limma: Linear Models for Microarray Data

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A., & Vingron, M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s96 · Cited by 2,440

Identifying differentially expressed genes using false discovery rate controlling procedures

Reiner, A., Yekutieli, D., & Benjamini, Y. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btf877 · Cited by 1,765

Use of within-array replicate spots for assessing differential expression in microarray experiments

Smyth, G. K., Michaud, J., & Scott, H. S. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti270 · Cited by 1,406

Analysis of Messy Data, Volume I: Designed Experiments

Schmee, J., Milliken, G. A., & Johnson, D. E. (1985) · Technometrics · doi:10.2307/1270212 · Cited by 922

Statistical Issues in cDNA Microarray Data Analysis

Smyth, G. K., Yang, J. Y. H., & Speed, T. P. (2003) · Humana Press eBooks · doi:10.1385/1-59259-364-x:111 · Cited by 471

Parameter estimation for the calibration and variance stabilization of microarray data

Huber, W. K., von Heydebreck, A., Sueltmann, H., Poustka, A., & Vingron, M. (2003) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1008 · Cited by 185

Design and analysis of comparative microarray experiments

Speed, T. P. (2003) · doi:10.1201/9780203011232-9 · Cited by 67

LRRN4 and UPK3B Are Markers of Primary Mesothelial Cells

Kanamori-Katayama, M., Kaiho, A., Ishizu, Y., Okamura-Oho, Y., Hino, O., Abe, M., Kishimoto, T., Sekihara, H., Nakamura, Y., Suzuki, H., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025391 · Cited by 92

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

Voigt, K., Sharma, C. M., Mitschke, J., Lambrecht, S. J., Voß, B., Hess, W. R., & Steglich, C. (2014) · The ISME Journal · doi:10.1038/ismej.2014.57 · Cited by 92

Arabidopsis CLAVATA 1 and CLAVATA 2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169‐dependent pathway

Hanemian, M., Barlet, X., Sorin, C., Yadeta, K. A., Keller, H., Favery, B., Simon, R. G., Thomma, B. P. H. J., Hartmann, C., Crespi, M. D., et al. (2016) · New Phytologist · doi:10.1111/nph.13913 · Cited by 92

A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress

Omidbakhshfard, M. A., Sujeeth, N., Gupta, S., Omranian, N., Guinan, K. J., Brotman, Y., Nikoloski, Z., Fernie, A. R., Mueller‐Roeber, B., & Gechev, T. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21020474 · Cited by 92

Analysis of the molecular nature associated with microsatellite status in colon cancer identifies clinical implications for immunotherapy

Bao, X., Zhang, H., Wu, W., Cheng, S., Dai, X., Zhu, X., Fu, Q., Tong, Z., Liu, L., Zheng, Y., et al. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-001437 · Cited by 92

Bisphenol A affects placental layers morphology and angiogenesis during early pregnancy phase in mice

Tait, S., Tassinari, R., Maranghi, F., & Mantovani, A. (2015) · Journal of Applied Toxicology · doi:10.1002/jat.3176 · Cited by 92

Loading-related regulation of gene expression in bone in the contexts of estrogen deficiency, lack of estrogen receptor α and disuse

Zaman, G., Saxon, L., Sunters, A., Hilton, H., Underhill, P., Williams, D., Price, J. S., & Lanyon, L. E. (2009) · Bone · doi:10.1016/j.bone.2009.10.021 · Cited by 95

Impact of Acute Metal Stress in Saccharomyces cerevisiae

Hosiner, D., Gerber, S., Lichtenberg‐Fraté, H., Glaser, W., Schüller, C., & Klipp, E. (2014) · PLoS ONE · doi:10.1371/journal.pone.0083330 · Cited by 92

Analysis of global changes in gene expression during activity-dormancy cycle in hybrid aspen apex

Karlberg, A., Englund, M., Petterle, A., Molnár, G., Sjödin, A., Bakó, L., & Bhalerao, R. P. (2010) · Plant Biotechnology · doi:10.5511/plantbiotechnology.27.1 · Cited by 92

Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a H olarctic songbird

Mason, N. A., & Taylor, S. A. (2015) · Molecular Ecology · doi:10.1111/mec.13140 · Cited by 93

