Prior to retiring in 2022, Alan's role as a bioinformatician was 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). He continues to work in a consulting capacity.
As an engineer with extensive experience in bioinformatics and computational biology, Alan supported the Harlan Lab, Greiner Lab, Brehm Lab, Kent Lab and Wang Lab by analyzing their diversified research and extracting data produced by the many experiments performed by our team of immunologists and biologists.
Alan 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, MD
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.
"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 Chan Diabetes Center of Excellence. "He enjoys talking about the biology too, and you can tell he's passionate about his work."
Publications
Derr AG, Arowosegbe A, Satish B, Redick SD, Qaisar N, Guo Z, Vanderleeden E, Trombly MI, Baer CE, Harlan DM, Greiner DL, Garber M, Wang JP. An Early Islet Transcriptional Signature is Associated with Local Inflammation in Autoimmune Diabetes. Diabetes. 2022 Nov 8:db220521. doi: 10.2337/db22-0521. Online ahead of print. PMID: 36346618
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. Diabetes. 2019 May;68(5):988-1001. doi: 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