Methods engineering of biomolecular and cellular assays

Methods engineering of biomolecular and cellular assays

Intersection of FOXO and RUNX1 gene-expression programs in single breast epithelial cells during morphogenesis and tumor progression. (2011) Proc Natl Acad Sci, 108, E803-12. [link to article]

Problem solving subject to constraints is the hallmark of engineering design (1). We adopt a design approach to invent new methods for interrogating cells and biomolecules. Our goal is to develop bioassays that are sensitive, quantitative, and as high-throughput and multiplex as possible. Most importantly, they should be reliable, generalizable, and shareable.

In the realm of signal transduction, we have developed and expanded high-throughput methods for profiling protein phosphatase activities (2, 3). These methods are now being applied to chronic viral infections along with a technique under development for a multiplex kinase activity assay. We also seek to extend or standardize established methods. For example, we have scaled quantitative real-time PCR to the entire human signaling receptome (4) and set standards for quantitative immunoblotting (5). Beyond empirical methods, we have completed a software platform for digital segmentation of brightfield images of 3D organoid cultures (to be submitted).

Selected Publications

  1. Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA. (2017) An engineering design approach to systems biology. Integr Biol, 9, 574-83. [Article]
  2. Shah M, Smolko CM, Kinicki S, Chapman ZD, Brautigan DL, Janes KA. (2017) Profiling subcellular phosphatase responses to coxsackievirus B3 infection of cardiomyocytes. Mol Cell Proteomics, 16, S244-S262. [Article]
  3. Janes KA. (2015) An analysis of critical factors for quantitative immunoblotting. Sci Signal, 8, rs2 [Article]
  4. Bose AK, Janes KA. (2013) A high-throughput assay for phosphoprotein-specific phosphatase activity in cellular extracts. Mol Cell Proteomics, 12, 797-806. [Article]
  5. Kang BH*, Jensen KJ*, Hatch JA, Janes KA. (2013) Simultaneous profiling of 194 distinct receptor transcripts in human cells. Sci Signal, 6, rs13. [Article]