We're excited to share that Alternate Allele Consulting contributed to a newly released bioRxiv preprint describing an innovative mass-spectrometry–based approach for mapping protease substrate specificity at unprecedented scale.

In this collaborative project, the research team designed and produced a naïve peptide substrate library of ~200,000 peptides and applied advanced LC/MS workflows to measure cleavage kinetics for tens of thousands of substrates in a single experiment. The method enables researchers to build detailed quantitative models—positional specificity matrices—that characterize how proteases recognize and cleave their substrates.

The study demonstrates this approach on two biologically important proteases, GluC and Fibroblast Activation Protein (FAP), revealing fine-grained determinants of protease specificity and expanding our ability to predict protease behavior across diverse peptide sequences.

Alternate Allele Consulting supported analysis and computational pipeline development for this work, contributing to a method that may help accelerate protease biology, therapeutic design, and protein engineering.

Alternate Allele Consulting is proud to have contributed to Infinity Bio's launch of EnviroSIGHT™, the world's first comprehensive non-viral microbial and protein allergen antibody analysis service. This breakthrough technology enables high-resolution profiling of immune responses to allergens, microbes, and toxins—unlocking new frontiers in systems immunology and chronic disease research.

EnviroSIGHT completes Infinity Bio's core antibody reactome service offerings. Combined with VirSIGHT (pan-virome) and HuSIGHT (pan-autoantibody)—all of which AAC contributed panel design expertise to—researchers now have access to the most comprehensive antibody assay ever developed, providing nearly one million antibody binding measurements in a single test. The EnviroSIGHT library covers pathogenic and opportunistic bacteria, diverse allergens from plants, fungi, food, and arthropods, beneficial gut microbiome components, parasites, pathogenic fungi, and venom proteins.

AAC's bioinformatics contributions to the panel design involved computational approaches to antigen selection from databases including the Immune Epitope Database (IEDB), ToxScan library, Segal microbiome library, and five allergen databases. Built on Infinity Bio's proprietary MIPSA technology (Molecular Indexing of Proteins by Self-Assembly), these panels represent a significant advancement in our ability to understand the immunological imprints of environmental exposures and their roles in infection, allergy, autoimmunity, and chronic inflammatory conditions.

This November marks a decade of Alternate Allele Consulting's partnership with DC Hunger Solutions, a nonprofit organization dedicated to building pathways out of poverty and helping individuals and families access the nutrition assistance they need.

Ten years ago, we developed the SNAP eligibility calculator for DC Hunger Solutions, a tool that helps Washington, DC residents quickly determine whether they qualify for the Supplemental Nutrition Assistance Program (SNAP). The calculator demystifies complex eligibility requirements and guides users through the application process, making it easier for those in need to access critical food assistance.

We're proud to continue supporting this mission by updating the calculator annually to reflect changes in SNAP regulations, income thresholds, and household requirements. It's been an honor to contribute our technical expertise to an organization that makes such a meaningful difference in our community.

Alternate Allele Consulting is pleased to announce the development of an R Software Development Kit (SDK) for tag.bio, enabling seamless integration between R and tag.bio's federated data mesh platform.

The R package provides access to tag.bio's distributed data resources as tidy data, following familiar R programming conventions. This approach allows bioinformatics researchers and data scientists to leverage their existing R workflows while accessing federated datasets across organizational boundaries.

Key features of the SDK include the ability to embed R functions and visualizations directly within tag.bio's web interface, as well as full integration of Rmarkdown reports as plugin applications. This tight integration enables researchers to build reproducible, shareable analytical workflows that combine the power of R with tag.bio's collaborative data platform.

Alternate Allele Consulting is proud to have contributed to a landmark study investigating the T cell repertoire in ankylosing spondylitis (AS), a chronic inflammatory disease strongly associated with the HLA-B27 allele. In this collaborative effort, researchers performed deep sequencing of more than 77 million TCRβ clonotypes across patient and control cohorts to search for shared sequence motifs potentially linked to disease biology.

The study identified 15 independent TCRβ motifs enriched in HLA-B27–positive AS patients compared to both healthy controls and B27-positive individuals without disease. These findings support the long-standing hypothesis that a common antigen, presented by HLA-B27 and recognized by CD8⁺ T cells, may contribute directly to AS pathogenesis.

We are pleased to announce our contribution to a newly published methods chapter in the Springer Methods in Molecular Biology series. The chapter, titled "RNA Gene Expression to Identify the Etiology of Acute Ischemic Stroke: The Biomarkers of Acute Stroke Etiology (BASE) Study)", presents a validated workflow for using whole-blood gene expression to classify ischemic stroke etiology — a major clinical challenge where a substantial fraction of patients leave the hospital without a definitive cause.

The chapter outlines standardized protocols for sample handling, RNA expression profiling, and downstream computational analysis, providing a reproducible framework for translational stroke biomarker research. Our team supported analytical components of this work, contributing to the development of robust expression-based classifiers for stroke subtype.