Transition of Plasmodium Sporozoites into Liver Stage-Like Forms Is Regulated by the RNA Binding Protein Pumilio

Gomes-Santos, C. S. S., Braks, J. A. M., Prudêncio, M., Carret, C., Gomes, A. R., Pain, A., Feltwell, T., Khan, S. M., Waters, A. P., Janse, C. J., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002046 · Cited by 92

ODDSOC2 Is a MADS Box Floral Repressor That Is Down-Regulated by Vernalization in Temperate Cereals

Greenup, A. G., Sasani, S., Oliver, S. N., Talbot, M. J., Dennis, E. S., Hemming, M. N., & Trevaskis, B. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.109.152488 · Cited by 92

Performance comparison of deep learning autoencoders for cancer subtype detection using multi-omics data

Franco, E. F., Rana, P., Cruz, A., Calderón, V. V., Azevedo, V., Ramos, R. T. J., & Ghosh, P. (2021) · Cancers · doi:10.3390/cancers13092013 · Cited by 92

Generation of Mouse and Human Organoid-Forming Intestinal Progenitor Cells by Direct Lineage Reprogramming

Miura, S., & Suzuki, A. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.08.020 · Cited by 91

Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2by RNA-Seq

Niederhuth, C. E., Patharkar, O. R., & Walker, J. C. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-37 · Cited by 91

Discovery of Novel Hypermethylated Genes in Prostate Cancer Using Genomic CpG Island Microarrays

Kron, K. J., Pethe, V. V., Briollais, L., Sadiković, B., Özçelik, H., Sunderji, A., Venkateswaran, V., Pinthus, J. H., Fleshner, N. E., van der Kwast, T., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004830 · Cited by 91

Gene expression in Eucalyptus branch wood with marked variation in cellulose microfibril orientation and lacking G‐layers

Qiu, D., Wilson, I. W., Gan, S., Washusen, R., Moran, G. F., & Southerton, S. G. (2008) · New Phytologist · doi:10.1111/j.1469-8137.2008.02439.x · Cited by 91

DNA methylation profiling in human lung tissue identifies genes associated with COPD

Morrow, J. D., Cho, M. H., Hersh, C. P., Pinto-Plata, V., Celli, B. R., Marchetti, N. T., Criner, G. J., Bueno, R., Washko, G. R., Glass, K., et al. (2016) · Epigenetics · doi:10.1080/15592294.2016.1226451 · Cited by 91

Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy

Islam, A. B. M. M. K., & Khan, M. A. (2020) · Scientific Reports · doi:10.1038/s41598-020-76404-8 · Cited by 94

The effects of dietary curcumin and rutin on colonic inflammation and gene expression in multidrug resistance gene-deficient (mdr1a−/−) mice, a model of inflammatory bowel diseases

Nones, K., Dommels, Y. E. M., Martell, S., Butts, C. A., McNabb, W. C., Park, Z. A., Zhu, S., HEDDERLEY, D. I., Barnett, M. P. G., & Roy, N. C. (2008) · British Journal Of Nutrition · doi:10.1017/s0007114508009847 · Cited by 91

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

Amin, V. R., Harris, R. A., Onuchic, V., Jackson, A. R., Charnecki, T., Paithankar, S., Subramanian, S. L., Riehle, K. P., Coarfa, C., & Milosavljevic, A. (2015) · Nature Communications · doi:10.1038/ncomms7370 · Cited by 93

Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley

Hollmann, J., Gregersen, P. L., & Krupinska, K. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru094 · Cited by 91

Developmental control of the Nlrp6 inflammasome and a substrate, IL-18, in mammalian intestine

Kempster, S. L., Bélteki, G., Forhead, A. J., Fowden, A. L., Catalano, R. D., Lam, B., McFarlane, I., Jones, D. S., & Smith, G. C. S. (2010) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00397.2010 · Cited by 91

Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol

Beckers, V., Poblete‐Castro, I., Tomasch, J., & Wittmann, C. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0470-2 · Cited by 92

A core transcriptional signature of human microglia: derivation and utility in describing region-dependent alterations associated with Alzheimer’s disease

