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Biotechnology Program (BIT)

Dr. Raymond Haggerty

Image of Dr. Raymond Haggerty

Project Description:

  • Microscopy
  • Image Analysis
  • Computational Biology
  • Bioinformatics

Techniques:

  • Bright-field microscopy
  • Fluorescent microscopy
  • Single-cell and time-lapse microscopy
  • Image feature extraction and analysis
  • Machine learning for biological applications
  • Mathematical and biophysical modeling

Project Description:

Microscopy allows us to see things that are invisible to the naked eye and image analysis allows us to extract quantitative information from microscopy experiments.  This allows us to explore a wealth of information from finding the localization of a protein of interest [1], exploring the dynamics of transcription when a cell is exposed to stress [2], helping us biophysically model how cells attain the right tension to undergo mitosis [3], or even determine the fate of stem cells [4].  Those previous examples are actually just projects I have been involved in- including some during my time as an undergraduate research student!  There are still even more diverse microscopy projects throughout many different fields of biology.

Summer research students will do imaging and analysis experiments on a variety of biological systems.  Prior experience using a microscope or programming is not necessary.  Most image analysis will take place using graphical user interface programs, but some students might also learn some programming.

References:

  • Haase J, Mishra PK, Stephens A, Haggerty RA, Quammen C, Taylor RM 2nd, Yeh E, Basrai MA, Bloom K. A 3D map of the yeast kinetochore reveals the presence of core and accessory centromere-specific histone. Curr Biol. 2013 Oct 7;23(19):1939-44. doi: 10.1016/j.cub.2013.07.083. Epub 2013 Sep 26.
  • Haggerty RA, Purvis JE. Inferring the structures of signaling motifs from paired dynamic traces of single cells. PLoS Comput Biol. 2021 Feb 4;17(2):e1008657. doi: 10.1371/journal.pcbi.1008657. 
  • Stephens AD, Haggerty RA, Vasquez PA, Vicci L, Snider CE, Shi F, Quammen C, Mullins C, Haase J, Taylor RM 2nd, Verdaasdonk JS, Falvo MR, Jin Y, Forest MG, Bloom K. Pericentric chromatin loops function as a nonlinear spring in mitotic force balance. J Cell Biol. 2013 Mar 18;200(6):757-72. doi: 10.1083/jcb.201208163.
  • Wolff SC, Kedziora KM, Dumitru R, Dungee CD, Zikry TM, Beltran AS, Haggerty RA, Cheng J, Redick MA, Purvis JE. Inheritance of OCT4 predetermines fate choice in human embryonic stem cells. Mol Syst Biol. 2018 Sep 3;14(9):e8140. doi: 10.15252/msb.20178140.