Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

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DAVID: Database for Annotation, Visualization, and Integrated Discovery

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The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

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DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists

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Identifying biological themes within lists of genes with EASE

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GOstat: find statistically overrepresented Gene Ontologies within a group of genes

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FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

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Ontological analysis of gene expression data: current tools, limitations, and open problems

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DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

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GOToolBox: functional analysis of gene datasets based on Gene Ontology

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High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)

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Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments

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DAVID gene ID conversion tool

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HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication

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GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists

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GObar: A Gene Ontology based analysis and visualization tool for gene sets

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

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The Molecular Signatures Database Hallmark Gene Set Collection

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Scenic: single-cell regulatory network inference and clustering.

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Gene ontology analysis for RNA-seq: accounting for selection bias

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Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

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STRING v9.1: protein-protein interaction networks, with increased coverage and integration

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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

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Metabolic regulation of gene expression by histone lactylation

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Circular RNAs are abundant, conserved, and associated with ALU repeats

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Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

Meyer, K. D., Saletore, Y., Zumbo, P., Elemento, O., Mason, C. E., & Jaffrey, S. R. (2012) · Cell · doi:10.1016/j.cell.2012.05.003 · Cited by 4,223 · see citing works

Host microbiota constantly control maturation and function of microglia in the CNS

Erny, D., Hrabě de Angelis, A. L., Jaitin, D., Wieghofer, P., Staszewski, O., David, E., Keren-Shaul, H., Mahlakoiv, T., Jakobshagen, K., Buch, T., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4030 · Cited by 3,569 · see citing works

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

Hugo, W., Zaretsky, J. M., Sun, L., Song, C., Moreno, B. H., Hu-Lieskovan, S., Berent-Maoz, B., Pang, J., Chmielowski, B., Cherry, G., et al. (2016) · Cell · doi:10.1016/j.cell.2016.02.065 · Cited by 3,448 · see citing works

An anatomically comprehensive atlas of the adult human brain transcriptome

Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., van de Lagemaat, L. N., Smith, K. A., Ebbert, A., Riley, Z. L., et al. (2012) · Nature · doi:10.1038/nature11405 · Cited by 3,083 · see citing works

Molecular Architecture of the Mouse Nervous System

Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., van der Zwan, J., Häring, M., Braun, E., Borm, L. E., La Manno, G., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.021 · Cited by 2,995 · see citing works

A survey of best practices for RNA-seq data analysis

Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794 · see citing works

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., Guimaraes, C., Panning, B., Ploegh, H. L., Bassik, M. C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.029 · Cited by 2,728 · see citing works

Depletion of Carcinoma-Associated Fibroblasts and Fibrosis Induces Immunosuppression and Accelerates Pancreas Cancer with Reduced Survival

Özdemir, B. C., Pentcheva-Hoang, T., Carstens, J. L., Zheng, X., Wu, C.-C., Simpson, T. R., Laklai, H., Sugimoto, H., Kahlert, C., Novitskiy, S. V., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.04.005 · Cited by 2,681 · see citing works

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

Zhang, Y., Sloan, S. A., Clarke, L. E., Caneda, C., Plaza, C. A., Blumenthal, P. D., Vogel, H., Steinberg, G. K., Edwards, M. S. B., Li, G., et al. (2016) · Neuron · doi:10.1016/j.neuron.2015.11.013 · Cited by 2,295 · see citing works

An atlas of active enhancers across human cell types and tissues

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Widespread transcription at neuronal activity-regulated enhancers

Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450 · see citing works

Integrated genomic characterization of pancreatic ductal adenocarcinoma

Raphael, B. J., Hruban, R. H., Aguirre, A. J., Moffitt, R. A., Yeh, J. J., Stewart, C., Robertson, A. G., Cherniack, A. D., Gupta, M., Getz, G., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.07.007 · Cited by 2,019 · see citing works

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.013 · Cited by 2,072 · see citing works

A tissue-specific atlas of mouse protein phosphorylation and expression

Huttlin, E. L., Jedrychowski, M. P., Elias, J. E., Goswami, T., Rad, R., Beausoleil, S. A., Villén, J., Haas, W., Sowa, M. E., & Gygi, S. P. (2010) · Cell · doi:10.1016/j.cell.2010.12.001 · Cited by 1,778 · see citing works

