Sameera D. Viswakula

Sameera D. Viswakula
University of Colombo · Department of Statistics

PhD (Genomic Biostatistics), MS (Statistics), BSc (Statistics special)

About

28
Publications
4,724
Reads
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115
Citations
Introduction
Strong background in probabilistic/statistical modeling and statistical computing using R, and C++. Hands on experience in handling NGS data using C++, Perl and Python languages, sequencing using Bowtie and manipulating using SRA/SAM Tools on Linux high performance computing clusters. Experience in developing new statistical frameworks to identify DNA – protein binding sites in ChIP-Seq data on UCSC Genome Browser and NCBI databases.
Additional affiliations
August 2011 - May 2015
Old Dominion University
Position
  • PhD

Publications

Publications (28)
Poster
Full-text available
This study aimed to develop and evaluate regression-based machine learning models for predicting and optimizing patient dose in chest X-ray examinations.
Article
Full-text available
Background The precise prediction of transcription factor binding sites (TFBSs) is pivotal for unraveling the gene regulatory networks underlying biological processes. While numerous tools have emerged for in silico TFBS prediction in recent years, the evolving landscape of computational biology necessitates thorough assessments of tool performance...
Preprint
Full-text available
Background The PIK3CA oncogene is one of the most mutated oncogenes in breast cancer, with ancestry-linked variations reported globally. The study aimed to discern the prevalence and prognostic role of PIK3CA mutations in Sri Lankan breast cancer patients for the first time, focusing on the correlation between somatic mutations and patient ancestry...
Article
Full-text available
Objective. The introduction of automatic tube current modulation (ATCM) has resulted in complex relationships between scanner parameters, patient body habitus, radiation dose, and image quality. ATCM adjusts tube current based on x-ray attenuation variations in the scan region, and overall patient dose depends on a combination of factors. This work...
Conference Paper
Full-text available
The precise prediction of transcription factor binding sites (TFBSs) is crucial for unravelling gene regulatory networks. Despite the emergence of in silico TFBS prediction tools, comprehensive evaluation of their performance remains limited. In this study, we assessed twelve widely used TFBS prediction tools and four de novo motif discovery tools...
Article
Full-text available
Objectives: Addressing the challenge of cost-effective asthma diagnosis amidst diverse symptom patterns among patients, this study aims to develop a machine learning-based asthma prediction tool for self-detection of asthma. Methods: Data from 6,665 participants in the Sri Lanka Health and Ageing Study (2018-2019) are used for this research. Thirte...
Conference Paper
This research study aims to assess how a specific treatment influences the levels of three proteins when left-censored observations are present in a limited sample size. The dataset contained paired data gathered from 20 subjects categorized into 4 groups with increasing dosages, collected before and after administrating the treatment. The primary...
Preprint
Full-text available
Background Depression is a common mental health disorder that affects a significant portion of the global population. In Sri Lanka, depression is a growing concern, especially among undergraduate students. This study aims to develop a machine learning model to predict the depression status of science undergraduates from a state university in Sri La...
Article
Full-text available
Background: Judicious fluid resuscitation and stringent monitoring of clinical parameters improve the outcome of dengue haemorrhagic fever (DHF). The usefulness of serum lactate to monitor adequate fluid therapy has not been adequately explored. Methods: An observational study was conducted in Sri Lanka, recruiting 162 DHF patients within 12 h o...
Preprint
Full-text available
Background: Hepatocellular carcinoma (HCC) is becoming a challenging global health concern with Asian and African countries carrying the highest burden of it. The rising prevalence of non-alcoholic steatohepatitis (NASH) associated HCC is linked with unhealthy dietary patterns and sedentary life styles. In addition, genetic predisposition may play...
Preprint
Full-text available
Background Dengue haemorrhagic fever (DHF) causes significant morbidity and mortality. Judicious fluid resuscitation is the cornerstone of managing vascular leakage in DHF and haematocrit (HCT) measurement is used to monitor the response to fluid resuscitation. Serum lactate level is a measure of tissue perfusion which can be a useful parameter to...
Presentation
Full-text available