Patir, A., Shih, B., McColl, B. W., & Freeman, T. C. (2019) · Glia · doi:10.1002/glia.23572 · Cited by 90

Overexpression of miR-214-3p in esophageal squamous cancer cells enhances sensitivity to cisplatin by targeting survivin directly and indirectly through CUG-BP1

Phatak, P., Byrnes, K. A., Mansour, D., Liu, L., Cao, S., Li, R., Rao, J. N., Turner, D. J., Wang, J.-Y., & Donahue, J. M. (2015) · Oncogene · doi:10.1038/onc.2015.271 · Cited by 91

Regulation of Seed Germination in the Close Arabidopsis RelativeLepidium sativum: A Global Tissue-Specific Transcript Analysis

Morris, K., Linkies, A., Müller, K., Oracz, K., Wang, X., Lynn, J. R., Leubner‐Metzger, G., & Finch‐Savage, W. E. (2011) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.169706 · Cited by 90

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

Kristiansson, E., Asker, N., Förlin, L., & Larsson, D. G. J. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-345 · Cited by 90

Construction of differential mRNA-lncRNA crosstalk networks based on ceRNA hypothesis uncover key roles of lncRNAs implicated in esophageal squamous cell carcinoma

Yang, S., Ning, Q., Zhang, G., Sun, H., Wang, Z., & Li, Y. (2016) · Oncotarget · doi:10.18632/oncotarget.13828 · Cited by 90

Differential transcriptional profiles mediated by exposure to the cannabinoids cannabidiol and Δ9‐tetrahydrocannabinol in BV‐2 microglial cells

Juknat, A., Pietr, M., Kozela, E., Rimmerman, N., Levy, R., Coppola, G., Geschwind, D. H., & Vogel, Z. (2011) · British Journal of Pharmacology · doi:10.1111/j.1476-5381.2011.01461.x · Cited by 90

Chronic exposure to cigarette smoke condensate in vitro induces epithelial to mesenchymal transition-like changes in human bronchial epithelial cells, BEAS-2B

Veljkovic, E., Jiricny, J., Menigatti, M., Rehrauer, H., & Han, W. (2010) · Toxicology in Vitro · doi:10.1016/j.tiv.2010.11.011 · Cited by 90

A technology platform to assess multiple cancer agents simultaneously within a patient’s tumor

Klinghoffer, R. A., Bahrami, S.-B., Hatton, B. A., Frazier, J. P., Moreno‐Gonzalez, A., Strand, A. D., Kerwin, W. S., Casalini, J. R., Thirstrup, D. J., You, S., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa7489 · Cited by 90

Transcriptional Responses of Arabidopsis thaliana during Wilt Disease Caused by the Soil-Borne Phytopathogenic Bacterium, Ralstonia solanacearum

Hu, J. H., Barlet, X., Deslandes, L., Hirsch, J., Feng, D. X., Somssich, I. E., & Marco, Y. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002589 · Cited by 90

Comparative Transcriptional and Genomic Analysis of Plasmodium falciparum Field Isolates

Mackinnon, M. J., Li, J., Mok, S., Kortok, M., Marsh, K., Preiser, P. R., & Bozdech, Z. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000644 · Cited by 90

Transcriptional analysis of abdominal fat in genetically fat and lean chickens reveals adipokines, lipogenic genes and a link between hemostasis and leanness

Resnyk, C., Carré, W., Wang, X., Porter, T. E., Simon, J., Bihan-Duval, É. L., Duclos, M. J. M. J., Aggrey, S. E., & Cogburn, L. A. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-557 · Cited by 93

Investigation of Malic Acid Production in Aspergillus oryzae under Nitrogen Starvation Conditions

Knuf, C., Nookaew, I., Brown, S. H., McCulloch, M., Berry, A., & Nielsen, J. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01445-13 · Cited by 94

Alpha-synuclein deficiency leads to increased glyoxalase I expression and glycation stress

Kurz, A., Rabbani, N., Walter, M. J., von Bonin, M., Thornalley, P. J., Auburger, G. W. J., & Gispert, S. (2010) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-010-0483-7 · Cited by 90

