Published in Bioinformatics on April 27, 2012
CSF1/CSF1R blockade reprograms tumor-infiltrating macrophages and improves response to T-cell checkpoint immunotherapy in pancreatic cancer models. Cancer Res (2014) 2.00
g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res (2016) 1.31
Elucidating novel serum biomarkers associated with pulmonary tuberculosis treatment. PLoS One (2013) 1.24
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res (2014) 1.23
Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods (2015) 1.00
Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver. Proc Natl Acad Sci U S A (2015) 0.99
HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis. Nucleic Acids Res (2014) 0.93
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc (2014) 0.92
Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Res (2013) 0.91
Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression. BMC Genomics (2015) 0.89
Tunable protein synthesis by transcript isoforms in human cells. Elife (2016) 0.88
High-fat diet reprograms the epigenome of rat spermatozoa and transgenerationally affects metabolism of the offspring. Mol Metab (2015) 0.88
Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells. BMC Genomics (2014) 0.88
Bioinformatic analysis of proteomics data. BMC Syst Biol (2014) 0.87
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA. PLoS One (2015) 0.86
Genomic alterations in BCL2L1 and DLC1 contribute to drug sensitivity in gastric cancer. Proc Natl Acad Sci U S A (2015) 0.86
Glycocapture-assisted global quantitative proteomics (gagQP) reveals multiorgan responses in serum toxicoproteome. J Proteome Res (2013) 0.85
A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs. BMC Genomics (2014) 0.84
Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Mol Cell Proteomics (2014) 0.84
A transcription factor hierarchy defines an environmental stress response network. Science (2016) 0.84
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data. Nucleic Acids Res (2014) 0.83
Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia. PLoS One (2013) 0.81
Comprehensive profiling of lysine acetylproteome analysis reveals diverse functions of lysine acetylation in common wheat. Sci Rep (2016) 0.81
SAMNetWeb: identifying condition-specific networks linking signaling and transcription. Bioinformatics (2014) 0.81
The proteomic landscape of the suprachiasmatic nucleus clock reveals large-scale coordination of key biological processes. PLoS Genet (2014) 0.81
ERG induces a mesenchymal-like state associated with chemoresistance in leukemia cells. Oncotarget (2014) 0.81
Acute targeting of general transcription factor IIB restricts cardiac hypertrophy via selective inhibition of gene transcription. Circ Heart Fail (2014) 0.81
Dynamic changes in global microRNAome and transcriptome reveal complex miRNA-mRNA regulated host response to Japanese Encephalitis Virus in microglial cells. Sci Rep (2016) 0.81
Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins. Genome Med (2016) 0.81
Microarray comparison of the gene expression profiles in the adult vs. embryonic day 14 rat liver. Biomed Rep (2014) 0.80
Acetylome analysis reveals the involvement of lysine acetylation in diverse biological processes in Phytophthora sojae. Sci Rep (2016) 0.80
An essential role for UTX in resolution and activation of bivalent promoters. Nucleic Acids Res (2016) 0.80
LENS: web-based lens for enrichment and network studies of human proteins. BMC Med Genomics (2015) 0.80
Blocking sense-strand activity improves potency, safety and specificity of anti-hepatitis B virus short hairpin RNA. EMBO Mol Med (2016) 0.80
Epigenome-Microbiome crosstalk: A potential new paradigm influencing neonatal susceptibility to disease. Epigenetics (2016) 0.79
Coregulation of genetic programs by the transcription factors NFIB and STAT5. Mol Endocrinol (2014) 0.79
CellLineNavigator: a workbench for cancer cell line analysis. Nucleic Acids Res (2012) 0.79
Comparative Tissue Proteomics of Microdissected Specimens Reveals Novel Candidate Biomarkers of Bladder Cancer. Mol Cell Proteomics (2015) 0.79
AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes. Bioinformatics (2015) 0.79
Systematic analysis of the lysine acetylome in Fusarium graminearum. BMC Genomics (2016) 0.79
