Piero Carninci

The paper profiles NHD microglia and shows they adopt an antigen-presenting state without TREM2 dependence, triggering glial-to-neuronal changes.

The paper identifies repeat element-anchored enhancer-promoter interactions (REEPIs) in hormone-resistant breast cancer and links them to transcriptional adaptation and regulatory reprogramming.

The paper introduces nucCAGE and PRIME to identify active cis-regulatory elements with high sensitivity and applies them to create a cell-type-resolved CRE atlas.

The paper maps RNA-chromatin interactions in human prefrontal cortex, revealing co-regulatory changes linked to brain evolution and disease pathways.

The paper identifies new gene products and transcript isoforms in macrophage differentiation and activation, revealing how alternative promoters influence innate immune functions.

The paper integrates enhancer-promoter interactions and RNA-DNA contacts to show RNA's role in modulating cis-regulatory networks during neural differentiation.

The paper shows Ku prevents aberrant mRNA splicing caused by intronic antisense Alu elements, which affects RNA metabolism and cell viability.

This study uses nanopore long-read sequencing to analyze genomic disruptions in Alzheimer's disease, finding increased retrotransposon activity and structural variants in aged brains.

The paper identifies ASCL1 as a key regulator of mTEC function and central tolerance by analyzing single-cell RNA sequencing data from thymoma patients and mouse models.

The paper identifies hypoacetylation-defined enhancers in luminal breast cancer cells and links them to subtype-specific gene regulation and patient classification.

The paper develops a machine learning method to identify cis-regulatory element profiles and their sequence features during neuronal differentiation using single-cell ATAC-seq and RNA-seq data.

The paper identifies RNA-initiating sites at STRs and links them to gene expression, revealing regulatory roles and interactions with Alu repeats.

The paper identifies trans-contacting intronic RNAs (TIRs) in neuronal cells that form nuclear scaffolds called introsomes, influencing 3D genome organization and gene expression.

This paper benchmarks multimodal single-cell data integration methods to improve kidney reference atlas quality by identifying adaptive states and rare cell types.

The paper identifies 3UTR-derived capped RNAs, showing they are abundant and originate from AGO2-mediated cleavage at G-quadruplexes, with implications for APP protein regulation.

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

This study identifies technical challenges in detecting somatic recombination of repeat elements using short and long read datasets and highlights PCR-induced artifacts.

The paper presents AIDA, a diverse single-cell RNA-seq atlas of immune cells, revealing sub-continental diversity impacts on immune cell properties and identifying functional genetic variants.

The paper identifies altered layer 1 astrocytes in schizophrenia using spatial and single-nucleus transcriptomics of the anterior cingulate cortex.

The paper introduces CapTrap-seq, a method for full-length RNA transcript sequencing, and shows it produces highly accurate transcript models in human tissues.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper introduces RADIP, a new technology for mapping RNA-chromatin interactions mediated by H3K27me3, and demonstrates its application in mouse embryonic stem cells.

The paper investigates sequence, structure, and functional features of SINE-derived RNAs in SINEUP non-coding RNAs, showing their role in post-transcriptional gene regulation through interactions with RBPs and ribosomal RNAs.

The paper constructs a single-cell atlas of transcribed cis-regulatory elements in the human genome, revealing gene regulation patterns and trait-gene relationships across cell populations.

This study identifies SINEUP RNAs with Internal Ribosomal Entry Site (IRES) sequences as effector domains, enhancing translation of target mRNAs through both linear and circular transcripts.

This study shows that the piRNA pathway is essential for adult neurogenesis by repressing protein synthesis and cellular senescence in mouse hippocampal neural progenitor cells.

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.

The paper investigates somatic recombination of Alu and L1 repeat elements in human genomes, finding tissue-specific patterns and links to neurodegenerative diseases.

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.