molecular Phylogenetics and Evolution DOI:10.1016/j.ympev.2016.03.031

• Amarasinghe S., Kathriarachchi H., and Udagama P. (2014) Conserved Regions of Plasmodium Vivax Potential Vaccine Candidate Antigens in Sri Lanka: Conscious In silico Analysis of Prospective Conformational Epitope Regions Asian Pacific Journal of Tropical Medicine. DOI: 10.1016/S1995-7645(14)60146-2

• Amarasinghe S., Watson-Haigh N.S., Gilliham M., Roy, S.J., Baumann U. (In Prep.) AtCIPK16 Mediates Salt Stress Through Phytohormones and Transcription Factors; (to be submitted to Environmental and Experimental Biology)

• Dias S., Amarasinghe S., Premerathne H. P., Kathriarachchi H., Udagama P., Escalante A.A. (In Prep.) Combined Analysis of the Genetic Diversity of CSP, MSP-1, MSP-3, AMA-1 and DBP Vaccine Candidate Antigens of Plasmodium vivax in Sri Lanka; (to be submitted to Elsevier Vaccine)

I have developed the long-read-tools.org

Improved Bioconductor/scPipe (Tian et al., 2018) to be able to process scATAC-Seq data

Selected Achievements

• Dean’s Commendation for Thesis Excellence (September 2018)

• Full fee scholarship from the University of Adelaide and ACPFG PhD scholarship, 2014

• The conference travel scholarship to attend BioInfoSummer 2014 in Melbourne, Australia

• Merit Award by the National Research Council, Sri Lanka for research paper published in Asian Pacific Journal of Tropical Medicine 10/2014; 7(12):832-840. DOI: 10.1016/S1995-7645(14)60146-2

• Best Science Student, Haverstock Secondary School, London, UK, 2000

• Proficiency prize for the exhibit in the Science section; science and mathematics exhibition, Sirimavo Bandaranaike Vidyalaya, 1997

• Proficiency prize for the exhibit in the Social Studies section; science and mathematics exhibition, Sirimavo Bandaranaike Vidyalaya, 1997

• Prize for 8A’s at G.C.E. O/L examination, Annual Prize Giving, Sirimavo Bandaranaika Vidyalaya, 2002

• Subject Prize (Buddhism), Annual Prize Giving, Sirimavo Bandaranaika Vidyalaya, 1998

• Class Prize for Grade 4, Annual Prize Giving, Sirimavo Bandaranaika Vidyalaya, 1995

• Merit for Proficiency in Grade 2, Annual Prize Giving, Sirimavo Bandaranaika Vidyalaya, 1993

Selected Conferences

• AGTA 2019 (presentation title: Long Reads for scATAC-seq), Pullman Albert Park, Melbourne

• Nanopore Day 2019 Melbourne, University of Melbourne

• Oz-single cell 2019, University of Melbourne, Melbourne

• Bioinfosummer 2016 (presentation title: Linking Transcriptome of Arabidopsis thaliana CIPK16 Transgenics with the Response to Initial Stages of Salt Stress), SAHMRI, Adelaide

• Joint Research Meeting 2016, Australian Centre for Plant Functional Genomics, University of Adelaide, Adelaide

• Combine student symposium 2015, Charles Perkins Centre, The University of Sydney

• ABACBS 2015, Charles Perkins Centre, The University of Sydney

• Bioinfosummer 2014 (presentation title: Narrowing Down on CIPK16 Orthologues: A Gene Involved in Enhanced Salt Tolerance), Clayton campus, Monash University, Melbourne

Selected Oral Presentations:

• Amarasinghe S., Tian L., Paoli-Iseppi R.E., Clark M.B., Jabbari J.S., Ritchie M.E. (2019) Long Reads for scATAC-seq, AGTA, Melbourne, 7-9th October 2019, Pullman Melbourne Albert Park

• Amarasinghe S., Kathriarachchi H., and Udagama P. (2012). Predicting the conformational Epitope Regions of Potential Asexual Erythrocytic Stage Vaccine Candidate Antigens of Plasmodium vivax using Bioinformatics Tools, Proceedings of the 6th Biennial Scientific Sessions of Allergy and Immunology Society of Sri Lanka (in collaboration with National Science Foundation), 14-15 June 2012, Medical Research Institute, Colombo

Selected Posters Presentations

• Amarasinghe S., Watson-Haigh N.S., Gilliham M., Roy, S.J., Baumann U. (2014). Narrowing Down On CIPK16 Orthologues: A Gene Involved In Enhanced Salt Tolerance. BioinfoSummer 2014 (Monash University, Clayton Campus, Melbourne, Australia)

Leadership Development Conferences

• Local: National Leader’s Development Seminar, Sri Lanka (2009. 2010, 2011)

• Overseas:

  National Leader’s Development Summit, Singapore (2009): Representing Sri Lanka

  UNLEASH, Leader’s Seminar, Malaysia (2011): Representing Sri Lanka

Professional Development, Office Bearing in Organizations and Societies

• Volunteered for a community engagement event of WEHI, “Art of Science”, September 2019

• Executive committee (Professional Development), Postdoctoral Association - Walter and Eliza Hall Institute (2018)

• Facilitator for the hands-on R workshop, WEHI, October 2018

• South Australia representative of COMBINE (a student-run Australian organisation for researchers in computational biology, bioinformatics, and related fields) (2017)

• Executive committee member of AgPoGs (currently known as P.A.W.S) – University of Adelaide (2016)

• Executive Leadership Body member of AIESEC Organization for consecutive 2 years (2010-2012)

• Member of Botanical Society, University of Colombo (2010-2011)

• The Editor of Photographic Society 2004/05, Sirimavo Bandaranaike Vidyalaya, Colombo 07

• The President, Computer Society 2004/05, Sirimavo Bandaranaike Vidyalaya, Colombo 07

Recreational Activities and Sports

• Member, University Tennis Team (Women, 2007/08), University of Colombo, Colombo 03

• Member, School Swimming Team, 2000-2005, Sirimavo Bandaranaike Vidyalaya, Colombo 07

• School Eastern Music orchestra, leading violin player, 2004/05, Sirimavo Bandaranaike Vidyalaya, Colombo 07

• The “Best Young Leader” award, CIMA awards Night, National Leader’s Development Seminar 2010, MIMT, Thulhiriya, Sri Lanka

• The “Best Organizing Committee” award for CDD 2010, CIMA awards Night, National Leader’s Development Seminar 2010, MIMT, Thulhiriya, Sri Lanka

• Inter-faculty sports meet (Tennis, women), 2008

• Bhathkande Sangeeth Exam, Lucknow, Class, Prathama in Violin Section, 2003

• Royal School of Music, Level II Violin, Merit, 2000

• Participation in School Swimming Competitions from 2000 to 2005

2019-2020 Masters in Bioinformatics Student: ‘Comprehensive benchmarking of scATAC-Seq data analysis tools’, supervision under guidance by Prof Matthew E.Ritchie.

2022-2025 PhD Student: ‘Landscape of the growing limb’, co-supervisor for bioinformatics component (10%)

I was in-charge teaching assistant for the special students of Bioinformatics from 3rd and 4th years at the Department of Plant Sciences, Faculty of Science, University of Colombo 10/2011-02/2013

• Conducted practical tutoring sessions for the undergraduates of the department

• Was involved in tutoring for other levels of undergraduates in the department