Integration of biological networks and gene expression data using Cytoscape.
paper
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- Authors
- Cline, Melissa S; Smoot, Michael; Cerami, Ethan; Kuchinsky, Allan; Landys, Nerius; Workman, Chris; Christmas, Rowan; Avila-Campilo, Iliana; Creech, Michael; Gross, Benjamin; Hanspers, Kristina; Isserlin, Ruth; Kelley, Ryan; Killcoyne, Sarah; Lotia, Samad; Maere, Steven; Morris, John; Ono, Keiichiro; Pavlovic, Vuk; Pico, Alexander R; Vailaya, Aditya; Wang, Peng-Liang; Adler, Annette; Conklin, Bruce R; Hood, Leroy; Kuiper, Martin; Sander, Chris; Schmulevich, Ilya; Schwikowski, Benno; Warner, Guy J; Ideker, Trey; Bader, Gary D
- Year
- 2007
- Journal
- Nature protocols
- PMID
- 17947979
- DOI
- 10.1038/nprot.2007.324
- PMCID
- PMC3685583
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.
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| Identifying developments over a decade in the digital health and telemedicine landscape in the UK using quantitative text mining. | Geifman N et al. | β | 2023 | β |
| Identifying the key genes of Epstein-Barr virus-regulated tumour immune microenvironment of gastric carcinomas. | Zhou H et al. | β | 2023 | β |
| Integrated analysis and clinical correlation analysis of hub genes, immune infiltration, and potential therapeutic agents related to lupus nephritis. | Lin W et al. | β | 2023 | β |
| Integrated analysis of inflammatory mRNAs, miRNAs, and lncRNAs elucidates the molecular interactome behind bovine mastitis. | Hasankhani A et al. | β | 2023 | β |
| Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify Molecular Mechanisms Associated with Intramuscular Fat Content in Beef Cattle. | Dehghanian Reyhan V et al. | β | 2023 | β |
| Integrated Metabolome and Transcriptome Analysis of Petal Anthocyanin Accumulation Mechanism in <i>Gloriosa superba</i> 'Rothschildiana' during Different Flower Development Stages. | Sun Y et al. | β | 2023 | β |
| Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism. | Jiang W et al. | β | 2023 | β |
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| Mitochondria and Endoplasmic Reticulum Stress in Retinal Organoids from Patients with Vision Loss. | Lee EJ et al. | β | 2023 | β |
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| Modeling Blast Crisis Using Mutagenized Chronic Myeloid Leukemia-Derived Induced Pluripotent Stem Cells (iPSCs). | Imeri J et al. | β | 2023 | β |
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| Modeling RET-Rearranged Non-Small Cell Lung Cancer (NSCLC): Generation of Lung Progenitor Cells (LPCs) from Patient-Derived Induced Pluripotent Stem Cells (iPSCs). | Marcoux P et al. | β | 2023 | β |
| MRP8/14 Is a Molecular Signature Triggered by Dopamine in HIV Latent Myeloid Targets That Increases HIV Transcription and Distinguishes HIV+ Methamphetamine Users with Detectable CSF Viral Load and Brain Pathology. | Basova LV et al. | β | 2023 | β |
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| Single-cell atlas reveals a distinct immune profile fostered by TΒ cell-BΒ cell crosstalk in triple negative breast cancer. | Ding S et al. | β | 2023 | β |
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| The Angiogenesis Inhibitor Isthmin-1 (ISM1) Is Overexpressed in Experimental Models of Glomerulopathy and Impairs the Viability of Podocytes. | Sahiri V et al. | β | 2023 | β |
| The potential effect and mechanism of Saikosaponin A against gastric cancer. | Wang C et al. | β | 2023 | β |
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| Uncovering the complex regulatory network of spring bud sprouting in tea plants: insights from metabolic, hormonal, and oxidative stress pathways. | Tang J et al. | β | 2023 | β |
| Weighted gene co-expression network analysis revealed T cell differentiation associated with the age-related phenotypes in COVID-19 patients. | Lin Y et al. | β | 2023 | β |
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| Exploring AI-2-mediated interspecies communications within rumen microbial communities. | Liu X et al. | β | 2022 | β |
