Standout Papers
- Introduction and expression of a rabbit beta-globin gene in mouse fibroblasts. (1979)
- Transformation of mammalian cells with genes from procaryotes and eucaryotes (1979)
- Mapping and quantifying mammalian transcriptomes by RNA-Seq (2008)
- Genome-Wide Mapping of in Vivo Protein-DNA Interactions (2007)
- Evidence for Developmentally Programmed Transdifferentiation in Mouse Esophageal Muscle (1995)
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation (2010)
- Disruption of the mouse MRF4 gene identifies multiple waves of myogenesis in the myotome (1995)
- Isolated sequences from the linked Myf-5 and MRF4 genes drive distinct patterns of muscle-specific expression in transgenic mice (1993)
- Altering Genotype and Phenotype by DNA-Mediated Gene Transfer (1980)
Citation Impact
Citing Papers
Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate
2019 StandoutScienceNobel
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
2015 StandoutNobel
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
2009 StandoutScience
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
2014 Standout
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
2008 Science
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
2010 StandoutScience
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
2008 StandoutScience
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
2016
Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation
2015
Hallmarks of Cancer: The Next Generation
2011 Standout
Differential expression analysis for sequence count data
2010 Standout
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
2011 Standout
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
2013
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
2018
Adaptive Myogenesis under Hypoxia
2005
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
2009 Standout
A Feature-Based Approach to Modeling Protein–DNA Interactions
2008
Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq
2010
CeMyoD accumulation defines the body wall muscle cell fate during C. elegans embryogenesis
1990 StandoutNobel
Differential analysis of gene regulation at transcript resolution with RNA-seq
2012 Standout
The retinoblastoma gene family in differentiation and development
1999
Circular RNAs are a large class of animal RNAs with regulatory potency
2013 StandoutNature
Alternative isoform regulation in human tissue transcriptomes
2008 StandoutNature
ChIP–seq: advantages and challenges of a maturing technology
2009
Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR
2011
Modular regulatory principles of large non-coding RNAs
2012 StandoutNature
Strand-specific deep sequencing of the transcriptome
2010
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
2010 Standout
Oxygen in Stem Cell Biology: A Critical Component of the Stem Cell Niche
2010
Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains
2008
Specific regulation of gene expression by antisense, sense and antigene nucleic acids
1990
UTX mediates demethylation of H3K27me3 at muscle-specific genes during myogenesis
2010
The protein Id: A negative regulator of helix-loop-helix DNA binding proteins
1990 Standout
Long-Term Proliferation and Dopaminergic Differentiation of Human Mesencephalic Neural Precursor Cells
2001
Sex-specific and lineage-specific alternative splicing in primates
2009
Mammalian microRNAs predominantly act to decrease target mRNA levels
2010 StandoutNature
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
2008
Modeling the dynamics of transcriptional gene regulatory networks for animal development
2008
Model-based Analysis of ChIP-Seq (MACS)
2008 Standout
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
2010 Standout
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
2011 Standout
Enterochromaffin Cells Are Gut Chemosensors that Couple to Sensory Neural Pathways
2017 StandoutNobel
Human-tumor-derived cell lines contain common and different transforming genes
1981
RNA sequencing shows no dosage compensation of the active X-chromosome
2010
Chromatin crosstalk in development and disease: lessons from REST
2007
Understanding mechanisms underlying human gene expression variation with RNA sequencing
2010 Nature
The Reality of Pervasive Transcription
2011
Biosynthesis of the reverse transcriptase of hepatitis B viruses involves de novo translational initiation not ribosomal frameshifting
1989 StandoutNatureNobel
CDYL Bridges REST and Histone Methyltransferases for Gene Repression and Suppression of Cellular Transformation
2008
Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing
2013
Normalization, testing, and false discovery rate estimation for RNA-sequencing data
2011
Fast gapped-read alignment with Bowtie 2
2012 Standout
Transcriptional co-activator PGC-1α drives the formation of slow-twitch muscle fibres
