Publications

Design of an optimal combination therapy with broadly neutralizing antibodies to suppress HIV-1

LaMont C., Otwinowski J., Vanshylla K., Gruell H., Klein F., Nourmohammad A., eLife, 19. July 2022, https://doi.org/10.7554/eLife.76004

Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing

Wang Y., Lei R., Nourmohammad A., Wu N.C., eLife 2021;10:e72516, 8. December 2021, https://doi.org/10.7554/eLife.72516

Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19

Montague Z., Lv H., Otwinowski J., DeWitt W.S., Isacchini G., Yip G.K., Ng W.W., Tsang O.T.-Y., Yuan M., Liu H., Wilson I.A., Peiris J.S.M., Wu N.C., Nourmohammad A., Ka Pun Mok C, Cell 35(8), 25. May 2021, https://doi.org/10.1016/j.celrep.2021.109173

Optimal evolutionary decision-making to store immune memory

Schnaack O.H., Nourmohammad A., eLife 10:e61346, 28. April 2021, https://doi.org/10.7554/eLife.61346

Deep generative selection models of T and B cell receptor repertoires with soNNia

Isacchini G., Walczak A.M., Mora T., Nourmohammad A., PNAS 118 (14) e2023141118, 6. April 2021, https://doi.org/10.1073/pnas.2023141118

Optimal Evolutionary Control for Artificial Selection on Molecular Phenotypes

Nourmohammad A. & Eksin C., Phys. Rev. X 11, 011044, 4. March 2021, https://doi.org/10.1103/PhysRevX.11.011044

Information-Geometric Optimization with Natural Selection

Otwinowski J, LaMont C.H., Nourmohammad A. , Entropy 2020, 22(9), 967, 31. August 2020, https://doi.org/10.3390/e22090967

SOS: online probability estimation and generation of T-and B-cell receptors

Isacchini G., Olivares C., Nourmohammad. A, Walczak A.M., Mora T., Bioinformatics, Volume 36, Issue 16, 4510–4512, 15. August 2020, https://doi.org/10.1093/bioinformatics/btaa574

Generative models of T-cell receptor sequences

Isacchini G., Sethna Z., Elhanati Y., Nourmohammad A., Walczak A.M., Mora T., Phys. Rev. E 101, 062414, 15. June 2020, https://doi.org/10.1103/PhysRevE.101.062414

Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape

Wu N. C., Otwinowski J., Thompson A. J., Nycholat C. M. Nourmohammad A. and Wilson I. A., Nat Commun 11, 1233, 6. March 2020, https://doi.org/10.1038/s41467-020-15102-5

The size of the immune repertoire of bacteria

Bradde S., Nourmohammad A., Goyal S., and Balasubramanian V., PNAS:201903666, 18. February 2020, https://doi.org/10.1073/pnas.1903666117

Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1

Nourmohammad A., Otwinowski J., Łuksza M., Mora T., M. Walczak A., Molecular Biology and Evolution, msz143, 18. June 2019, https://doi.org/10.1093/molbev/msz143

Adaptive Evolution of Gene Expression in Drosophila

Nourmohammad A., Rambeau J., Held T., Kovacova V., Berg J., Lässig M., Cell Reports Volume 20 Issue 6: 1385 - 1395, 13. July 2017,                    https://doi.org/10.1016/j.celrep.2017.07.033

Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections

Nourmohammad A., Otwinowski J., Plotkin J.B., PLoS Genetics 12: e1006171, 21. July 2016, https://doi.org/10.1371/journal.pgen.1006171