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| Identifying key genes of classic papillary thyroid cancer in women aged more than 55 years old using bioinformatics analysis. | Li CC et al. | β | 2022 | β |
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| Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum. | Davis EC et al. | β | 2022 | β |
| Microbial Multitrophic Communities Drive the Variation of Antibiotic Resistome in the Gut of Soil Woodlice (Crustacea: Isopoda). | Xiang Q et al. | β | 2022 | β |
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| MicroRNAs Promote the Progression of Sepsis-Induced Cardiomyopathy and Neurovascular Dysfunction Through Upregulation of NF-kappaB Signaling Pathway-Associated HDAC7/ACTN4. | Luo Q et al. | β | 2022 | β |
| Modeling Global Genomic Instability in Chronic Myeloid Leukemia (CML) using patient-derived induced pluripotent stem cells (iPSC) | Telliam G et al. | β | 2022 | β |
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| New insights of necroptosis and immune infiltration in sepsis-induced myocardial dysfunction from bioinformatics analysis through RNA-seq in mice. | Du Y et al. | β | 2022 | β |
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| Profiling the Spatial Expression Pattern and ceRNA Network of lncRNA, miRNA, and mRNA Associated with the Development of Intermuscular Bones in Zebrafish. | Ye W et al. | β | 2022 | β |
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| Seasonal Dynamics of Bacterial Community Structure in Diesel Oil-Contaminated Soil Cultivated with Tall Fescue (<i>Festuca arundinacea</i>). | Lee YY et al. | β | 2022 | β |
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| To explore the potential molecular mechanism of complex rose-bergamot essential oil on anti-anxiety with facial spots based on network pharmacology. | Xin J et al. | β | 2022 | β |
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| Requirement of the Mowat-Wilson Syndrome Gene Zeb2 in the Differentiation and Maintenance of Non-photoreceptor Cell Types During Retinal Development. | Wei W et al. | β | 2019 | β |
| Reversal of Vocal Fold Mucosal Fibrosis Using siRNA against the Collagen-Specific Chaperone Serpinh1. | Kishimoto Y et al. | β | 2019 | β |
| RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens. | Khan S et al. | β | 2019 | β |
| Serum extracellular vesicles contain SPARC and LRG1 as biomarkers of colon cancer and differ by tumour primary location. | Zhong ME et al. | β | 2019 | β |
| Sex-specific Tau methylation patterns and synaptic transcriptional alterations are associated with neural vulnerability during chronic neuroinflammation. | Didonna A et al. | β | 2019 | β |
| SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons. | Zaslavsky K et al. | β | 2019 | β |
| Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in <i>Escherichia coli</i> K12. | Huddleston JP et al. | β | 2019 | β |
| Studying alcohol use disorder using Drosophila melanogaster in the era of 'Big Data'. | Engel GL et al. | β | 2019 | β |
| Systems based analysis of human embryos and gene networks involved in cell lineage allocation. | Smith HL et al. | β | 2019 | β |
| Targeting JUN, CEBPB, and HDAC3: A Novel Strategy to Overcome Drug Resistance in Hypoxic Glioblastoma. | Gao Y et al. | β | 2019 | β |
| The Cytoscape BioGateway App: explorative network building from the BioGateway triple store. | HolmΓ₯s S et al. | β | 2019 | β |
| The Med31 Conserved Component of the Divergent Mediator Complex in Tetrahymena thermophila Participates in Developmental Regulation. | Garg J et al. | β | 2019 | β |
| The Old and the New: Discovery Proteomics Identifies Putative Novel Seminal Fluid Proteins in Drosophila. | Karr TL et al. | β | 2019 | β |
| The sensitivity to Hsp90 inhibitors of both normal and oncogenically transformed cells is determined by the equilibrium between cellular quiescence and activity. | Echeverria PC et al. | β | 2019 | β |
| The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: insights into cancer resistance mechanisms. | Altwasser R et al. | β | 2019 | β |
| Transcriptional and functional diversity of human macrophage repolarization. | Gharib SA et al. | β | 2019 | β |
