We are working to improve single-cell approaches to systems biology. These techniques are crucial because individual cells respond heterogeneously to identical chemical and genetic perturbations, and because clinical samples are often limited to small numbers of cells. Translating new and existing techniques for genome- and proteome-wide analysis to the single cell level will facilitate their application to biomedicine. By combining cutting-edge microscopy, next-generation sequencing, and microfabrication, we enable novel, unbiased measurements for investigation of heterogeneous biological systems. We focus mainly on single-cell transcriptomics along with single molecule and single cell approaches to proteomics, where current tools lag far behind those available for nucleic acid analysis.
Shiroguchi, K., Jia, T.Z., Sims, P.A., Xie. X.S. Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Single Molecule Barcodes. Proc. Natl. Acad. Sci. USA, (published online, 2012).
Featured in Chemical & Engineering News, Nature Methods, NIH NHGRI Genome Advance of the Month, GenomeWeb / In Sequence, and Faculty of 1000.
Sims, J.S., Militello, K.T., Sims, P.A., Patel, V.P., Kasper, J.M., Wirth, D.F. Patterns of gene-specific and total transcriptional activity during the Plasmodium falciparum intraerythrocytic developmental cycle. Eurkaryot. Cell, 8, 327-338 (2009).
Featured as the Cover Article in ChemPhysChem.
Featured in Chemical & Engineering News.
Sims, P.A., Wong, C.F., Vuga, D., McCammon, J.A., Sefton, B.M. Relative contributions of desolvation, inter-, and intramolecular interactions to binding affinity in protein kinase systems. J. Comp. Chem., 26, 668-681 (2005).