A. Nourmohammad (2022) T-cell responses deciphered. Science 376: 796-797

C. Kreer, C. Lupo, M. S. Ercanoglu, L. Gieselmann, N. Spisak, J. Grossbach, M. Schlotz, P. Schommers, H. Gruell, L. Dold, A. Beyer, A. Nourmohammad, T. Mora, A. M. Walczak, F. Klein (2022) Determining probabilities of HIV-1 bNAb development in healthy and chronically infected individuals, bioRXiv:2022.07.11.499584

Y. Wang, R. Lei, A. Nourmohammad, N. C. Wu (2021) Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing. eLife 10:e72516. biorXiv: 2021.07.10.451918

Z. Montague*, H. Lv*, J. Otwinowski, W. S. DeWitt, G. Isacchini, G. K. Yip, W. W. Ng, O. T. Tsang, M. Yuan, H. Liu, I. A. Wilson, M. Peiris, N. C. Wu^, A. Nourmohammad^, C. K. Mok^ (2021) Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity. Cell Reports 35(8) 109173 arXiv:2007.06762

G. Isacchini, A. Walczak, T. Mora, A. Nourmohammad (2021) Deep generative selection models of T and B cell receptor repertoires with soNNia, Proc Nat Acad Sci 118 (14) e2023141118

G. Isacchini, C. Olivares, A. Nourmohammad, A.M. Walczak, T. Mora (2020) SOS: Online probability estimation and generation of T and B cell receptors. Bioinformatics, btaa574, manuscript, website

G. Isacchini, Z. Sethna, Y. Elhanati, A. Nourmohammad, A.M. Walczak, T. Mora (2020) On generative models of T-cell receptor sequences. Phys. Rev. E 101, 062414. manuscript

N.C. Wu, J. Otwinowski, A.J. Thompson, C.M. Nycholat, J.C. Paulson, A. Nourmohammad and I. A. Wilson (2020) Major hemagglutinin antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape. Nature Communications 11(1233): DOI: 10.1038/s41467-020-15102-5.

A. Nourmohammad^, J. Otwinowski, M. Łuksza, T. Mora, A.M. Walczak (2019) Fierce selection and interference in B-cell repertoire response to chronic HIV-1. Molecular Biology and Evolution 36(10): 2184–2194.

T. Hagai, X. Chen, R.J. Miragaia, R. Rostom, T. Gomes, N. Kunowska, J. Henriksson, J. Park, V. Proserpio, G. Donati, L. Bossini-Castillo, F.A. Vieira Braga, G. Naamati, J. Fletcher, E. Stephenson, P. Vegh, G. Trynka, I. Kondova, M. Dennis, M. Haniffa, A. Nourmohammad, M. Lässig and S.A. Teichmann (2018) Gene expression variability across cells and species shapes innate immunity, Nature 563, 197–202. manuscript

O. Schnaack, L. Peliti, A. Nourmohammad (2022) Learning and organization of memory for evolving patterns. Phys. Rev. X 12, 021063

O. Schnaack, L. Peliti, A. Nourmohammad (2021) Risk-utility tradeoff shapes memory strategies for evolving patterns. arXiv:2110.15008

O. Schnaack, A. Nourmohammad^ (2020) Optimal evolutionary decision-making to store immune memory. arXiv:2007.01363, manuscript

S. Bradde^, A. Nourmohammad^, S. Goyal^, V. Balasubramanian^ (2020) The size of the immune repertoire of bacteria. Proc Nat Acad Sci, 117 (10) 5144-5151. manuscript

A. Nourmohammad^*, J. Otwinowski* and J.B. Plotkin (2016) Host-pathogen coevolution and the emergence of broadly neutralizing antibodies in chronic infections. PLoS Genetics 12, 7, e1006171. manuscript, SI.