2002 StandoutNature
Design and analysis of ChIP-seq experiments for DNA-binding proteins
2008
Transcriptome genetics using second generation sequencing in a Caucasian population
2010 Nature
Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells
2008
RNA-Seq: a revolutionary tool for transcriptomics
2008 Standout
N6-methyladenosine-dependent regulation of messenger RNA stability
2013 StandoutNature
An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs
2011
Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions
2011
Cloud-scale RNA-sequencing differential expression analysis with Myrna
2010
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
2012
Sequence-selective DNA recognition by synthetic ligands
1991
From RNA-seq reads to differential expression results
2010
A survey of sequence alignment algorithms for next-generation sequencing
2010
Detecting differential usage of exons from RNA-seq data
2012
Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
2010
Global quantification of mammalian gene expression control
2011 StandoutNature
Human DNA methylomes at base resolution show widespread epigenomic differences
2009 StandoutNature
lincRNAs act in the circuitry controlling pluripotency and differentiation
2011 StandoutNature
FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders
2015
Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells
2009
Correlation of mRNA and protein in complex biological samples
2009
Integrative transformation of Caenorhabditis elegans
1986 StandoutNobel
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
2013
The evolution of gene expression levels in mammalian organs
2011 StandoutNatureNobel
Sequencing technologies — the next generation
2009 Standout
Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells
2009
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
2013 StandoutNobel
Cell‐type specific analysis of translating RNAs in developing flowers reveals new levels of control
2010
The isolation of structural genes from libraries of eucaryotic DNA
1978 Standout
The human beta-globin gene and a functional viral thymidine kinase gene in developing mice.
1981
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
2013 Standout
Hormone-responsive expression of an endogenous proviral gene of mouse mammary tumor virus after molecular cloning and gene transfer into cultured cells.
1981
Integration, transcription, and control of a Drosophila heat shock gene in mouse cells.
1981 StandoutNobel
Number and distribution of polyadenylated RNA sequences in yeast
1977 StandoutNobel
Modeling and automation of sequencing-based characterization of RNA structure
2011 StandoutNobel
Adenovirus early region 1A enables viral and cellular transforming genes to transform primary cells in culture
1983 Nature
Messenger RNA prevalence in sea urchin embryos measured with cloned cDNAs.
1980
Introduction and expression of a fetal human globin gene in mouse fibroblasts.
1982 StandoutNobel
Rabbit β-globin mRNA production in mouse L cells transformed with cloned rabbit β-globin chromosomal DNA
1979 Nature
Sterols accelerate degradation of hamster 3-hydroxy-3-methylglutaryl coenzyme A reductase encoded by a constitutively expressed cDNA.
1985 StandoutNobel
Microinjection of a rabbit beta-globin gene into zygotes and its subsequent expression in adult mice and their offspring.
1981
Genetic and physical linkage of exogenous sequences in transformed cells
1980
The structure and evolution of the human β-globin gene family
1980
Ovalbumin is synthesized in mouse cells transformed with the natural chicken ovalbumin gene.
1980
5-Azacytidine-Induced Reactivation of a Herpes Simplex Thymidine Kinase Gene
1982 Science
Cotransfer of circular and linear prokaryotic and eukaryotic DNA sequences into mouse cells.
1980
Biological properties of human c-Ha-ras1 genes mutated at codon 12
1984 Nature
A structure for amplified DNA
1983 StandoutNobel
Few transcribed RNAs are translated in avian erythroid cells
1978
Ectopic Expression of the Serotonin 1c Receptor and the Triggering of Malignant Transformation
1989 StandoutScienceNobel
Cloning of Human Mineralocorticoid Receptor Complementary DNA: Structural and Functional Kinship with the Glucocorticoid Receptor
1987 StandoutScience
Introduction of a viral thymidine kinase gene and the human β-globin gene into developmentally multipotential mouse teratocarcinoma cells
1980 StandoutNobel
Gene amplification and gene correction in somatic cells
1982 StandoutNobel
Accurate transcription initiation on a purified mouse β-globin DNA fragment in a cell-free system
1980
Site-Specific Cleavage of a Yeast Chromosome by Oligonucleotide-Directed Triple-Helix Formation
1990 Science
Expression of a MyoD family member prefigures muscle pattern in Drosophila embryos.