Map of differential transcript expression in the normal human large intestine

LaPointe, L. C., Dunne, R. A., Brown, G. S., Worthley, D. L., Molloy, P. L., Wattchow, D. A., & Young, G. P. (2007) · Physiological Genomics · doi:10.1152/physiolgenomics.00185.2006 · Cited by 90

Arabidopsis NITRILASE 1 Contributes to the Regulation of Root Growth and Development through Modulation of Auxin Biosynthesis in Seedlings

Lehmann, T. J., Janowitz, T., Sánchez‐Parra, B., Alonso, M.-M. P., Trompetter, I., Piotrowski, M., & Pollmann, S. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00036 · Cited by 90

Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs

Kitazaki, K., Fukushima, A., Nakabayashi, R., Okazaki, Y., Kobayashi, M., Mori, T., Nishizawa, T., Reyes-Chin-Wo, S., Michelmore, R. W., Saito, K., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-25686-0 · Cited by 90

The molecular signature of CD8+ T cells undergoing deletional tolerance

Parish, I. A., Rao, S., Smyth, G. K., Juelich, T., Denyer, G. S., Davey, G. M., Strasser, A., & Heath, W. R. (2009) · Blood · doi:10.1182/blood-2008-10-185223 · Cited by 92

Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption

Scalcinati, G., Otero, J. M., Vleet, J. R. H., Jeffries, T. W., Olsson, L., & Nielsen, J. (2012) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2012.00808.x · Cited by 89

Carbosilane dendrimer nanotechnology outlines of the broad HIV blocker profile

Chonco, L., Pion, M., Vacas‐Córdoba, E., Rasines, B., Maly, M., Serramía, M. J., López-Fernández, L. A., de la Mata, F. J., Álvarez, S., Gómez, R., et al. (2012) · Journal of Controlled Release · doi:10.1016/j.jconrel.2012.04.050 · Cited by 89

DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells

Zhang, X., Ulm, A., Somineni, R. P., Oh, S., Weirauch, M. T., Zhang, H.-X., Chen, X., Lehn, M. A., Janssen, E. M., & Ji, H. (2014) · Epigenetics & Chromatin · doi:10.1186/1756-8935-7-21 · Cited by 93

Improving culture performance and antibody production in CHO cell culture processes by reducing the Warburg effect

Buchsteiner, M., Quek, L., Gray, P. P., & Nielsen, L. K. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26724 · Cited by 100

Acute exposure to microplastics induces metabolic disturbances and gut dysbiosis in adult zebrafish (Danio rerio)

Medriano, C. A., & Bae, S. (2022) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2022.114125 · Cited by 91

A molecular network of conserved factors keeps ribosomes dormant in the egg

Leesch, F., Lorenzo‐Orts, L., Pribitzer, C., Grishkovskaya, I., Roehsner, J., Chugunova, A. A., Matzinger, M., Roitinger, E., Belačić, K., Kandolf, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05623-y · Cited by 92

Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells

Diesch, J., Sanij, E., Gilan, O., Love, C. G., Tran, H., Fleming, N. I., Ellul, J., Marcia, A., Haviv, I., Pearson, R. B., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088950 · Cited by 95

The Role of T cell PPAR γ in mice with experimental inflammatory bowel disease

Guri, A. J., Mohapatra, S. K., Horne, W. T., Hontecillas, R., & Bassaganya-Riera, J. (2010) · BMC Gastroenterology · doi:10.1186/1471-230x-10-60 · Cited by 89

Integrative genome‐wide analysis reveals a robust genomic glioblastoma signature associated with copy number driving changes in gene expression

de Tayrac, M., Etcheverry, A., Aubry, M., Saïkali, S., Hamlat, A., Quillien, V., Treut, A. L., Galibert, M., & Mosser, J. (2008) · Genes Chromosomes and Cancer · doi:10.1002/gcc.20618 · Cited by 89

Bacterial origin of a diverse family of UDP-glycosyltransferase genes in the Tetranychus urticae genome

Ahn, S., Dermauw, W., Wybouw, N., Heckel, D. G., & Leeuwen, T. V. (2014) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2014.04.003 · Cited by 93

The forkhead transcription factor FOXK2 acts as a chromatin targeting factor for the BAP1-containing histone deubiquitinase complex

