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Macrophage Transcriptional Profile Identifies Lipid Catabolic Pathways That Can Be Therapeutically Targeted after Spinal Cord Injury

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Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development

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MicroRNA Markers for the Diagnosis of Pancreatic and Biliary-Tract Cancers

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microRNA-148a Is a Prognostic oncomiR That Targets MIG6 and BIM to Regulate EGFR and Apoptosis in Glioblastoma

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Functional analysis of African Xanthomonas oryzae pv. oryzae TALomes reveals a new susceptibility gene in bacterial leaf blight of rice

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Leishmania donovani Infection Causes Distinct Epigenetic DNA Methylation Changes in Host Macrophages

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Diversity of Biological Effects Induced by Longwave UVA Rays (UVA1) in Reconstructed Skin

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The GI – CDF module of Arabidopsis affects freezing tolerance and growth as well as flowering

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Establishment and characterization of models of chemotherapy resistance in colorectal cancer: Towards a predictive signature of chemoresistance

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Neuroinflammatory Signals in Alzheimer Disease and APP/PS1 Transgenic Mice

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A dual-species co-cultivation system to study the interactions between Roseobacters and dinoflagellates

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miR-34a Repression in Proneural Malignant Gliomas Upregulates Expression of Its Target PDGFRA and Promotes Tumorigenesis

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Generation of folliculogenic human epithelial stem cells from induced pluripotent stem cells

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Epigenetic remodeling during arsenical-induced malignant transformation

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The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes

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Cellular, synaptic, and biochemical features of resilient cognition in Alzheimer’s disease

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Global Gene Expression Patterns of Nostoc punctiforme in Steady-State Dinitrogen-Grown Heterocyst-Containing Cultures and at Single Time Points during the Differentiation of Akinetes and Hormogonia

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Methylation profiling with a panel of cancer related genes: Association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer

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Genes Required for Aerial Growth, Cell Division, and Chromosome Segregation Are Targets of WhiA before Sporulation in Streptomyces venezuelae

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DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

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Transcriptomic analysis of probable asymptomatic and symptomatic alzheimer brains

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Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organsPreprint

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ER71 directs mesodermal fate decisions during embryogenesis

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Functional‐genomics‐based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses

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HMGA1: A Master Regulator of Tumor Progression in Triple-Negative Breast Cancer Cells

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Plastic and Evolved Responses to Global Change: What Can We Learn from Comparative Transcriptomics?: Table 1.

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Early nitrogen‐deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho‐) proteome levels between nitrate and ammonium nutrition

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Considerations for target oxygen saturation in COVID-19 patients: are we under-shooting?

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Endoplasmic reticulum is a major target of cadmium toxicity in yeast

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Toona sinensis and its major bioactive compound gallic acid inhibit LPS-induced inflammation in nuclear factor-κB transgenic mice as evaluated by in vivo bioluminescence imaging

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Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street?1

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PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis

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Accumulation of Multipotent Progenitors with a Basal Differentiation Bias during Aging of Human Mammary Epithelia

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Dynamically regulated miRNA-mRNA networks revealed by exercise

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The effects of perinatal testosterone exposure on the DNA methylome of the mouse brain are late-emerging

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ORIGINAL ARTICLE: The Transcriptome of the Fetal Inflammatory Response Syndrome

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Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth

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Positively correlated miRNA-mRNA regulatory networks in mouse frontal cortex during early stages of alcohol dependence

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MicroRNA-214 controls skin and hair follicle development by modulating the activity of the Wnt pathway

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The extracellular EXO protein mediates cell expansion in Arabidopsis leaves

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Altered expression of histamine signaling genes in autism spectrum disorder

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The prediction of late-onset preeclampsia: Results from a longitudinal proteomics study

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Appyters: Turning Jupyter Notebooks into data-driven web apps

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MicroRNA Regulatory Network Analysis Using miRNet 2.0

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Tryptophan-Derived Metabolites Are Required for Antifungal Defense in the Arabidopsis mlo2 Mutant

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Molecular Strategies of the Caenorhabditis elegans Dauer Larva to Survive Extreme Desiccation

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Bypass Mechanisms of the Androgen Receptor Pathway in Therapy-Resistant Prostate Cancer Cell Models

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MicroRNA/gene profiling unveils early molecular changes and nuclear factor erythroid related factor 2 (NRF2) activation in a rat model recapitulating human hepatocellular carcinoma (HCC)

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Stochastic Expression of the Interferon-β Gene

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Genome-Wide Association Analysis in Asthma Subjects Identifies SPATS2L as a Novel Bronchodilator Response Gene

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Loss of BAF (mSWI/SNF) Complexes Causes Global Transcriptional and Chromatin State Changes in Forebrain Development

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Chronic psychological stress and high-fat high-fructose diet disrupt metabolic and inflammatory gene networks in the brain, liver, and gut and promote behavioral deficits in mice

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Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum

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Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression

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YB-1, the E2F Pathway, and Regulation of Tumor Cell Growth

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Differential gene expression in functional classes of interstitial cells of Cajal in murine small intestine