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

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The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J.-P., St-Denis, N. A., Li, T., Miteva, Y. V., Hauri, S., Sardiu, M. E., Low, T. Y., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2557 · Cited by 1,686 · see citing works

YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA

Shi, H., Wang, X., Lu, Z., Zhao, B. S., Ma, H., Hsu, P. J., Liu, C., & He, C. (2017) · Cell Research · doi:10.1038/cr.2017.15 · Cited by 1,815 · see citing works

HIF1α–dependent glycolytic pathway orchestrates a metabolic checkpoint for the differentiation of TH17 and Treg cells

Shi, L. Z., Wang, R., Huang, G., Vogel, P., Neale, G., Green, D. R., & Chi, H. (2011) · Journal of Experimental Medicine · doi:10.1084/jem.20110278 · Cited by 1,803 · see citing works

Translation of CircRNAs

Pamudurti, N. R., Bartok, O., Jens, M., Ashwal-Fluss, R., Stottmeister, C., Ruhe, L., Hanan, M., Wyler, E., Perez-Hernandez, D., Ramberger, E., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.02.021 · Cited by 1,810 · see citing works

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy

Siddiqui, I., Schaeuble, K., Chennupati, V., Fuertes Marraco, S. A., Calderon-Copete, S., Pais Ferreira, D., Carmona, S. J., Scarpellino, L., Gfeller, D., Pradervand, S., et al. (2019) · Immunity · doi:10.1016/j.immuni.2018.12.021 · Cited by 1,679 · see citing works

ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death

Han, J., Back, S. H., Hur, J., Lin, Y.-H., Gildersleeve, R., Shan, J., Yuan, C. L., Krokowski, D., Wang, S., Hatzoglou, M., et al. (2013) · Nature Cell Biology · doi:10.1038/ncb2738 · Cited by 1,691 · see citing works

Identification and characterization of essential genes in the human genome

Wang, T., Birsoy, K., Hughes, N. W., Krupczak, K. M., Post, Y., Wei, J. J., Lander, E. S., & Sabatini, D. M. (2015) · Science · doi:10.1126/science.aac7041 · Cited by 1,617 · see citing works

The microglial sensome revealed by direct RNA sequencing

Hickman, S. E., Kingery, N. D., Ohsumi, T. K., Borowsky, M. L., Wang, L.-C., Means, T. K., & El Khoury, J. (2013) · Nature Neuroscience · doi:10.1038/nn.3554 · Cited by 1,511 · see citing works

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands

Lamas, B., Richard, M. L., Leducq, V., Pham, H.-P., Michel, M.-L., Da Costa, G., Bridonneau, C., Jegou, S., Hoffmann, T. W., Natividad, J. M., et al. (2016) · Nature Medicine · doi:10.1038/nm.4102 · Cited by 1,482 · see citing works

A unifying model for mTORC1-mediated regulation of mRNA translation

Thoreen, C. C., Chantranupong, L., Keys, H. R., Wang, T., Gray, N. S., & Sabatini, D. M. (2012) · Nature · doi:10.1038/nature11083 · Cited by 1,477 · see citing works

Pollutants bioavailability and toxicological risk from microplastics to marine mussels

Avio, C. G., Gorbi, S., Milan, M., Benedetti, M., Fattorini, D., d'Errico, G., Pauletto, M., Bargelloni, L., & Regoli, F. (2015) · Environmental Pollution · doi:10.1016/j.envpol.2014.12.021 · Cited by 1,413 · see citing works

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

Gosselin, D., Link, V. M., Romanoski, C. E., Fonseca, G. J., Eichenfield, D. Z., Spann, N. J., Stender, J. D., Chun, H. B., Garner, H., Geissmann, F., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.023 · Cited by 1,307 · see citing works

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

Bruderer, R., Bernhardt, O. M., Gandhi, T., Miladinović, S. M., Cheng, L.-Y., Messner, S., Ehrenberger, T., Zanotelli, V., Butscheid, Y., Escher, C., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.044305 · Cited by 1,238 · see citing works

Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth

Tang, H., Hammack, C., Ogden, S. C., Wen, Z., Qian, X., Li, Y., Yao, B., Shin, J., Zhang, F., Lee, E. M., et al. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.02.016 · Cited by 1,292 · see citing works

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., Desai, T. J., Krasnow, M. A., & Quake, S. R. (2014) · Nature · doi:10.1038/nature13173 · Cited by 1,342 · see citing works