Ji, Z., Mohammed, H., Webber, A., Ridsdale, J., Han, N., Carroll, J. S., & Sharrocks, A. D. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku274 · Cited by 95

Functional Identification of Cancer-Specific Methylation of CDO1 , HOXA9 , and TAC1 for the Diagnosis of Lung Cancer

Wrangle, J. M., Machida, E. O., Danilova, L., Hulbert, A., Franco, N. C., Zhang, W., Glöckner, S. C., Tessema, M., Neste, L. V., Easwaran, H., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-2109 · Cited by 89

Comparative study on gene set and pathway topology-based enrichment methods

Bayerlová, M., Jung, K., Krämer, F., Klemm, F., Bleckmann, A., & Beißbarth, T. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0751-5 · Cited by 90

Gene regulation and priming by topoisomerase IIα in embryonic stem cells

Thakurela, S., Garding, A., Jung, J., Schübeler, D., Burger, L., & Tiwari, V. K. (2013) · Nature Communications · doi:10.1038/ncomms3478 · Cited by 91

Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes

Acevedo, N., Reinius, L. E., Vitezic, M., Fortino, V., Söderhäll, C., Honkanen, H., Veijola, R., Simell, O., Toppari, J., Ilonen, J., et al. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0064-6 · Cited by 92

Genomic Signatures and Dose-Dependent Transitions in Nasal Epithelial Responses to Inhaled Formaldehyde in the Rat

Andersen, M. E., M.A., H. J. C. I., Bermudez, E., Willson, G. A., & Thomas, R. S. (2008) · Toxicological Sciences · doi:10.1093/toxsci/kfn097 · Cited by 90

Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar

Pechanova, O., Hsu, C.-Y., Adams, J. P., Pechan, T., Vandervelde, L., Drnevich, J. M., Jawdy, S. S., Adeli, A., Suttle, J. C., Lawrence, A. M., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-674 · Cited by 88

Combined mRNA microarray and proteomic analysis of eutopic endometrium of women with and without endometriosis

Fassbender, A., Verbeeck, N., Börnigen, D., Kyama, C. M., Bokor, A., Vodolazkaia, A., Peeraer, K., Tomassetti, C., Meuleman, C., Gevaert, O., et al. (2012) · Human Reproduction · doi:10.1093/humrep/des127 · Cited by 87

WDR5 Expression Is Prognostic of Breast Cancer Outcome

Dai, X., Guo, W., Zhan, C., Liu, X., Bai, Z., & Yang, Y. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124964 · Cited by 87

Inhibition of miR-9 de-represses HuR and DICER1 and impairs Hodgkin lymphoma tumour outgrowth in vivo

Leucci, E., Zriwil, A., Gregersen, L. H., Jensen, K. T., Obad, S., Bellan, C., Leoncini, L., Kauppinen, S., & Lund, A. H. (2012) · Oncogene · doi:10.1038/onc.2012.15 · Cited by 89

Genetic Dissection of Cardiac Remodeling in an Isoproterenol-Induced Heart Failure Mouse Model

Wang, J., Rau, C., Avetisyan, R., Ren, S. V., Romay, M. C., Stolin, G., Gong, K., Wang, Y., & Lusis, A. J. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006038 · Cited by 90

Cell wall dynamics during apple development and storage involves hemicellulose modifications and related expressed genes

Dheilly, E., Gall, S. L., Guillou, M., Renou, J., Bonnin, E., Orsel, M., & Lahaye, M. (2016) · BMC Plant Biology · doi:10.1186/s12870-016-0887-0 · Cited by 87

Computational Methods for Single-Cell RNA Sequencing

Hie, B., Peters, J. M., Nyquist, S. K., Shalek, A. K., Berger, B., & Bryson, B. D. (2020) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-012220-100601 · Cited by 89

Pan‐Cancer Single‐Cell and Spatial‐Resolved Profiling Reveals the Immunosuppressive Role of APOE+ Macrophages in Immune Checkpoint Inhibitor Therapy

Liu, C., Xie, J., Lin, B., Tian, W., Wu, Y., Shan, X., Hong, L., Li, X., Liu, L., Jin, Y., et al. (2024) · Advanced Science · doi:10.1002/advs.202401061 · Cited by 90

