Shanika L. Amarasinghe

Shanika L. Amarasinghe
Monash University (Australia) · Australian Regenerative Medicine Institute

PhD (Bioinformatics); B.Sc (Hon's) in Bioinformatics; FBCS

About

14
Publications
5,101
Reads
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606
Citations
Citations since 2016
10 Research Items
605 Citations
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2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
Introduction
Shanika (a.k.a. Shani) is a bioinformatics postdoc with more than 10 years of experience. She is trained in analysing large next-generation sequencing data (e.g. single-cell, long-reads), identifying novel genetic variants, protein modelling and phylogenetic analysis. She is open for academic and professional collaborations and networks as an ECR in Australia.
Additional affiliations
September 2018 - June 2022
The Walter and Eliza Hall Institute of Medical Research
Position
  • Postdoctoral Research Fellow - Bioinformatics
Description
  • Joined as a part of Ritchie Laboratory (Epigenetics and Development Division). Working on single cell RNA-Seq, single-cell ATAC-Seq and long-read sequencing data and related tool development. We also work on benchmarking a dataset that can be used in analyzing newly developed single-cell and long-read data analysis tools. I have also guided multiple collaborations involving the analysis of high-throughput CRISPR-Cas9 genetic screen data.
April 2013 - March 2014
Faculty of Medicine, University of Colombo, Sri Lanka
Position
  • Scientist (Bioinformatics)
Description
  • Involved in first human genome analyzing and novel SNP calling from the aspects of bioinformatics. This was done using tools such as SAM, BWA and VCFTools. Created a genome/exome analyzing pipeline for HGU Created and maintained the HGU official website
October 2011 - February 2013
University of Colombo
Position
  • Research Assistant
Description
  • In-change TA for students from 3rd/4th year (Hons) in Bioinformatics Carried out hands on bioinformatics and molecular biology practicals for 3rd/4th year (Hons) students in Bioinformatics
Education
April 2014 - March 2017
University of Adelaide
Field of study
  • Bioinformatics
June 2007 - November 2011
University of Colombo
Field of study
  • Bioinformatics

Publications

Publications (14)
Article
Calcineurin B-like protein interacting protein kinases (CIPKs) are key regulators of pre-transcriptional and post-translational responses to abiotic stress. Arabidopsis thaliana CIPK16 (AtCIPK16) was identified from a forward genetic screen as a gene that mediates lower shoot salt accumulation and improved salinity tolerance in Arabidopsis and tran...
Article
Full-text available
Objective: Mapping and modeling of conformational B cell epitope regions of highly conserved and protective regions of three merozoite candidate vaccine proteins of Plasmodium vivax, i.e.Merozoite Surface Protein-1 (PvMSP-1), Apical Membrane Antigen -1 Domain II (PvAMA1-DII) and Region II of the Duffy Binding Protein (PvDBPII), and analyzing the im...
Conference Paper
Predicting the Conformational Epitope Regions of Potential Asexual Erythrocytic Stage Vaccine Candidate Antigens of Plasmodium vivax using Bioinformatics Tools Amarasinghe Shanika1, Kathriarachchi Hashendra1, Udagama Preethi2 1Department of Plant Sciences, 2Department of Zoology, Faculty of Science, University of Colombo, Cumarathunga Munidasa Mawa...
Article
MR1 is a highly conserved microbial immune-detection system in mammals. It captures vitamin B–related metabolite antigens from diverse microbes and presents them at the cell surface to stimulate MR1-restricted lymphocytes including mucosal-associated invariant T (MAIT) cells. MR1 presentation and MAIT cell recognition mediate homeostasis through ho...
Preprint
The current lack of benchmark datasets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and differential expression analysis workflows. Here, we present a benchmark experiment using two human lung adenocarcinoma cell lines that were each profiled in triplicate together with synthetic,...
Preprint
Full-text available
Hexanucleotide expansion mutations in C9ORF72 are a cause of familial amyotrophic lateral sclerosis. We previously reported that long arginine-rich dipeptide repeats (DPR), mimicking abnormal proteins expressed from the hexanucleotide expansion, caused translation stalling when expressed in cell culture models. Whether this stalling provides a mech...
Article
Full-text available
A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline ( FLAMES ) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved funct...
Article
Full-text available
Background: The data produced by long-read third-generation sequencers have unique characteristics compared to short-read sequencing data, often requiring tailored analysis tools for tasks ranging from quality control to downstream processing. The rapid growth in software that addresses these challenges for different genomics applications is diffi...
Preprint
Full-text available
Alternative splicing shapes the phenotype of cells in development and disease. Long-read RNA-sequencing recovers full-length transcripts but has limited throughput at the single-cell level. Here we developed single-cell full-length transcript sequencing by sampling (FLT-seq), together with the computational pipeline FLAMES to overcome these issues...
Preprint
Full-text available
Soil salinity causes large productivity losses for agriculture worldwide. Next-generation crops that can tolerate salt stress are required for the sustainability of global food production. Previous research in Arabidopsis thaliana aimed at uncovering novel factors underpinning improved plant salinity tolerance identified the protein kinase AtCIPK16...
Article
Full-text available
Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast pace of development of such tools can be overwhelming. To assist in the design and analysis of lon...
Article
Soil salinity causes large productivity losses for agriculture worldwide. Barley has been identified as one of the more salt tolerant staple crops compared to wheat and rice. Identification of genes and allelic variations underlying various salt tolerance mechanisms in barley will be a practical contribution towards the development of cereal lines...

