Genomics
We introduce a novel data-driven framework for the design of targeted gene panels for estimating exome-wide biomarkers in cancer immunotherapy. Our first goal is to develop a generative model for the profile of mutation across the exome,…
The detection of genomic regions unusually rich in a given pattern is an important undertaking in the analysis of next generation sequencing data. Recent studies of chromosomal translocations in activated B lymphocytes have identified…
Despite of the fast development of highly effective vaccines to control the current COVID$-$19 pandemic, the unequal distribution and availability of these vaccines worldwide and the number of people infected in the world lead to the…
We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples, and to prepare these cells for bulk whole genome sequencing without cultivation. We characterize this approach by…
The phylogenetic tree of SARS-CoV-2 (nCov-19) viruses is reconstructed according to the similarity of genome sequences. The tree topology of Betacoronavirus is remarkably consistent with biologist's systematics. Because the tree…
We develop a greedy algorithm that is fast and scalable in the detection of a nested partition extracted from a dendrogram obtained from hierarchical clustering of a multivariate series. Our algorithm provides a $p$-value for each clade…
Accurate drug response prediction (DRP) is a crucial yet challenging task in precision medicine. This paper presents a novel Attention-Guided Multi-omics Integration (AGMI) approach for DRP, which first constructs a Multi-edge Graph (MeG)…
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.…
Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variation present in every human genome, and supports the discovery…
The availability of genomic data is essential to progress in biomedical research, personalized medicine, etc. However, its extreme sensitivity makes it problematic, if not outright impossible, to publish or share it. As a result, several…
Pathway enrichment analysis has become a widely used knowledge-based approach for the interpretation of biomedical data. Its popularity has led to an explosion of both enrichment methods and pathway databases. While the elegance of pathway…
Deep sequencing has become one of the most popular tools for transcriptome profiling in biomedical studies. While an abundance of computational methods exists for "normalizing" sequencing data to remove unwanted between-sample variations…
This paper describes a novel approach to modeling homphily, i.e. the tendency of nodes that share (or differ in) certain attributes to be linked; we consider dynamic networks in which nodes can be added over time but not removed. Our…
COVID-19 pandemic, is still unknown and is an important open question. There are speculations that bats are a possible origin. Likewise, there are many closely related (corona-) viruses, such as SARS, which was found to be transmitted…
Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…
Motivation: Cutting the cost of DNA sequencing technology led to a quantum leap in the availability of genomic data. While sharing genomic data across researchers is an essential driver of advances in health and biomedical research, the…
Background: Bladder cancer is the 10th most common cancer worldwide, and its prevalence is increasing, especially in developing countries. Objective: In the present study, we employed gene expression profiles from the GSE163209 data set in…
Breast cancer is the most common cancer in women worldwide, and discovering the biomarkers of this disease became so vital nowadays and Cell in Cell structure could be one of them, and it may be used as an available proxy for tumor…
In this paper we apply the structure of genomes as second-order Markov processes specified by the distributions of successive triplets of bases to two bioinformatics problems: identification of outliers in genome databases and read…
The increasing spread of COVID-19, caused by the virus SARS-CoV-2, raises concerns about the extent to which mutations have occurred across the viral genome. We present a partial replication of an earlier 2021 study by Wang, R. et al. that…