Nexco | Laboratory of Cell and Membrane Biology, EPFL

From Bench to Publications: When Faster Bespoke Analyses Combined with Deep Biological Insights Shape Research Direction

Leveraging RNA-seq and ChIP-seq to understand cellular responses to perturbations

"Nexco Analytics provides expert bioinformatics with deep scientific collaboration, making them an invaluable research partner"

Francisco Mesquita, PhD, is a senior scientist at the EPFL, Lausanne, whose research focuses on membrane biology at the host-pathogen interface. Dr. Mesquita frequently harnesses different omics technologies, particularly RNA-seq and ChIP-seq, to identify key molecular mechanisms crucial for understanding how cells and their membranes respond to perturbations. However, before collaborating with Nexco Analytics, he struggled to process, analyze, and interpret large-scale omics experiments and extract biologically meaningful insights to inform his research direction.

As part of the van der Goot lab, Dr. Mesquita studies various aspects of cell and membrane biology, including membrane properties of the endoplasmic reticulum and plasma membrane, the dynamics of a type of posttranslational modification called S-palmitoylation, and how host cell pathways respond to infections and toxins.

Dr. Mesquita struggled to process, analyze, and interpret large-scale omics experiments and extract biologically meaningful insights to inform his research direction.

Here are the challenges he faced and how Nexco Analytics helped:

Dr. Mesquita struggled to process large quantities of omics data efficiently

He found standard data analysis pipelines too rigid or superficial for his complex experiments

This limited the biologically meaningful interpretations he could make

He had difficulty finding biologically savvy data analysts who could also contribute biological interpretations to help shape experimental hypotheses

"Before working with Nexco Analytics, we needed a bioinformatics partner who could efficiently process large omics datasets while providing biologically meaningful interpretations. Standard computational pipelines were often too rigid or lacked the depth required for our research. We also wanted a team that could integrate with our projects, contribute scientific insights, and help shape experimental directions."

Nexco Analytics provided large-scale RNA-seq and ChIP-seq data processing, with pathway and ontology analysis

Nexco Analytics’ data analysts held in-person meetings with Dr. Mesquita, where they offered novel analytical and insightful biological ideas to help shape his research direction

They created custom analytical strategies and solutions tailored to Dr. Mesquita’s projects

Nexco Analytics integrated publicly available omics data to help independently validate and strengthen his findings

"What set Nexco Analytics apart was their ability to actively engage with our research, providing valuable insights and suggesting new research avenues."

Dr. Mesquita improved his research efficiency and expanded his research scope

With Nexco Analytics, he benefited from highly efficient data processing and in-depth, custom analyses that were hard to achieve before

He identified key regulatory pathways and made novel findings crucial to his publications

He benefited from continual engagement, flexibility, and support in data analysis and deep biological interpretation from Nexco Analytics

Dr. Mesquita’s collaboration with Nexco Analytics was integral to publications, grant applications, and conference presentations

"The biggest benefit of working with Nexco Analytics is their scientific engagement and flexibility. They don’t just analyze data—they contribute to the research itself. They provide expert bioinformatics with deep scientific collaboration, making them an invaluable research partner. Their work has contributed to our publications, grant applications, and conference presentations, improving research efficiency and expanding our scientific scope. I would highly recommend Nexco Analytics to any researcher needing expert bioinformatics analysis with a strong collaborative approach."