Gene expression profiling of peri-implant healing of PLGA-Li+ implants suggests an activated Wnt signaling pathway in vivo. PLoS One (2014) 0.78
Proteome-wide analysis of lysine acetylation in the plant pathogen Botrytis cinerea. Sci Rep (2016) 0.78
Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures. PeerJ (2013) 0.78
Expression-based network biology identifies immune-related functional modules involved in plant defense. BMC Genomics (2014) 0.78
Elucidation of Relevant Neuroinflammation Mechanisms Using Gene Expression Profiling in Patients with Amyotrophic Lateral Sclerosis. PLoS One (2016) 0.77
Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry. BMC Genomics (2015) 0.77
Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism. BMC Genomics (2015) 0.77
Nuclear receptor-mediated alleviation of alcoholic fatty liver by polyphenols contained in alcoholic beverages. PLoS One (2014) 0.77
Genomic responses during acute human anaphylaxis are characterized by upregulation of innate inflammatory gene networks. PLoS One (2014) 0.77
Multiple sporadic colorectal cancers display a unique methylation phenotype. PLoS One (2014) 0.77
Regulation of toll-like receptor signaling by the SF3a mRNA splicing complex. PLoS Genet (2015) 0.77
Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules. Sci Rep (2016) 0.77
Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism. BMC Syst Biol (2014) 0.76
Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging. Nucleic Acids Res (2015) 0.76
Networks of Host Factors that Interact with NS1 Protein of Influenza A Virus. Front Microbiol (2016) 0.76
Genome-wide analysis of functional and evolutionary features of tele-enhancers. G3 (Bethesda) (2014) 0.76
Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis. EMBO Rep (2015) 0.76
Nonsynonymous Single-Nucleotide Variations on Some Posttranslational Modifications of Human Proteins and the Association with Diseases. Comput Math Methods Med (2015) 0.76
Cooperative Transcriptional Activation of Antimicrobial Genes by STAT and NF-κB Pathways by Concerted Recruitment of the Mediator Complex. Cell Rep (2015) 0.76
Global Profiling of the Cellular Alternative RNA Splicing Landscape during Virus-Host Interactions. PLoS One (2016) 0.76
Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python). Genet Res Int (2016) 0.75
Systematic analysis of the lysine acetylome reveals diverse functions of lysine acetylation in the oleaginous yeast Yarrowia lipolytica. AMB Express (2017) 0.75
A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors. Oncotarget (2015) 0.75
Synergic Functions of miRNAs Determine Neuronal Fate of Adult Neural Stem Cells. Stem Cell Reports (2017) 0.75
Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme. Nat Commun (2016) 0.75
Mice produced by mitotic reprogramming of sperm injected into haploid parthenogenotes. Nat Commun (2016) 0.75
First insights into the nature and evolution of antisense transcription in nematodes. BMC Evol Biol (2016) 0.75
ISAAC - InterSpecies Analysing Application using Containers. BMC Bioinformatics (2014) 0.75
Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions. BMC Microbiol (2016) 0.75
High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells. BMC Genomics (2015) 0.75
Integrated analysis of transcriptome in cancer patient-derived xenografts. PLoS One (2015) 0.75
High prevalence of TP53 mutations is associated with poor survival and an EMT signature in gliosarcoma patients. Exp Mol Med (2017) 0.75
Retrovirus-Mediated Expression of E2A-PBX1 Blocks Lymphoid Fate but Permits Retention of Myeloid Potential in Early Hematopoietic Progenitors. PLoS One (2015) 0.75
Investigation of differentially-expressed microRNAs and genes in cervical cancer using an integrated bioinformatics analysis. Oncol Lett (2017) 0.75
Energy metabolism in Mycobacterium gilvum PYR-GCK: insights from transcript expression analyses following two states of induction. PLoS One (2014) 0.75
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. Sci Rep (2016) 0.75
Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma. BMC Genomics (2016) 0.75
Prediction of Possible Biomarkers and Novel Pathways Conferring Risk to Post-Traumatic Stress Disorder. PLoS One (2016) 0.75
rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining. BMC Bioinformatics (2017) 0.75