| Transcriptional Reprogramming of Pea Leaves at Early Reproductive Stages. | Gallardo K et al. | β | 2019 | β |
| Transcriptome comparative analysis of immune tissues from asymptomatic and diseased Epinephelus moara naturally infected with nervous necrosis virus. | Wang L et al. | β | 2019 | β |
| Transcriptomic analysis of the oleaginous yeast <i>Lipomyces starkeyi</i> during lipid accumulation on enzymatically treated corn stover hydrolysate. | Pomraning KR et al. | β | 2019 | β |
| Transcriptomic evidence that cortisol alters perinatal epicardial adipose tissue maturation. | Richards EM et al. | β | 2019 | β |
| Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests. | Dukunde A et al. | β | 2019 | β |
| Wide transcriptional investigation unravel novel insights of the on-tree maturation and postharvest ripening of 'Abate Fetel' pear fruit. | Busatto N et al. | β | 2019 | β |
| A hnRNP Kβ»AR-Related Signature Reflects Progression toward Castration-Resistant Prostate Cancer. | Capaia M et al. | β | 2018 | β |
| A landscape of synthetic viable interactions in cancer. | Gu Y et al. | β | 2018 | β |
| A microRNA feedback loop regulates global microRNA abundance during aging. | Inukai S et al. | β | 2018 | β |
| A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles. | Chae S et al. | β | 2018 | β |
| Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. | Zhang Y et al. | β | 2018 | β |
| Analyzing and Designing Cell Factories with OptFlux. | VilaΓ§a P et al. | β | 2018 | β |
| An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle. | De Oliveira PSN et al. | β | 2018 | β |
| Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach. | Chen W et al. | β | 2018 | β |
| Aryl hydrocarbon receptor (AHR) is a novel druggable pathway controlling malignant progenitor proliferation in chronic myeloid leukemia (CML). | Gentil M et al. | β | 2018 | β |
| Associating H<sub>2</sub>O<sub>2-</sub>and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage. | Ganief N et al. | β | 2018 | β |
| A Systems Biology Study in Tomato Fruit Reveals Correlations between the Ascorbate Pool and Genes Involved in Ribosome Biogenesis, Translation, and the Heat-Shock Response. | Stevens RG et al. | β | 2018 | β |
| Blood transcriptional and microRNA responses to short-term exposure to disinfection by-products in a swimming pool. | EspΓn-PΓ©rez A et al. | β | 2018 | β |
| Building Molecular Interaction Networks from Microarray Data for Drug Target Screening. | Yuen SC et al. | β | 2018 | β |
| Cancer Associated Fibroblasts: The Architects of Stroma Remodeling. | Santi A et al. | β | 2018 | β |
| Codon usage and modular interactions between messenger RNA coding regions and small RNAs in Escherichia coli. | Tello M et al. | β | 2018 | β |
| Combined Human Genome-wide RNAi and Metabolite Analyses Identify IMPDH as a Host-Directed Target against Chlamydia Infection. | Rother M et al. | β | 2018 | β |
| Comparison of gene expression profiles between human erythroid cells derived from fetal liver and adult peripheral blood. | Tangprasittipap A et al. | β | 2018 | β |
| Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species. | Song X et al. | β | 2018 | β |
| Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. | Giuliani S et al. | β | 2018 | β |
| Context-dependent prediction of protein complexes by SiComPre. | Rizzetto S et al. | β | 2018 | β |
| Conventional and emerging roles of the energy sensor Snf1/AMPK in <i>Saccharomyces cerevisiae</i>. | Coccetti P et al. | β | 2018 | β |
| Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius. | Vogt MS et al. | β | 2018 | β |
| DAZL Regulates Germ Cell Survival through a Network of PolyA-Proximal mRNA Interactions. | Zagore LL et al. | β | 2018 | β |
| Deconvolution of Human Brain Cell Type Transcriptomes Unraveled Microglia-Specific Potential Biomarkers. | Ayana R et al. | β | 2018 | β |
| De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. | Qi H et al. | β | 2018 | β |
| Dietary Glycation Products Regulate Immune Homeostasis: Early Glycation Products Promote Prostate Cancer Cell Proliferation through Modulating Macrophages. | Chen Y et al. | β | 2018 | β |
