- H. Venkatachalapathy, C. Brzakala, E. Batchelor, S.M. Azarin†, and C.A. Sarkar†. "Inertial effect of cell state velocity on the quiescence-proliferation fate decision in breast cancer." npj Systems Biology and Applications, 10:111 (2024). †Co-corresponding authors. Link
- K.A. Lemke, C.A. Sarkar, and S.M. Azarin. "Rapid retinoic acid-induced trophoblast cell model from human induced pluripotent stem cells." Scientific Reports, 14: 18204 (2024). Link
- J.J. Kang, A. Ohoka, and C.A. Sarkar. "Designing multivalent and multispecific biologics." Annual Review of Chemical and Biomolecular Engineering, 15:293-314 (2024). Link
- H. Venkatachalapathy, Z. Yang, S.M. Azarin, C.A. Sarkar†, and E. Batchelor†. "Pulsed stimuli entrain p53 to synchronize single cells and modulate cell-fate determination." bioRxiv, 2023.10.24.563786 (2023). †Co-corresponding authors. Link
- A. Ohoka and C.A. Sarkar. "Facile display of homomultivalent proteins for in vitro selections." ACS Synthetic Biology, 12:634-638 (2023). Link
- J.C. Stark†, M.A. Gray†, S. Wisnovsky, I. Ibarlucea-Benitez, N.M. Riley, M.K. Ribi, M. Lustig, W.J. Errington, B. Bruncsics, C.A. Sarkar, T. Valerius, J.V. Ravetch, and C.R. Bertozzi. "Antibody-lectin chimeras for glyco-immune checkpoint blockade." bioRxiv, 2022.10.26.513931 (2022). †Contributed equally. Link
- B. Bruncsics†, W.J. Errington†, and C.A. Sarkar. "MVsim is a toolset for quantifying and designing multivalent interactions." Nature Communications, 13:5029 (2022). †Contributed equally. Link | MVsim
- Q. Zhang, S.M. Azarin, and C.A. Sarkar. "Model-guided engineering of DNA sequences with predictable site-specific recombination rates." Nature Communications, 13:4152 (2022). Link
- G.C. Markou and C.A. Sarkar. "A cell-free approach to identify binding hotspots in plant immune receptors." Scientific Reports, 12:501 (2022). Link
- G.C. Markou, A. Ohoka, and C.A. Sarkar. "Engineering a minimal leucine-rich repeat IgG-binding module." Applied Biochemistry and Biotechnology, 194:1636-1644 (2022). Link
- H. Venkatachalapathy, S.M. Azarin, and C.A. Sarkar. "Trajectory-based energy landscapes of gene regulatory networks." Biophysical Journal, 120:687-698 (2021). Link
- W.J. Errington†, B. Bruncsics†, and C.A. Sarkar. "Mechanisms of non-canonical binding dynamics in multivalent protein-protein interactions." Proceedings of the National Academy of Sciences USA, 116:25659-25667 (2019). †Contributed equally. Link
- N.A. Shah and C.A. Sarkar. "Variable cellular decision-making behavior in a constant synthetic network topology." BMC Bioinformatics, 20:237 (2019). Link
- Z. Ye and C.A. Sarkar. "Towards a quantitative understanding of cell identity." Trends in Cell Biology, 28:1030-1048 (2018). Link
- F.W. Sadler, I. Dodevski, and C.A. Sarkar. "RNA thermometers for the PURExpress system." ACS Synthetic Biology, 7:292-296 (2018). Link
- A.L. Kane, B. Al-Shayeb, P.V. Holec, S. Rajan, N.E. Le Mieux, S.C. Heinsch, S. Psarska, K.G. Aukema, C.A. Sarkar, E.A. Nater and J.A. Gralnick. "Toward bioremediation of methylmercury using silica encapsulated Escherichia coli harboring the mer operon." PLOS ONE, 11:e0147036 (2016). Link
- N.A. Shah, M. Levesque, A. Raj, and C.A. Sarkar. "Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue." Journal of Cell Science, 128:3009-3017 (2015). Link
- I. Dodevski†, G.C. Markou†, and C.A. Sarkar. "Conceptual and methodological advances in cell-free directed evolution." Current Opinion in Structural Biology, 33:1-7 (2015). †Contributed equally. Link
- N.A. Shah and C.A. Sarkar. "Computationally guided design of robust gene circuits." Methods in Molecular Biology, 1244:167-178 (2015). Link
- D.T.W. Ng and C.A. Sarkar. "NP-Sticky: a web server for optimizing DNA ligation with non-palindromic sticky ends." Journal of Molecular Biology, 426:1861-1869 (2014). Link | NP-Sticky
- M.S. Magaraci†, A. Veerakumar†, P. Qiao, A. Amurthur, J.Y. Lee, J.S. Miller‡, M. Goulian, and C.A. Sarkar‡. "Engineering Escherichia coli for light-activated cytolysis of mammalian cells." ACS Synthetic Biology, 3:944-948 (2014). †Contributed equally; ‡co-corresponding authors. Link
- H.M. Mehta, M. Futami, T. Glaubach, Q. Yang, D.W. Lee, J.R. Andolina, Z. Whichard, M. Quinn, H. Lu, W.-M. Kao, B. Przychodzen, C.A. Sarkar, A. Minella, J.P. Maciejewski, and S.J. Corey. "Alternatively spliced, truncated GCSF receptor promotes leukemogenic properties and sensitivity to JAK inhibition." Leukemia, 28:1041-1051 (2014). Link
- C.A. Sarkar. "Concentrating (on) native proteins to control cell fate." Science, 341:1349-1351 (2013). Link
- 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, 8:958-966 (2013). Link
- 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. Link | Cover
- 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). Link
- 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). Link
- 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). Link
- 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). Link
- 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). Link
- 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). Link
- N.A. Shah and C.A. Sarkar. "Robust network topologies for generating switch-like cellular responses." PLOS Computational Biology, 7:e1002085 (2011). Link
- S. Palani and C.A. Sarkar. "Synthetic conversion of a graded receptor signal into a tunable, reversible switch." Molecular Systems Biology, 7:480 (2011). Link
- 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). Link
- 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. Link
- 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. Link
- 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). Link
- 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). Link
- 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
- C.A. Sarkar. "Principles of Computational Cell Biology – From Protein Complexes to Cellular Networks." The Quarterly Review of Biology, 84:303-303 (2009). Link
- 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). Link
- 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. Link
- 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). Link
- 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. Link
- 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). Link
- 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). Link
- 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). Link
- 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). Link