Peter Simsfaculty & research

Peter sims

Peter Sims photo PETER SIMS
Email: pas2182@columbia.edu
Phone: 212-851-5369
Location ICRC-1002B



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.

Selected Publications

 

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).

Sims, P.A., Greenleaf, W.J., Duan, H., Xie, X.S. Fluorogenic DNA sequencing in PDMS microreactors. Nature Methods, 8, 575-580 (2011).

  • Featured in Chemical & Engineering News, Nature Methods, NIH NHGRI Genome Advance of the Month, GenomeWeb / In Sequence, and Faculty of 1000.

Sims, P.A., Xie, X.S. Probing dynein and kinesin stepping with mechanical manipulation in a living cell. ChemPhysChem, 10, 1511-1516 (2009).

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).

Nan, X., Sims, P.A., Xie, X.S. Organelle tracking in a living cell with microsecond time resolution and nanometer spatial precision. ChemPhysChem, 9, 707-712 (2008).

  • Featured as the Cover Article in ChemPhysChem.

Lu, P.J., Sims, P.A., Oki, H., MacArthur, J., Weitz, D.A. Target-locking acquisition with real-time confocal (TARC) microscopy. Optics Express, 15, 8702-8712 (2007).

 

Nan, X., Sims, P.A., Chen, P., Xie, X.S. Observation of individual microtubule motor steps in living cells with endocytosed quantum dots. J. Phys. Chem. B, 109, 24220-24224 (2005).

  • 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).