Background & Research

I am currently a science writer in the Sabeti Lab at the Broad Institute of MIT and Harvard. Previously, I was a postdoctoral researcher at Harvard Medical School, where my work focused on understanding the emergence of drug resistance in melanoma. I received my PhD at Cornell University, where I developed computational models of the biochemical networks that govern multiple aspects of immune responses.

Publications 

These works can also be found through Google Scholar.

* These authors contributed equally.

  1. Petros BA, Paull JS, Tomkins-Tinch CH, Loftness BC, DeRuff KC, Nair P, Gionet GL,Benz A, Brock-Fisher T, Hughes M, Yurkovetskiy L, Mulaudzi S, Leenerman E, Nyalile T, Moreno GK, Specht I, Sani K, Adams G, Babet SV, Baron E, Blank JT, Boehm C, Botti-Lodovico Y, Brown J, Buisker AR, Burcham T, Chylek L, Cronan P, Dauphin A, Desreumaux V, Doss M, Flynn B, Gladden-Young A, Glennon O, Harmon HD, Hook TV , Kary A, King C, Loreth C, Marrs L, McQuade KJ, Milton TT, Mulford JM, Oba K, Pearlman L, Schifferli M, Schmidt MJ, Tandus GM, Tyler A, Vodzak ME, Bevill KK, Colubri A, MacInnis BL, Ozsoy AZ, Parrie E, Sholtes K, Siddle KJ, Fry B, Luban J,Park DJ, Marshall J, Bronson A, Schaffner SF, Sabeti PC. (2022) Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework. Med 3(12):883-900.e13 [link]

  2. Chylek LA, Wang S, Sorger PK. Mechanisms of emergent phenomena in signal transduction systems (in preparation).

  3. Vemulapalli V, Chylek LA, Erickson A, Pfeiffer A, Gabriel KH, LaRochelle J, Subramanian K, Cao R, Stegmaier K, Mohseni M, LaMarche MJ, Acker MG, Sorger PK, Gygi SP, Blacklow SC. (2021) Time resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling. eLife 10, e64251 [link]

  4. Tyan K, Levin A, Avalos-Pacheco A, Plana D, Rand EA, Yang H, Maliszewski LE, Chylek LA, Atta L, Tye MA, Carmack MM, Oglesby NS, Burgin S, Yu SH, LeBoeuf NR, Kemp JM. (2020) Considerations for the Selection and Use of Disinfectants Against SARS-CoV- 2 in a Healthcare Setting. Open Forum Infectious Diseases 7, ofaa396. [link]

  5. Gerosa L, Chidley C, Fröhlich F, Sanchez G, Lim SK, Muhlich J, Chen J-Y, Vallabhaneni S, Baker GJ, Schapiro D, Atanasova MI, Chylek LA, Shi T, Yi, L Nicora CD, Claas A, Ng TSC, Kohler RH, Lauffenburger DA, Weissleder R, Miller MA, Qian W-J, Wiley JS, Sorger PK. (2020) Receptor-driven ERK pulses enable persistence of BRAF-mutant melanoma cells adapted to RAF and MEK inhibitors. Cell Systems 11, 478-494.e9 [link]

  6. Chylek LA. (2019) Using mechanistic models for analysis of proteomic data. In Modeling Biomolecular Site Dynamics: Methods and Protocols, Methods in Molecular Biology, vol. 1945, 256-270 (WS Hlavacek, editor). Springer. [link]

  7. Lin YT, Chylek LA, Lemons NW, Hlavacek WS.(2018) Using equation-free computation to accelerate network-free stochastic simulation of chemical kinetics. J Phys Chem B. 122, 6351- 6356. [link]

  8. Harmon B,* Chylek LA,* Liu Y,* Mahajan A, Schudel BR, Holowka DA, Baird BA, Wilson BS, Hlavacek WA, Singh AK. (2017) Timescale separation of positive and negative signaling creates history-dependent responses to IgE receptor stimulation. Scientific Reports 7, 15586. *These authors contributed equally. [link]

  9. Chylek LA, Holowka DA, Baird BA, Hlavacek WS. Quantitative modeling of mast cell signaling. In Systems Immunology: An Introduction to Modeling Methods for Scientists (Das J, Jayaprakash C, Editors), CRC Press, Boca Raton, FL, Ch 13, pp 213-226. ISBN-13: 978- 1-4987-1740-3 [link]

  10. Chylek LA. Understanding IgE receptor signaling through computational modeling and quantitative experiments. (2016). PhD thesis, Cornell University.

  11. BR Thomas, LA Chylek, J Colvin, S Sirimulla, AHA Clayton, WS Hlavacek, RG Posner. (2015) GenFit: a fitting tool compatible with BioNetGen, NFsim, and distributed computing environments. Bioinformatics pii, btv655. [link]

  12. Chylek LA, Harris LA, Faeder JR, Hlavacek WS (2015) Modeling for (physical) biologists: an introduction to the rule-based approach. Phys. Biol. 12:045007 [link]

  13. Andris C and Chylek LA. 'Good' hard vs. 'Bad' hard. The Chronicle of Higher Education. Feb 4th, 2015. [link]

  14. Chylek LA, Wilson BS, Hlavacek WS. (2014) Modeling biomolecular site dynamics in immunoreceptor signaling systems. Advances in Experimental Medicine and Biology 844, 245-262 (S. J. Corey, M. Kimmel and J. N. Leonard, Editors), Springer. [link]

  15. Chylek LA,* Akimov V,* Dengjel J,* Rigbolt KTG, Hu B, Hlavacek WS, Blagoev, B. (2014) Phosphorylation site dynamics of early T-cell receptor signaling. PLOS ONE 9, e104240. *These authors contributed equally. [link]

  16. Chylek LA, Chylek LA, Holowka DA, Baird BA, Hlavacek WS. (2014) An interaction library for the FcεRI signaling network. Frontiers in Immunology 5, 172. [link]

  17. Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. (2014) Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. WIREs Systems Biology and Medicine 6, 13-36. [link]

  18. Chylek LA. (2013) Decoding the language of phosphorylation site dynamics. Science Signaling 6, jc2. [link]

  19. Chylek LA, Stites EC, Posner RG, Hlavacek WS. (2013) Innovations of the rule-based modeling approach. In Systems Biology: Integrative Biology and Simulation Tools Vol. 1, Ch. 9, pp. 273-300 (A. Prokop and B. Csukás, Editors), Springer, Dordrecht. ISBN: 978-94-007-6802-4 (Print) ISBN: 978-94-007-6803-1 (Online) [link]

  20. Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. (2011) Guidelines for visualizing and annotating rule-based models. Molecular BioSystems 7, 2779 - 2795 (A top-ten most accessed article of June 2011) [link]