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Haddock is the lead author of Practical computing for biologists (Sinauer, 2011). He has contributed to over 100 research papers on bioluminescence and related phenomena in open ocean and deep sea animals including Ctenophora, Siphonophora, Radiolaria, and Medusae. His co-written paper "Broad phylogenomic sampling improves resolution of the animal tree of life" has been cited over 1675 times, while the review article "Bioluminescence in the sea" has been cited over 475 times.