selected publications
- Pronounced early differentiation underlies zebra finch gonadal germ cell development. Developmental biology. 2024 Academic Article GET IT
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing. Scientific data. 2024 Academic Article GET IT
- The single-cell opioid responses in the context of HIV (SCORCH) consortium. Molecular psychiatry. 2024 Review GET IT
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods. 2024 Academic Article GET IT
- Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain. Nature neuroscience. 2024 Academic Article GET IT
- 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
-
A guide to the BRAIN Initiative Cell Census Network data ecosystem.
PLoS biology.
2023
Academic Article
GET IT
Times cited: 9 - From words to complete phrases: insight into single-cell isoforms using short and long reads. Transcription. 2023 Review GET IT
- Accurate isoform discovery with IsoQuant using long reads. Nature biotechnology. 2023 Academic Article GET IT
- The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing. Nature methods. 2023 Academic Article GET IT
- ScisorWiz: Visualizing Differential Isoform Expression in Single-Cell Long-Read Data. Bioinformatics (Oxford, England). 2022 Academic Article GET IT
- Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns. Genome research. 2022 Academic Article GET IT
- Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9. Scientific reports. 2022 Academic Article GET IT
-
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
Nature biotechnology.
2022
Academic Article
GET IT
Times cited: 50 - Schizophrenia is defined by cell-specific neuropathology and multiple neurodevelopmental mechanisms in patient-derived cerebral organoids. Molecular psychiatry. 2021 Academic Article GET IT
-
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.
Nature communications.
2021
Academic Article
GET IT
Times cited: 95 -
Getting the Entire Message: Progress in Isoform Sequencing.
Frontiers in genetics.
2019
Information Resource
GET IT
Times cited: 29 - SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron. 2019 Academic Article GET IT
-
The tech for the next decade: promises and challenges in genome biology.
Genome biology.
2019
Conference Paper
GET IT
Times cited: 2 -
Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions.
Frontiers in genetics.
2019
Academic Article
GET IT
Times cited: 27 -
Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.
Nature biotechnology.
2018
Academic Article
GET IT
Times cited: 74 -
Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome.
Genome research.
2017
Academic Article
GET IT
Times cited: 45 -
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.
Nature communications.
2017
Academic Article
GET IT
Times cited: 225 -
Promoter-like epigenetic signatures in exons displaying cell type-specific splicing.
Genome biology.
2015
Academic Article
GET IT
Times cited: 23 -
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.
Genome research.
2015
Academic Article
GET IT
Times cited: 135 -
Absence of canonical marks of active chromatin in developmentally regulated genes.
Nature genetics.
2015
Academic Article
GET IT
Times cited: 60 -
Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events.
Nature biotechnology.
2015
Academic Article
GET IT
Times cited: 143 -
Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing.
RNA (New York, N.Y.).
2015
Academic Article
GET IT
Times cited: 16 -
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
GET IT
Times cited: 185 -
A single-molecule long-read survey of the human transcriptome.
Nature biotechnology.
2013
Academic Article
GET IT
Times cited: 479 -
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.
G3 (Bethesda, Md.).
2013
Academic Article
GET IT
Times cited: 51 -
An integrated encyclopedia of DNA elements in the human genome.
Nature.
2012
Academic Article
GET IT
Times cited: 12641 -
Landscape of transcription in human cells.
Nature.
2012
Academic Article
GET IT
Times cited: 4116 -
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
GET IT
Times cited: 345 -
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Genome research.
2012
Academic Article
GET IT
Times cited: 4128 -
Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer.
PLoS biology.
2011
Academic Article
GET IT
Times cited: 82 -
A user's guide to the encyclopedia of DNA elements (ENCODE).
PLoS biology.
2011
Academic Article
GET IT
Times cited: 902 -
From chromatin to splicing: RNA-processing as a total artwork.
Epigenetics.
2010
Academic Article
GET IT
Times cited: 20 -
Nucleosome positioning as a determinant of exon recognition.
Nature structural & molecular biology.
2009
Academic Article
GET IT
Times cited: 317