Tricyclic Antidepressants Promote Ceramide Accumulation to Regulate Collagen Production in Human Hepatic Stellate Cells. Sci Rep (2017) 0.75
A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis. PLoS One (2015) 0.75
SiBIC: a web server for generating gene set networks based on biclusters obtained by maximal frequent itemset mining. PLoS One (2013) 0.75
The severity of hereditary porphyria is modulated by the porphyrin exporter and Lan antigen ABCB6. Nat Commun (2016) 0.75
Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells. World J Surg Oncol (2016) 0.75
Extracting tumor tissue immune status from expression profiles: correlating renal cancer prognosis with tumor-associated immunome. Oncotarget (2015) 0.75
Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. Int J Mol Sci (2014) 0.75
Cell types differ in global coordination of splicing and proportion of highly expressed genes. Sci Rep (2016) 0.75
MLL4 prepares the enhancer landscape for Foxp3 induction via chromatin looping. Nat Immunol (2017) 0.75
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res (2007) 17.46
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics (2007) 12.76
DAVID gene ID conversion tool. Bioinformation (2008) 9.16
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res (2007) 17.46
HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc Natl Acad Sci U S A (2002) 17.22
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46
Initiation of Antiretroviral Therapy in Early Asymptomatic HIV Infection. N Engl J Med (2015) 15.06
Inflammatory and coagulation biomarkers and mortality in patients with HIV infection. PLoS Med (2008) 13.72
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics (2007) 12.76
DAVID gene ID conversion tool. Bioinformation (2008) 9.16
Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res (2003) 8.08
HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells. Nat Immunol (2008) 5.01
Initial sequence and comparative analysis of the cat genome. Genome Res (2007) 4.67
Inflammation, coagulation and cardiovascular disease in HIV-infected individuals. PLoS One (2012) 3.68
Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc Natl Acad Sci U S A (2003) 3.47
PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics (2003) 3.11
Extracting biological meaning from large gene lists with DAVID. Curr Protoc Bioinformatics (2009) 2.88
The role of miR-31 and its target gene SATB2 in cancer-associated fibroblasts. Cell Cycle (2010) 2.69
Idiopathic CD4+ lymphocytopenia: natural history and prognostic factors. Blood (2008) 2.27
Changes in inflammatory and coagulation biomarkers: a randomized comparison of immediate versus deferred antiretroviral therapy in patients with HIV infection. J Acquir Immune Defic Syndr (2011) 2.21
A Randomized, Controlled Trial of ZMapp for Ebola Virus Infection. N Engl J Med (2016) 2.09
In vivo expansion of CD4CD45RO-CD25 T cells expressing foxP3 in IL-2-treated HIV-infected patients. J Clin Invest (2005) 1.96
HIV infection-associated immune activation occurs by two distinct pathways that differentially affect CD4 and CD8 T cells. Proc Natl Acad Sci U S A (2008) 1.95
Incomplete CD4 T cell recovery in HIV-1 infection after 12 months of highly active antiretroviral therapy is associated with ongoing increased CD4 T cell activation and turnover. J Acquir Immune Defic Syndr (2003) 1.82
IL-2-induced CD4+ T-cell expansion in HIV-infected patients is associated with long-term decreases in T-cell proliferation. Blood (2004) 1.82
Induction of prolonged survival of CD4+ T lymphocytes by intermittent IL-2 therapy in HIV-infected patients. J Clin Invest (2005) 1.82
High prevalence of osteonecrosis of the femoral head in HIV-infected adults. Ann Intern Med (2002) 1.74
The evaluation of subcutaneous proleukin (interleukin-2) in a randomized international trial: rationale, design, and methods of ESPRIT. Control Clin Trials (2002) 1.73
The identification of microRNAs in a genomically unstable region of human chromosome 8q24. Mol Cancer Res (2008) 1.71
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics (2008) 1.68
When to start therapy for HIV infection: a swinging pendulum in search of data. Ann Intern Med (2003) 1.63
Bovine apolipoprotein B-100 is a dominant immunogen in therapeutic cell populations cultured in fetal calf serum in mice and humans. Blood (2007) 1.52
