Publications

  1. P.A. Barendt, N.A. Shah, G.A. Barendt, P.A. Kothari, and C.A. Sarkar. "Evidence for context-dependent complementarity of non-Shine-Dalgarno ribosome binding sites to Escherichia coli rRNA." ACS Chemical Biology, in press (2013). Abstract | PDF
  2. P.A. Barendt†, D.T.W. Ng†, C.N. McQuade, and C.A. Sarkar. "Streamlined protocol for mRNA display." ACS Combinatorial Science, 15:77–81 (2013). †Contributed equally. Abstract | PDF | Cover
  3. D.T.W. Ng and C.A. Sarkar. "Engineering signal peptides for enhanced protein secretion from Lactococcus lactis." Applied and Environmental Microbiology, 79:347-356 (2013). Abstract | PDF | Supplement
  4. S.T. Jung, W. Kelton, T.H. Kang, D.T.W. Ng, J.T. Andersen, I. Sandlie, C.A. Sarkar, and G. Georgiou. "Effective phagocytosis of low Her2 tumor cell lines with engineered, aglycosylated IgG displaying high FcγRIIa affinity and selectivity." ACS Chemical Biology, 8:368-375 (2013). Abstract | PDF | Supplement
  5. D.T.W. Ng and C.A. Sarkar. "Model-guided ligation strategy for optimal assembly of DNA libraries." Protein Engineering, Design, and Selection, 25:669-678 (2012). Abstract | PDF | Supplement
  6. P.A. Barendt, N.A. Shah, G.A. Barendt, and C.A. Sarkar. "Broad-specificity mRNA-rRNA complementarity in efficient protein translation." PLOS Genetics, 8:e1002598 (2012). Abstract | PDF | Supplement
  7. S. Palani and C.A. Sarkar. "Transient noise amplification and gene expression synchronization in a bistable mammalian cell-fate switch." Cell Reports, 1:215-224 (2012). Abstract | PDF | Supplement
  8. E.C. O'Shaughnessy and C.A. Sarkar. "Analyzing and engineering cell signaling modules with synthetic biology." Current Opinion in Biotechnology, 23:785-790 (2012). Abstract | PDF
  9. N.A. Shah and C.A. Sarkar. "Robust network topologies for generating switch-like cellular responses." PLOS Computational Biology, 7:e1002085 (2011). Abstract | PDF | Supplement
  10. S. Palani and C.A. Sarkar. "Synthetic conversion of a graded receptor signal into a tunable, reversible switch." Molecular Systems Biology, 7:480 (2011). Abstract | PDF | Supplement
  11. D.T.W. Ng and C.A. Sarkar. "Nisin-inducible secretion of a biologically active single-chain insulin analog by Lactococcus lactis NZ9000." Biotechnology and Bioengineering, 108:1987-1996 (2011). Abstract | PDF | Supplement
  12. E.C. O'Shaughnessy, S. Palani, J.J. Collins†, and C.A. Sarkar†. "Tunable signal processing in synthetic MAP kinase cascades." Cell, 144:119-131 (2011). †Co-corresponding authors. Abstract | PDF | Supplement
  13. C. Zahnd, C.A. Sarkar†, and A. Plückthun†. "Computational analysis of off-rate selection experiments to optimize affinity maturation by directed evolution." Protein Engineering, Design, and Selection, 23:175-184 (2010). †Co-corresponding authors. Abstract | PDF
  14. Z.L. Whichard, C.A. Sarkar, M. Kimmel, and S.J. Corey. "Hematopoiesis and its disorders: a systems biology approach." Blood, 115:2339-2347 (2010). Abstract | PDF
  15. S. Palani and C.A. Sarkar. "Integrating extrinsic and intrinsic cues into a minimal model of lineage commitment for hematopoietic progenitors." PLOS Computational Biology, 5:e1000518 (2009). Abstract | PDF | Supplement
  16. P.A. Barendt and C.A. Sarkar. "Cell-Free Display Systems for Protein Engineering" in Protein Engineering and Design, Jennifer Cochran and Sheldon Park, eds., Taylor and Francis Group, Boca Raton, FL (2009). Link
  17. C.A. Sarkar. "Principles of Computational Cell Biology -- From Protein Complexes to Cellular Networks." The Quarterly Review of Biology, 84:303-303 (2009). PDF
  18. P. Milovnik, D. Ferrari, C.A. Sarkar, and A. Plückthun. "Selection and characterization of DARPins specific for the neurotensin receptor 1." Protein Engineering, Design, and Selection, 22:357-366 (2009). Abstract | PDF
  19. C.A. Sarkar†, I. Dodevski†, M. Kenig, S. Dudli, A. Mohr, E. Hermans, and A. Plückthun. "Directed evolution of a G-protein coupled receptor for expression, stability, and binding selectivity." Proceedings of the National Academy of Sciences USA, 105:14808-14813 (2008). †Contributed equally. Abstract | PDF | Supplement
  20. S. Palani and C.A. Sarkar. "Positive receptor feedback during lineage commitment can generate ultrasensitivity to ligand and confer robustness to a bistable switch." Biophysical Journal, 95:1575-1589 (2008). Abstract | PDF | Supplement
  21. S. Kubetzko†, C.A. Sarkar†, and A. Plückthun. "Protein PEGylation decreases observed target association rates via a dual blocking mechanism." Molecular Pharmacology, 68:1439-1454 (2005). †Contributed equally. Abstract | PDF | Supplement
  22. C.A. Sarkar, K. Lowenhaupt, P.J. Wang, T. Horan, and D.A. Lauffenburger. "Parsing the effects of binding, signaling, and trafficking on the mitogenic potencies of granulocyte colony-stimulating factor analogues." Biotechnology Progress, 19:955-964 (2003). Abstract | PDF
  23. M.S. Ricci, C.A. Sarkar, E.M. Fallon, D.A. Lauffenburger, and D.N Brems. "pH dependence of structural stability of interleukin-2 and granulocyte colony-stimulating factor." Protein Science, 12:1030-1038 (2003). Abstract | PDF
  24. C.A. Sarkar and D.A. Lauffenburger. "Cell-level pharmacokinetic model of granulocyte colony-stimulating factor: implications for ligand lifetime and potency in vivo." Molecular Pharmacology, 63:147-158 (2003). Abstract | PDF
  25. C.A. Sarkar, K. Lowenhaupt, T. Horan, T.C. Boone, B. Tidor, and D.A. Lauffenburger. "Rational cytokine design for increased lifetime and enhanced potency using pH-activated 'histidine switching.'" Nature Biotechnology, 20:908-913 (2002). Abstract | PDF