• G. Visani, M. N. Pun, W. Galvin, E. Daniel, K. Borisiak, U. Wagura, A. Nourmohammad (2024) HERMES: Holographic Equivariant neuRal network model for Mutational Effect and Stability prediction, arXiv:2407.06703

• G. Visani, W. Galvin, M. N. Pun, A. Nourmohammad (2024) H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing. Machine Learning in Computational Biology meeting, PMLR 240:230-249. [arXiv]

• G.M. Visani, M.N. Pun, A. Nourmohammad (2024) Holographic-(V)AE: an end-to-end SO(3)-Equivariant (Variational) Autoencoder in Fourier Space. Phys. Rev. Research 6, 023006 [arXiv]

• G. Isacchini, V. Quiniou, P. Barennes, V. Mhanna, H. Vantomme, P. Stys, E. Mariotti-Ferandiz, D. Klatzmann, A. Walczak^, T. Mora^, and A. Nourmohammad^ (2024) Local and global variability in developing human T-cell repertoires,  PRX Life 2, 013011  [arxiv]

• M.N. Pun, A. Ivanov, Q. Bellamy, Z. Montague, C. LaMont, P. Bradley, J. Otwinowski,  A. Nourmohammad (2024) Learning the shape of  protein micro-environments  with  a holographic convolutional neural network. Proc Nat Acad  121 (6) e2300838121 [bioRxiv]

• K. Abadie, E. Clark, R. M. Valanparambil, O. Ukogu, W. Yang, R. Daza, K. K.H. Ng, J. Fathima, A. Wang, A. Bhandoola, A. Nourmohammad, R. Ahmed, J. Shendure, J. Cao, H. Y. Kueh (2024) Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision, Immunity  ISSN 1074-7613 [bioRxiv]

• 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 (2023) Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals. Nat Commun 14,7137. [bioRXiv]

• M. Lässig^, V. Mustonen^, and A. Nourmohammad^ (2023) Steering and controlling evolution — from bioengineering to fighting pathogens. Nature Rev Genet: https://doi.org/10.1038/s41576-023-00623-8

• A. Nourmohammad, G. Visani, M.N. Pun (2022) Machine-learning model reveals protein folding physics. Physics 15, 183 

• C. LaMont, J. Otwinowski, K. Vanshylla, H. Gruell, F. Klein, A. Nourmohammad (2022) Design of an optimal combination therapy with broadly neutralizing antibodies to suppress HIV-1. eLife 11:e76004. [arXiv]

press coverage (eLife)
press coverage (UW) 

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

Physics Magazine coverage

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

• G. Isacchini*, N. Spisak*, A. Nourmohammad^, T. Mora^,  A. Walczak^ (2022) Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories: MINIMALIST.  Phys. Rev. E 105, 055309, [arXiv]

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

• 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]

• 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]

Press coverage

• O. Schnaack, A. Nourmohammad^ (2021) Optimal evolutionary decision-making to store immune memory, eLife 10:e61346, [arXiv]

Physics Magazine coverage

• 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, [bioRXiv] 

• A. Nourmohammad^, C. Eksin, (2021) Optimal evolutionary control for artificial selection on molecular phenotypes. Phys. Rev. X 11, 011044, [bioRxiv]

• J. Otwinowski, C. LaMont, A. Nourmohammad (2020) Information-geometric optimization with natural selection, Entropy, 22(9), 967, manuscript

• 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, [website], [arXiv]

• 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. [arXiv]

• 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). 

• 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. [arXiv]

Featured on the cover
commentary by M. Deem in PNAS

• 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. [arXiv]

• 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

        F1000Prime Recommended

• A. Nourmohammad^, J. Rambeau, T. Held, V. Kovacova, J. Berg and M. Lässig^ (2017) Adaptive evolution of gene expression in Drosophila. Cell Reports 20, 6, 1385-1395. [arXiv]

      F1000Prime Recommended

• 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. [arXiv]

• T. Held, A. Nourmohammad,  and M. Lässig (2014) Adaptive evolution of molecular phenotypes. Journal of Statistical Mechanics: Theory and Experiment 2014, P09029. manuscript.

• A. Nourmohammad*,  S. Schiffels* and M. Lässig (2013) Evolution of molecular phenotypes under stabilizing selection. Journal of Statistical Mechanics: Theory and Experiment 2013, P01012. [arXiv]

• A. Nourmohammad, T. Held and M. Lässig (2013) Universality and predictability in molecular quantitative genetics. Current Opinion in Genetics & Development 23, 6, 684-693. [bioRxiv]

• A. Nourmohammad and M. Lässig (2011) Formation of regulatory modules by local sequence duplication. PLoS Computational Biology 7, 10, e1002167. 

• R.H. Abdolvahab, F. Roshani, A. Nourmohammad,  M. Sahimi and M.R.R. Tabar (2008) Analytical and numerical studies of sequence dependence of passage times for translocation of heterobiopolymers through nanopores. The Journal of Chemical Physics 129, 23. 

bold: SPE members,      *: co-first author,        ^: corresponding author (equal contribution)