| Direct reprogramming of fibroblasts into neural stem cells by single non-neural progenitor transcription factor Ptf1a. | Xiao D et al. | β | 2018 | β |
| Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. | Torres-Oliva M et al. | β | 2018 | β |
| Dysbiosis and Ecotypes of the Salivary Microbiome Associated With Inflammatory Bowel Diseases and the Assistance in Diagnosis of Diseases Using Oral Bacterial Profiles. | Xun Z et al. | β | 2018 | β |
| Dysregulated genes and their functional pathways in luteinized granulosa cells from PCOS patients after cabergoline treatment. | Ferrero H et al. | β | 2018 | β |
| Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake. | Jones AC et al. | β | 2018 | β |
| Efficient and robust proteome-wide approaches for cross-linking mass spectrometry. | Klykov O et al. | β | 2018 | β |
| Evaluation of molecular brain changes associated with environmental stress in rodent models compared to human major depressive disorder: A proteomic systems approach. | Cox DA et al. | β | 2018 | β |
| Exploring chromatin hierarchical organization via Markov State Modelling. | Tan ZW et al. | β | 2018 | β |
| Expression ratio of the TGFΞ²-inducible gene MYO10 is prognostic for overall survival of squamous cell lung cancer patients and predicts chemotherapy response. | Dvornikov D et al. | β | 2018 | β |
| FERMT2 links cortical actin structures, plasma membrane tension and focal adhesion function to stabilize podocyte morphology. | Yasuda-Yamahara M et al. | β | 2018 | β |
| Finding novel relationships with integrated gene-gene association network analysis of <i>Synechocystis sp.</i> PCC 6803 using species-independent text-mining. | Kreula SM et al. | β | 2018 | β |
| Functional Analysis of Hif1 Histone Chaperone in <i>Saccharomyces cerevisiae</i>. | Dannah NS et al. | β | 2018 | β |
| Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells. | Biase FH et al. | β | 2018 | β |
| Gene expression analysis indicates reduced memory and cognitive functions in the hippocampus and increase in synaptic reorganization in the frontal cortex 3Β weeks after MDMA administration in Dark Agouti rats. | Petschner P et al. | β | 2018 | β |
| Gene expression profiling in colon of mice exposed to food additive titanium dioxide (E171). | Proquin H et al. | β | 2018 | β |
| Gene Profiling in Patients with Systemic Sclerosis Reveals the Presence of Oncogenic Gene Signatures. | Dolcino M et al. | β | 2018 | β |
| Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma. | Tessier L et al. | β | 2018 | β |
| Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca<sup>2+</sup> Channel Blocker. | Ma K et al. | β | 2018 | β |
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| Gut Sphingolipid Composition as a Prelude to Necrotizing Enterocolitis. | Rusconi B et al. | β | 2018 | β |
| Harnessing synthetic lethality to predict the response to cancer treatment. | Lee JS et al. | β | 2018 | β |
| Host-Virus Protein Interaction Network Reveals the Involvement of Multiple Host Processes in the Life Cycle of Hepatitis E Virus. | Subramani C et al. | β | 2018 | β |
| Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. | Levchenko A et al. | β | 2018 | β |
| Hyperthermophilic Composting Accelerates the Removal of Antibiotic Resistance Genes and Mobile Genetic Elements in Sewage Sludge. | Liao H et al. | β | 2018 | β |
| Identification and analysis of hub genes and networks related to hypoxia preconditioning in mice (No 035215). | Cheng H et al. | β | 2018 | β |
| Identification of genes required for eye development by high-throughput screening of mouse knockouts. | Moore BA et al. | β | 2018 | β |
| Identification of PP1-Gadd34 substrates involved in the unfolded protein response using K-BIPS, a method for phosphatase substrate identification. | Dedigama-Arachchige PM et al. | β | 2018 | β |
| Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. | Cesar ASM et al. | β | 2018 | β |
| Identifier Mapping in Cytoscape. | Treister A et al. | β | 2018 | β |
