Shivashankar H. Nagaraj
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View article: Pharmacogenomics-Driven Multimodal Data Integration Improves Predictions of Adverse Drug Reactions in Cancer Patients using Machine Learning
Pharmacogenomics-Driven Multimodal Data Integration Improves Predictions of Adverse Drug Reactions in Cancer Patients using Machine Learning Open
Accurately predicting adverse drug reactions (ADRs) in cancer remains challenging. We applied a pharmacogenomics-driven machine learning framework that integrates genomic, environmental, and comorbidity data to enhance ADR prediction. Usin…
View article: Regional autozygosity association with albumin-to-creatinine ratio reveals a novel FTO region in an Indigenous Australian population
Regional autozygosity association with albumin-to-creatinine ratio reveals a novel FTO region in an Indigenous Australian population Open
The genetic distinctiveness of Indigenous Australian populations is well established, yet the Tiwi population remains underrepresented in genetic research. Due to their prolonged geographic isolation, these populations are prone to increas…
View article: Identification of Small Open Reading Frame-encoded Proteins in the Human Genome
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome Open
One of the main goals of the Human Genome Project is to identify all protein-coding genes. There are ∼ 20,500 protein-coding genes annotated in the human reference databases. However, in the last few years, proteogenomics studies have pred…
View article: Bridging genomics’ greatest challenge: The diversity gap
Bridging genomics’ greatest challenge: The diversity gap Open
Achieving diverse representation in biomedical data is critical for healthcare equity. Failure to do so perpetuates health disparities and exacerbates biases that may harm patients with underrepresented ancestral backgrounds. We present a …
View article: Machine Learning Enabled Prediction of Biologically Relevant Gene Expression Using <scp>CT</scp>‐Based Radiomic Features in Non‐Small Cell Lung Cancer
Machine Learning Enabled Prediction of Biologically Relevant Gene Expression Using <span>CT</span>‐Based Radiomic Features in Non‐Small Cell Lung Cancer Open
Background Non‐small‐cell lung cancer (NSCLC) remains a global health challenge, driving morbidity and mortality. The emerging field of radiogenomics utilizes statistical methods to correlate radiographic tumor features with genomic charac…
View article: Genomic characterization of clinically significant blood group variants in Aboriginal Australians.
Genomic characterization of clinically significant blood group variants in Aboriginal Australians. Open
The comprehensive analyses of blood group genetic variant profiles identified in this study will provide insight and an opportunity to improve Aboriginal health by aiding in the identification of appropriate blood products for population-s…
View article: A Systematic Review Exploring Empirical Pharmacogenomics Research Within Global Indigenous Populations
A Systematic Review Exploring Empirical Pharmacogenomics Research Within Global Indigenous Populations Open
Background This systematic review aims to highlight the scope of pharmacogenomics research within global Indigenous populations. This review also explores the barriers and facilitators of pharmacogenomics research within this population. M…
View article: Mapping the Pharmacogenetic Landscape in a Ugandan Population: Implications for Personalized Medicine in an Underrepresented Population
Mapping the Pharmacogenetic Landscape in a Ugandan Population: Implications for Personalized Medicine in an Underrepresented Population Open
Africans are extremely underrepresented in global genomic research. African populations face high burdens of communicable and non‐communicable diseases and experience widespread polypharmacy. As population‐specific genetic studies are cruc…
View article: Pharmacological induction of chromatin remodeling drives chemosensitization in triple-negative breast cancer
Pharmacological induction of chromatin remodeling drives chemosensitization in triple-negative breast cancer Open
Targeted therapies have improved outcomes for certain cancer subtypes, but cytotoxic chemotherapy remains a mainstay for triple-negative breast cancer (TNBC). The epithelial-to-mesenchymal transition (EMT) is a developmental program co-opt…
View article: VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins Open
SWATH is a data acquisition strategy acclaimed for generating quantitatively accurate and consistent measurements of proteins across multiple samples. Its utility for proteomics studies in nonlaboratory animals, however, is currently compr…
View article: Novel genetic markers for chronic kidney disease in a geographically isolated population of Indigenous Australians: Individual and multiple phenotype genome-wide association study
Novel genetic markers for chronic kidney disease in a geographically isolated population of Indigenous Australians: Individual and multiple phenotype genome-wide association study Open
Background Chronic kidney disease (CKD) is highly prevalent among Indigenous Australians, especially those in remote regions. The Tiwi population has been isolated from mainland Australia for millennia and exhibits unique genetic character…
View article: Genetic Characterization of Blood Group Antigens for Polynesian Heritage Norfolk Island Residents
Genetic Characterization of Blood Group Antigens for Polynesian Heritage Norfolk Island Residents Open
Improvements in blood group genotyping methods have allowed large scale population-based blood group genetics studies, facilitating the discovery of rare blood group antigens. Norfolk Island, an external and isolated territory of Australia…
View article: Machine Learning-Based Prediction of Distant Recurrence in Invasive Breast Carcinoma Using Clinicopathological Data: A Cross-Institutional Study
Machine Learning-Based Prediction of Distant Recurrence in Invasive Breast Carcinoma Using Clinicopathological Data: A Cross-Institutional Study Open
Breast cancer is the most common type of cancer worldwide. Alarmingly, approximately 30% of breast cancer cases result in disease recurrence at distant organs after treatment. Distant recurrence is more common in some subtypes such as inva…
View article: The pharmacogenomic landscape of an Indigenous Australian population
