2 citations · 3 across the 4 of their papers we have counts for
5 papers
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…
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…
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…
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…
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…