100 citations · 275 across the 25 of their papers we have counts for
29 papers
T-cell repertoire response in individuals with post-acute sequelae of COVID-19
Zachary Montague, Rhea M Grover, Andrew Baumgartner +3
T-cells are central to SARS-CoV-2 clearance and immunological memory, yet their contribution to the persistence of post-acute sequelae of COVID-19 (PASC) remains poorly understood.…
Design principles of the cytotoxic CD8+ T-cell response
Obinna A. Ukogu, Zachary Montague, Grégoire Altan-Bonnet +1
Cytotoxic T lymphocytes eliminate infected or malignant cells, safeguarding surrounding tissues. Although experimental and systems-immunology studies have cataloged many molecular…
T-cell receptor specificity landscape revealed through de novo peptide design
Gian Marco Visani, Michael N. Pun, Anastasia A. Minervina +3
T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived pep…
Adaptive efficiency of information processing in immune-pathogen co-evolution
Quinn N Bellamy, Zachary Montague, Luca Peliti +1
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can d…
Loop-Diffusion: an equivariant diffusion model for designing and scoring protein loops
Kevin Borisiak, Gian Marco Visani, Armita Nourmohammad
Predicting protein functional characteristics from structure remains a central problem in protein science, with broad implications from understanding the mechanisms of disease to d…
HERMES: Holographic Equivariant neuRal network model for Mutational Effect and Stability prediction
Gian Marco Visani, William Galvin, Zac Jones +5
Predicting the stability and fitness effects of amino acid mutations in proteins is a cornerstone of biological discovery and engineering. Various experimental techniques have been…
H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing
Gian Marco Visani, William Galvin, Michael Neal Pun +1
Accurately modeling protein 3D structure is essential for the design of functional proteins. An important sub-task of structure modeling is protein side-chain packing: predicting t…
Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals
Giulio Isacchini, Valentin Quiniou, Hélène Vantomme +6
The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens. TCRs are acq…
Learning the shape of protein micro-environments with a holographic convolutional neural network
Michael N. Pun, Andrew Ivanov, Quinn Bellamy +5
Proteins play a central role in biology from immune recognition to brain activity. While major advances in machine learning have improved our ability to predict protein structure f…
Holographic-(V)AE: an end-to-end SO(3)-Equivariant (Variational) Autoencoder in Fourier Space
Gian Marco Visani, Michael N. Pun, Arman Angaji +1
Group-equivariant neural networks have emerged as a data-efficient approach to solve classification and regression tasks, while respecting the relevant symmetries of the data. Howe…
Design of an optimal combination therapy with broadly neutralizing antibodies to suppress HIV-1
Colin LaMont, Jakub Otwinowski, Kanika Vanshylla +3
Broadly neutralizing antibodies (bNAbs) are promising targets for vaccination and therapy against HIV. Passive infusions of bNAbs have shown promise in clinical trials as a potenti…
Risk-utility tradeoff shapes memory strategies for evolving patterns
Oskar H Schnaack, Luca Peliti, Armita Nourmohammad
Keeping a memory of evolving stimuli is ubiquitous in biology, an example of which is immune memory for evolving pathogens. However, learning and memory storage for dynamic pattern…
Learning and organization of memory for evolving patterns
Oskar H Schnaack, Luca Peliti, Armita Nourmohammad
Storing memory for molecular recognition is an efficient strategy for responding to external stimuli. Biological processes use different strategies to store memory. In the olfactor…
MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad +2
Simulation-based inference enables learning the parameters of a model even when its likelihood cannot be computed in practice. One class of methods uses data simulated with differe…
Deep generative selection models of T and B cell receptor repertoires with soNNia
Giulio Isacchini, Aleksandra M Walczak, Thierry Mora +1
Subclasses of lymphocytes carry different functional roles to work together to produce an immune response and lasting immunity. Additionally to these functional roles, T and B-cell…
Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity
Zachary Montague, Huibin Lv, Jakub Otwinowski +12
COVID-19 patients show varying severity of the disease ranging from asymptomatic to requiring intensive care. Although a number of SARS-CoV-2 specific monoclonal antibodies have be…
Optimal evolutionary decision-making to store immune memory
Oskar H Schnaack, Armita Nourmohammad
The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, whi…
SOS: Online probability estimation and generation of T and B cell receptors
Giulio Isacchini, Carlos Olivares, Armita Nourmohammad +2
Recent advances in modelling VDJ recombination and subsequent selection of T and B cell receptors provide useful tools to analyze and compare immune repertoires across time, indivi…
Optimal evolutionary control for artificial selection on molecular phenotypes
Armita Nourmohammad, Ceyhun Eksin
Controlling an evolving population is an important task in modern molecular genetics, including directed evolution for improving the activity of molecules and enzymes, in breeding…
Information-geometric optimization with natural selection
Jakub Otwinowski, Colin LaMont
Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between populat…
On generative models of T-cell receptor sequences
Giulio Isacchini, Zachary Sethna, Yuval Elhanati +3
T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and mali…
The size of the immune repertoire of bacteria
Serena Bradde, Armita Nourmohammad, Sidhartha Goyal +1
Some bacteria and archaea possess an immune system, based on the CRISPR-Cas mechanism, that confers adaptive immunity against phage. In such species, individual bacteria maintain a…
Fierce selection and interference in B-cell repertoire response to chronic HIV-1
Armita Nourmohammad, Jakub Otwinowski, Marta Łuksza +2
During chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host's adaptive immune system. While it is clear that HIV exerts strong selection on the adapti…
Host-pathogen coevolution and the emergence of broadly neutralizing antibodies in chronic infections
Armita Nourmohammad, Jakub Otwinowski, Joshua B. Plotkin
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as…