selected publications
- Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types. 2025 GET IT
- A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain. Cell reports. 2025 Academic Article GET IT
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A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.
Nature communications.
2025
Academic Article
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Times cited: 1 - NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas. Cell reports. 2025 Academic Article GET IT
- NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas. 2025 GET IT
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Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.
Nature biotechnology.
2025
Academic Article
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Times cited: 1 - Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations. NPJ precision oncology. 2025 Academic Article GET IT
- A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types. 2025 GET IT
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Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics.
Genome research.
2024
Review
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Times cited: 9 -
Pronounced early differentiation underlies zebra finch gonadal germ cell development.
Developmental biology.
2024
Academic Article
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Times cited: 2 -
Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing.
Scientific data.
2024
Academic Article
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Times cited: 4 -
The single-cell opioid responses in the context of HIV (SCORCH) consortium.
Molecular psychiatry.
2024
Academic Article
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Times cited: 4 -
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Nature methods.
2024
Academic Article
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Times cited: 64 -
Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain.
Nature neuroscience.
2024
Academic Article
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Times cited: 45 - ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's Disease. 2024 GET IT
- cloudrnaSPAdes: isoform assembly using bulk barcoded RNA sequencing data. Bioinformatics (Oxford, England). 2024 Academic Article GET IT
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. 2023 GET IT
- cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data. 2023 GET IT
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A guide to the BRAIN Initiative Cell Census Network data ecosystem.
PLoS biology.
2023
Academic Article
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Times cited: 21 -
From words to complete phrases: insight into single-cell isoforms using short and long reads.
Transcription.
2023
Review
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Times cited: 10 -
Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development.
2023
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Times cited: 15 -
Accurate isoform discovery with IsoQuant using long reads.
Nature biotechnology.
2023
Academic Article
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Times cited: 86 -
The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing.
Nature methods.
2023
Academic Article
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Times cited: 20 -
ScisorWiz: visualizing differential isoform expression in single-cell long-read data.
Bioinformatics (Oxford, England).
2022
Academic Article
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Times cited: 16 -
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.
Genome research.
2022
Academic Article
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Times cited: 27 -
Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9.
Scientific reports.
2022
Academic Article
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Times cited: 7 -
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
Nature biotechnology.
2022
Academic Article
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Times cited: 72 -
Schizophrenia is defined by cell-specific neuropathology and multiple neurodevelopmental mechanisms in patient-derived cerebral organoids.
Molecular psychiatry.
2021
Academic Article
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Times cited: 87 -
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.
Nature communications.
2021
Academic Article
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Times cited: 128 -
Getting the Entire Message: Progress in Isoform Sequencing.
Frontiers in genetics.
2019
Review
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Times cited: 33 -
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.
Neuron.
2019
Academic Article
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Times cited: 553 -
The tech for the next decade: promises and challenges in genome biology.
Genome biology.
2019
Conference Paper
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Times cited: 2 -
Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions.
Frontiers in genetics.
2019
Academic Article
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Times cited: 34 -
Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.
Nature biotechnology.
2018
Academic Article
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Times cited: 235 -
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.
Genome medicine.
2017
Review
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Times cited: 48 -
Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome.
Genome research.
2017
Academic Article
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Times cited: 49 -
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.
Nature communications.
2017
Academic Article
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Times cited: 279 - Erratum to: Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. 2016 GET IT
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Promoter-like epigenetic signatures in exons displaying cell type-specific splicing.
Genome biology.
2015
Academic Article
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Times cited: 25 -
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.
Genome research.
2015
Academic Article
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Times cited: 154 -
Absence of canonical marks of active chromatin in developmentally regulated genes.
Nature genetics.
2015
Academic Article
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Times cited: 64 -
Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events.
Nature biotechnology.
2015
Academic Article
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Times cited: 155 -
Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing.
RNA (New York, N.Y.).
2015
Academic Article
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Times cited: 19 -
Defining a personal, allele-specific, and single-molecule long-read transcriptome.
Proceedings of the National Academy of Sciences of the United States of America.
2014
Academic Article
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Times cited: 192 -
A single-molecule long-read survey of the human transcriptome.
Nature biotechnology.
2013
Academic Article
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Times cited: 514 -
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.
G3 (Bethesda, Md.).
2013
Academic Article
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Times cited: 54 -
An integrated encyclopedia of DNA elements in the human genome.
Nature.
2012
Academic Article
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Times cited: 13490 -
Landscape of transcription in human cells.
Nature.
2012
Academic Article
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Times cited: 4338 -
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.
Genome research.
2012
Academic Article
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Times cited: 362 -
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Genome research.
2012
Academic Article
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Times cited: 4330 -
Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer.
PLoS biology.
2011
Academic Article
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Times cited: 88 -
A user's guide to the encyclopedia of DNA elements (ENCODE).
PLoS biology.
2011
Academic Article
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Times cited: 902 -
From chromatin to splicing: RNA-processing as a total artwork.
Epigenetics.
2010
Academic Article
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Times cited: 20 -
Nucleosome positioning as a determinant of exon recognition.
Nature structural & molecular biology.
2009
Academic Article
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Times cited: 317