Advanced Biosensing Techniques and Applications

ART: A Compositional Physical Theory for the End-to-End Design of Solid-Phase Immunosensors

The paper introduces ART, a physical theory for designing solid-phase immunoassays by modeling coupled processes and demonstrating its application through examples.

A Multiplex Protein Microarray Platform for Preclinical Tissue Binding and Cross-Reactivity of Therapeutic Antibodies

The paper introduces a multiplex protein microarray platform to assess tissue binding and cross-reactivity of therapeutic antibodies, showing distinct profiles for different antibodies and species.

SCKAnalyzer: A Web Tool for Single-Cycle Kinetics Analysis and Simulation

SCKAnalyzer processes and fits single-cycle kinetics data from biosensors, offering simulation and analysis tools for biomolecular interactions.

pyKinaXe: a fast and robust turnkey kinase activity profiler

pyKinaXe is a Python package that automates the analysis of PamChip data, offering faster and more efficient kinase activity profiling compared to existing tools.

Multimodal Sensitivity Enhancement of Binding-based Diagnostic Assays Using Functional Hydrogels

This paper introduces a hydrogel-based strategy to enhance sensitivity and multiplexability in binding-based diagnostic assays across multiple modalities.

Plasma titration provides a physical ruler for cross-platform proteomics

The paper introduces Plasmix, a plasma reference suite, to improve cross-platform proteomics integration by identifying proteins with consistent titration responses across platforms.

The unexplainable plasma protein measurements from Proximity Extension Assays

The paper evaluates Olink Explore plasma protein assays by analyzing genetic associations, cross-platform concordance, and tissue atlases to identify targets with low variance explainability.

Machine learning cross-platform proteomic imputation enables protein quality scoring and replication of epidemiological associations

This paper develops a machine learning framework to impute cross-platform proteomic data, improving replication of epidemiological findings and protein quality scoring.

High-density peptide arrays detect tuberculosis through immune remodeling, not only antigen recognition alone

The paper uses high-density peptide arrays to detect tuberculosis by analyzing immune repertoire remodeling rather than antigen-specific recognition, achieving high accuracy in HIV-negative individuals.

Cell-free immuno-profiling on a genetically programmed biochip

This paper develops a cell-free biochip platform to profile antibody-antigen interactions and epitope specificity using SARS-CoV-2 antigens and human sera.

cpiVAE: Robust and Interpretable Cross-Platform Proteomics Imputation

cpiVAE improves cross-platform proteomics imputation between Olink and SomaScan, achieving higher correlation than KNN and WNN, and enabling better phenotype associations.

PiP-plex: A Particle-in-Particle System for Multiplexed Quantification of Proteins Secreted by Single Cells

PiP-plex enables multiplexed quantification of single-cell protein secretion using a particles-in-particle system, detecting cytokine responses in THP-1 cells to lipopolysaccharide.

A High-throughput Multi-Species Platform Using Biolayer Interferometry Immunosorbent Assay (BLI-ISA) as an Alternative to Indirect ELISA for Vaccine Development

This paper introduces a BLI-ISA protocol as a faster and more efficient alternative to ELISA for comparing antigen-specific antibody levels in vaccine development.

Evaluation of Multiplexed Liquid Glycan Array (LiGA) for Serological Detection of Glycan-binding Antibodies

This paper evaluates the multiplexed liquid glycan array (LiGA) for detecting ABO blood group antibodies in human serum, identifying its strengths and limitations.

Characterization of antiviral compounds using Bio-Layer Interferometry

This paper optimizes Bio-Layer Interferometry (BLI) protocols to measure binding affinities of antiviral compounds with viral proteins, demonstrating sub-nanomolar KD values and covalent interactions.

A multiplex extracellular interactome screening method employing high-avidity nanoparticles

The paper introduces a multiplex method to screen CSP extracellular interactions using nanoparticles and fluorescent beads, showing improved sensitivity and dynamic range over ELISA-based assays.

Overcoming effects of heterogeneous binding on BLI analysis

This study identifies analyte aggregation as a cause of heterogeneous binding in BLI and proposes a method to improve binding characteristic accuracy.

High-temporal-resolution point-of-care multiplex biomarker monitoring in small animals using microfluidic digital ELISA

This paper develops a microfluidic digital ELISA platform for rapid, high-temporal-resolution biomarker monitoring in small animals using whole blood, demonstrating its utility in a murine sepsis model.

Effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification using the SomaScan and Olink assays

This study evaluates how in vitro hemolysis and freeze-thaw cycles affect protein abundance measurements in SomaScan and Olink assays, identifying affected analytes and proposing quality control measures.

Lambda Theta Reflectometry: a new technique to measure optical film thickness applied to planar protein arrays

This paper introduces Lambda Theta Reflectometry (LTR), a new reflectometric technique for measuring optical film thickness, and validates its accuracy using SiO2 layers.

Novel sensor-integrated proteome on chip (SPOC) platform with thousands of folded proteins on a 1.5 sq-cm biosensor chip to enable high-throughput real-time label-free screening for kinetic analysis.

The paper introduces a high-throughput proteomic platform called SPOC that enables real-time label-free screening of protein interactions with kinetic analysis capabilities.

Lossless Single-Molecule Counting To Absolute QuantifyProteoforms

The paper introduces PICO, a novel immunoassay for absolute quantification of proteoforms, validated with recombinant and non-recombinant targets and demonstrating combinatorial multiplexing capabilities.

SomaScan Bioinformatics: Normalization, Quality Control, and Assessment of Pre-Analytical Variation

The paper describes bioinformatic methods for normalization, quality control, and variability assessment of SomaScan proteomics data.

The applying of immuno-RCA for the high-sensitivity detection of the ABO blood group antibodies on the printed glycoarray

This paper develops an immuno-RCA method for highly sensitive detection of ABO blood group antibodies on a printed glycoarray, achieving sensitivity down to 1 ng/ml.

An effective method of measuring nanobody binding kinetics and competition-based epitope mapping using biolayer interferometry

The paper describes a method using biolayer interferometry to measure nanobody binding kinetics and perform competition-based epitope mapping.

Ranking Antibody Binding Epitopes and Proteins Across Samples from Whole Proteome Tiled Linear Peptides

The paper introduces HERON, an R package for identifying immunogenic epitopes from ultradense peptide binding arrays across multiple samples.

Variability of 7K and 11K SomaScan plasma proteomics assays

Across Baltimore Longitudinal Study of Aging replicates, fully normalized SomaScan 11K has median inter-plate coefficient of variation 5% (7K: 4.5%), intra-plate 3%, 7K inter-batch 8%.

Massively parallel identification of single-cell immunophenotypes

This paper introduces biocytometry, a method for multiparametric immunophenotyping with high sensitivity and throughput, showing strong alignment with existing technologies and potential applications in disease monitoring and drug development.

Application of Cancer Cell Line Encyclopedia for Measuring Correlation Between Transcriptomics and Proteomics as a Guide for System-level Insights

The paper evaluates the SomaScan proteome profiling platform using CCLE cancer cell lines, showing its ability to distinguish cell lines by proteome signatures and correlate with transcriptome data.

NULISA: a novel proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing

NULISA is a proteomic platform with attomolar sensitivity and high multiplexing, enabling detection of low-abundance proteins in liquid biopsies.