Beyond the Data: Bioinformatics at Albany Medical College

Reprinted from the Alumni Association Winter 2025 Bulletin.

Ramon Bossardi Ramos, PhD, is an assistant professor, molecular and cellular physiology, and the director of the bioinformatics core in the Department of Molecular and Cellular Physiology at Albany Medical College, where he plays a dual role as a researcher and core director. His lab specializes in multiomics data analysis, focusing on bioinformatics, epigenetics, and the impact of inflammation on endothelial health. Dr. Ramos’s work addresses critical questions in endothelial biology and vascular inflammation, contributing to foundational research and the development of bioinformatics capabilities across the college.

Dr. Bossardi-Ramos began his scientific journey at the Federal University of Rio Grande do Sul (UFRGS) in Brazil, studying the molecular bases of multifactorial diseases. His research trajectory took him to Johns Hopkins University for his first postdoctoral fellowship, where he deepened his expertise in epigenetics, particularly gene imprinting and DNA methylation. Following this, he completed a second postdoctoral fellowship at Albany Medical College, investigating IL-6 signaling’s effects on endothelial DNA and the protective role of SOCS3.

Transitioning to a faculty position at Albany Medical College, Dr. Bossardi-Ramos was awarded a prestigious Career Development Award (CDA) from the American Heart Association, which has been instrumental in establishing his independent research program. This funding supports his dual mission of advancing endothelial inflammation research and building a robust bioinformatics core.

We spoke with Dr. Ramos about how his dual expertise in research and bioinformatics core management allows him to bridge cutting-edge computational analysis with translational research, enhancing the college’s capacity to pursue innovative studies in cardiovascular and inflammatory diseases. Below are highlights of our discussion.

What is bioinformatics?

Bioinformatics is an interdisciplinary field combining biology, computer science, and statistics to analyze biological data, such as DNA sequences and gene expression. It goes beyond data management, using algorithms and models to uncover molecular mechanisms, predict disease outcomes, and find potential treatments.

 At Albany Medical College, bioinformatics is part of our research efforts on complex diseases, including sepsis, cardiovascular disease, and cancer, through collaborations across multiple disciplines. By integrating data from technologies like RNA sequencing and epigenetic profiling, I work with researchers in all four basic science departments and clinical medicine to uncover disease mechanisms and identify biomarkers. These efforts accelerate early diagnosis, enable personalized treatments, and enhance Albany Medical Center's research profile.

Our work has led to published papers and active grant submissions, supporting innovative studies that contribute to our mission of advancing patient outcomes. The return on these efforts strengthens the College’s role as a leader in cutting-edge bioinformatics in the region, enabling us to bring pioneering research insights directly into clinical applications.

What are the objectives of bioinformatics?

At its core, bioinformatics aims to use computational tools to decode the vast and complex information found in biological data. The primary objectives include organizing, analyzing, and interpreting this data to uncover insights about how genes and proteins function, how diseases progress, and how biological systems interact. By translating raw biological data into actionable knowledge, bioinformatics enables researchers to make discoveries that can lead to breakthroughs in diagnostics, drug development, and personalized medicine.

The bioinformatics core is dedicated to bridging research and clinical application, ultimately contributing to improved patient care and personalized therapies.

How is bioinformatics working/helping Albany Medical College?

Bioinformatics is a part of research that supports investigators in biological questions with a data-driven approach. We analyze vast amounts of genetic and molecular data through bioinformatics, helping to reveal the mechanisms underlying diseases. Over the past two years, I have made significant contributions to the College’s research mission. We have published 10 papers in collaboration with research groups. The collaboration is broad reaching, involving 21 investigators across departments, and has strengthened grant proposals.

My work involves many analyses, from RNA sequencing and ATAC-seq to single-cell sequencing and DNA methylation studies. Beyond research, bioinformatics contributes to educational initiatives at Albany Medical College. Courses like Medical Informatics and a Bioinformatics Journal Club empower the next generation of researchers with the computational skills to analyze and interpret complex biological data.

What more do we need to be successful with this program?

Continued investment in advanced technology and resources is crucial to fully realizing the potential of our bioinformatics program at Albany Medical College. As we continue to push the boundaries of personalized medicine, bioinformatics requires highly specialized software tools, enhanced data storage solutions, and support for cutting-edge methodologies like machine learning and AI.

