Published in Database (Oxford) on September 14, 2011
Positive feedback between PU.1 and the cell cycle controls myeloid differentiation. Science (2013) 2.31
Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits. Cell (2014) 1.73
Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response. Cell (2013) 1.32
Global and stage specific patterns of Krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells. PLoS One (2013) 1.03
Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. Elife (2014) 0.86
New levels of transcriptome complexity at upper thermal limits in wild Drosophila revealed by exon expression analysis. Genetics (2013) 0.82
Wolbachia Influences the Production of Octopamine and Affects Drosophila Male Aggression. Appl Environ Microbiol (2015) 0.81
Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland. Radiat Oncol (2012) 0.81
Longevity Genes Revealed by Integrative Analysis of Isoform-Specific daf-16/FoxO Mutants of Caenorhabditis elegans. Genetics (2015) 0.80
Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. Elife (2016) 0.79
GABA-A and NMDA receptor subunit mRNA expression is altered in the caudate but not the putamen of the postmortem brains of alcoholics. Front Cell Neurosci (2014) 0.78
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Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
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Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (2003) 16.80
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Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res (2007) 13.47
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An established preadipose cell line and its differentiation in culture. II. Factors affecting the adipose conversion. Cell (1975) 8.29
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BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics (2008) 5.24
PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification. Nucleic Acids Res (2009) 5.03
Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev (2008) 4.93
Anatomical profiling of nuclear receptor expression reveals a hierarchical transcriptional network. Cell (2006) 4.64
QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics (2008) 3.62
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics (2004) 3.44
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol (2005) 3.24
A gateway-compatible yeast one-hybrid system. Genome Res (2004) 3.23
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Evolution of C2H2-zinc finger genes and subfamilies in mammals: species-specific duplication and loss of clusters, genes and effector domains. BMC Evol Biol (2008) 1.51
Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific. Genome Biol (2004) 1.30
Primique: automatic design of specific PCR primers for each sequence in a family. BMC Bioinformatics (2007) 1.27
High-throughput quantification of splicing isoforms. RNA (2009) 1.16
Experimental advances in the characterization of metazoan gene regulatory networks. Brief Funct Genomic Proteomic (2009) 0.84
A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol (2008) 38.22
ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res (2003) 17.39
Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89
PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform (2002) 8.77
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res (2006) 6.13
High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform (2002) 4.95
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res (2005) 4.15
KAP1 controls endogenous retroviruses in embryonic stem cells. Nature (2010) 4.02
The dynamic architecture of Hox gene clusters. Science (2011) 3.58
A first version of the Caenorhabditis elegans Promoterome. Genome Res (2004) 3.29
Exhaustion of tumor-specific CD8⁺ T cells in metastases from melanoma patients. J Clin Invest (2011) 3.28
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol (2005) 3.24
Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol (2011) 2.94
Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet (2009) 2.76
The Microbe browser for comparative genomics. Nucleic Acids Res (2009) 2.71
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science (2013) 2.66
Topology and dynamics of the zebrafish segmentation clock core circuit. PLoS Biol (2012) 2.41
The conserved transcriptome in human and rodent male gametogenesis. Proc Natl Acad Sci U S A (2007) 2.30
Gene expression profiling identifies molecular subtypes of inflammatory breast cancer. Cancer Res (2005) 2.26
Probable zoonotic leprosy in the southern United States. N Engl J Med (2011) 2.22
Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol (2012) 2.12
Nemo: an evolutionary and population genetics programming framework. Bioinformatics (2006) 2.10
Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res (2005) 2.05
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat (2004) 1.97
Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes. Hum Mol Genet (2005) 1.96
Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet (2007) 1.92
Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat Protoc (2008) 1.89
Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. Plant J (2012) 1.84
Morphological and molecular characterization of adult midgut compartmentalization in Drosophila. Cell Rep (2013) 1.71
Roles of Vibrio fischeri and nonsymbiotic bacteria in the dynamics of mucus secretion during symbiont colonization of the Euprymna scolopes light organ. Appl Environ Microbiol (2002) 1.67
Gene expression profiling for molecular characterization of inflammatory breast cancer and prediction of response to chemotherapy. Cancer Res (2004) 1.61
Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat Methods (2007) 1.49
C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO. Mech Ageing Dev (2006) 1.44
Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L. EMBO J (2011) 1.40
Phylogenetic trees: visualizing, customizing and detecting incongruence. Bioinformatics (2005) 1.38
Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genet (2012) 1.31
GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. Database (Oxford) (2010) 1.31
C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metab (2005) 1.28
Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell. J Virol (2011) 1.25
Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein. PLoS Pathog (2012) 1.25
MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics (2009) 1.24
Automated protein-DNA interaction screening of Drosophila regulatory elements. Nat Methods (2011) 1.21
Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet (2011) 1.20
Perinatal exposure to bisphenol a increases adult mammary gland progesterone response and cell number. Mol Endocrinol (2011) 1.09
The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae. Mol Cell (2010) 1.07
Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nat Methods (2013) 1.06
Complex expression dynamics and robustness in C. elegans insulin networks. Genome Res (2013) 1.06
Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO. Mol Cell (2012) 1.05
Global and stage specific patterns of Krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells. PLoS One (2013) 1.03
Comparative genomics of Esx genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation. Infect Immun (2011) 1.01
The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res (2009) 1.01
MutaDATABASE: a centralized and standardized DNA variation database. Nat Biotechnol (2011) 0.99
Primer-initiated sequence synthesis to detect and assemble structural variants. Nat Methods (2010) 0.98
A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics (2011) 0.96
Conserved role for the Drosophila Pax6 homolog Eyeless in differentiation and function of insulin-producing neurons. Proc Natl Acad Sci U S A (2008) 0.95
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. Nucleic Acids Res (2012) 0.94
Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method. Methods Mol Biol (2012) 0.93
Genome-wide definition of the SigF regulon in Mycobacterium tuberculosis. J Bacteriol (2012) 0.93
Zinc-metalloproteases in insects: ACE and ECE. Insect Biochem Mol Biol (2004) 0.92
DNA-centered approaches to characterize regulatory protein-DNA interaction complexes. Mol Biosyst (2009) 0.90
Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing. PLoS One (2009) 0.88
iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Res (2012) 0.87
Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo. Chaos (2013) 0.86
Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility. Hum Reprod (2012) 0.86
A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. Mol Syst Biol (2013) 0.86
Pax6 and eye development in Arthropoda. Arthropod Struct Dev (2006) 0.86
Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. Brief Funct Genomics (2010) 0.84
Few crucial links assure checkpoint efficiency in the yeast cell-cycle network. Bioinformatics (2006) 0.83
Structural variation-associated expression changes are paralleled by chromatin architecture modifications. PLoS One (2013) 0.82
Representing perturbed dynamics in biological network models. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 0.82
Neprilysins: an evolutionarily conserved family of metalloproteases that play important roles in reproduction in Drosophila. Genetics (2014) 0.81
Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico. Biosystems (2010) 0.81
WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data. Nucleic Acids Res (2010) 0.81
Mutational analysis of the eyeless gene and phenotypic rescue reveal that an intact Eyeless protein is necessary for normal eye and brain development in Drosophila. Dev Biol (2009) 0.80
Genome-wide profiling of DNA-binding proteins using barcode-based multiplex Solexa sequencing. Methods Mol Biol (2012) 0.79
Isolation and characterization of an angiotensin converting enzyme substrate from vitellogenic ovaries of Neobellieria bullata. Peptides (2002) 0.79
Enrichment of N-terminal cysteinyl-peptides by covalent capture. J Proteomics (2008) 0.78
Structure, evolutionary conservation, and functions of angiotensin- and endothelin-converting enzymes. Int Rev Cytol (2004) 0.78
MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. BMC Genomics (2006) 0.77
Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics (2013) 0.77
PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data. BMC Microbiol (2012) 0.77
Presence of angiotensin converting enzyme (ACE) interactive factors in ovaries of the grey fleshfly Neobellieria bullata. Comp Biochem Physiol B Biochem Mol Biol (2002) 0.76
A mammalian transcription factor-specific peptide repository for targeted proteomics. Proteomics (2015) 0.76
A high-throughput gateway-compatible yeast one-hybrid screen to detect protein-DNA interactions. Methods Mol Biol (2012) 0.76
Editorial overview: Genome architecture and expression. Curr Opin Genet Dev (2017) 0.75
Angiotensin-converting enzyme inhibition studies by natural leech inhibitors by capillary electrophoresis and competition assay. Eur J Biochem (2004) 0.75
Bicaudal C1 promotes pancreatic NEUROG3+ endocrine progenitor differentiation and ductal morphogenesis. Development (2016) 0.75