1990
DNA methylation in the human γδβ-globin locus in erythroid and nonerythroid tissues
1980
Introduction of a rabbit β-globin gene into the mouse germ line
1981 Nature
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
2012 Standout
New human transforming genes detected by a tumorigenicity assay.
1984
Transformation of frog embryos with a rabbit beta-globin gene.
1981
Computational methods for transcriptome annotation and quantification using RNA-seq
2011
Cloned mouse mammary tumor virus DNA is biologically active in transfected mouse cells and its expression is stimulated by glucocorticoid hormones
1981
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
2013 Standout
Expression of a β-globin gene is enhanced by remote SV40 DNA sequences
1981
Nucleosomal packaging of the thymidine kinase gene of herpes simplex virus transferred into mouse cells: an actively expressed single-copy gene.
1980
Tissue Engineering--Current Challenges and Expanding Opportunities
2002 StandoutScience
Identification of DNA sequences required for transcription of the human α1-globin gene in a new SV40 host-vector system
1981
Regulated expression of human interferon beta 1 gene after transduction into cultured mouse and rabbit cells.
1982 Nobel
Sequence-Selective Recognition of DNA by Strand Displacement with a Thymine-Substituted Polyamide
1991 StandoutScience
Regulated expression of human growth hormone genes in mouse cells
1982 StandoutNobel
DNA sequences that mediate attenuation of transcription from the mouse protooncogene myc.
1989 StandoutNobel
Somatic expression of herpes thymidine kinase in mice following injection of a fusion gene into eggs
1981
Transforming DNA integrates into the host chromosome
1981 StandoutNobel
High efficiency transformation by direct microinjection of DNA into cultured mammalian cells
1980 StandoutNobel
Promoter Sequences of Eukaryotic Protein-Coding Genes
1980 Science
Molecular cloning and characterization of the human β-like globin gene cluster
1980
Selective elimination of mRNAs in vivo: complementary oligodeoxynucleotides promote RNA degradation by an RNase H-like activity.
1987 StandoutNobel
Characteristics of an SV40-plasmid recombinant and its movement into and out of the genome of a murine cell
1980
Induction of human beta-interferon synthesis with poly(rI . rC) in mouse cells transfected with cloned cDNA plasmids.
1982
High Throughput Short Read Alignment via Bi-directional BWT
2009
Deduced primary structure of the alpha subunit of the GTP-binding stimulatory protein of adenylate cyclase.
1986 StandoutNobel
Recognition of Thymine Adenine Base Pairs by Guanine in a Pyrimidine Triple Helix Motif
1989 Science
Sequence complexity of the RNA accumulated in oocytes of Arbacia punctulata
1976
Coordinate modulation of transfected HSV thymidine kinase and human globin genes
1983 StandoutNobel
Introduction of rat growth hormone gene into mouse fibroblasts via a retroviral DNA vector: expression and regulation.
1982
Isolation and characterization of a new cellular oncogene encoding a protein with multiple potential transmembrane domains
1986
Determination of cellular RNA concentrations by electron microscopy of R loop-containing DNA.
1981 StandoutNobel
The human LDL receptor: A cysteine-rich protein with multiple Alu sequences in its mRNA
1984 StandoutNobel
Deoxyribonucleic acid-mediated gene transfer in mammalian cells: molecular analysis of unstable transformants and their progression to stability.
1981
Transformation of mammalian cells with an amplifiable dominant-acting gene.
1980 StandoutNobel
Developmental expression of two cloned sequences coding for rare sea urchin embryo messages
1980
Membrane-bound domain of HMG CoA reductase is required for sterol-enhanced degradation of the enzyme
1985 StandoutNobel
Isolation of the chicken thymidine kinase gene by plasmid rescue
1980 Nature
Inducibility of human β-interferon gene in mouse L-cell clones
1982 Nature
DNA-mediated gene transfer of a circular plasmid into murine cells.
1979
Expression of the gag-pol fusion protein of Moloney murine leukemia virus without gag protein does not induce virion formation or proteolytic processing
1988
Regulated expression of an extrachromosomal human beta-interferon gene in mouse cells.