Equity research is among the most important information sources for making investment decisions on equities. The purpose of this study is to utilize statistical measures to evaluate the estimates and recommendations forecasted in equity research reports. Measures are applied to a publicly sourced data set of 16699 forecasts by 27 brokerages coverin...
Article
Background: Corona virus disease 2019 (COVID-19) is caused by a novel corona virus which originated in China and spread worldwide to become a global pandemic. Objectives: To identify the demographic and clinical characteristics of children below the age of 14 years with COVID-19 in Sri Lanka. Method: This was a retrospective, cross sectional descri...
Article
Full-text available
Dengue is one of the most important vector-borne infection in Sri Lanka currently leading to vast economic and social burden. Neither a vaccine nor drug is still not being practiced, vector controlling is the best approach to control disease transmission in the country. Therefore, early warning systems are imminent requirement. The aim of the study...
Conference Paper
Full-text available
Seed priming is one promising strategy that has been employed in enhancing stress tolerance in plants. The present study aimed to assess the effectiveness of five seed priming treatments (hydropriming and 1% concentration of KCl, CaCl2, KNO3, and ZnSO4) on seed germination and growth at early seedling stage of five Sri Lankan rice varieties (kaluhe...
Article
Full-text available
Dengue is the most important mosquito-borne viral infection disease in Sri Lanka triggering extensive economic and social burden in the country. Even after numerous source reduction programmes, more than 30,000 incidences are reporting in the country every year. The last and greatest dengue epidemic in the country was reported in July, 2017 with mo...
Article
Full-text available
Dengue is the most important mosquito-borne viral infection in Sri Lanka causing an enormous social and economic burden in the country. In the absence of therapeutic drugs and the developed vaccines are under investigation, vector control is the best strategy to reduce the disease transmission. Therefore, the development of novel tools to control d...
Article
Full-text available
Background: Breast cancer (BC) is known to be the most common malignancy in females whereas colorectal cancer (CRC) incidence also higher in both genders in Sri Lanka. TP53 is an important tumour suppressor gene and its somatic mutations are reported in approximately 27% of BC and 43% of CRC cases. Analysis of TP53 gene variants not only provides...
Conference Paper
A Scientific method of selecting all possible fraudulent combinations from the weekly pre-auction, where tea samples are bided by the tea exporting companies to be purchased for exporting purposes is critical to mitigate frauds in tea exports from Sri Lanka. Therefore, building a proper mechanism to predict fraudulent samples received by the tea ta...
Article
Full-text available
Background: Dengue is one of the major health problems in Sri Lanka causing an enormous social and economic burden to the country. An accurate early warning system can enhance the efficiency of preventive measures. The aim of the study was to develop and validate a simple accurate forecasting model for the District of Gampaha, Sri Lanka. Three tim...
Article
Full-text available
Abstract Leptospirosis is a zoonostic infectious disease, caused by a pathogenic species of the Genus Leptospira. In recent years, a markedly increased number of leptospirosis cases have been reported in the District of Gampaha, in the Western Province of Sri Lanka. Typically, the risk of the disease in the district is seasonal with a small spike o...
Article
Full-text available
We sought to evaluate the success of prehospital, non-drug assisted endotracheal intubation performed by Virginia prehospital care providers and to develop a model designed to predict the probability of success of endotracheal intubation.Methods We conducted a retrospective observational study on prehospital, non-drug assisted endotracheal intubati...
Article
The tremendous demand on computer memory and computing time for prediction of complex secondary structures limits the applicability of most RNA secondary structure prediction programs available to short RNA sequences. We propose to approach this problem by segmenting a long RNA sequence into shorter non-overlapping chunks, predicting the secondary...
Article
Full-text available
Conditional logistic regression models have been extensively used in the field of medicine and mainly applied in matched case control studies. However, none of the major statistical packages, i.e. SAS, MINITAB, SPSS provide diagnostics to assess the goodness-of-fit of these models. In addition the freely downloadable package R provides no functions...

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