MDI Biological Laboratory
Senior Staff Scientist, Director of Comparative Genomics and Data Science Core

Joel H. Graber, Ph.D.

Modern biomedical research is increasingly data-intensive and requires computational expertise and robust procedures that ensure rigorous and reproductive analysis.

The MDI Biological Laboratory's Comparative Genomics and Data Science (CGDS) Core is focused on collaboration, analysis and education in the computational analysis of genome-scale data. Their efforts are distributed between the linked goals of (1) providing our collaborating research groups with experimental data analysis/management and computational resources, and (2) providing training in computational biology within MDIBL and also as the Maine INBRE (IDeA Networks of Biomedical Research Excellence) research program.

Biomedical research is dependent on data management and increasingly sophisticated analysis workflows that are both rigorous and reproducible. The Core has the experience and knowledge to provide training, analysis, and infrastructure that enable our collaborating researchers to accomplish their research goals.

As director of the CGDS core, it is Dr. Graber's role to ensure that MDI Bio Lab's computational data analysis resources are up-to-date and sufficiently adaptable to answer the specific questions of interest for each research group. The Core's work is highly collaborative, beginning before data is collected with discussions and statistical assessment of projected experiments, continuing through all steps of data analysis, providing explanations of the rationale and consequences of computational options and finally ending with the generation of tables and figures and their interpretation for publication and presentation.

Core personnel depend upon, and contribute to, community-supported and open-source software packages and workflows. This work is focused on robust and rigorous vetting, storage, and analysis of genomic data. Reproducibility is ensured by using workflows and software that implement careful version control of all software and external data resources, combined with complete and detailed logging of all analytic procedures. Rigor is established and enhanced by generating all workflows in a modular manner that facilitates characterization of the consequences of variation in choices of program, data resources or parameters.

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Education

  • Ph.D., Cornell University, Experimental Accelerator Physics, 1993
  • B.S., Michigan Technological University, Physics, 1987
  • B.S., Michigan Technological University, Computer Science, 1987

Student Projects

Research Fellow projects working within the Comparative Genomics and Data Science Core are focused on analysis and interpretation of genome-scale biological and biomedical data. In recent years, the Core team has also defined and supervised several Masters Degree projects for students from our associated educational institutions. 

Projects are generally carried out in collaboration with wet-bench researchers from MDI Bio Lab as well as visiting or INBRE-partner research groups, focusing on rigorous analysis of genome-scale data. Core personnel also support computational projects that emphasize “best practices” in developing rigorous and reproducible tools, workflows, and databases. Summer projects are discrete, targeted towards analysis or tool development, and can be carried out over the course of 10 weeks. The CGDS Core is also open to academic year internships focused on longer-term projects.

Lab Members

Celeste NobregaBioinformatician II

Celeste Nobrega received her B.A. in bioinformatics from Wheaton College in 2022. Her history with MDI Bio Lab began as an REU student with the CGDS Core in 2020, where she studied the transcriptomic response of zebrafish to chronic cortisol exposure. She continued this work through her undergraduate Honors Thesis in 2021–22. After graduating, she spent three years in cancer research at the Broad Institute of MIT and Harvard, deepening her expertise in transcriptomic analysis. In 2025, she found her way back to MDI Bio Lab, where she now works as a bioinformatician in the CGDS Core. She is passionate about bridging the gap between bench scientists and computational work, sharing her knowledge through lectures and hands-on courses. Alongside her teaching, she continues to develop her skills across all things transcriptomics. Much of her current work centers on bulk RNA-seq analysis for investigators across the INBRE network, including deconvolution with single-cell references, differential polyadenylation, comparative genomics and open-ended data science problem-solving.

Riley GrindleBioinformatician I

Riley Grindle earned his B.Sc. in Molecular Biology and Computer Science from the University of Maine in 2023 and is currently pursuing a Master's in bioinformatics, with a concentration in data science, at Northeastern University's Roux Institute. He has been a bioinformatician with the CGDS core since 2023, specializing in single-cell and spatial transcriptomics and in optimizing these workflows for cloud environments. In addition to this work, he has become an ambassador for the Nextflow programming community, applying many of its principles to lead development on several internal pipelines: scscape (single-cell downstream analysis), txmupdate (transcriptome refinement), and orthologymap (cross-species gene comparison).

Matthew CoxBioinformatician I

Matthew Cox received his B.S. from the University of Maine in 2022 and joined MDI Bio Lab that same year as a research assistant, studying aging in C. elegans and Drosophila under metabolic and environmental stress. In 2024, he began a Master's in Data Analytics (concentration in Machine Intelligence) at Northeastern University's Roux Institute while helping manage MDI Bio Lab's African turquoise killifish colony. He has since transitioned to MDI Bio Lab's CGDS core, where he analyzes transcriptomic data for Dr. Hermann Haller's lab, which investigates vascular aging dynamics and therapeutics, and completed his Master's in 2026.

Markus SujanskyBioinformatician I

Markus Sujansky earned his B.Sc. in Biology and Computer Science at Boston College in 2025, joining MDI Bio Lab's Computational Genomics and Data Science Core later that year. His time at MDI Bio Lab had begun two summers previously, though, as a SURF fellow in the CGDS core, during which he fell in love with the research process and computational science puzzle. In his role, he serves as the lead bioinformatician attaché to the Plasticity Group, a subset of MDI Bio Lab's labs interested in studying cellular plasticity as a mechanism of regeneration. To this end, he developed scSAMap, a Nextflow Pipeline focused on robust cross-species single-cell/nucleus comparative analysis, and remains interested in the rapidly expanding multi-omic applications of data science in the field.