| Identifying mouse developmental essential genes using machine learning. | Tian D et al. | β | 2018 | β |
| <i>In silico</i> Identification of the Indispensable Quorum Sensing Proteins of Multidrug Resistant <i>Proteus mirabilis</i>. | Pawar S et al. | β | 2018 | β |
| Immune Response to <i>Rotavirus</i> and Gluten Sensitivity. | Puccetti A et al. | β | 2018 | β |
| Impact of Dietary Carbohydrate/Protein Ratio on Hepatic Metabolism in Land-Locked Atlantic Salmon (<i>Salmo salar</i> L.). | Betancor MB et al. | β | 2018 | β |
| Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks. | Lages J et al. | β | 2018 | β |
| Integrated in silico and in vivo approaches to investigate effects of BDE-99 mediated by the nuclear receptors on developing zebrafish. | Zhang L et al. | β | 2018 | β |
| Integrated network analysis reveals the importance of microbial interactions for maize growth. | Tao J et al. | β | 2018 | β |
| Integrated physiology and proteome analysis of embryo and endosperm highlights complex metabolic networks involved in seed germination in wheat (Triticum aestivum L.). | Liu Y et al. | β | 2018 | β |
| Integrated Transcript and Metabolite Profiles Reveal That <i>Eb</i>CHI Plays an Important Role in Scutellarin Accumulation in <i>Erigeron breviscapus</i> Hairy Roots. | Chen R et al. | β | 2018 | β |
| Integrate Imaging Flow Cytometry and Transcriptomic Profiling to Evaluate Altered Endocytic CD1d Trafficking. | Sharma M et al. | β | 2018 | β |
| Integrative analysis of the inter-tumoral heterogeneity of triple-negative breast cancer. | Chiu AM et al. | β | 2018 | β |
| Interleukin-1Ξ² Signaling in Dendritic Cells Induces Antiviral Interferon Responses. | Aarreberg LD et al. | β | 2018 | β |
| In vivo brain GPCR signaling elucidated by phosphoproteomics. | Liu JJ et al. | β | 2018 | β |
| Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium. | Darville LNF et al. | β | 2018 | β |
| Leptin Stimulates Cellular Glycolysis Through a STAT3 Dependent Mechanism in Tilapia. | Douros JD et al. | β | 2018 | β |
| Long noncoding RNA AC003092.1 promotes temozolomide chemosensitivity through miR-195/TFPI-2 signaling modulation in glioblastoma. | Xu N et al. | β | 2018 | β |
| Long Non-Coding RNAs Play a Role in the Pathogenesis of Psoriatic Arthritis by Regulating MicroRNAs and Genes Involved in Inflammation and Metabolic Syndrome. | Dolcino M et al. | β | 2018 | β |
| Loss of the E3 ubiquitin ligase MKRN1 represses diet-induced metabolic syndrome through AMPK activation. | Lee MS et al. | β | 2018 | β |
| Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. | Zhu GR et al. | β | 2018 | β |
| Maladaptive phenotypic plasticity in cardiac muscle growth is suppressed in high-altitude deer mice. | Velotta JP et al. | β | 2018 | β |
| Malaria infected red blood cells release small regulatory RNAs through extracellular vesicles. | Babatunde KA et al. | β | 2018 | β |
| Mechanistic insight into ROS and neutral lipid alteration induced toxicity in the human model with fins (Danio rerio) by industrially synthesized titanium dioxide nanoparticles. | Verma SK et al. | β | 2018 | β |
| Metabolome Integrated Analysis of High-Temperature Response in <i>Pinus radiata</i>. | EscandΓ³n M et al. | β | 2018 | β |
| MetExploreViz: web component for interactive metabolic network visualization. | Chazalviel M et al. | β | 2018 | β |
| MicroRNA Profiling in Aging Brain of PSEN1/PSEN2 Double Knockout Mice. | Ham S et al. | β | 2018 | β |
| miR147b: A novel key regulator of interleukin 1 beta-mediated inflammation in human astrocytes. | van Scheppingen J et al. | β | 2018 | β |
| Molecular insights into paediatric breast fibroepithelial tumours. | Tay TKY et al. | β | 2018 | β |
| Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations. | AlakΓ€rppΓ€ E et al. | β | 2018 | β |
| Necessity and Sufficiency of Ldb1 in the Generation, Differentiation and Maintenance of Non-photoreceptor Cell Types During Retinal Development. | Xiao D et al. | β | 2018 | β |
| NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples. | Yu H et al. | β | 2018 | β |
| Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana. | Liu S et al. | β | 2018 | β |