Quantitative single-cell RNA-seq with unique molecular identifiers

Islam, S., Zeisel, A., Joost, S., La Manno, G., Zajac, P., Kasper, M., Lönnerberg, P., & Linnarsson, S. (2014) · Nature Methods · doi:10.1038/nmeth.2772 · Cited by 1,183 · see citing works

Personal omics profiling reveals dynamic molecular and medical phenotypes

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Transcriptional landscape of the prenatal human brain

Miller, J. A., Ding, S.-L., Sunkin, S. M., Smith, K. A., Ng, L., Szafer, A., Ebbert, A., Riley, Z. L., Royall, J. J., Aiona, K., et al. (2014) · Nature · doi:10.1038/nature13185 · Cited by 1,325 · see citing works

Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism

Sanders, S. J., Ercan-Sencicek, A. G., Hus, V., Luo, R., Murtha, M. T., Moreno-De-Luca, D., Chu, S. H., Moreau, M. P., Gupta, A. R., Thomson, S. A., et al. (2011) · Neuron · doi:10.1016/j.neuron.2011.05.002 · Cited by 1,263 · see citing works

NASH limits anti-tumour surveillance in immunotherapy-treated HCC

Pfister, D., Núñez, N. G., Pinyol, R., Govaere, O., Pinter, M., Szydlowska, M., Gupta, R., Qiu, M., Deczkowska, A., Weiner, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03362-0 · Cited by 1,294 · see citing works

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

Marques, S., Zeisel, A., Codeluppi, S., van Bruggen, D., Mendanha Falcão, A., Xiao, L., Li, H., Häring, M., Hochgerner, H., Romanov, R. A., et al. (2016) · Science · doi:10.1126/science.aaf6463 · Cited by 1,246 · see citing works

Microglial brain region-dependent diversity and selective regional sensitivities to aging

Grabert, K., Michoel, T., Karavolos, M. H., Clohisey, S., Baillie, J. K., Stevens, M. P., Freeman, T. C., Summers, K. M., & McColl, B. W. (2016) · Nature Neuroscience · doi:10.1038/nn.4222 · Cited by 1,151 · see citing works

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

Adamson, B., Norman, T. M., Jost, M., Cho, M. Y., Nuñez, J. K., Chen, Y., Villalta, J. E., Gilbert, L. A., Horlbeck, M. A., Hein, M. Y., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.048 · Cited by 1,215 · see citing works

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

Camp, J. G., Badsha, F., Florio, M., Kanton, S., Gerber, T., Wilsch-Bräuninger, M., Lewitus, E., Sykes, A., Hevers, W., Lancaster, M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1520760112 · Cited by 1,130 · see citing works

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

Ji, A. L., Rubin, A. J., Thrane, K., Jiang, S., Reynolds, D. L., Meyers, R. M., Guo, M. G., George, B. M., Mollbrink, A., Bergenstråhle, J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.039 · Cited by 1,117 · see citing works

Architectural protein subclasses shape 3D organization of genomes during lineage commitment

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Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity

You, X., Vlatkovic, I., Babic, A., Will, T., Epstein, I., Tushev, G., Akbalik, G., Wang, M., Glock, C., Quedenau, C., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.3975 · Cited by 1,149 · see citing works

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Abeshouse, A., Adebamowo, C., Adebamowo, S. N., Akbani, R., Akeredolu, T., Ally, A., Anderson, M. L., Anur, P., Appelbaum, E. L., Armenia, J., et al. (2017) · Cell · doi:10.1016/j.cell.2017.10.014 · Cited by 1,069 · see citing works

Deep learning-based multi-omics integration robustly predicts survival in liver cancer

Chaudhary, K., Poirion, O. B., Lu, L., & Garmire, L. X. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-0853 · Cited by 1,091 · see citing works

Gene co-expression analysis for functional classification and gene–disease predictions

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Highly Multiplexed Subcellular RNA Sequencing in Situ

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TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop

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Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

Xue, Z., Huang, K., Cai, C., Cai, L., Jiang, C.-Y., Feng, Y., Liu, Z., Zeng, Q., Cheng, L., Sun, Y. E., et al. (2013) · Nature · doi:10.1038/nature12364 · Cited by 963 · see citing works

Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1

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Differential Ly-6C expression identifies the recruited macrophage phenotype, which orchestrates the regression of murine liver fibrosis

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