The pharmacogenomic landscape of an Indigenous Australian population Open
Background: Population genomic studies of individuals of Indigenous ancestry have been extremely limited comprising <0.5% of participants in international genetic databases and genome-wide association studies, contributing to a “genomic…
View article: Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression
Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression Open
The epithelial-mesenchymal transition (EMT) is a developmental program co-opted by tumor cells that aids the initiation of the metastatic cascade. Tumor cells that undergo EMT are relatively chemoresistant, and there are currently no thera…
View article: Predicting Distant Recurrences in Invasive Breast Carcinoma Patients Using Clinicopathological Data: A cross-institutional and AI-based study
Predicting Distant Recurrences in Invasive Breast Carcinoma Patients Using Clinicopathological Data: A cross-institutional and AI-based study Open
Breast cancer ranks second in the most common cancer in women worldwide with 30% of cases resulting into recurrence of the disease at distant organs post the treatment. While clinicians have utilized several clinicopathological measurement…
View article: hSSB1 (NABP2/OBFC2B) modulates the DNA damage and androgen‐induced transcriptional response in prostate cancer
hSSB1 (NABP2/OBFC2B) modulates the DNA damage and androgen‐induced transcriptional response in prostate cancer Open
Background Activation and regulation of androgen receptor (AR) signaling and the DNA damage response impact the prostate cancer (PCa) treatment modalities of androgen deprivation therapy (ADT) and radiotherapy. Here, we have evaluated a ro…
View article: Using whole-genome sequencing to characterize clinically significant blood groups among healthy older Australians
Using whole-genome sequencing to characterize clinically significant blood groups among healthy older Australians Open
There have been no comprehensive studies of a full range of blood group polymorphisms within the Australian population. This problem is compounded by the absence of any databases carrying genomic information on chronically transfused patie…
View article: The genomic landscape of blood groups in Indigenous Australians in remote communities
The genomic landscape of blood groups in Indigenous Australians in remote communities Open
Background Red blood cell (RBC) membrane‐associated blood group systems are clinically significant. Alloimmunisation is a persistent risk associated with blood transfusion owing to the antigen polymorphisms among these RBC‐associated blood…
View article: Unlocking capacities of genomics for the COVID-19 response and future pandemics
Unlocking capacities of genomics for the COVID-19 response and future pandemics Open
During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing method…
View article: Deep Learning-Based Pan-Cancer Classification Model Reveals Tissue-of-Origin Specific Gene Expression Signatures
Deep Learning-Based Pan-Cancer Classification Model Reveals Tissue-of-Origin Specific Gene Expression Signatures Open
Cancer tissue-of-origin specific biomarkers are needed for effective diagnosis, monitoring, and treatment of cancers. In this study, we analyzed transcriptomics data from 37 cancer types provided by The Cancer Genome Atlas (TCGA) to identi…
View article: RBCeq: A robust and scalable algorithm for accurate genetic blood typing
RBCeq: A robust and scalable algorithm for accurate genetic blood typing Open
This work was supported in part by Advance Queensland Research Fellowship, MRFF Genomics Health Futures Mission (76,757), and the Australian Red Cross LifeBlood. The Australian governments fund the Australian Red Cross Lifeblood for the pr…
View article: ImaGene: a web-based software platform for tumor radiogenomic evaluation and reporting
ImaGene: a web-based software platform for tumor radiogenomic evaluation and reporting Open
Summary Radiographic imaging techniques provide insight into the imaging features of tumor regions of interest, while immunohistochemistry and sequencing techniques performed on biopsy samples yield omics data. Relationships between tumor …
View article: The Gene-Drug Duality: Exploring the Pharmacogenomics of Indigenous Populations
The Gene-Drug Duality: Exploring the Pharmacogenomics of Indigenous Populations Open
While pharmacogenomic studies have facilitated the rapid expansion of personalized medicine, the benefits of these findings have not been evenly distributed. Genomic datasets pertaining to Indigenous populations are sorely lacking, leaving…
View article: Unlocking capacities of viral genomics for the COVID-19 pandemic response
Unlocking capacities of viral genomics for the COVID-19 pandemic response Open
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies,…
View article: Using Whole Genome Sequencing to Characterize Clinically Significant Blood Groups Among Healthy Older Australians
Using Whole Genome Sequencing to Characterize Clinically Significant Blood Groups Among Healthy Older Australians Open
There have been no comprehensive studies of a full range of blood group polymorphisms within the Australian population. The problem is compounded by the absence of any databases carrying genomic information on chronically transfused patien…
View article: Deep learning-based pan-cancer classification model reveals cancer-specific gene expression signatures
Deep learning-based pan-cancer classification model reveals cancer-specific gene expression signatures Open
The identification of cancer-specific biomarkers and therapeutic targets is one of the primary goals of cancer genomics. Thousands of cancer genomes, exomes, and transcriptomes have been sequenced to date. In this study, we conducted a pan…
View article: BGvar - a comprehensive resource for blood group immunogenetics
BGvar - a comprehensive resource for blood group immunogenetics Open
Background Blood groups form the basis of effective and safe blood transfusion. There are about 41 well recognized human blood group systems presently known. Blood groups are molecularly determined by the presence of specific antigens on t…
View article: Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors
Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors Open
View article: Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data
Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data Open