| Novel Method for Noninvasive Sampling of the Distal Airspace in Acute Respiratory Distress Syndrome. | McNeil JB et al. | β | 2018 | β |
| Plant Bio-Wars: Maize Protein Networks Reveal Tissue-Specific Defense Strategies in Response to a Root Herbivore. | Castano-Duque L et al. | β | 2018 | β |
| Plant data visualisation using network graphs. | Mohamad-Matrol AA et al. | β | 2018 | β |
| Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. | McIntyre W et al. | β | 2018 | β |
| Proteomic analysis of sperm proteins in infertile men with high levels of reactive oxygen species. | Ayaz A et al. | β | 2018 | β |
| Proteomic Analysis of Ubiquitinated Proteins in Rice (<i>Oryza sativa</i>) After Treatment With Pathogen-Associated Molecular Pattern (PAMP) Elicitors. | Chen XL et al. | β | 2018 | β |
| Quantitative Proteomic Analysis of Changes Related to Age and Calorie Restriction in Rat Liver Tissue. | Kim Y et al. | β | 2018 | β |
| RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17Ξ±-ethynylestradiol. | Yadetie F et al. | β | 2018 | β |
| Sex Determination in <i>Ceratopteris richardii</i> Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte. | Atallah NM et al. | β | 2018 | β |
| Short-term transcriptome and microRNAs responses to exposure to different air pollutants in two population studies. | EspΓn-PΓ©rez A et al. | β | 2018 | β |
| Simulation Study of cDNA Dataset to Investigate Possible Association of Differentially Expressed Genes of Human THP1-Monocytic Cells in Cancer Progression Affected by Bacterial Shiga Toxins. | Muhammad SA et al. | β | 2018 | β |
| Single-Cell Approach to Influenza-Specific CD8<sup>+</sup> T Cell Receptor Repertoires Across Different Age Groups, Tissues, and Following Influenza Virus Infection. | Sant S et al. | β | 2018 | β |
| Sirtuin 1-Chromatin-Binding Dynamics Points to a Common Mechanism Regulating Inflammatory Targets in SIV Infection and in the Aging Brain. | Bortell N et al. | β | 2018 | β |
| Spatial distribution and exposure risks of ambient chlorinated polycyclic aromatic hydrocarbons in Tokyo Bay area and network approach to source impacts. | Ohura T et al. | β | 2018 | β |
| Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. | Contreras-LΓ³pez O et al. | β | 2018 | β |
| SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines. | Fiscon G et al. | β | 2018 | β |
| Systems Pharmacology-Based Approach of Connecting Disease Genes in Genome-Wide Association Studies with Traditional Chinese Medicine. | Kim J et al. | β | 2018 | β |
| Targeting nuclear receptor NR4A1-dependent adipocyte progenitor quiescence promotes metabolic adaptation to obesity. | Zhang Y et al. | β | 2018 | β |
| The developmental transcriptome of the human heart. | Pervolaraki E et al. | β | 2018 | β |
| The Human Gut Virome in Hypertension. | Han M et al. | β | 2018 | β |
| The Interactomic Analysis Reveals Pathogenic Protein Networks in <i>Phomopsis longicolla</i> Underlying Seed Decay of Soybean. | Li S et al. | β | 2018 | β |
| The Proteome of Prostate Cancer Bone Metastasis Reveals Heterogeneity with Prognostic Implications. | Iglesias-Gato D et al. | β | 2018 | β |
| The role of inter-species interactions in Salinispora specialized metabolism. | Patin NV et al. | β | 2018 | β |
| The Synergistic Combination of Everolimus and Paroxetine Exerts Post-ischemic Neuroprotection In Vitro. | Suvanish Kumar VS et al. | β | 2018 | β |
| Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development. | Marques S et al. | β | 2018 | β |
| Transcriptional Profiling Suggests Extensive Metabolic Rewiring of Human and Mouse Macrophages during Early Interferon Alpha Responses. | Ahmed D et al. | β | 2018 | β |
| Transcriptome analyses identify key genes and potential mechanisms in a rat model of osteoarthritis. | Li HZ et al. | β | 2018 | β |
| Transcriptome Analysis Revealed Impaired cAMP Responsiveness in PHF21A-Deficient Human Cells. | Porter RS et al. | β | 2018 | β |
| Transcriptome profiling of whisker follicles in methamphetamine self-administered rats. | Song SH et al. | β | 2018 | β |
