Benthos Prime Central

Established in 2022 and headquartered in Houston, TX, USA, Benthos Prime Central is a next-generation Translational Omics company. We offer comprehensive wet-lab and bioinformatics services in bulk and single-cell transcriptomics, proteomics, and metabolomics. Positioned at the intersection of omics, data science, and translational biology, we develop innovative multi-omic platforms that leverage big data to bridge the gap between significant biological challenges and therapeutic solutions for translational researchers.

Enabling Translational Scientists with Meaningful Omics Data
Finding a resource that combines complex experimental expertise, troubleshooting capabilities, deep disease knowledge, and advanced omics bioinformatics is rare. Converting your experiments into actionable therapeutic insights requires the integration of all these elements.
At Benthos Prime Central, we form a team that brings together these components, integrating omics at various levels to deliver actionable, therapeutically meaningful outcomes. We believe omics datasets should be more than just lists of genes, proteins, or spatial pixels — whether bulk, single-cell, or spatial, across transcriptomics, proteomics, or metabolomics. Traditional approaches like gene identification and pathway analysis often overlook biological context, turning expensive experiments into underutilized resources. Benthos Prime Central bridges this gap by integrating biology and bioinformatics, transforming both raw and pre-analyzed datasets into biologically meaningful insights. Our pipelines include: EV omics for enriching EV-specific molecules, lncRNA-specific analyses, Single-cell function-focused analyses and more.
Services “here”
Developing Innovative Bioinformatics Solutions
Traditional bioinformatics often treats datasets in a one-dimensional way, missing the complexity of biological regulation, which operates at multiple levels through coordinated interactions. This limitation can hinder reliable biomarker discoveries and effective therapeutic interventions. At Benthos Prime Central, we understand that each experiment and regulatory layer adds unique value to the understanding of cellular systems and pathways. We specialize in creating multi-dimensional, multi-omics solutions that deeply integrate biological information, enhancing the depth and relevance of your research. Whether you have RNA-seq data or a pilot single-cell transcriptomics experiment, we provide multi-omics integration without the need for costly additional experiments.
For example:
If you're working with miRNA profiling of extracellular vesicles (EVs), we assess the functional impact of your EVs on different organs and cell types, adding therapeutic value and cost-saving insights.
We also offer proprietary tools like GWASmeRNA, which predicts functional genomics associations for GWAS results lacking identified functions in the genome, linking them to RNA methylation pathways for deeper insights.
At Benthos Prime Central, we provide innovative tools to address a wide range of biological challenges, turning your data into actionable insights in a cost-effective and scientifically sound way.
Solutions “here”

Single-cell and single-nucleus transcriptomics (scRNA-seq, snRNA-seq)
Spatial transcriptomics
Single-cell DNA methylation
Long noncoding RNA sequencing (lncRNA) and lncRNA discovery (lncRNA-seq)
Single cell full-length transcriptome sequencing for RNA isoforms (SMART-seq)
Chromatin-IP (ChIP-seq)
RNA-IP (RIP-seq)
PRO-seq (RNA Polymerase, enhancer RNA active sites)
Direct RNA sequencing by nanopore for RNA modifications (epitranscriptomics)
Exosomes and extracellular vesicles RNA (transcriptomics) and protein (proteomics)
BIOINFORMATICS Analysis of omics datasets

Experimental and bioinformatics pipeline design and application
ASO, siRNA design for RNA-based drug discovery and gene knockdown
Interpretation for biology and therapeutic discovery of large omics datasets
Omics-based discovery and therapeutics pathway directions
Rapid preparation of data and figures for grants and manuscripts editing for improved success
Interpretation of publicly available Omics datasets for therapeutics
Small and large animal study design
Scientific editing to optimize clarity, accuracy and impact of a diverse range of scientific communications for successful manuscript publications and grants

