B cells, plasma cells and antibody repertoires in the tumour microenvironment

GV Sharonov, EO Serebrovskaya… - Nature Reviews …, 2020 - nature.com
Recent data show that B cells and plasma cells located in tumours or in tumour-draining
lymph nodes can have important roles in shaping antitumour immune responses. In tumour …

The molecular mechanisms that underlie the immune biology of anti-drug antibody formation following treatment with monoclonal antibodies

A Vaisman-Mentesh, M Gutierrez-Gonzalez… - Frontiers in …, 2020 - frontiersin.org
Monoclonal antibodies (mAbs) are a crucial asset for human health and modern medicine,
however, the repeated administration of mAbs can be highly immunogenic. Drug …

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

JA Ruffolo, LS Chu, SP Mahajan, JJ Gray - Nature communications, 2023 - nature.com
Antibodies have the capacity to bind a diverse set of antigens, and they have become critical
therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six …

Antibody design using LSTM based deep generative model from phage display library for affinity maturation

K Saka, T Kakuzaki, S Metsugi, D Kashiwagi… - Scientific reports, 2021 - nature.com
Molecular evolution is an important step in the development of therapeutic antibodies.
However, the current method of affinity maturation is overly costly and labor-intensive …

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

JA Ruffolo, JJ Gray - Biophysical Journal, 2022 - cell.com
1Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA,
2Department of Chemical and Biomolecular Engineering, Johns Hopkins University …

Deciphering antibody affinity maturation with language models and weakly supervised learning

JA Ruffolo, JJ Gray, J Sulam - arXiv preprint arXiv:2112.07782, 2021 - arxiv.org
In response to pathogens, the adaptive immune system generates specific antibodies that
bind and neutralize foreign antigens. Understanding the composition of an individual's …

Fusion protein linkers: property, design and functionality

X Chen, JL Zaro, WC Shen - Advanced drug delivery reviews, 2013 - Elsevier
As an indispensable component of recombinant fusion proteins, linkers have shown
increasing importance in the construction of stable, bioactive fusion proteins. This review …

Machine learning for biologics: opportunities for protein engineering, developability, and formulation

H Narayanan, F Dingfelder, A Butté, N Lorenzen… - Trends in …, 2021 - cell.com
Successful biologics must satisfy multiple properties including activity and particular
physicochemical features that are globally defined as developability. These multiple …

Antigen receptor repertoire profiling from RNA-seq data

DA Bolotin, S Poslavsky, AN Davydov, FE Frenkel… - Nature …, 2017 - nature.com
To the Editor: Somatic recombination and accumulation of mutations in VDJ segments result
in vast heterogeneity of T-cell receptor (TCR) and immunoglobulin repertoires1, 2. High …

The state-of-play and future of antibody therapeutics

Z Elgundi, M Reslan, E Cruz, V Sifniotis… - Advanced drug delivery …, 2017 - Elsevier
It has been over four decades since the development of monoclonal antibodies (mAbs)
using a hybridoma cell line was first reported. Since then more than thirty therapeutic …