| Transcriptomics analyses reveal the molecular roadmap and long non-coding RNA landscape of sperm cell lineage development. | Liu L et al. | β | 2018 | β |
| Tumor endothelial marker 8 promotes cancer progression and metastasis. | HΓΈye AM et al. | β | 2018 | β |
| UCSF ChimeraX: Meeting modern challenges in visualization and analysis. | Goddard TD et al. | β | 2018 | β |
| Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome. | Ho B et al. | β | 2018 | β |
| Venom gland transcriptomics and microRNA profiling of juvenile and adult yellow-bellied sea snake, Hydrophis platurus, from Playa del Coco (Guanacaste, Costa Rica). | Durban J et al. | β | 2018 | β |
| When Transcriptomics and Metabolomics Work Hand in Hand: A Case Study Characterizing Plant CDF Transcription Factors. | PΓ©rez-Alonso MM et al. | β | 2018 | β |
| Widespread Genotype-Phenotype Correlations in Intellectual Disability. | Casanova EL et al. | β | 2018 | β |
| Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm. | Roth M et al. | β | 2018 | β |
| Accumulation of prohibitin is a common cellular response to different stressing stimuli and protects melanoma cells from ER stress and chemotherapy-induced cell death. | Tortelli TC et al. | β | 2017 | β |
| A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa). | Liu S et al. | β | 2017 | β |
| Acute Exposure to Pacific Ciguatoxin Reduces Electroencephalogram Activity and Disrupts Neurotransmitter Metabolic Pathways in Motor Cortex. | Kumar G et al. | β | 2017 | β |
| Analyzing trapped protein complexes by Virotrap and SFINX. | Titeca K et al. | β | 2017 | β |
| An integrated shotgun proteomics and bioinformatics approach for analysis of brain proteins from MCAO model using serial affinity chromatograph with four active ingredients from Shengmai preparations as ligands. | Fan XX et al. | β | 2017 | β |
| An Integrative Approach to Decipher the Chemical Antagonism between the Competing Endophytes Paraconiothyrium variabile and Bacillus subtilis. | Vallet M et al. | β | 2017 | β |
| A proteomic approach to identify metalloproteins and metal-binding proteins in liver from diabetic rats. | Braga CP et al. | β | 2017 | β |
| ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells. | Park NI et al. | β | 2017 | β |
| A Signature of Circulating microRNAs Predicts the Susceptibility of Acute Mountain Sickness. | Liu B et al. | β | 2017 | β |
| Astrocyte-specific overexpressed gene signatures in response to methamphetamine exposure in vitro. | Bortell N et al. | β | 2017 | β |
| A Systems Biology Approach to Understanding Alcoholic Liver Disease Molecular Mechanism: The Development of Static and Dynamic Models. | Shafaghati L et al. | β | 2017 | β |
| Bioinformatics analysis of gene expression alterations in microRNAβ122 knockout mice with hepatocellular carcinoma. | He B et al. | β | 2017 | β |
| Cellular Signaling Pathways in Insulin Resistance-Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus. | Muhammad SA et al. | β | 2017 | β |
| Cerebrospinal fluid extracellular vesicle enrichment for protein biomarker discovery in neurological disease; multiple sclerosis. | Welton JL et al. | β | 2017 | β |
| Charting the transcriptional landscape of cells of renin lineage following podocyte depletion. | McClelland AD et al. | β | 2017 | β |
| Comparative analysis of gene regulatory networks of highly metastatic breast cancer cells established by orthotopic transplantation and intra-circulation injection. | Nakayama J et al. | β | 2017 | β |
| Comparative transcriptomic analysis of <i>Gardnerella vaginalis</i> biofilms vs. planktonic cultures using RNA-seq. | Castro J et al. | β | 2017 | β |
| Comprehensive classification of the PIN domain-like superfamily. | Matelska D et al. | β | 2017 | β |
| Computational analysis of multimorbidity between asthma, eczema and rhinitis. | Aguilar D et al. | β | 2017 | β |
| Construction of Functional Gene Networks Using Phylogenetic Profiles. | Shin J et al. | β | 2017 | β |
| Cross-species gene modules emerge from a systems biology approach to osteoarthritis. | Mueller AJ et al. | β | 2017 | β |
