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Interdisciplinary Work Featured by BMC Genomics

M. D. McNally • DATE: September 29, 2016

Interdisciplinary Work Featured by BMC Genomics

Professor Milenkovic

A recent paper co-authored by Milenkovic’s Complex Networks lab (Computer Science and Engineering) and Pfrender lab (Biology) from the University of the Notre Dame has been featured on the main page of the BMC Genomics journal. The paper has 11 authors, including Boyoung Yoo (the first co-author of the paper who is currently a Ph.D. student at Stanford University) and Taryn Green, both of whom were working as undergraduate researchers in Milenkovic lab at the time of the study.

The paper's biology focus is on studying in the freshwater crustacean Daphnia daily rhythmic patterns of behavior and physiology that may be regulated by a molecular circadian clock, by analyzing genome-wide temporal transcriptomics data. This work adds to a growing body of literature suggesting that the genetic mechanisms governing rhythmicity in crustaceans may be divergent from other arthropod lineages including insects.

The computational novelty of the paper comes from using a comprehensive network modeling and analysis approach on top of traditional statistical "differential gene expression" analyses of the Daphnia transcriptomics data, in order to identify novel co-regulated rhythmic genes that have similar network topological properties and functional annotations as rhythmic genes identified by the traditional analyses. In the process, the network approach was also applied to prediction of novel protein functional annotations. Thus, the paper highlights the power of network modeling in the biology domain, as it shows that network analyses can reveal novel knowledge that traditional non-network approaches might not be able to uncover.