A5043958930- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Algorithms and Data Compression
- Genetic factors in colorectal cancer
- Recommender Systems and Techniques
- Chromosomal and Genetic Variations
- Customer churn and segmentation
- Advanced Data Storage Technologies
- Advanced Bandit Algorithms Research
- Imbalanced Data Classification Techniques
- AI in cancer detection
- Evolution and Genetic Dynamics
- Cell Image Analysis Techniques
- Gene expression and cancer classification
- Genomics and Rare Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Advanced Graph Neural Networks
- Esophageal Cancer Research and Treatment
- Stock Market Forecasting Methods
- Epigenetics and DNA Methylation
Rice University
2019-2024
Macquarie University
2020-2021
Sharif University of Technology
2016-2017
Intelligence is the ability to learn from experience and use domain experts’ knowledge adapt new situations. In this context, an intelligent Recommender System should be able experience, as it vital know that items will recommended. Traditionally, Systems have been recognized playlist generators for video/music services (e.g., Netflix Spotify), e-commerce product recommenders Amazon eBay), or social content Facebook Twitter). However, in modern enterprises are highly data-/knowledge-driven...
Single-cell DNA sequencing technologies are enabling the study of mutations and their evolutionary trajectories in cancer. Somatic copy number aberrations (CNAs) have been implicated development progression various types A wide array methods for CNA detection has either developed specifically or adapted to single-cell data. Understanding strengths limitations that unique each these is very important obtaining accurate profiles from We benchmarked three widely used methods–Ginkgo, HMMcopy,...
Abstract Copy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the initiation, progression, and potential treatment While such have traditionally been available via “bulk sequencing,” more recently introduced techniques for single-cell DNA sequencing (scDNAseq) provide type that makes CNA inference possible at resolution. We introduce a new birth-death evolutionary model Bayesian method, NestedBD, trees...
Abstract Cancers develop and progress as mutations accumulate, with the advent of single-cell DNA RNA sequencing, researchers can observe these their transcriptomic effects predict proteomic changes remarkable temporal spatial precision. However, to connect genomic consequences, cells either only data or must be mapped a common domain. For this purpose, we present MaCroDNA, method that uses maximum weighted bipartite matching per-gene read counts from RNA-seq data. Using ground truth...
Abstract Motivation Single-nucleotide variants (SNVs) are the most common variations in human genome. Recently developed methods for SNV detection from single-cell DNA sequencing data, such as SCIΦ and scVILP, leverage evolutionary history of cells to overcome technical errors associated with protocols. Despite being accurate, these not scalable extensive genomic breadth whole-genome (scWGS) whole-exome (scWES) data. Results Here, we report on a new method, Phylovar, which extends...
Abstract Copy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the initiation, progression, and potential treatment While such have traditionally been available via “bulk sequencing”, more recently introduced techniques for single-cell DNA sequencing (scDNAseq) provide type that makes CNA inference possible at resolution. In this paper, we introduce a new birth-death evolutionary model as well Bayesian method,...
Abstract Single-cell DNA sequencing technologies are enabling the study of mutations and their evolutionary trajectories in cancer. Somatic copy number aberrations (CNAs) have been implicated development progression various types A wide array methods for CNA detection has either developed specifically or adapted to single-cell data. Understanding strengths limitations that unique each these is very important obtaining accurate profiles from Here we review major steps followed by when...
Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment these reads play an important role in any downstream analysis. Similarly, reducing the overall cost related to time consumption aligner. The tradeoff between accuracy speed main challenge designing long read aligners. We propose Meta-aligner which aligns very reference genome efficiently accurately. incorporates available short/long aligners as subcomponents uses...
Abstract Single-cell sequencing provides a powerful approach for elucidating intratumor heterogeneity by resolving cell-to-cell variability. However, it also poses additional challenges including elevated error rates, allelic dropout and non-uniform coverage. A recently introduced single-cell-specific mutation detection algorithm leverages the evolutionary relationship between cells denoising data. due to its probabilistic nature, this method does not scale well with number of cells. Here,...
Abstract Fast and accurate alignment of long-reads plays an important role in reducing the overall cost long-read sequencing. In this paper, we propose Meta-aligner, efficient aligner that exploits statistics reference genome to improve performance terms time complexity achieving significantly higher recall for very noisy long reads. The first step algorithm adopts well-known short-read aligners order rapidly align a large fraction reads through progressive process aligning read fragments...
Abstract Single-nucleotide variants (SNVs) are the most common variations in human genome. Recently developed methods for SNV detection from single-cell DNA sequencing (scDNAseq) data, such as SCIΦ and scVILP, leverage evolutionary history of cells to overcome technical errors associated with protocols. Despite being accurate, these not scalable extensive genomic breadth whole-genome (scWGS) whole-exome (scWES) data. Here we report on a new method, Phylovar, which extends phylogeny-guided...
Abstract Cancers develop and progress as mutations accumulate, with the advent of single-cell DNA RNA sequencing, researchers can observe these mutations, their transcriptomic effects, predict proteomic changes remarkable temporal spatial precision. However, to connect genomic consequences, cells either only data or must be mapped a common domain. For this purpose, we present MaCroDNA, novel method which uses maximum weighted bipartite matching per-gene read counts from RNA-seq data. Using...
<ns3:p>In October 2019, 46 scientists from around the world participated in first National Center for Biotechnology Information (NCBI) Structural Variation (SV) Codeathon at Baylor College of Medicine. The charge this annual working session was to identify ongoing challenges topics SV and graph genomes, response design reliable methods facilitate their study. Over three days, seven groups each designed developed new open-sourced improve bioinformatic analysis genomic SVs represented...
Abstract With the advent of single-cell DNA sequencing, it is now possible to infer evolutionary history thousands tumor cells obtained from a single patient. This history, which takes shape tree, reveals mode evolution specific cancer under study and, in turn, helps with clinical diagnosis, prognosis, and therapeutic treatment. In this we focus on question determining their inferred history. particular, employ recursive neural networks that capture tree structures classify into one four...
Establishing a new business may involve Knowledge acquisition in various areas, from personal to and marketing sources. This task is challenging as it requires examining data islands uncover hidden patterns unknown correlations such purchasing behavior, consumer buying signals, demographic socioeconomic attributes of different locations. paper introduces novel framework for extracting identifying important features banking non-banking sources address this challenge. We present an...