1982
Identification of two distinct regulatory regions adjacent to the human β-interferon gene
1983
Analysis of transcriptional regulatory signals of the HSV thymidine kinase gene: Identification of an upstream control region
1981 StandoutNobel
Replication and expression of thymidine kinase and human globin genes microinjected into mouse fibroblasts.
1980
The structure of the thymidine kinase gene promoter: Nuclease hypersensitivity correlates with expression
1982 StandoutNobel
TopHat: discovering splice junctions with RNA-Seq
2009 Standout
Second Structural Motif for Recognition of DNA by Oligonucleotide-Directed Triple-Helix Formation
1991 Science
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
2013 Standout
The regulated expression of β-globin genes introduced into mouse erythroleukemia cells
1983 StandoutNobel
Complex population of mRNA sequences in large polyadenylylated nuclear RNA molecules.
1978
Transfer of human globin genes to erythroleukemic mouse cells.
1982
The mouse metallothionein-I gene is transcriptionally regulated by cadmium following transfection into human or mouse cells
1982
DNA Methylation and Gene Function
1980 StandoutScience
Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain
2010
Modulation of transfected gene expression mediated by changes in chromatin structure
1982
Methylation of foreign DNA sequences in eukaryotic cells.
1980
Genetic Transformation of Drosophila with Transposable Element Vectors
1982 StandoutScience
The nucleotide sequence of the human β-globin gene
1980
Hormonal inducibility of rat α2u globulin genes in transfected mouse cells
1981 Nature
Transformation of the gene for hypoxanthine phosphoribosyltransferase
1979
Isolation of transforming DNA: Cloning the hamster aprt gene
1980 StandoutNobel
Works of B Wold being referenced
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
2007 StandoutScience
Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity
2012
Computation for ChIP-seq and RNA-seq studies
2009
Sequence census methods for functional genomics
2007
Systematic evaluation of factors influencing ChIP-seq fidelity
2012
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
2010 Standout
Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
2006
Skeletal muscle determination and differentiation: story of a core regulatory network and its context
1996
Scaffolding a Caenorhabditis nematode genome with RNA-seq
2010
Mapping and quantifying mammalian transcriptomes by RNA-Seq
2008 Standout
Herculin, a fourth member of the MyoD family of myogenic regulatory genes.
1990
Poly-L-ornithine-mediated transformation of mammalian cells.
1987
Altering Genotype and Phenotype by DNA-Mediated Gene Transfer
1980 StandoutScienceNobel
Transformation of mammalian cells with genes from procaryotes and eucaryotes
1979 StandoutNobel
Muscle creatine kinase sequence elements regulating skeletal and cardiac muscle expression in transgenic mice.
1989
Culture in Reduced Levels of Oxygen Promotes Clonogenic Sympathoadrenal Differentiation by Isolated Neural Crest Stem Cells
2000
Appearance and persistence of maternal RNA sequences in sea urchin development
1977
Stable reduction of thymidine kinase activity in cells expressing high levels of anti-sense RNA
1985
Structural gene sets active in embryos and adult tissues of the sea urchin
1976
Large-Scale Quality Analysis of Published ChIP-seq Data
2013
Muscle Creatine Kinase Sequence Elements Regulating Skeletal and Cardiac Muscle Expression in Transgenic Mice
1989
In Vivo Footprinting of a Muscle Specific Enhancer by Ligation Mediated PCR
1989 Science
Introduction and expression of a rabbit beta-globin gene in mouse fibroblasts.
1979 StandoutNobel
Enhanced Proliferation, Survival, and Dopaminergic Differentiation of CNS Precursors in Lowered Oxygen
2000
Interleukin-2 Transcription Is Regulated In Vivo at the Level of Coordinated Binding of Both Constitutive and Regulated Factors
1994
Inhibition of DNA Binding Proteins by Oligonucleotide-Directed Triple Helix Formation
1989 Science
Sea urchin embryo mRNA sequences expressed in the nuclear RNA of adult tissues
1978