We are also eager to build a bridge between research and clinical applications. With further support, we could establish a bioinformatics-driven clinical genomics program to bring precision medicine directly into patient care, helping physicians make data-informed decisions tailored to an individual’s genetic profile. This has enormous potential for patients with complex conditions, where personalized approaches could significantly improve outcomes.

Ultimately, donations and partnerships with philanthropic organizations could transform our efforts to achieve these goals. Such support would accelerate research discoveries and bring us closer to a future where data-driven insights from bioinformatics translate directly into better health outcomes for our patients and the broader community.

Are you collaborating with other colleges or universities?

Our bioinformatics core actively collaborates both within Albany Medical College and with leading institutions worldwide. Internally, we work with investigators across multiple departments, providing bioinformatics support to enhance their research. Externally, we partner with renowned universities and research centers, forming a network that strengthens our projects with diverse expertise and resources. These collaborations enable us to drive innovation, tackle complex questions, and expand the impact of our research on a global scale.

Which type of skills are required to be good at your job?

Strong analytical skills and a solid understanding of biology are essential to be effective as a bioinformatician. We must be comfortable with computer programming, as much of our work involves writing code to analyze large datasets. Critical thinking is crucial, allowing us to interpret complex data and uncover meaningful patterns contributing to medical research. Lastly, communication skills are important as we collaborate with researchers from various fields to make sense of data in a way that can drive clinical advances.

Do you rely on multiple databases in your computing?

Most of the data used in bioinformatics core analyses comes from our own researchers, who generate high-quality data through cutting-edge projects. This data feeds directly into our bioinformatics analyses, enabling us to find new insights into disease mechanisms and potential treatments by combining Albany Medical College-generated data with insights from global databases.

We also rely on multiple databases to analyze and interpret biological data. These databases store gene sequences, protein structures, and clinical data. There are federal databases (such as those from the NIH), which are publicly accessible, proprietary databases that offer specialized curated data, and focused research databases for areas like cancer genomics.

Are there specific programming languages?

In bioinformatics, I use programming languages like R, Python, and Bash. R is excellent for statistical analysis and data visualization, helping us interpret complex biological data. Python is very versatile, allowing us to automate tasks and handle large datasets efficiently. Bash is used for managing files and running commands on our servers, which is essential for processing large-scale data quickly. Together, these languages enable us to turn raw biological data into meaningful insights.

What do you enjoy about this role?

What I enjoy most about my role is the opportunity to uncover insights that can impact health care. Bioinformatics allows me to explore the complexities of biology through data, bridging science and technology to answer challenging questions. I also love the collaborative nature of the work—partnering with researchers across disciplines and translating data into discoveries that could one day improve patient outcomes. Knowing that each analysis brings us closer to new therapies and a better understanding of disease is rewarding.

What is difficult?

One of the biggest challenges in bioinformatics is managing and analyzing vast amounts of complex data. Each dataset can be millions of data points, requiring careful organization, powerful computational resources, and specialized skills to extract meaningful insights. Another difficulty is keeping up with the fast-paced advancements in biology and technology; there’s always a new learning tool or method. Finally, translating complex findings into actionable insights that other researchers and clinicians can use adds more complexity to the work.

Are there challenges or equipment needs that could improve outcomes?

The bioinformatics core at Albany Medical College has grown significantly, with collaborations spanning 22 research groups and a lab to manage. With only one bioinformatician handling this workload, there’s a real opportunity to enhance our research impact by expanding support. Access to additional staff and advanced computing resources would allow us to keep pace with increasing data demands and provide even faster, more in-depth analysis. This support would ultimately empower us to make quicker strides in critical areas like sepsis, cancer, and cardiovascular research, benefiting our investigators and the patients who rely on these advancements.

What are you hopeful about in this field?

I am incredibly hopeful about the transformative power of bioinformatics to revolutionize health care. As we delve deeper into complex conditions like cardiovascular disease, sepsis and cancer, bioinformatics allows us to decode the molecular details that could lead to groundbreaking therapies and personalized treatments. The potential to predict disease outcomes, identify novel drug targets, and develop treatments tailored to each patient's unique genetic profile is within reach.

With the proper support, our bioinformatics core at Albany Medical College could be at the forefront of these advancements. Expanding our resources would allow us to accelerate discoveries that could change lives, not only by improving patient outcomes here but also by setting a new standard in medical research. This is a pivotal time for investment in bioinformatics, and with increased backing, we can push the boundaries of what is possible in medicine.