Scientific and Biomedical Expertise
Prabhu Mathiyalagan is a globally experienced biomedical scientist and entrepreneur. He has led innovation in advanced human disease omics at two of New York City’s top institutions — New York University and Mount Sinai Hospital — where he built a strong foundation in real-world therapeutic discovery and development. He has multidisciplinary expertise spanning cardiovascular biology, pulmonary arterial hypertension, fibrosis, autoimmune diseases, blood pressure regulation, peripheral artery disease, stem cells, and tissue regeneration. His molecular and omics specialties include genetics, epigenetics, functional genomics, epitranscriptomics, RNA therapeutics, extracellular vesicles, single-cell and spatial transcriptomics, long noncoding RNA (lncRNA) therapy, and RNA engineering.
Professional Journey
Prabhu began his scientific journey in India with a Master’s in Biotechnology and Immunology at Bharathidasan University, focusing on HLA genetics. He earned his Ph.D. at Monash University, Australia, studying long noncoding RNAs and chromatin regulation of cardiac genes. In the U.S., he worked at Mount Sinai Hospital on RNA modifications and extracellular vesicles in cardiovascular disease, and at NYU on functional genomics in blood pressure and autoimmune diseases. At Haya Therapeutics in Switzerland, he advanced RNA-based drug discovery, biomarker development, and translational omics in the biotech industry.
Innovator of Proprietary Omics Platforms for Translational Research
Bridging academic rigor with real-world therapeutic impact, he has contributed to both academia and the biotech/pharma sectors, often serving as a global omics consultant to research labs, startups, and pharmaceutical companies. Prabhu has developed several proprietary platforms—including EVOrgansense™, GWASmeRNA™, RNAmethylQ™, RNA KnockMasterX™, and Artificial RNAgence™—to fill critical gaps in omics-driven discovery. He has authored numerous scientific publications, led high-performing research teams, and received major awards and grants including from the American Heart Association, NHLBI, and Keystone Symposia. He currently consults for multiple academic laboratories and biotechnology companies, and serves as a guest editor for several peer-reviewed scientific journals.

6 months ago

Working with Dr. Mathiyalagan and his company Benthos is allowing us to delve deeper into mechanisms of regenerative biology. It has greatly added to our ability to understand important molecular signaling pathways regulating various regenerative processes, and we hope to work together on many projects in the future! Benthos provides outstanding service in a timely manner, and at lower cost than many other similar services, with the bioinformatics expertise of Dr. Mathiyalagan, one of the most knowledgeable scientists I have encountered in this field!

We collaborate with Benthos Prime Central for our single nucleus transcriptomics project, and their insights and support has been invaluable. Their team provided us with expert guidance on sample preparation, data acquisition, and analysis, allowing us to achieve results with high precision. They were not only thorough in their technical support but also responsive to our specific needs throughout the project. Thanks to their help, we successfully generated a comprehensive transcriptomic profile that has greatly advanced our understanding of our study. I highly recommend Benthos Prime Central for their dedication to quality and experience in the field of single nucleus transcriptomics.

6 months ago

Jane Faber

Professor Hina Chaudhry

We have had an excellent experience with Benthos Prime Central's single-cell transcriptomics services and their EV miRNA omics analysis. Benthos Prime Central's EVOrgansense platform has enabled assessing the impact of our EVs on specific organs and tissues. Prabhu is very knowledgeable and consistently provided high-quality, accurate, and insightful analyses, significantly enhancing our research capabilities. We greatly value his expertise, responsiveness, and commitment to supporting our scientific goals.

6 months ago

Jane Faber

Professor Hina Chaudhry

I contacted Dr. Mathiyalagan and his team about a complicated 4D spatial transcriptomic study in which spatial resolution was paired with temporal changes of a specific cardiac population highlighted by the expression of an inducible YFP transgene. This required analyses like demultiplexing, QC and sequence alignment, expression quantification for each spot, dimensionality reduction (PCA), spatial clustering, tSNE, UMAP and differential expression. In addition, it entailed aggregate analysis by pooling samples together for differential gene expression analysis between groups using 10x loupe browser. Overall, they customized the spatial transcriptomic with YFP detection. The compelling data revealed important biological mechanisms, which we will now be able to publish. Dr. Mathiyalagan and his colleagues responded to all of my emails within minutes and helped me evaluate data and resolve challenges. I highly suggest Benthos Prime Central, Dr. Mathiyalagan's extensive scientific expertise, and his staff for analyses and sample processing.