An Epigenetic Signature in Peripheral Blood Associated with the Haplotype on 17q21.31, a Risk Factor for Neurodegenerative Tauopathy

Li, Y., Chen, J., Sears, R., Gao, F., Klein, E., Karydas, A., Geschwind, M. D., Rosen, H. J., Boxer, A. L., Guo, W., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004211 · Cited by 87

Comparison of dorsal root ganglion gene expression in rat models of traumatic and HIV‐associated neuropathic pain

Maratou, K., Wallace, V. C. J., Hasnie, F. S., Okuse, K., Hosseini, R., Jina, N., Blackbeard, J., Pheby, T., Orengo, C. A., Dickenson, A. H., et al. (2008) · European Journal of Pain · doi:10.1016/j.ejpain.2008.05.011 · Cited by 89

Dual role of transcription and transcript stability in the regulation of gene expression inEscherichia colicells cultured on glucose at different growth rates

Esquerré, T., Laguerre, S., Turlan, C., Carpousis, A. J., Girbal, L., & Cocaign‐Bousquet, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1150 · Cited by 87

Research Resource: Interplay between the Genomic and Transcriptional Networks of Androgen Receptor and Estrogen Receptor α in Luminal Breast Cancer Cells

Need, E. F., Selth, L. A., Harris, T. J., Birrell, S. N., Tilley, W. D., & Buchanan, G. (2012) · Molecular Endocrinology · doi:10.1210/me.2011-1314 · Cited by 87

Differential Gene Expression in Cultured Osteoblasts and Bone Marrow Stromal Cells From Patients With Paget's Disease of Bone

Naot, D., Bava, U., Matthews, B. G., Callon, K. E., Gamble, G. D., Black, M. A., Song, S., PITTO, R. P., Cundy, T., Cornish, J., et al. (2006) · Journal of Bone and Mineral Research · doi:10.1359/jbmr.061108 · Cited by 88

Pronounced Phenotype in Activated Regulatory T Cells during a Chronic Helminth Infection

Layland, L. E., Mages, J., Loddenkemper, C., Hoerauf, A. M., Wagner, H., Lang, R., & da Costa, C. P. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0901435 · Cited by 87

Effect of reproductive tract environment following controlled ovarian hyperstimulation treatment on embryo development and global transcriptome profile of blastocysts: implications for animal breeding and human assisted reproduction

Gad, A. Y., Besenfelder, U., Rings, F., Ghanem, N., Salilew‐Wondim, D., Hossain, M. M., Tesfaye, D., Lonergan, P., Becker, A., Cinar, U., et al. (2011) · Human Reproduction · doi:10.1093/humrep/der110 · Cited by 87

The HGF/c-MET Pathway Is a Driver and Biomarker of VEGFR-inhibitor Resistance and Vascular Remodeling in Non–Small Cell Lung Cancer

Cascone, T., Xu, L., Lin, H. Y., Liu, W., Tran, H. T., Liu, Y., Howells, K., Haddad, V., Hanrahan, E. O., Nilsson, M. B., et al. (2017) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-3216 · Cited by 92

Epigenome‐wide association of PTSD from heterogeneous cohorts with a common multi‐site analysis pipeline

Ratanatharathorn, A. D., Boks, M. P., Maihofer, A. X., Aiello, A. E., Amstadter, A. B., Ashley‐Koch, A. E., Baker, D. G., Beckham, J. C., Bromet, E. J., Dennis, M. F., et al. (2017) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32568 · Cited by 91

Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors

Kim, K., Shin, J., Lee, S.-H., Kweon, H.-S., Maloof, J. N., & Choi, G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011066108 · Cited by 86

Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system

Pulgar, R., Hödar, C., Travisany, D., Zuñiga, A., Domínguez, C., Maass, A., González, M., & Cambiazo, V. (2015) · BMC Genomics · doi:10.1186/s12864-015-1716-9 · Cited by 88

Social stress increases expression of hemoglobin genes in mouse prefrontal cortex

