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Alan Derr - Bioinformatician

Cammett Scholar for Type 1 Diabetes Research,
Diabetes Center of Excellence, UMass Medical School


Bioinformatics, Brandeis University
MS, Electrical Engineering, Columbia University
BS, Electrical Engineering, Rensselaer Polytechnic Institute


Analyzing T1D Data at UMass Medical School

Alan's role as a bioinformatician is to analyze the vast volume of data generated during the study of human insulin producing beta cells and the immune cells that attack human islets in people living with type 1 diabetes (T1D).  

As an engineer with extensive experience in bioinformatics and computational biology, Alan supports the Harlan Lab, Greiner Lab, Brehm Lab, Kent Lab and Wang Lab. He applies his expertise to analyze their diversified research which includes comparing human islet cells from donors with T1D to that of non-diabetic islets, exploring the onset of T1D in a unique rat model, and recapitulating T1D in our novel humanized model of type 1 diabetes. Alan is responsible for extracting data produced by the many experiments performed by our team of immunologists and biologists.

Alan is also working to develop single-cell RNA-Seq analysis tools, pipelines, and methods. He developed and wrote the ESAT (End-sequencing Analysis Toolkit), a program designed to analyze RNA-Seq data derived from end-sequencing methods, which has become extremely useful in the quantification of data from single-cell RNA-Seq technologies.

Cammett Scholar for Type 1 Diabetes Research


(left to right)  John Cammett - Alan Derr - David Harlan

Alan was awarded the Cammett Scholar for type 1 diabetes research, supported by a generous gift from UMass Diabetes Center of Excellence Visiting Advocacy Committee member John Cammett. Mr. Cammett has type 1 diabetes and is inspired by his mother who has lived with T1D for nearly 60 years. He serves on the JDRF finance committee and provides business expertise and financial support to new therapies and technologies. 

"Alan Derr is the rare bioinformatician who speaks in a way non-science people can understand," said David Harlan, MD, co-director of the UMass Diabetes Center of Excellence. "Alan enjoys talking about the biology too, and you can tell he's passionate about his work."


Russell MA, Redick SD, Blodgett DM, Richardson SJ, Leete P, Krogvold L, Dahl-Jørgensen K, Bottino R, Brissova M, Spaeth JM, Babon JAB, Haliyur R, Powers AC, Yang C, Kent SC, Derr AG, Kucukural A, Garber MG, Morgan NG, Harlan DM. HLA Class II Antigen Processing and Presentation Pathway Components Demonstrated by Transcriptome and Protein Analyses of Islet β-Cells From Donors With Type 1 Diabetes. Diabetes2019 May;68(5):988-1001doi: 10.2337/db18-0686. PubMed PMID: 30833470; PubMed Central PMCID: PMC6477908.

Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res. 2016 Oct;26(10):1397-1410. PubMed PMID: 27470110; PubMed Central PMCID: PMC5052061.

Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun F, Song L, Carone BR, Ricci EP, Li XZ, Fauquier L, Moore MJ, Sullivan R, Mello CC, Garber M, Rando OJ.
Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science. 2016 Jan 22;351(6271):391-396. PubMed PMID: 26721685; PubMed Central PMCID: PMC4888079.

A complete list of published work can be found in My Bibliography