Subina Mehta

Subina Mehta
University of Minnesota Twin Cities | UMN · Department of Biochemistry, Molecular Biology and Biophysics (CBS)

Master of Science

About

34
Publications
3,018
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
154
Citations

Publications

Publications (34)
Preprint
There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analys...
Article
Full-text available
Intestinal proteases mediate digestion and immune signalling, while increased gut proteolytic activity disrupts the intestinal barrier and generates visceral hypersensitivity, which is common in irritable bowel syndrome (IBS). However, the mechanisms controlling protease function are unclear. Here we show that members of the gut microbiota suppress...
Article
Full-text available
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely acc...
Article
Full-text available
Chronic inflammation of the colon causes genomic and/or transcriptomic events, which can lead to expression of non-canonical protein sequences contributing to oncogenesis. To better understand these mechanisms, Rag2−/−Il10−/− mice were infected with Helicobacter hepaticus to induce chronic inflammation of the cecum and the colon. Transcriptomic dat...
Article
Full-text available
Background The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecul...
Article
The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on...
Article
metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple c...
Preprint
Full-text available
The Coronavirus Disease 2019 (COVID19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection...
Preprint
The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformati...
Article
In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabitating potential pathogens in COV...
Article
Full-text available
jats:p>To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measu...
Article
Full-text available
For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. LFQ enables peptide-level quantitation, which is useful in proteomics (analyzing peptides carrying post-translational modificat...
Article
Multi-omics approaches focused on mass-spectrometry (MS)-based data, such as metaproteomics, utilize genomic and/or transcriptomic sequencing data to generate a comprehensive protein sequence database. These databases can be very large, containing millions of sequences, which reduces the sensitivity of matching tandem mass spectrometry (MS/MS) data...
Preprint
Full-text available
For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. In LFQ workflows, protein abundance changes are inferred from peptide-level information, including microbial peptides (for meta...
Article
Full-text available
Background Proteogenomics integrates genomics, transcriptomics, and mass spectrometry (MS)-based proteomics data to identify novel protein sequences arising from gene and transcript sequence variants. Proteogenomic data analysis requires integration of disparate ‘omic software tools, as well as customized tools to view and interpret results. The fl...
Preprint
Full-text available
To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional role of expressed microbial genes/proteins. This can be accomplished through metaproteomics, which characterizes the protein complement of the microbiome. Several software tools exist for analyzing microbiomes at the functional level by measuring their c...
Article
Workflows for large-scale (MS)-based shotgun proteomics can potentially lead to costly errors in the form of incorrect peptide spectrum matches (PSMs). To improve robustness of these workflows, we have investigated the use of the precursor mass discrepancy (PMD) to detect and filter potentially false PSMs that have, nonetheless, a high confidence s...
Preprint
Background: Proteogenomics integrates genomics, transcriptomics and mass spectrometry (MS)-based proteomics data to identify novel protein sequences arising from gene and transcript sequence variants. Proteogenomic data analysis requires integration of disparate omic software tools, as well as customized tools to view and interpret results. The fle...
Preprint
Full-text available
Multi-omics approaches focused on mass-spectrometry (MS)-based data, such as metaproteomics, utilize genomic and/or transcriptomic sequencing data to generate a comprehensive protein sequence database. These databases can be very large, containing millions of sequences, which reduces the sensitivity of matching tandem mass spectrometry (MS/MS) data...
Preprint
Full-text available
Workflows for large-scale (MS)-based shotgun proteomics can potentially lead to costly errors in the form of incorrect peptide spectrum matches (PSMs). To improve robustness of these workflows, we have investigated the use of the precursor mass discrepancy (PMD) to detect and filter potentially false PSMs that have, nonetheless, a high confidence s...
Article
Full-text available
Microbiome research offers promising insights into the impact of microorganisms on biological systems. Metaproteomics, the study of microbial proteins at the community level, integrates genomic, transcriptomic, and proteomic data to determine the taxonomic and functional state of a microbiome. However, standard metaproteomics software is subject to...
Poster
Full-text available
The effect of microbiota on human health, disease and environment has been demonstrated through metagenomics and metaproteomics research. Metaproteomics is capable of analyzing the proteins expressed by microorganisms and provides information regarding the functions of the individual community members. While it is important to identify proteins, fu...
Chapter
Affinity proteomics (AP-MS) is growing in importance for characterizing protein-protein interactions (PPIs) in the form of protein complexes and signaling networks. The AP-MS approach necessitates several different software tools, integrated into reproducible and accessible workflows. However, if the scientist (e.g., a bench biologist) lacks a comp...
Article
Full-text available
Galaxy provides an accessible platform where multi-step data analysis workflows integrating disparate software can be run, even by researchers with limited programming expertise. Applications of such sophisticated workflows are many, including those which integrate software from different ‘omic domains (e.g. genomics, proteomics, metabolomics). In...
Article
Next-generation sequencing technologies, coupled with advances in mass spectrometry-based proteomics, have facilitated system-wide quantitative profiling of expressed mRNA transcripts and proteins. Proteo-transcriptomic analysis compares the relative abundance levels of transcripts and their corresponding proteins, illuminating discordant gene prod...
Article
moFF is a modular and operating system independent tool for quantitative analysis of label-free mass-spectrometry based proteomics data. The moFF workflow, comprising matching-between-runs and apex quantification, can be applied to any upstream search engine’s output, along with the corresponding Thermo or mzML raw file. We here present moFF 2.0, w...
Article
Full-text available
Galaxy provides an accessible platform where multi-step data analysis workflows integrating disparate software can be run, even by researchers with limited programming expertise. Applications of such sophisticated workflows are many, including those which integrate software from different ‘omic domains (e.g. genomics, proteomics, metabolomics). In...
Article
The chromosome-centric human proteome project (C-HPP) seeks to comprehensively characterize all protein products coded by the genome, including those expressed sequence variants confirmed via proteogenomics methods. The closely related biology and disease human proteome project (B/D-HPP) seeks to understand the biological and pathological associati...
Poster
Full-text available
Protein/peptide-level quantification (either labeled or label-free) is routinely used in shotgun proteomics data analysis for determining the abundance of proteins in a given sample. However, accurate, rapid and robust label-free quantification is still a major challenge in the field of quantitative proteomics. Label-free quantification (LFQ) based...
Poster
Full-text available
Mass Spectrometry (MS) based quantitative proteomics provides information regarding protein expression and abundance in a given sample. Protein / Peptide level quantitation (either labeled or label-free) is routinely used in analysis of shotgun proteomics data. For multi-omics studies such as proteogenomics and metaproteomics, peptide-detection and...
Article
Full-text available
The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins...
Conference Paper
Background: Noroviruses (NoV) from genogroup II, genotype 4 (GII.4) strains have historically caused the majority of NoV outbreaks worldwide and are associated with increased hospitalization and mortality rates relative to other NoV genotypes. The emergence of the NoV GII.4 Sydney 2012 variant strain, first identified in Sydney Australia in March 2...

Network

Cited By

Projects

Projects (2)