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Systems Analysis of a RIG-I Agonist Inducing Broad Spectrum Inhibition of Virus Infectivity

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Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

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Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms

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Large Scale Aggregate Microarray Analysis Reveals Three Distinct Molecular Subclasses of Human Preeclampsia

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Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach

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Predictability of human differential gene expression

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Gene expression during normal and FSHD myogenesis

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Comprehensive transcriptome and immunophenotype analysis of renal and cardiac MSC-like populations supports strong congruence with bone marrow MSC despite maintenance of distinct identities

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Histone deacetylase inhibition in colorectal cancer cells reveals competing roles for members of the oncogenic miR‐17‐92 cluster

Humphreys, K. J., Cobiac, L., Leu, R. K. L., der Hoek, M. B. V., & Michael, M. (2012) · Molecular Carcinogenesis · doi:10.1002/mc.21879 · Cited by 117

Expression profiling of mouse subplate reveals a dynamic gene network and disease association with autism and schizophrenia

Hoerder‐Suabedissen, A., Oeschger, F. M., Krishnan, M. L., Belgard, T. G., Wang, W. Z., Lee, S., Webber, C., Petretto, E. G., Edwards, A. D., & Molnár, Z. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218510110 · Cited by 118

Heterografting with nonself rootstocks induces genes involved in stress responses at the graft interface when compared with autografted controls

Cookson, S. J., Clemente‐Moreno, M. J., Hévin, C., Mendome, L. Z. N., Delrot, S., Magnin, N., Trossat-Magnin, C., & Ollat, N. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru145 · Cited by 122

Two Histone Deacetylases, FfHda1 and FfHda2, Are Important for Fusarium fujikuroi Secondary Metabolism and Virulence

Studt, L., Schmidt, F. J., Jahn, L., Sieber, C. M. K., Connolly, L., Niehaus, E., Freitag, M., Humpf, H., & Tudzynski, B. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01557-13 · Cited by 117

Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers

Kashyap, M. K., Marimuthu, A., Kishore, C. J. H., Peri, S., Keerthikumar, S., Prasad, T. S. K., Mahmood, R., Rao, S., Ranganathan, P., Sanjeeviah, R. C., et al. (2009) · Cancer Biology & Therapy · doi:10.4161/cbt.8.1.7090 · Cited by 118

cAMP Response Element-Binding Protein Is a Primary Hub of Activity-Driven Neuronal Gene Expression

Benito, E., Valor, L. M., Jimenez-Minchan, M., Huber, W. K., & Barco, Á. (2011) · Journal of Neuroscience · doi:10.1523/jneurosci.4554-11.2011 · Cited by 119

Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti

Pini, F., Nisco, N. J. D., Ferri, L., Penterman, J. N., Fioravanti, A., Brilli, M., Mengoni, A., Bazzicalupo, M., Viollier, P. H., Walker, G. C., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005232 · Cited by 116

DNA Methylation in the Medial Prefrontal Cortex Regulates Alcohol-Induced Behavior and Plasticity

Barbier, E., Tapocik, J. D., Juergens, N., Pitcairn, C., Borich, A., Schank, J. R., Sun, H., Schuebel, K. E., Zhou, Z., Yuan, Q., et al. (2015) · Journal of Neuroscience · doi:10.1523/jneurosci.4571-14.2015 · Cited by 116

Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned

Price, E. M., & Robinson, W. P. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00083 · Cited by 117

Escherichia coli- and Staphylococcus aureus-induced mastitis differentially modulate transcriptional responses in neighbouring uninfected bovine mammary gland quarters

Jensen, K., Günther, J., Talbot, R., Petzl, W., Zerbe, H., Schuberth, H., Seyfert, H., & Glass, E. J. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-36 · Cited by 116

Transcriptomic characterization of fibrolamellar hepatocellular carcinoma

Simon, E. P., Freije, C. A., Farber, B. A., Lalazar, G., Darcy, D. G., Honeyman, J. N., Chiaroni-Clarke, R. C., Dill, B. D., Molina, H., Bhanot, U. K., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1424894112 · Cited by 115

TheIDA/IDA-LIKEandPIP/PIP-LIKEgene families inArabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide

Vie, A. K., Najafi, J., Liu, B., Winge, P., Butenko, M. A., Hornslien, K. S., Kumpf, R. P., Aalen, R. B., Bones, A. M., & Brembu, T. (2015) · Journal of Experimental Botany · doi:10.1093/jxb/erv285 · Cited by 115

A Genetically Hard-Wired Metabolic Transcriptome in Plasmodium falciparum Fails to Mount Protective Responses to Lethal Antifolates

Ganesan, K., Ponmee, N., Jiang, L., Fowble, J. W., White, J. C., Kamchonwongpaisan, S., Yuthavong, Y., Wilairat, P., & Rathod, P. K. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000214 · Cited by 115

SigCom LINCS: data and metadata search engine for a million gene expression signatures

Evangelista, J. E., Clarke, D. J. B., Xie, Z., Lachmann, A., Jeon, M., Chen, K., Jagodnik, K. M., Jenkins, S. L., Kuleshov, M. V., Wojciechowicz, M. L., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac328 · Cited by 118

Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity

Fröhlich, K., Brombacher, E., Fahrner, M., Vogele, D., Kook, L., Pinter, N., Bronsert, P., Timme‐Bronsert, S., Schmidt, A., Baerenfaller, K., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30094-0 · Cited by 117

Exploring the associations between microRNA expression profiles and environmental pollutants in human placenta from the National Children's Study (NCS)

Li, Q., Deyssenroth, M. A., Li, A., Dassanayake, P. S., Darrah, T. H., Friedman, A. E., Friedman, M. R., Lambertini, L., Landrigan, P. J., Stodgell, C., et al. (2015) · Epigenetics · doi:10.1080/15592294.2015.1066960 · Cited by 115

Full-term Pregnancy Induces a Specific Genomic Signature in the Human Breast

Russo, J., Balogh, G., & Russo, I. H. (2008) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-07-0678 · Cited by 115

Microbial-Host Co-metabolites Are Prodromal Markers Predicting Phenotypic Heterogeneity in Behavior, Obesity, and Impaired Glucose Tolerance

Dumas, M.-E., Rothwell, A. R., Hoyles, L., Aranias, T., Chilloux, J., Calderari, S., Noll, E. M., Péan, N., Boulangé, C. L., Blancher, C., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.039 · Cited by 114

Transcriptome from circulating cells suggests dysregulated pathways associated with long-term recurrent events following first-time myocardial infarction

Suresh, R., Li, X., Chiriac, A. E., Goel, K., Terzic, A., Pérez-Terzic, C. M., & Nelson, T. J. (2014) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2014.04.017 · Cited by 116

Circulating serum microRNAs as novel diagnostic and prognostic biomarkers for multiple myeloma and monoclonal gammopathy of undetermined significance

Kubiczkova, L., Kryukov, F., Slabý, O., Dementyeva, E., Jarkovský, J., Nekvindová, J., Radová, L., Grešlíková, H., Kuglík, P., Vetešníková, E., et al. (2013) · Haematologica · doi:10.3324/haematol.2013.093500 · Cited by 114

A novel computational approach for drug repurposing using systems biology

Peyvandipour, A., Saberian, N., Shafi, A., Donato, M., & Drăghici, S. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty133 · Cited by 117

Bovine pretransfer endometrium and embryo transcriptome fingerprints as predictors of pregnancy success after embryo transfer

Salilew‐Wondim, D., Hoelker, M., Rings, F., Ghanem, N., Ulas-Cinar, M., Peippo, J., Tholen, E., Looft, C., Schellander, K., & Tesfaye, D. (2010) · Physiological Genomics · doi:10.1152/physiolgenomics.00047.2010 · Cited by 121

Effects of Low Progesterone on the Endometrial Transcriptome in Cattle1

Forde, N., Mehta, J. P., Minten, M. A., Crowe, M. A., Roche, J. F., Spencer, T. E., & Lonergan, P. (2012) · Biology of Reproduction · doi:10.1095/biolreprod.112.103424 · Cited by 114

Regulation of alternative splicing by the circadian clock and food related cues

McGlincy, N. J., Valomon, A., Chesham, J. E., Maywood, E. S., Hastings, M. H., & Ule, J. (2012) · Genome biology · doi:10.1186/gb-2012-13-6-r54 · Cited by 115

Midbrain dopamine neurons in Parkinson׳s disease exhibit a dysregulated miRNA and target-gene network

Briggs, C. E., Wang, Y., Kong, B., Woo, T.-U. W., Iyer, L. K., & Sonntag, K. C. (2015) · Brain Research · doi:10.1016/j.brainres.2015.05.021 · Cited by 113

Genome-wide analysis of diel gene expression in the unicellular N2-fixing cyanobacterium Crocosphaera watsonii WH 8501

Shi, T., Shilova, I. N., Rabouille, S., & Zehr, J. P. (2010) · The ISME Journal · doi:10.1038/ismej.2009.148 · Cited by 113

Transcriptome Profiling of Human Pre-Implantation Development

Zhang, P., Zucchelli, M., Bruce, S., Hambiliki, F., Stavreus-Evers, A. C., Levkov, L., Skottman, H., Kerkelä, E., Kere, J., & Hovatta, O. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007844 · Cited by 117

The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function

Loedige, I., Gaidatzis, D., Sack, R., Meister, G., & Filipowicz, W. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1032 · Cited by 113

Limma: linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor

Smyth, G. K. (2013)

limmaGUI: A graphical user interface for linear modeling of microarray data

Wettenhall, J. M., & Smyth, G. K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth449 · Cited by 720

Empirical array quality weights in the analysis of microarray data

Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, A., Holloway, A., & Smyth, G. K. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-261 · Cited by 312

Examples

Yes, L. (2010)

LLAMA: AN ONLINE MICROARRAY LINEAR ANALYSIS TOOLPreprint

Routley, B. S., & Muldoon, M. R. (2005) · MIMS EPrints (University of Southampton)