Questions

Questions (2)
Question
Hi to the experts of RNA-Seq analysis,
I have this burning question of knowing your experience about following;
There is my favorite gene from Arabidopsis which I over-expressed in a Arabidopsis system in different controls and treatment conditions. I used LIMMA analysis pipeline to derive the differentially expressed gene lists (DEGs).
My question; is it possible that I not see the over-expressed gene in any of the contrasts I make (e.g. even in the contrast between transgenic control vs. wild-type control) ?
Thanks a lot for your comments in advance.
Shani.
Question
Can anyone please tell me how to find the genome sequence of Cleome spinosa or Cleome gynandra ?
I know Cleome spinosa is fully sequenced and that the assembly is available. I cannot seem to locate it.
Thank you very much.

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Cited By

Projects

Projects (2)
Project
Identification of the genetic variation that underlies the leaf Na+ accumulation differences in barley cultivars using RNA-Seq data for gene expression analysis and variant analysis
Project
Background: CBL interacting protein kinases (CIPKs) are key regulators of post-translational and pre-transcriptional responses to abiotic stresses. Many plant species have numerous forms of CIPKs (26 in Arabidopsis, 28 in poplar, 30 in rice) which appear to have very specific roles during abiotic stress. From a forward genetics screen we have previously identified AtCIPK16 as an important gene responsible for reduced shoot salt accumulation and improved salinity tolerance in Arabidopsis (Roy et al., 2013). Transgenic Arabidopsis, barley and wheat have all been shown to have improved salinity tolerance through enhanced salt exclusion from the shoot. The hypothesis for improved salinity tolerance is that the kinase is regulating the expression of genes in the nucleus and/or targeting ion transporters/channels on the plasma membrane. However, it is not clear whether cereals such as barley have an equivalent protein to AtCIPK16 which has a similar function or how this family of proteins evolved to have such a diverse function. Aims of the Project: 1. Understanding the evolutionary relationship of CIPK proteins in grasses in order to provide the biological importance of a functionally “similar” protein to CIPK16 in A. thaliana. 2. Understanding of the downstream regulatory network controlled by AtCIPK16 in Arabidopsis thaliana and Hordeum vulgare (barley). 3. Improve the current understanding of the functionality in the CBL-CIPK signaling pathway in context of barley.