Monoclonal and Polyclonal Antibodies Research

Protein visualization and manipulation in Drosophila through the use of epitope tags recognized by nanobodies

The paper introduces two short NanoTag epitopes and their nanobodies for in vivo protein visualization and manipulation in Drosophila, demonstrating their utility in multiple assays and CRISPR-based tagging.

Llamanade: an open-source computational pipeline for robust nanobody humanization

Llamanade is an open-source pipeline that humanizes nanobodies using sequence and structural analysis, improving their translational potential for therapeutic applications.

A high-throughput, automated, cell-free expression and screening platform for antibody discovery

This paper develops an automated cell-free platform for rapid antibody discovery and screening, demonstrating its effectiveness with SARS-CoV-2 neutralizing antibodies.

A hybridoma-derived monoclonal antibody with high homology to the aberrant myeloma light chain

The paper identifies a high-homology light chain sequence from a hybridoma that is antigen-specific, highlighting challenges in variable domain sequencing.

ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces

This study demonstrates how ssDNA recombineering in bacteria enables hyper-diversification of nanobodies, resulting in variants that recognize new antigens while retaining original specificity.

Antibody Upstream Sequences Diversity and Its Biological Implications Revealed by Repertoire Sequencing

The paper identifies and characterizes the diversity of antibody upstream sequences (AUS) across multiple species using Rep-Seq and 5RACE, revealing new variants and their implications for antibody biology.

Study of Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (Clustal- X) of Monoclonal mice/human antibodies

The paper compares BLAST and Clustal-X alignments of monoclonal antibody light and heavy chains to assess sequence homology and identify conserved regions.

Selection and structural characterisation of anti-TREM2 scFvs that reduce levels of shed ectodomain

The paper identifies and characterizes anti-TREM2 scFv antibodies that inhibit soluble TREM2 production.

Knowledge-based antibody repertoire simulation, a novel allele detection tool evaluation and application

The paper evaluates novel allele detection tools using simulated and real antibody repertoire sequencing data and identifies 43 novel alleles.

Generation of photocaged nanobodies for in vivo applications using genetic code expansion and computationally guided protein engineering

This paper develops photocaged nanobodies for in vivo applications using genetic code expansion and computational methods to control protein interactions with light.

Design of smart antibody mimetics with photosensitive switches

This paper introduces light-controllable antibody mimetics, moonbody and sunbody, enabling rapid and reversible antigen recognition and precise control of cellular processes using light.

Optimized antibody humanization by intra and inter VH-VL binding energy sorting

The paper introduces a computational pipeline for antibody humanization that uses VH-VL binding energy sorting to optimize humanized antibodies and validates it against experimental data.

Data mining patented antibody sequences

The paper analyzes antibody sequences from patents to assess their utility for therapeutic antibody engineering and finds they reflect clinical sequences.

A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-Pertussis toxoid antibodies

The paper introduces a method to identify novel cross-clonotype antibodies by clustering based on predicted paratope features, validated on a Pertussis toxoid dataset.

Essentially leading antibody production: An investigation of amino acids, myeloma and natural V-region signal peptides in producing Pertuzumab and Trastuzumab variants

The paper investigates how varying signal peptides and amino acid counts affect recombinant antibody production rates in HEK293 cells, developing a predictive model for transient production.

Brain Antibody Sequence Evaluation (BASE): an easy-to-use software for complete data analysis in single cell immunoglobulin cloning

BASE is a software tool for analyzing single-cell immunoglobulin cloning data, providing automated analysis with high accuracy and additional plasmid sequence confirmation.

New insights on the interaction mechanism of rhTNF with its antagonists Adalimumab and Etanercept

The paper investigates the interaction of rhTNF with Adalimumab and Etanercept, revealing new binding patterns and stoichiometry of their complexes.

AncesTree: an interactive immunoglobulin lineage tree visualizer

AncesTree provides an interactive GUI for visualizing immunoglobulin lineage trees and mutations derived from Phylip analysis of antibody repertoires.

Predicting Antibody Developability from Sequence using Machine Learning

This paper develops a machine learning pipeline to predict antibody developability from sequence, achieving high sensitivity and specificity on a dataset of 2400 antibodies.

Engineering Highly Homogenous Tetravalent IgGs with Enhanced Sperm Agglutination Potency

The paper designs tetravalent anti-sperm IgGs with enhanced agglutination potency compared to the parent IgG, while maintaining production yields and thermostability.

Engineering highly multivalent sperm-binding IgG antibodies for potent non-hormonal female contraception

The paper engineers multivalent IgG antibodies that agglutinate sperm more potently than monovalent IgGs, achieving high contraceptive efficacy in sheep.

An Array of 60,000 Antibodies for Proteome-Scale Antibody Generation and Target Discovery

The paper develops PETAL, a library of 62,208 mAbs against 15,199 peptides, enabling proteome-scale antibody generation and target discovery across species.

Chemogenetic control of nanobodies

This paper describes an engineered nanobody that modulates GFP binding with small molecules, enabling controlled study of GFP fusion proteins in biological processes.

Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding.

The paper analyzes the structure and sequence of the antibody DE loop, revealing its role in antigen binding and its variability in HIV-1 antibodies.

cAb-Rep: A Database of Curated Antibody Repertoires for Exploring antibody diversity and Predicting Antibody Prevalence

cAb-Rep is a curated database of human B cell immunoglobulin sequence repertoires, providing annotated datasets for studying antibody diversity and prevalence.

Looking for Therapeutic Antibodies in Next Generation Sequencing Repositories

The paper compares therapeutic antibodies to NGS-derived antibody sequences to identify sequence matches and convergence between natural and artificial antibody development.

Deep learning enables therapeutic antibody optimization in mammalian cells by deciphering high-dimensional protein sequence space

Mammalian display of CRISPR-introduced trastuzumab mutant libraries trains a network that picks antigen binders out of a hundred-million-variant virtual library; 30 of 30 tested variants bound.

A toolbox of nanobodies developed and validated for diverse neuroscience research applications

The paper develops and validates a set of nanobodies for targeting proteins in brain neurons, providing a toolbox for visualization and modulation of subcellular sites.

A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain

The paper describes a method to generate and validate recombinant monoclonal antibodies for neuroscience research, enabling multiplex immunolabeling of brain tissue.

RANbodies: reporter-nanobody fusions as versatile, small, sensitive immunohistochemical reagents

The paper introduces RANbodies, nanobody-reporter fusions that enable sensitive and scalable detection of molecules in cells and tissues.