Sushmita Roy
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View article: Defining the role of β-cell IRE1α/XBP1 pathway and its gene regulatory network components in non-obese diabetic mice
Defining the role of β-cell IRE1α/XBP1 pathway and its gene regulatory network components in non-obese diabetic mice Open
The unfolded protein response sensor, IRE1α, acts through its regulated IRE1α-dependent decay (RIDD) activity or transcription factor XBP1 to determine cell fate and survival. While blunting RIDD activity prevents diabetes in type 1 diabet…
View article: Uncovering Functional Gene Regulatory Networks in Bulk and Single-Cell Data through Robust Transcription Factor Activity Estimation and Model-Guided Experimental Validation
Uncovering Functional Gene Regulatory Networks in Bulk and Single-Cell Data through Robust Transcription Factor Activity Estimation and Model-Guided Experimental Validation Open
Reconstructing genome-scale gene regulatory networks (GRNs) remains a difficult problem in systems biology, and many experimental and computational methods have been developed to address this problem. Recent computational methods have aime…
View article: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization Open
Three-dimensional (3D) genome organization, which determines how the DNA is packaged inside the nucleus, has emerged as a key component of the gene regulation machinery. High-throughput chromosome conformation data sets, such as Hi-C, have…
View article: Prevalence of Atherogenic Lipoprotein Phenotype among the Obese Medical Students in Bangladesh
Prevalence of Atherogenic Lipoprotein Phenotype among the Obese Medical Students in Bangladesh Open
Background: Medical students are expected to be conscious about nutrition and healthy active life styles. So, study of obesity & atherogenic lipoproteins among medical students may reflect the prevalence of this cardiovascular risk factor …
View article: Perspective on recent developments and challenges in regulatory and systems genomics
Perspective on recent developments and challenges in regulatory and systems genomics Open
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective…
View article: Student’s Perspective Towards Online Teaching-Learning Activity
Student’s Perspective Towards Online Teaching-Learning Activity Open
Background: Online learning is a form of education that takes place over the Internet. With the advancement of information and communication technologies, the acceptance of online education is increasing. It is an alternative to traditiona…
View article: A facile chemical strategy to synthesize precise AAV-protein conjugates for targeted gene delivery
A facile chemical strategy to synthesize precise AAV-protein conjugates for targeted gene delivery Open
The efficacy of current gene therapy approaches using adeno associated virus (AAV) vectors is limited by the poor control over their tissue tropism. Untargeted AAV vectors require high doses to achieve therapeutic efficacy, which is associ…
View article: Human iPSC-derived Committed Cardiac Progenitors Generate Cardiac Tissue Grafts in a Swine Ischemic Cardiomyopathy Model without Triggering Ventricular Arrhythmias
Human iPSC-derived Committed Cardiac Progenitors Generate Cardiac Tissue Grafts in a Swine Ischemic Cardiomyopathy Model without Triggering Ventricular Arrhythmias Open
Background: The adult human heart following a large myocardial infarction is unable to regenerate heart muscle and instead forms scar with the risk of progressive heart failure. Large animal studies have shown that intramyocardial injectio…
View article: Current and future directions in network biology
Current and future directions in network biology Open
Summary Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although t…
View article: Current and future directions in network biology
Current and future directions in network biology Open
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field…
View article: Examining dynamics of three-dimensional genome organization with multi-task matrix factorization
Examining dynamics of three-dimensional genome organization with multi-task matrix factorization Open
Three-dimensional (3D) genome organization, which determines how the DNA is packaged inside the nucleus, has emerged as a key component of the gene regulation machinery. High-throughput chromosome conformation datasets, such as Hi-C, have …
View article: Benchmarking graph representation learning algorithms for detecting modules in molecular networks
Benchmarking graph representation learning algorithms for detecting modules in molecular networks Open
Background: A common task in molecular network analysis is the detection of community structures or modules. Such modules are frequently associated with shared biological functions and are often disrupted in disease. Detection of community…
View article: Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation
Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation Open
Understanding the impact of regulatory variants on complex phenotypes is a significant challenge because the genes and pathways that are targeted by such variants and the cell type context in which regulatory variants operate are typically…
View article: The Single-Cell Transcriptome Program of Nodule Development Cellular Lineages in<i>Medicago truncatula</i>
The Single-Cell Transcriptome Program of Nodule Development Cellular Lineages in<i>Medicago truncatula</i> Open
Summary Legumes can establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules after root exposure to lipo-chito-oligosaccharides secreted by the bacteria. Nodule development initiates with anticlinal mitotic di…
View article: ISMB/ECCB 2023 proceedings
ISMB/ECCB 2023 proceedings Open
International audience
View article: Source Code for Paper "Benchmarking graph representation learning algorithms for detecting modules in molecular networks"
Source Code for Paper "Benchmarking graph representation learning algorithms for detecting modules in molecular networks" Open
Source code used for "Comparison of deep and shallow graph representation learning algorithms for detecting modules in molecular networks" paper
View article: Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets Open
Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. Single-cell technologies such as single cell RNA-sequenci…
View article: A network-based model of<i>Aspergillus fumigatus</i>elucidates regulators of development and defensive natural products of an opportunistic pathogen
A network-based model of<i>Aspergillus fumigatus</i>elucidates regulators of development and defensive natural products of an opportunistic pathogen Open
Aspergillus fumigatus is a notorious pathogenic fungus responsible for various harmful, sometimes lethal, diseases known as aspergilloses. Understanding the gene regulatory networks that specify the expression programs underlying this fung…
View article: Dataset for Paper "Benchmarking graph representation learning algorithms for detecting modules in molecular networks"
Dataset for Paper "Benchmarking graph representation learning algorithms for detecting modules in molecular networks" Open
Datasets used for "Benchmarking graph representation learning algorithms for detecting modules in molecular networks"
View article: Comparison of deep and shallow graph representation learning algorithms for detecting modules in molecular networks
Comparison of deep and shallow graph representation learning algorithms for detecting modules in molecular networks Open
LFR benchmark graphs for "Comparison of deep and shallow graph representation learning algorithms for detecting modules in molecular networks" paper
View article: Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets Open
The uploaded files are source datasets for the scMTNI algorithm. scMTNI is a multi-task learning framework that integrates the cell lineage structure, scRNA-seq and scATAC-seq measurements to enable joint inference of cell type-specific GR…
View article: Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets Open
The uploaded files are source datasets for the scMTNI algorithm. scMTNI is a multi-task learning framework that integrates the cell lineage structure, scRNA-seq and scATAC-seq measurements to enable joint inference of cell type-specific GR…
View article: Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets Open
The uploaded files are source datasets for the scMTNI algorithm. scMTNI is a multi-task learning framework that integrates the cell lineage structure, scRNA-seq and scATAC-seq measurements to enable joint inference of cell type-specific GR…
View article: Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets Open
The uploaded files are source datasets for the scMTNI algorithm. scMTNI is a multi-task learning framework that integrates the cell lineage structure, scRNA-seq and scATAC-seq measurements to enable joint inference of cell type-specific GR…