Published in Bioinformatics on December 13, 2005
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat Methods (2011) 1.95
msmsEval: tandem mass spectral quality assignment for high-throughput proteomics. BMC Bioinformatics (2007) 1.17
ScanRanker: Quality assessment of tandem mass spectra via sequence tagging. J Proteome Res (2011) 0.94
Serum proteome changes in acromegalic patients following transsphenoidal surgery: novel biomarkers of disease activity. Eur J Endocrinol (2010) 0.86
Tandem mass spectrometry data quality assessment by self-convolution. BMC Bioinformatics (2007) 0.82
Integrated data management and validation platform for phosphorylated tandem mass spectrometry data. Proteomics (2010) 0.82
A novel approach to denoising ion trap tandem mass spectra. Proteome Sci (2009) 0.82
Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction. BMC Genomics (2010) 0.81
Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences. Proteomics (2007) 0.81
Quality assessment of tandem mass spectra using support vector machine (SVM). BMC Bioinformatics (2009) 0.78
Copy number variation and selection during reprogramming to pluripotency. Nature (2011) 8.24
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell (2011) 7.41
Exosomes with immune modulatory features are present in human breast milk. J Immunol (2007) 3.47
High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol (2010) 3.21
Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes. J Exp Med (2008) 2.79
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics (2009) 2.70
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics (2006) 2.37
Genomic views of STAT function in CD4+ T helper cell differentiation. Nat Rev Immunol (2011) 2.09
Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov (2013) 1.93
Gene expression profiling during differentiation of human monocytes to macrophages or dendritic cells. J Leukoc Biol (2007) 1.90
Difference in gene expression between human fetal liver and adult bone marrow mesenchymal stem cells. Haematologica (2005) 1.90
Gene expression signatures of seven individual human embryonic stem cell lines. Stem Cells (2005) 1.86
Timing of infant feeding in relation to childhood asthma and allergic diseases. J Allergy Clin Immunol (2012) 1.62
Improving missing value estimation in microarray data with gene ontology. Bioinformatics (2005) 1.57
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics (2007) 1.54
Constitutively active cytoplasmic c-Jun N-terminal kinase 1 is a dominant regulator of dendritic architecture: role of microtubule-associated protein 2 as an effector. J Neurosci (2005) 1.54
Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins. Biol Psychiatry (2012) 1.50
Peroxiredoxins and tropomyosins as plasma biomarkers for lung cancer and asbestos exposure. Lung Cancer (2012) 1.49
Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res (2005) 1.42
Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis: the cardiovascular risk in young Finns study. PLoS Genet (2010) 1.39
Genetic and epigenetic stability of human pluripotent stem cells. Nat Rev Genet (2012) 1.38
Early target genes of IL-12 and STAT4 signaling in th cells. J Immunol (2004) 1.31
Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity (2010) 1.28
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity (2013) 1.27
Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics (2008) 1.22
Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages. PLoS Pathog (2011) 1.22
Genome-wide identification of novel genes involved in early Th1 and Th2 cell differentiation. J Immunol (2007) 1.21
Identification of novel IL-4/Stat6-regulated genes in T lymphocytes. J Immunol (2003) 1.20
Identification of a hormone-regulated dynamic nuclear actin network associated with estrogen receptor alpha in human breast cancer cell nuclei. Mol Cell Proteomics (2010) 1.19
Differential expression of IFN regulatory factor 4 gene in human monocyte-derived dendritic cells and macrophages. J Immunol (2005) 1.15
Actin and RIG-I/MAVS signaling components translocate to mitochondria upon influenza A virus infection of human primary macrophages. J Immunol (2009) 1.12
Identification of genes involved in the initiation of human Th1 or Th2 cell commitment. Eur J Immunol (2005) 1.12
Cytosolic RNA recognition pathway activates 14-3-3 protein mediated signaling and caspase-dependent disruption of cytokeratin network in human keratinocytes. J Proteome Res (2010) 1.11
Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biol (2009) 1.10
Association analysis of common variants of STAT6, GATA3, and STAT4 to asthma and high serum IgE phenotypes. J Allergy Clin Immunol (2005) 1.08
PARP-14, a member of the B aggressive lymphoma family, transduces survival signals in primary B cells. Blood (2009) 1.08
Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma. Clin Cancer Res (2006) 1.05
Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes. J Immunol (2003) 1.02
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics (2009) 1.02
Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol Cell Proteomics (2010) 1.02
Gene expression profiling of immune-competent human cells exposed to engineered zinc oxide or titanium dioxide nanoparticles. PLoS One (2013) 1.02
Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response. Mol Syst Biol (2007) 1.02
RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells (2012) 1.01
Autoimmune regulator induced changes in the gene expression profile of human monocyte-dendritic cell-lineage. Mol Immunol (2004) 1.01
Proteomic analysis of glial fibrillary acidic protein in Alzheimer's disease and aging brain. Neurobiol Dis (2005) 1.01
Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays. IEEE/ACM Trans Comput Biol Bioinform (2010) 1.01
A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. Proteomics (2005) 1.00
Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PLoS Comput Biol (2013) 1.00
Identification of early gene expression changes during human Th17 cell differentiation. Blood (2012) 0.99
CD73 participates in cellular multiresistance program and protects against TRAIL-induced apoptosis. J Immunol (2008) 0.99
A mitochondrial ribosomal and RNA decay pathway blocks cell proliferation. Curr Biol (2013) 0.99
Oxidative modification of proteins in the frontal cortex of Alzheimer's disease brain. Neurobiol Aging (2005) 0.99
Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood. Transl Res (2012) 0.98
A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinformatics (2006) 0.98
Global phospholipidomics analysis reveals selective pulmonary peroxidation profiles upon inhalation of single-walled carbon nanotubes. ACS Nano (2011) 0.97
Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation. Mol Cell Proteomics (2008) 0.97
Transcriptional and epigenetic regulation of T-helper lineage specification. Immunol Rev (2014) 0.97
Unique gene expression signature by human embryonic stem cells cultured under serum-free conditions correlates with their enhanced and prolonged growth in an undifferentiated stage. Stem Cells (2005) 0.97
An insight into molecular mechanisms of human T helper cell differentiation. Ann Med (2008) 0.96
Distinct sets of developmentally regulated genes that are expressed by human oocytes and human embryonic stem cells. Fertil Steril (2006) 0.96
Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinformatics (2008) 0.96
Expression of human pim family genes is selectively up-regulated by cytokines promoting T helper type 1, but not T helper type 2, cell differentiation. Immunology (2005) 0.95
Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis. J Chem Inf Model (2014) 0.95
Identification of new Golgi complex specific proteins by direct organelle proteomic analysis. Proteomics (2006) 0.95
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets. Brief Bioinform (2009) 0.95
Reactive oxygen species deficiency induces autoimmunity with type 1 interferon signature. Antioxid Redox Signal (2014) 0.94
PRELI is a mitochondrial regulator of human primary T-helper cell apoptosis, STAT6, and Th2-cell differentiation. Blood (2008) 0.94
Activating transcription factor 3 is a positive regulator of human IFNG gene expression. J Immunol (2010) 0.94
Obatoclax, saliphenylhalamide, and gemcitabine inhibit influenza a virus infection. J Biol Chem (2012) 0.94
SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. Blood (2010) 0.93
Reproducibility-optimized test statistic for ranking genes in microarray studies. IEEE/ACM Trans Comput Biol Bioinform (2008) 0.93
Netrin-4 promotes glioblastoma cell proliferation through integrin β4 signaling. Neoplasia (2012) 0.93
Identification of proteins associated with ligand-activated estrogen receptor α in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS. Proteomics (2010) 0.92
Improved statistical modeling of tumor growth and treatment effect in preclinical animal studies with highly heterogeneous responses in vivo. Clin Cancer Res (2012) 0.92
Toward more realistic drug-target interaction predictions. Brief Bioinform (2014) 0.92
GIMAP Proteins in T-Lymphocytes. J Signal Transduct (2010) 0.92
New separation-free assay technique for SNPs using two-photon excitation fluorometry. Nucleic Acids Res (2004) 0.92
Tetrahydrobiopterin in the treatment of children with autistic disorder: a double-blind placebo-controlled crossover study. J Clin Psychopharmacol (2005) 0.92
Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling. J Autoimmun (2010) 0.91