Stankiewicz, A. M., Gościk, J., Swiergiel, A. H., Majewska, A., Wieczorek, M., Juszczak, G. R., & Lisowski, P. (2014) · BMC Neuroscience · doi:10.1186/s12868-014-0130-6 · Cited by 89

Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes

Dmitriev, P., Barat, A., Polesskaya, A., O’Connell, M. J., Robert, T., Dessen, P., Walsh, T., Lazar, V., Turki, A., Carnac, G., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-265 · Cited by 89

Epigenome-wide association study of peripheral blood mononuclear cells in systemic lupus erythematosus: Identifying DNA methylation signatures associated with interferon-related genes based on ethnicity and SLEDAI

Joseph, S. J., George, N. I., Green-Knox, B., Treadwell, E. L., Word, B. R., Yim, S., & Lyn‐Cook, B. D. (2018) · Journal of Autoimmunity · doi:10.1016/j.jaut.2018.09.007 · Cited by 88

Placental expression profile of imprinted genes impacts birth weight

Deyssenroth, M. A., Green, B. B., Armstrong, D. A., Sharp, A. J., Lambertini, L., Marsit, C. J., & Chen, J. (2015) · Epigenetics · doi:10.1080/15592294.2015.1073881 · Cited by 86

Mutant Analysis in Arabidopsis Provides Insight into the Molecular Mode of Action of the Auxinic Herbicide Dicamba

Gleason, C., Foley, R. C., & Singh, K. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017245 · Cited by 89

Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases

Harris, A. R., Nagy‐Szakal, D., Pedersen, N. K., Opekun, A. R., Bronský, J., Munkholm, P. S., Jespersgaard, C., Andersen, P., Melegh, B., Ferry, G. D., et al. (2012) · Inflammatory Bowel Diseases · doi:10.1002/ibd.22956 · Cited by 88

Distribution based nearest neighbor imputation for truncated high dimensional data with applications to pre-clinical and clinical metabolomics studies

Shah, J., Rai, S. N., DeFilippis, A. P., Hill, B. G., Bhatnagar, A., & Brock, G. N. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1547-6 · Cited by 86

Brd4 modulates the innate immune response through Mnk2–eIF4E pathway-dependent translational control of IκBα

Bao, Y., Wu, X., Chen, J., Hu, X., Zeng, F., Cheng, J., Jin, H., Lin, X., & Chen, L. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1700109114 · Cited by 90

lncRNA DLEU2 acts as a miR-181a sponge to regulate SEPP1 and inhibit skeletal muscle differentiation and regeneration

Wang, Y., Zhao, Z.-J., Kang, X.-R., Bian, T., Shen, Z.-M., Jiang, Y., Sun, B., Hu, H.-B., & Chen, Y.-S. (2020) · Aging · doi:10.18632/aging.104095 · Cited by 85

Association of Childhood Chronic Physical Aggression with a DNA Methylation Signature in Adult Human T Cells

Provençal, N., Suderman, M. J., Guillemin, C., Vitaro, F., Côté, S. M., Hallett, M., Tremblay, R. E., & Szyf, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089839 · Cited by 85

Genome-Wide Identification of Alternative Splice Forms Down-Regulated by Nonsense-Mediated mRNA Decay in Drosophila

Hansen, K. D., Lareau, L. F., Blanchette, M., Green, R. E., Meng, Q., Rehwinkel, J., Gallusser, F., Izaurralde, E., Rio, D. C., Dudoit, S., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000525 · Cited by 88

The epigenetic signature of systemic insulin resistance in obese women

Arner, P., Sahlqvist, A., Sinha, I., Xu, H. Y., Yao, X., Waterworth, D. M., Rajpal, D. K., Loomis, A. K., Freudenberg, J., Johnson, T., et al. (2016) · Diabetologia · doi:10.1007/s00125-016-4074-5 · Cited by 86

c-Myc overexpression and endocrine resistance in breast cancer

McNeil, C. M., Sergio, C. M., Anderson, L. R., Inman, C. K., Eggleton, S. A., Murphy, N., Millar, E. K. A., Crea, P., Kench, J. G., Alles, M. C., et al. (2006) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/j.jsbmb.2006.09.028 · Cited by 85

Loss of Tribbles pseudokinase-3 promotes Akt-driven tumorigenesis via FOXO inactivation