| Differential Protein Expression Marks the Transition From Infection With <i>Opisthorchis viverrini</i> to Cholangiocarcinoma. | Khoontawad J et al. | β | 2017 | β |
| Does an increased body mass index affect endometrial gene expression patterns in infertile patients? AΒ functional genomics analysis. | Comstock IA et al. | β | 2017 | β |
| Downregulation of genes related to immune and inflammatory response in IVF implantation failure cases under controlled ovarian stimulation. | Pathare ADS et al. | β | 2017 | β |
| Dynamics and robustness of the cardiac progenitor cell induced pluripotent stem cell network during cell phenotypes transition. | Yao Y et al. | β | 2017 | β |
| Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities. | Patin NV et al. | β | 2017 | β |
| EGR1 regulates cellular metabolism and survival in endocrine resistant breast cancer. | Shajahan-Haq AN et al. | β | 2017 | β |
| Evaluating the associations between human circadian rhythms and dysregulated genes in liver cancer cells. | Polo A et al. | β | 2017 | β |
| Exploring Blueberry Aroma Complexity by Chromatographic and Direct-Injection Spectrometric Techniques. | Farneti B et al. | β | 2017 | β |
| First comprehensive proteome analysis of lysine crotonylation in seedling leaves of Nicotiana tabacum. | Sun H et al. | β | 2017 | β |
| From word models to executable models of signaling networks using automated assembly. | Gyori BM et al. | β | 2017 | β |
| Functional annotation of Alzheimer's disease associated loci revealed by GWASs. | Han Z et al. | β | 2017 | β |
| GALNT6 expression enhances aggressive phenotypes of ovarian cancer cells by regulating EGFR activity. | Lin TC et al. | β | 2017 | β |
| Gene and MicroRNA Expression Are Predictive of Tumor Response in Rectal Adenocarcinoma Patients Treated With Preoperative Chemoradiotherapy. | Millino C et al. | β | 2017 | β |
| Gene Expression Analysis before and after Treatment with Adalimumab in Patients with Ankylosing Spondylitis Identifies Molecular Pathways Associated with Response to Therapy. | Dolcino M et al. | β | 2017 | β |
| Gene-metabolite network analysis in different nonalcoholic fatty liver disease phenotypes. | Liu XL et al. | β | 2017 | β |
| Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature. | Lamurias A et al. | β | 2017 | β |
| Genome-scale metabolic models applied to human health and disease. | Cook DJ et al. | β | 2017 | β |
| Genome-wide association study unravels the genetic control of the apple volatilome and its interplay with fruit texture. | Farneti B et al. | β | 2017 | β |
| Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation. | Tai PWL et al. | β | 2017 | β |
| GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software. | Mittal V et al. | β | 2017 | β |
| High-Resolution Expression Profiling of Peripheral Blood CD8<sup>+</sup> Cells in Patients with Multiple Sclerosis Displays Fingolimod-Induced Immune Cell Redistribution. | Roch L et al. | β | 2017 | β |
| HSF-1 is a regulator of miRNA expression in Caenorhabditis elegans. | Brunquell J et al. | β | 2017 | β |
| Identification and Characterization of Domesticated Bacterial Transposases. | Bertels F et al. | β | 2017 | β |
| Identification of context-dependent expression quantitative trait loci in whole blood. | Zhernakova DV et al. | β | 2017 | β |
| Identification of genetic networks that act in the somatic cells of the testis to mediate the developmental program of spermatogenesis. | Fairchild MJ et al. | β | 2017 | β |
| Identification of Histone Deacetylase (HDAC) as a drug target against MRSA via interolog method of protein-protein interaction prediction. | Uddin R et al. | β | 2017 | β |
| Identification of <i>SPOP</i> related metabolic pathways in prostate cancer. | Yan M et al. | β | 2017 | β |
| Identification of miRNA-mRNA crosstalk in CD4<sup>+</sup> T cells during HIV-1 infection by integrating transcriptome analyses. | Liao Q et al. | β | 2017 | β |
| Identification of novel diagnostic biomarkers for thyroid carcinoma. | Wang X et al. | β | 2017 | β |
| Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. | Giner-Lamia J et al. | β | 2017 | β |
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