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View article: BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences
BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences Open
A bstract Modern genomics produces billions of sequencing records per run, which are typically stored as gzip-compressed FASTQ files. While this format is widely used, it is not optimal for high-throughput processing due to its reliance on…
View article: Pathogenic Viruses, Genome Integrations, and Viral::Human Chimeric Transcripts Detected by VirusIntegrationFinder Across >30k Human Tumor and Normal Samples
Pathogenic Viruses, Genome Integrations, and Viral::Human Chimeric Transcripts Detected by VirusIntegrationFinder Across >30k Human Tumor and Normal Samples Open
Viruses are a leading cause of human morbidity and mortality. Certain viruses, including human papillomaviruses (HPVs), play a significant role in the etiology of cancer. Detection of viral DNA insertions in the human genome from next gene…
View article: STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads
STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads Open
Summary Allele-specific expression (ASE) is an important genetic phenomenon that impacts an individual’s phenotype and is relevant in various biological and medical contexts. Next-generation RNA sequencing technologies provide an unprecede…
View article: A mucus production programme promotes classical pancreatic ductal adenocarcinoma
A mucus production programme promotes classical pancreatic ductal adenocarcinoma Open
Objective The optimal therapeutic response in cancer patients is highly dependent upon the differentiation state of their tumours. Pancreatic ductal adenocarcinoma (PDA) is a lethal cancer that harbours distinct phenotypic subtypes with pr…
View article: Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA sequencing datasets
Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA sequencing datasets Open
View article: Comparative transcriptomics reveals human-specific cortical features
Comparative transcriptomics reveals human-specific cortical features Open
The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates are poorly understood. We used comparative single-nucleus transcriptomics to analyze samples of the middle temporal gyrus (MTG) f…
View article: Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution
Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution Open
Enhanced cognitive function in humans is hypothesized to result from cortical expansion and increased cellular diversity. However, the mechanisms that drive these phenotypic innovations remain poorly understood, in part because of the lack…
View article: Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3–FOXO1 in rhabdomyosarcoma
Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3–FOXO1 in rhabdomyosarcoma Open
Recurrent chromosomal rearrangements found in rhabdomyosarcoma (RMS) produce the PAX3–FOXO1 fusion protein, which is an oncogenic driver and a dependency in this disease. One important function of PAX3–FOXO1 is to arrest myogenic different…
View article: The ENCODE Uniform Analysis Pipelines
The ENCODE Uniform Analysis Pipelines Open
View article: Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector
Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector Open
View article: The ENCODE Uniform Analysis Pipelines
The ENCODE Uniform Analysis Pipelines Open
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across…
View article: The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models Open
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets fr…
View article: Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA-sequencing datasets
Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA-sequencing datasets Open
Glioblastoma multiforme (GBM) is an aggressive, heterogeneous grade IV brain tumor. Glioblastoma stem cells (GSCs) initiate the tumor and are known culprits of therapy resistance. Mounting evidence has demonstrated a regulatory role of lon…
View article: Supplementary Tables for "Comparative single cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution"
Supplementary Tables for "Comparative single cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution" Open
Supplementary Tables to reproduce results reported in "Comparative single cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution"
View article: Conserved coexpression at single cell resolution across primate brains
Conserved coexpression at single cell resolution across primate brains Open
Enhanced cognitive function in humans is hypothesized to result from cortical expansion and increased cellular diversity. However, the mechanisms that drive these phenotypic differences remain poorly understood, in part due to the lack of …
View article: Comparative transcriptomics reveals human-specific cortical features
Comparative transcriptomics reveals human-specific cortical features Open
Humans have unique cognitive abilities among primates, including language, but their molecular, cellular, and circuit substrates are poorly understood. We used comparative single nucleus transcriptomics in adult humans, chimpanzees, gorill…
View article: Author Correction: Perspectives on ENCODE
Author Correction: Perspectives on ENCODE Open
In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, US…
View article: Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes Open
View article: Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse
Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse Open
View article: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses
Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses Open
The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In this study, we explored the consensus ge…
View article: Comparative cellular analysis of motor cortex in human, marmoset and mouse
Comparative cellular analysis of motor cortex in human, marmoset and mouse Open
View article: Targeted <i>in silico</i> characterization of fusion transcripts in tumor and normal tissues via FusionInspector
Targeted <i>in silico</i> characterization of fusion transcripts in tumor and normal tissues via FusionInspector Open
Motivation Gene fusions play a key role as driver oncogenes in tumors, and their reliable discovery and detection are important for cancer research, diagnostics, prognostics and guiding personalized therapy. While discovering gene fusions …
View article: A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery Open
The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the inference of the impacts of somatic variants to pathway analysis to biomarker development and subtype dis…
View article: STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data
STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data Open
We present STARsolo , a comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR . Using simulated data that closely resembles realistic scRNA-seq, we demonstrate t…
View article: Multi-tissue integrative analysis of personal epigenomes
Multi-tissue integrative analysis of personal epigenomes Open
Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for…
View article: Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses
Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses Open
The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In this study, we explored the consensus ge…
View article: Landscape of transcription in human cells
Landscape of transcription in human cells Open
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific sub-cellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic sub-cellul…
View article: Expanded encyclopaedias of DNA elements in the human and mouse genomes
Expanded encyclopaedias of DNA elements in the human and mouse genomes Open
View article: Perspectives on ENCODE
Perspectives on ENCODE Open
View article: A limited set of transcriptional programs define major cell types
A limited set of transcriptional programs define major cell types Open
We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define …