Salazar‐Roa, M., Lorente, M., García-Taboada, E., Pérez-Gómez, E., Dávila, D., Zúñiga-García, P., Flores, J. M., Rodríguez, A., Hegedüs, Z., Mosén-Ansorena, D., et al. (2014) · Cell Death and Differentiation · doi:10.1038/cdd.2014.133 · Cited by 88

Connectivity mapping identifies HDAC inhibitors for the treatment of t(4;11)-positive infant acute lymphoblastic leukemia

Stumpel, D. J. P. M., Schneider, P., Seslija, L., Osaki, H., Williams, O., Pieters, R., & Stam, R. W. (2011) · Leukemia · doi:10.1038/leu.2011.278 · Cited by 85

Transcriptome analysis of high‐temperature adult‐plant resistance conditioned by Yr39 during the wheat– Puccinia striiformis f. sp. tritici interaction

Coram, T. E., Settles, M. L., & Chen, X. (2008) · Molecular Plant Pathology · doi:10.1111/j.1364-3703.2008.00476.x · Cited by 85

Upregulation of IL‐6, IL‐8 and CXCL‐1 production in dermal fibroblasts by normal/malignant epithelial cells in vitro: Immunohistochemical and transcriptomic analyses

Kolář, M., Szabó, P., Dvořánková, B., Lacina, L., Gabius, H., Strnad, H., Šáchová, J., Vlček, Č., Plzák, J., Chovanec, M., et al. (2012) · Biology of the Cell · doi:10.1111/boc.201200018 · Cited by 85

Members of the barley NAC transcription factor gene family show differential co-regulation with senescence-associated genes during senescence of flag leaves

Christiansen, M. W., & Gregersen, P. L. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru046 · Cited by 85

The Role of Particulate Matter-Associated Zinc in Cardiac Injury in Rats

Kodavanti, U. P., Schladweiler, M. C. J., Gilmour, P. S., Wallenborn, J. G., Mandavilli, B. S., Ledbetter, A. D., Christiani, D. C., Runge, M. S., Karoly, E. D., Costa, D. L., et al. (2007) · Environmental Health Perspectives · doi:10.1289/ehp.10379 · Cited by 85

A Gene Expression Signature for Chemoradiosensitivity of Colorectal Cancer Cells

Spitzner, M., Emons, G., Krämer, F., Gaedcke, J., Rave‐Fränk, M., Scharf, J., Burfeind, P., Becker, H., Beißbarth, T., Ghadimi, Β. M., et al. (2010) · International Journal of Radiation Oncology*Biology*Physics · doi:10.1016/j.ijrobp.2010.06.023 · Cited by 87

The dynamics of pyrethroid resistance in Anopheles arabiensis from Zanzibar and an assessment of the underlying genetic basis

Jones, C. M., Haji, K. A., Khatib, B. O., Bagi, J., Mcha, J. H., Devine, G. J., Daley, M. F., Kabula, B. I., Ali, A., Majambere, S., et al. (2013) · Parasites & Vectors · doi:10.1186/1756-3305-6-343 · Cited by 85

Epigenomic profiling of preterm infants reveals DNA methylation differences at sites associated with neural function

Sparrow, S. A., Manning, J. R., Cartier, J., Anblagan, D., Bastin, M. E., Piyasena, C., Pataky, R., Moore, E. J., Semple, S. I., Wilkinson, A. G., et al. (2016) · Translational Psychiatry · doi:10.1038/tp.2015.210 · Cited by 88

Molecular crosstalk between tumour and brain parenchyma instructs histopathological features in glioblastoma

Bougnaud, S., Golebiewska, A., Oudin, A., Keunen, O., Harter, P. N., Mäder, L., Azuaje, F. J., Fritah, S., Stieber, D., Kaoma, T., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.7454 · Cited by 88

The Senescence-associated Secretory Phenotype Mediates Oncogene-induced Senescence in Pediatric Pilocytic Astrocytoma

Buhl, J. L., Selt, F., Hielscher, T., Guiho, R., Ecker, J., Sahm, F., Ridinger, J., Riehl, D., Usta, D., Ismer, B., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1965 · Cited by 84

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)