Deshan Perera
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View article: Enhancing disease risk gene discovery by integrating transcription factor-linked <i>trans</i> -variants into transcriptome-wide association analyses
Enhancing disease risk gene discovery by integrating transcription factor-linked <i>trans</i> -variants into transcriptome-wide association analyses Open
Transcriptome-wide association studies (TWAS) have been successful in identifying disease susceptibility genes by integrating cis-variants predicted gene expression with genome-wide association studies (GWAS) data. However, trans-variants …
View article: Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell
Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell Open
Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of …
View article: cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions
cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions Open
Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants un…
View article: Enhancing Disease Risk Gene Discovery by Integrating Transcription Factor-Linked Trans-located Variants into Transcriptome-Wide Association Analyses
Enhancing Disease Risk Gene Discovery by Integrating Transcription Factor-Linked Trans-located Variants into Transcriptome-Wide Association Analyses Open
Transcriptome-wide association studies (TWAS) have been successful in identifying disease susceptibility genes by integrating cis-variants predicted gene expression with genome-wide association studies (GWAS) data. However, trans-located v…
View article: Tissue-specific transfer-learning enables retasking of a general comprehensive model to a specific domain
Tissue-specific transfer-learning enables retasking of a general comprehensive model to a specific domain Open
Machine learning (ML) has proven successful in biological data analysis. However, may require massive training data. To allow broader use of ML in the full spectrum of biology and medicine, including sample-sparse domains, re-directing est…
View article: CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data
CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data Open
Statistical tests for molecular evolution provide quantifiable insights into the selection pressures that govern a genome's evolution. Increasing sample sizes used for analysis leads to higher statistical power. However, this requires more…
View article: Interaction-integrated linear mixed model reveals 3D-genetic basis underlying Autism
Interaction-integrated linear mixed model reveals 3D-genetic basis underlying Autism Open
Genetic interactions play critical roles in genotype-phenotype associations. We developed a novel interaction-integrated linear mixed model (ILMM) that integrates a priori knowledge into linear mixed models. ILMM enables statistical integr…
View article: CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data
CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data Open
Statistical tests for molecular evolution provide quantifiable insights into the selection pressures that govern a genome’s evolution. Increasing sample sizes used for analysis leads to higher statistical power. However, this requires more…
View article: In silico study of SARS‐CoV‐2 spike protein RBD and human ACE‐2 affinity dynamics across variants and Omicron subvariants
In silico study of SARS‐CoV‐2 spike protein RBD and human ACE‐2 affinity dynamics across variants and Omicron subvariants Open
The coronavirus disease 2019 virus outbreak continues worldwide, with many variants emerging, some of which are considered variants of concern (VOCs). The WHO designated Omicron as a VOC and assigned it under variant B.1.1.529. Here, we us…
View article: cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions
cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions Open
Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants un…
View article: Reconstructing SARS-CoV-2 infection dynamics through the phylogenetic inference of unsampled sources of infection
Reconstructing SARS-CoV-2 infection dynamics through the phylogenetic inference of unsampled sources of infection Open
The COVID-19 pandemic has illustrated the importance of infection tracking. The role of asymptomatic, undiagnosed individuals in driving infections within this pandemic has become increasingly evident. Modern phylogenetic tools that take i…
View article: A Novel In Silico Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery
A Novel In Silico Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery Open
Current in silico proteomics require the trifecta analysis, namely, prediction, validation, and functional assessment of a modeled protein. The main drawback of this endeavor is the lack of a single protocol that utilizes a proper set of b…
View article: Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding
Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding Open
DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple ind…
View article: A novel computational approach to reconstruct SARS-CoV-2 infection dynamics through the inference of unsampled sources of infection
A novel computational approach to reconstruct SARS-CoV-2 infection dynamics through the inference of unsampled sources of infection Open
Infectious diseases such as the COVID19 pandemic cemented the importance of disease tracking. The role of asymptomatic, undiagnosed individuals in driving infection has become evident. Their unaccountability results in ineffective preventi…
View article: Statistical model integrating interactions into genotype-phenotype association mapping: an application to reveal 3D-genetic basis underlying Autism
Statistical model integrating interactions into genotype-phenotype association mapping: an application to reveal 3D-genetic basis underlying Autism Open
Biological interactions are prevalent in the functioning organisms. Correspondingly, statistical geneticists developed various models to identify genetic interactions through genotype-phenotype association mapping. The current standard pro…
View article: A benchmarked in-silico driven pipeline capable of complete trifecta protein analysis
A benchmarked in-silico driven pipeline capable of complete trifecta protein analysis Open
Background Current in-silico based proteomics requires the prediction, validation and functional analysis of a modelled protein. The main drawback in this protocol is the lack of a singular protocol that utilizes a proper set of benchmarke…
View article: Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort
Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort Open
Modern computational methods using patient Human Immunodeficiency Virus type 1 (HIV-1) genetic sequences can model population-wide viral transmission dynamics. Accurate transmission inferences can play a critical role in the characterizati…
View article: 1,3-Dinitrobenze-Induced Genotoxicity Through Altering Nuclear Integrity of Diploid and Polyploidy Germ Cells
1,3-Dinitrobenze-Induced Genotoxicity Through Altering Nuclear Integrity of Diploid and Polyploidy Germ Cells Open
1,3-Dinitrobenzene (mDNB) is a widely used intermediate in commercial products and causes testicular injury. However, genotoxic effects upon low-level exposure are poorly understood. The present study evaluated the effects of very low-chro…