Brian J. Beliveau

The paper introduces POCA, a photosensitizer platform for proximity labeling of proteins, RNA, and DNA in fixed cells without genetic engineering, demonstrating its utility across multiple molecular targets.

The paper identifies age-related molecular changes in mouse spleens using proteomics and transcriptomics, showing cell-type-specific remodeling and gender differences in post-transcriptional buffering.

DNA O-MAP identifies molecular neighborhoods around specific genomic loci using programmable probes and proteomics.

CellCycleNet predicts cell cycle phases from 3D nuclear-stained images, outperforming SVM models and showing strong generalization across microscopes.

The paper uses O-MAP to study a cardiac-specific RNA factory around TTN RNA, revealing its chromatin interactions, RNA composition, and role of RBM20 in gene regulation.

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

The paper processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

The paper introduces Tigerfish, a software tool for designing oligonucleotide probes targeting repetitive DNA intervals across genomes, and demonstrates its application on human chromosomes.

The paper introduces pSABER, a method for amplifying in situ hybridization signals in cellular and histopathological samples, achieving 25-fold amplification over conventional methods.

The paper introduces O-MAP, a method for discovering RNA-interacting proteins, transcripts, and genomic loci in situ with high precision and without genetic manipulation.

This paper introduces Decode-PAINT, a method for high-resolution chromatin imaging, and demonstrates its application to study X chromosome structure in cells.

PaintSHOP provides an interactive platform for designing oligonucleotide FISH experiments, integrating machine learning to predict probe specificity and generate standardized probe sets.

The paper investigates the 3D organization of Drosophila melanogaster pericentromeric heterochromatin domains and their spatial interactions with euchromatic regions enriched in H3K9me2/3 marks.

SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues by using oligo-based probes with long DNA concatemers for sensitive fluorescent detection.

The paper identifies the sequence composition of Drosophila melanogaster centromeres, showing they are composed of retroelement islands flanked by satellite repeats, with G2/Jockey-3 being the most enriched retroelement.

This paper describes a method for producing high-purity single-stranded DNA for various applications.

The paper uses super-resolution imaging and integrative modeling to achieve 10 kb resolution of chromosome folding.

OligoMiner designs genome-scale oligo FISH probes with customizable parameters and evaluates probe specificity using supervised learning, demonstrating scalability across model organisms.