Mathangi Thiagarajan
A5077996792- Cancer Genomics and Diagnostics
- Ferroptosis and cancer prognosis
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- RNA modifications and cancer
- Microbial Community Ecology and Physiology
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Cancer Research and Treatments
- Gene expression and cancer classification
- Radiomics and Machine Learning in Medical Imaging
- Pancreatic and Hepatic Oncology Research
- Renal cell carcinoma treatment
- Advanced Proteomics Techniques and Applications
- Ubiquitin and proteasome pathways
- Metabolomics and Mass Spectrometry Studies
- Bacteriophages and microbial interactions
- Cancer-related Molecular Pathways
- Protist diversity and phylogeny
- Parasitic Infections and Diagnostics
- Iron Metabolism and Disorders
- Microtubule and mitosis dynamics
- Colorectal Cancer Treatments and Studies
- Reproductive Biology and Fertility
- Cancer, Lipids, and Metabolism
Frederick National Laboratory for Cancer Research
2019-2024
Leidos (United States)
2017-2024
Leidos Biomedical Research Inc. (United States)
2017-2021
J. Craig Venter Institute
2006-2016
Harvard University
2011
University of Baltimore
2009
University of Maryland, Baltimore
2009
Microarrays have emerged as the premier tool for studying gene expression on a genomic scale.Advances in precision of array printers and scanners well improved laboratory protocols (11) allow assays tremendous complexity scope.Scientists seeking to harness potential this technique are often challenged by large quantities data produced.Well-designed, user-friendly software is key tracking, integrating, qualifying, ultimately deriving scientific insight from experimental results.In support our...
Microbial communities carry out the majority of biochemical activity on planet, and they play integral roles in processes including metabolism immune homeostasis human microbiome. Shotgun sequencing such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but resulting data typically comprise short reads hundreds different organisms are at best challenging assemble comparably single-organism genomes. Here, we describe an alternative...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline soma functions that are embodied by distinct nuclei within single cell. germline-like micronucleus (MIC) its genome held in reserve sexual reproduction. soma-like macronucleus (MAC), which possesses processed from of the MIC, center gene expression does not directly contribute DNA to progeny. We report here shotgun sequencing, assembly, analysis...
To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization 110 tumors 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, acetylproteomics. Multi-omics clustering revealed four subgroups defined by key driver mutations, country, gender. Proteomic phosphoproteomic data illuminated downstream copy number aberrations, somatic...
To elucidate the deregulated functional modules that drive clear cell renal carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration proteogenomic measurements uniquely protein dysregulation cellular mechanisms impacted by alterations, including...
Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification metabolomic data on 99 treatment-naive GBMs provides insights GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 PLCG1) as potential switches mediating oncogenic pathway activation, well targets for EGFR-, TP53-, RB1-altered tumors. Immune...
Abstract Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of tick, Ixodes scapularis (Say), which vectors that cause Lyme disease, human granulocytic anaplasmosis, babesiosis diseases. The large reflects accumulation repetitive DNA, new lineages retro-transposons, gene architecture patterns resembling ancient metazoans rather pancrustaceans. Annotation scaffolds representing ∼57% genome, reveals 20,486 protein-coding genes...
The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this "proteogenomics" approach was applied to 122 treatment-naive primary breast cancers accrued preserve post-translational modifications, including protein phosphorylation acetylation. Proteogenomics challenged standard cancer diagnoses, provided detailed analysis the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint...
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences perturbations to the p53 Wnt/β-catenin pathways, identified potential role for circRNAs in epithelial-mesenchymal transition, provided information about proteomic markers clinical genomic tumor subgroups, including relationships known druggable pathways. An extensive genome-wide...
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 tissues. Proteomic, phosphoproteomic, glycoproteomic analyses were used to characterize proteins their modifications. In addition, whole-genome sequencing, whole-exome methylation, RNA sequencing...
Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa, however, not well known, genomes have been analyzed from only the latter two lineages. Tiny “picoplanktonic” members of prymnesiophyte lineage long inferred to be ecologically important but remain poorly characterized. Here, we examine pico-prymnesiophyte evolutionary history ecology using...
Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape LSCC, providing deeper exposition LSCC biology potential implications. identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 overexpressing target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such LSD1 EZH2 to SOX2-overexpressing tumors. Our data support...
We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins phosphosites, prioritizes copy number drivers, highlights an oncogenic role for RNA processing genes. investigation mutual exclusivity between FAT1 truncating mutations 11q13.3 amplifications reveals dysregulated actin dynamics as common functional consequence. Phosphoproteomics characterizes two...
Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater marine habitats, underlying mechanisms to this structuring yet remain unknown. We hypothesized that of natural bacterial is linked striking divide microbiomes. To test hypothesis, metagenomic sequencing microbial along a 1,800 km transect Baltic Sea area, encompassing continuous...
Clear cell renal carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- intratumoral heterogeneity (ITH) results in varying prognosis treatment outcomes. To obtain the comprehensive profile ccRCC, we perform integrative histopathologic, proteogenomic, metabolomic analyses on 305 ccRCC tumor segments 166 paired adjacent normal tissues from 213 cases. Combining histologic molecular profiles reveals ITH 90% ccRCCs, with 50% demonstrating immune...
Post-translational modifications (PTMs) play key roles in regulating cell signaling and physiology both normal cancer cells. Advances mass spectrometry enable high-throughput, accurate, sensitive measurement of PTM levels to better understand their role, prevalence, crosstalk. Here, we analyze the largest collection proteogenomics data from 1,110 patients with profiles across 11 types (10 National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium [CPTAC]). Our study reveals...
Deep exome resequencing is a powerful approach for delineating patterns of protein-coding variation among genes, pathways, individuals and populations.We analyzed data from 2,440 European African ancestry as part the National Heart, Lung, Blood Institute's Exome Project, aim which to discover novel genes mechanisms that contribute heart, lung blood disorders.Each was sequenced mean coverage 116×, allowing detailed inferences about population genomic both common rare coding variation.We...
Understanding the microbial content of air has important scientific, health, and economic implications. While studies have primarily characterized taxonomic samples by sequencing 16S or 18S ribosomal RNA gene, direct analysis genomic airborne microorganisms not been possible due to extremely low density biological material in environments. We developed sampling amplification methods enable adequate DNA recovery allow metagenomic profiling collected from indoor outdoor Air were a large urban...
Abstract Summary: JCVI Metagenomics Reports (METAREP) is a Web 2.0 application designed to help scientists analyze and compare annotated metagenomics datasets. It utilizes Solr/Lucene, high-performance scalable search engine, quickly query large data collections. Furthermore, users can use its SQL-like syntax filter refine METAREP provides graphical summaries for top taxonomic functional classifications as well GO, NCBI Taxonomy KEGG Pathway Browser. Users absolute relative counts of...
The characterization of global marine microbial taxonomic and functional diversity is a primary goal the Global Ocean Sampling Expedition. As part this study, 19 water samples were collected aboard Sorcerer II sailing vessel from southern Indian in an effort to more thoroughly understand lifestyle strategies inhabitants ultra-oligotrophic region. No investigations whole virioplankton assemblages have been conducted on waters or across multiple size fractions thus far. Therefore, goals study...
Abstract Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and Current waters during seasonal upwelling event, providing an opportunity examine the impact of episodic pulses cold nutrient-rich water into surface microbial communities. The set consists ∼5.8 million predicted proteins across seven sites, three different size classes: 0.1–0.8, 0.8–3.0 3.0–200.0 μm. Taxonomic metabolic analyses suggest that...
Many gene products exhibit great structural heterogeneity because of an array modifications. These modifications are not directly encoded in the genomic template but often affect functionality proteins. Protein glycosylation plays a vital role proper protein functions. However, analysis glycoproteins has been challenging compared with other modifications, such as phosphorylation. Here, we perform integrated proteomic and glycoproteomic 83 prospectively collected high-grade serous ovarian...