Safety, tolerability, and mechanisms of antiretroviral activity of pegylated interferon Alfa-2a in HIV-1-monoinfected participants: a phase II clinical trial. J Infect Dis (2010) 1.51
IL-1R-MyD88 signaling in keratinocyte transformation and carcinogenesis. J Exp Med (2012) 1.48
Characteristics and Clinical Management of a Cluster of 3 Patients With Ebola Virus Disease, Including the First Domestically Acquired Cases in the United States. Ann Intern Med (2015) 1.47
Myocardial injury after noncardiac surgery: a large, international, prospective cohort study establishing diagnostic criteria, characteristics, predictors, and 30-day outcomes. Anesthesiology (2014) 1.47
Mutation in CEP290 discovered for cat model of human retinal degeneration. J Hered (2007) 1.46
Telomere length and heavy-chain mutation status in familial chronic lymphocytic leukemia. Leuk Res (2002) 1.44
Cutting edge: L-selectin (CD62L) expression distinguishes small resting memory CD4+ T cells that preferentially respond to recall antigen. J Immunol (2003) 1.42
Cutting edge: Ku70 is a novel cytosolic DNA sensor that induces type III rather than type I IFN. J Immunol (2011) 1.41
Cellular immune responses to human papillomavirus (HPV)-16 L1 in healthy volunteers immunized with recombinant HPV-16 L1 virus-like particles. J Infect Dis (2003) 1.40
Safety (toxicity), pharmacokinetics, immunogenicity, and impact on elements of the normal immune system of recombinant human IL-15 in rhesus macaques. Blood (2011) 1.39
Randomized controlled trial of motivational enhancement therapy with nontreatment-seeking adolescent cannabis users: a further test of the teen marijuana check-up. Psychol Addict Behav (2011) 1.38
Treatment of intestinal helminths does not reduce plasma concentrations of HIV-1 RNA in coinfected Zambian adults. J Infect Dis (2005) 1.37
Genome-wide compensatory changes accompany drug- selected mutations in the Plasmodium falciparum crt gene. PLoS One (2008) 1.36
Human immunodeficiency virus viremia induces plasmacytoid dendritic cell activation in vivo and diminished alpha interferon production in vitro. J Virol (2008) 1.36
IL-27, a novel anti-HIV cytokine, activates multiple interferon-inducible genes in macrophages. AIDS (2008) 1.33
Pre-ART levels of inflammation and coagulation markers are strong predictors of death in a South African cohort with advanced HIV disease. PLoS One (2012) 1.31
Macrophage-tropic simian/human immunodeficiency virus chimeras use CXCR4, not CCR5, for infections of rhesus macaque peripheral blood mononuclear cells and alveolar macrophages. J Virol (2003) 1.29
Detection of KIR3DS1 on the cell surface of peripheral blood NK cells facilitates identification of a novel null allele and assessment of KIR3DS1 expression during HIV-1 infection. J Immunol (2007) 1.29
Human immunodeficiency virus type 1 derivative with 7% simian immunodeficiency virus genetic content is able to establish infections in pig-tailed macaques. J Virol (2007) 1.27
Explaining, predicting, and treating HIV-associated CD4 cell loss: after 25 years still a puzzle. JAMA (2006) 1.27
High recombination rates and hotspots in a Plasmodium falciparum genetic cross. Genome Biol (2011) 1.27
Loss of naïve cells accompanies memory CD4+ T-cell depletion during long-term progression to AIDS in Simian immunodeficiency virus-infected macaques. J Virol (2006) 1.27
Safety and immunogenicity of multiple and higher doses of an inactivated influenza A/H5N1 vaccine. J Infect Dis (2009) 1.26
Diminished production of monocyte proinflammatory cytokines during human immunodeficiency virus viremia is mediated by type I interferons. J Virol (2006) 1.24
A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS. J Data Mining Genomics Proteomics (2013) 1.23
Noninfectious papilloma virus-like particles inhibit HIV-1 replication: implications for immune control of HIV-1 infection by IL-27. Blood (2006) 1.21
Identification and functional clustering of global gene expression differences between human age-related cataract and clear lenses. Mol Vis (2003) 1.21
HIV-1 vaccines and adaptive trial designs. Sci Transl Med (2011) 1.21
Murine leukemias with retroviral insertions at Lmo2 are predictive of the leukemias induced in SCID-X1 patients following retroviral gene therapy. PLoS Genet (2009) 1.19