David M. Umulis
Agricultural &
Biological Engineering
Purdue University
225 S. University St.
W. Lafayette, IN 47907
Phone: 765.494.1223
dumulis@purdue.edu 

Welcome to the ABE Computational Biology Group Webpage:

The focus of our research is to investigate the regulation of signal transduction in development. Specifically, we are interested in elucidating mechanisms of robustness, cell fate decisions, and tissue patterning by morphogen gradients. Engineers and biologists with some math/physics background are particularly capable of addressing these questions because development in many contexts relies on fluid flow, mass transport, chemical reactions, process control, and thermodynamics. One major goal of our lab is to foster interdisciplinary research projects to tackle problems in biology using quantitative image analysis and systems biology approaches such as mathematical models and bioinformatics.

Lab news & updates:

July 7, 2012. Graduate student Wei Dou is getting married!! Congratulations!

June 1, 2012 Dr. Umulis returns fromc0-leading a Study Abroad program in China. Tibet was very fascinating for many reasons.

Recent lab papers:

 

  1. Dou W, Zhang D, Jung YK, Cheng JX, Umulis DM.  Label-free imaging of lipid-droplet intracellular motion in early Drosophila embryos using femtosecond Stimulated Raman Loss microscopy. (To appear: Biophysical Journal)
  2. Dou W, Yang X, Bosnan T, Brooks A, Pargett M, Raftery L, Umulis DM. Evaluation of quantitative imaging methods for BMP-mediated morphogen patterning. FEBS Letters (Accepted).
  3. Raftery LA, Umulis DM. Regulation of BMP activity and range in Drosophila development.  Current Opinion in Cell Biology, 24:1-8. (2011)
  4. Karim M, Buzzard G, Umulis DM. Secreted, receptor-associated BMP regulators reduce stochastic noise intrinsic to many extracellular morphogen distributions. Available online ahead of print. Journal of the Royal Society: Interface, Available online ahead of print. (2011)
  5. Karim M, Umulis DM, Buzzard G. Steady state probability approximation applied to stochastic model of biological network. IEEE Proceedings: GENSIPS (); Selected for special issue of BMC Genomics (To appear).
  6. Hengenius JB, Gribskov M, Rundell AE, Fowlkes CC, and Umulis DM. Analysis of Gap Gene regulation in an Organism-scale model of the Drosophila melanogaster Embryo. PLoS ONE, 6(11): e26797. (2011)
  7. Peluso CE, Umulis DM, Kim YJ, O’Connor MB, and Serpe M. Shaping BMP morphogen gradients through enzyme-substrate interactions. Developmental Cell, 21(2) pp. 375 - 383. (2011)
  8. Harris R, Pargett M, Sutcliffe C, Umulis DM, Ashe HL.  Brat promotes stem cell differentiation via control of a bistable switch that restricts BMP signaling. Developmental Cell, 20, 1:72-83. (2011)
  9. Wang HW, Chai N, Hu S, Dou W, Umulis DM, Wang LV, Sturek M, Lucht R, Cheng JX. Label-free bond selective imaging by listening to vibrationally excited molecules. Physical Review Letters, 106:238106.  (2011).
  10. Claussen J, Hengenius J, Wickner M, Fisher T, Umulis DM*, Porterfield DM* Effects of Carbon Nanotube-Tethered Nanosphere Density on Amperometric Biosensing: Simulation and Experiment. Journal of Physical Chemistry C. 115(43):20896-904. (2011) *Co-corresponding author.
  11. Umulis DM, O. Shimmi, O’Connor MB, Othmer HG.  Organism-scale modeling of early Drosophila patterning via bone morphogenetic proteins. Developmental Cell, 18, 2:260-74. (2010) PMCID: PMC2848394