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.

6 months ago

Jane Faber

Professor Hina Chaudhry

“We worked closely with Prabhu and his team on several multi-omics projects, including human patient-derived scRNA-seq and bulk RNA-seq analysis, and were very satisfied with the support. They went beyond standard pipelines and helped tailor the analysis to our specific disease context, including cell-type deconvolution for bulk RNA-seq and network-level scRNA-seq analysis such as CellChat, SCENIC, and pseudotime. They also helped integrate multiple datasets into a clear biological story, which was very useful for our translational goals. In addition, they quickly developed a SNP panel strategy for genotype-based demultiplexing of pooled snRNA-seq samples using public datasets, which was especially helpful for our grant application timeline. Overall, the work was fast, responsive, and scientifically solid, and added real value to our project.”

“Working with Benthos Prime Central on our multi-omics study was a highly valuable experience. The project involved integration of single-cell transcriptomics, DNA methylation, and bulk RNA-seq across multiple human tissues and comparison groups. Their team brought more than just analytical support. They contributed to shaping the overall direction of the study. By thoughtfully integrating datasets across modalities and tissues, they helped reveal disease mechanisms that were not apparent from individual analyses alone, including previously uncharacterized pathways with potential relevance to disease prevention. They also provided meaningful input in organizing complex results into a clear and compelling biological narrative. Their support in figure preparation and manuscript development helped improve both the clarity and coherence of the final work. Overall, Benthos Prime Central demonstrated a strong combination of technical expertise, biological understanding, and collaborative scientific thinking. They are well suited for complex, multi-layered omics projects that require both depth of analysis and interpretability.”

6 months ago

Jane Faber

Professor Hina Chaudhry

“We engaged Benthos Prime Central to run RNA-seq for our samples and have their support for RNA-seq and iPS-specific transcriptomic analysis. From the outset, their team provided thoughtful guidance on experimental design, sample preparation, and appropriate omics strategies, which helped strengthen the overall direction of the project. The analysis itself was thorough and extended beyond conventional pathway-level interpretation, yielding deeper insights into the underlying transcriptomic changes. Their experience with bulk transcriptomics was evident in both the quality of the analysis and the clarity of the results presented. Throughout the project, communication was clear and collaborative, and the work was delivered on time. Their ability to bridge experimental considerations with downstream data analysis made them a valuable partner from planning through to final interpretation.”

“We had the opportunity to collaborate with Benthos Prime Central on a portfolio of advanced transcriptomics initiatives spanning single-nucleus RNA sequencing (snRNA-seq) in murine tissues, single-cell RNA sequencing (scRNA-seq) in human stem cell systems, and integrative analyses across bulk RNA-seq and lncRNA datasets in both human and mouse tissues. What sets their team apart is their ability to go far beyond conventional analytics. They applied sophisticated computational frameworks; including trajectory, and pseudotime modeling, and cross-platform data integration paired with rigorous pathway-level interrogation. This enabled the identification of rare and previously uncharacterized cellular populations and the construction of cohesive, biologically meaningful narratives across complex datasets. Importantly, their work connected multi-omics data to stem cell biology and regenerative processes, providing valuable mechanistic insights with clear translational relevance. The integration of diverse datasets into a unified, systems-level understanding was particularly impressive. Benthos Prime Central brings together deep computational expertise with nuanced biological interpretation, consistently delivering clear, actionable insights. We strongly recommend them as a premier partner for complex single-cell and multi-omics programs, particularly those aimed at uncovering novel biology and advancing therapeutic innovation.”

6 months ago

Jane Faber

Professor Hina Chaudhry

“We collaborated with Benthos Prime Central on integrative epigenomics and transcriptomics analyses in human tissue, with a particular focus on DNA methylation and comprehensive mapping of CpG islands across miRNA genes. Their work stood out for its precision and depth, combining site-specific DNA methylation analysis and CpG islands with careful mapping of miRNA loci to uncover regulatory relationships between epigenetic modifications and non-coding RNA expression. They went beyond standard workflows by designing targeted assays and primers to interrogate methylation-dependent regulation at specific genomic regions. Importantly, they extended these insights into exosomal transcriptomics, linking tissue-level epigenetic regulation to circulating molecular signals with potential biomarker relevance. This systems-level yet highly targeted approach provided novel biological insights that would not have been captured through conventional analyses. Benthos Prime Central brings a rare combination of technical rigor and biological interpretation, and we would strongly recommend them for advanced multi-omics and epigenomics projects with translational focus.”

“I've had the genuine pleasure of collaborating with Dr. Prabhu Mathiyalagan and his team at Benthos Prime Central for nearly a year, and it's been an incredibly rewarding experience. We've worked together on a range of exciting and complex projects - from whole genome DNA methylation and single-cell transcriptomics to immune profiling and multiomics integration involving mRNA and noncoding RNA. What stands out most about Prabhu is his deep scientific insight and the clarity he brings to every conversation. He and his team have been instrumental not just in the data analysis, but also in shaping the conceptual direction of our work. Their expertise in extracellular vesicle biology has added a valuable dimension to our research. Beyond the science, it's been a true pleasure working with someone so thoughtful, responsive, and collaborative. Prabhu fosters a spirit of partnership that makes even the most challenging projects feel manageable and exciting. I’m grateful for the trust and synergy we’ve built and look forward to continuing this journey together.”

6 months ago

Jane Faber

Professor Hina Chaudhry

“We worked closely with Prabhu and Benthos Prime Central on our zebrafish scRNA-seq project and had a great experience throughout the collaboration. The team went beyond a standard single-cell analysis pipeline and took the time to understand the biological context of our project. They incorporated our feedback through multiple rounds of analysis, including refinement of cell populations, improved cell-type annotation using multiple reference datasets, and tailored interpretation based on relevant literature. They also performed advanced analyses, including cell-cell communication, pseudotime trajectory analysis, and in-depth differential expression analysis, while continuously adapting the approach to our specific scientific questions. Overall, the team was highly responsive and scientifically rigorous.”