Biology subjects

Rincon, N.

Publications and source records attributed to Rincon, N..

3 recordsLinked to original sources

bioRxiv2026

MS-BCR-DB: an integrated BCR repertoire database to mine humoral multiple sclerosis signatures

Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS) in which B cells play a critical role. While B-cell receptor (BCR) sequencing studies in MS are increasing, progress in understanding MS-associated BCR repertoire features and convergent patterns across patients has been limited by small cohorts, heterogeneous experimental methodologies, and fragmented data storage. To overcome these challenges, we developed the MS-BCR-Database, the first publicly accessible and uniformly processed collection of human MS BCR sequencing datasets. We harmonized raw BCR-sequencing data into an AIRR-compliant database incorporating clinical and technical metadata, enabling coherent cross-study analyses. Using this resource, we identified putative disease-associated BCR-sequence features, including CNS-biased V-gene usage, marked oligoclonal expansion in cerebrospinal fluid, and convergent clonotype clusters shared exclusively among MS patients. Integration with antigen-annotated BCR databases revealed matches to antibodies recognizing both viral antigens, including Epstein-Barr virus, and CNS self-proteins. The MS-BCR-Database provides a scalable foundation for mechanistic discovery and biomarker development in MS, while establishing a broadly applicable resource for integrative analyses of BCR repertoires.

bioinformatics↗

bioRxiv2022

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

The original CHESS database of human genes was assembled from nearly 10,000 RNA sequencing experiments in 53 human body sites produced by the Genotype-Tissue Expression (GTEx) project, and then augmented with genes from other databases to yield a comprehensive collection of protein-coding and noncoding transcripts. The construction of the new CHESS 3 database employed improved transcript assembly algorithms, a new machine learning classifier, and protein structure predictions to identify genes and transcripts likely to be functional and to eliminate those that appeared more likely to represent noise. The new catalog contains 41,356 genes on the GRCh38 reference human genome, of which 19,839 are protein-coding, and a total of 158,377 transcripts. These include 14,863 novel protein-coding transcripts. The total number of transcripts is substantially smaller than earlier versions due to improved transcriptome assembly methods and to a stricter protocol for filtering out noisy transcripts. Notably, CHESS 3 contains all of the transcripts in the MANE database, and at least one transcript corresponding to the vast majority of protein-coding genes in the RefSeq and GENCODE databases. CHESS 3 has also been mapped onto the complete CHM13 human genome, which gives a more-complete gene count of 43,773 genes and 19,968 protein-coding genes. The CHESS database is available at http://ccb.jhu.edu/chess.

genomics↗

bioRxiv2022

Highly accurate isoform identification for the human transcriptome

We explore a new hypothesis in genome annotation, namely whether computationally predicted protein structures can help to identify which of multiple possible gene isoforms represents a functional protein product. Guided by structure predictions, we evaluated over 140,000 isoforms of human protein-coding genes assembled from over 10,000 RNA sequencing experiments across many human tissues. We illustrate our new method with examples where structure provides a guide to function in combination with expression and evolutionary evidence. Additionally, we provide the complete set of structures as a resource to better understand the function of human genes and their isoforms. These results demonstrate the promise of protein structure prediction as a genome annotation tool, allowing us to refine even the most highly-curated catalog of human proteins. One-Sentence SummaryWe describe the use of 3D protein structures on a genome-wide scale to evaluate human protein isoforms for biological functionality.

genomics↗