DAVID: Database for Annotation, Visualization, and Integrated Discovery

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232

Database resources of the National Center for Biotechnology Information: update

Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,695

Identifying biological themes within lists of genes with EASE

Hosack, D. A., Dennis, G., Sherman, B. T., Lane, H. C., & Lempicki, R. A. (2003) · Genome biology · doi:10.1186/gb-2003-4-10-r70 · Cited by 1,961

The Ensembl genome database project

Hubbard, T. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.38 · Cited by 1,610

Computational analysis of microarray data

Quackenbush, J. (2001) · Nature Reviews Genetics · doi:10.1038/35076576 · Cited by 1,481

Database resources of the National Center for Biotechnology Information

Wheeler, D. L. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.10 · Cited by 583

GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

Rebhan, M., Caspi, V. C., Prilusky, J., & Lancet, D. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.8.656 · Cited by 502

NetAffx: Affymetrix probesets and annotations

Liu, G. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg121 · Cited by 487

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

Wen, B., Wu, H., Shinkai, Y., Irizarry, R. A., & Feinberg, A. P. (2009) · Nature Genetics · doi:10.1038/ng.297 · Cited by 634

Pro-Inflammatory CD11c+CD206+ Adipose Tissue Macrophages Are Associated With Insulin Resistance in Human Obesity

Wentworth, J. M., Naselli, G., Brown, W. A., Doyle, L., Phipson, B., Smyth, G. K., Wabitsch, M., O’Brien, P. E., & Harrison, L. C. (2010) · Diabetes · doi:10.2337/db09-0287 · Cited by 636

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues

Krautkramer, K. A., Kreznar, J. H., Romano, K. A., Vivas, E. I., Barrett-Wilt, G. A., Rabaglia, M. E., Keller, M. P., Attie, A. D., Rey, F. E., & Denu, J. M. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.025 · Cited by 607

Regulated Accumulation of Desmosterol Integrates Macrophage Lipid Metabolism and Inflammatory Responses

Spann, N. J., Garmire, L. X., McDonald, J. G., Myers, D. S., Milne, S. B., Shibata, N., Reichart, D. R., Fox, J. N., Shaked, I., Heudobler, D., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.054 · Cited by 630

Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis

Johnson, M. B., Kawasawa, Y. I., Mason, C. E., Krsnik, Ž., Coppola, G., Bogdanović, D., Geschwind, D. H., Mane, S. M., State, M. W., & Šestan, N. (2009) · Neuron · doi:10.1016/j.neuron.2009.03.027 · Cited by 603

Non-CpG methylation of the PGC-1α promoter through DNMT3B controls mitochondrial density.

Barrès, R., Osler, M. E., Yan, J., Rune, A., Fritz, T., Caidahl, K., Krook, A., & Zierath, J. R. (2009) · Cell Metabolism · doi:10.1016/j.cmet.2009.07.011 · Cited by 602

Toxicity Mechanisms in Escherichia coli Vary for Silver Nanoparticles and Differ from Ionic Silver

Ivask, A., Badawy, A. M. E., Kaweeteerawat, C., Boren, D., Fischer, H., Ji, Z., Chang, C. H., Liu, R., Tolaymat, T. M., Telesca, D., et al. (2013) · ACS Nano · doi:10.1021/nn4044047 · Cited by 618

Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery

Towbin, B. D., González-Aguilera, C., Sack, R., Gaidatzis, D., Kalck, V., Meister, P., Askjaer, P., & Gasser, S. M. (2012) · Cell · doi:10.1016/j.cell.2012.06.051 · Cited by 597

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome

Gury-BenAri, M., Thaiss, C. A., Serafini, N., Winter, D. R., Giladi, A., Lara-Astiaso, D., Levy, M., Salame, T. M., Weiner, A., David, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.07.043 · Cited by 587

Next-generation genomics: an integrative approach

Hawkins, R. D., Hon, G. C., & Ren, B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2795 · Cited by 608

GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists

Carmona‐Sáez, P., Chagoyen, M., Tirado, F., Carazo, J. M., & Pascual-Montano, A. (2007) · Genome biology · doi:10.1186/gb-2007-8-1-r3 · Cited by 591

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

Hon, G. C., Hawkins, R. D., Caballero, O. L., Lo, C., Lister, R., Pelizzola, M., Valsesia, A., Ye, Z., Kuan, S., Edsall, L. E., et al. (2012) · Genome Research · doi:10.1101/gr.125872.111 · Cited by 583

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes

Graubert, T. A., Shen, D., Ding, L., Okeyo-Owuor, T., Shirai, C. L., Shao, J., Krysiak, K., Harris, C. C., Koboldt, D. C., Larson, D. E., et al. (2011) · Nature Genetics · doi:10.1038/ng.1031 · Cited by 604

Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome

Liu, G.-H., Barkho, B. Z., Ruiz, S., Diep, D., Qu, J., Yang, S.-L., Panopoulos, A. D., Suzuki, K., Kurian, L., Walsh, C., et al. (2011) · Nature · doi:10.1038/nature09879 · Cited by 575

Molecular Characterization of Basal-Like and Non-Basal-Like Triple-Negative Breast Cancer

Prat, A., Adamo, B., Cheang, M. C. U., Anders, C. K., Carey, L., & Perou, C. M. (2013) · The Oncologist · doi:10.1634/theoncologist.2012-0397 · Cited by 591

Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes

Rowley, J. W., Oler, A. J., Tolley, N. D., Hunter, B. N., Low, E. N., Nix, D. A., Yost, C. C., Zimmerman, G. A., & Weyrich, A. S. (2011) · Blood · doi:10.1182/blood-2011-03-339705 · Cited by 579

Plasma proteomic signature of age in healthy humans

Tanaka, T., Biancotto, A., Moaddel, R., Moore, A. Z., Gonzalez‐Freire, M., Aon, M. A., Candia, J., Zhang, P., Cheung, F., Fantoni, G., et al. (2018) · Aging Cell · doi:10.1111/acel.12799 · Cited by 562

microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder

Perkins, D. O., Jeffries, C. D., Jarskog, L. F., Thomson, J. M., Woods, K., Newman, M. A., Parker, J. S., Jin, J., & Hammond, S. M. (2007) · Genome Biology · doi:10.1186/gb-2007-8-2-r27 · Cited by 574

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

Sherman, B. T., Huang, D. W., Tan, Q., Guo, Y., Bour, S. P., Liu, D., Stephens, R., Baseler, M., Lane, H. C., & Lempicki, R. A. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-426 · Cited by 559

Identification of novel NRF2-regulated genes by ChIP-Seq: influence on retinoid X receptor alpha

Chorley, B. N., Campbell, M. R., Wang, X., Karaca, M., Sambandan, D., Bangura, F., Xue, P., Pi, J., Kleeberger, S. R., & Bell, D. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks409 · Cited by 573

RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3

Tavares, L., Dimitrova, E., Oxley, D., Webster, J. A., Poot, R. A., Demmers, J., Bezstarosti, K., Taylor, S., Ura, H., Koide, H., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.029 · Cited by 583

Traditional Chinese Medicine (TCM) in the treatment of COVID-19 and other viral infections: Efficacies and mechanisms

Huang, K., Zhang, P., Zhang, Z., Youn, J. Y., Wang, C., Zhang, H., & Cai, H. “. (2021) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2021.107843 · Cited by 565

A survey of current trends in computational drug repositioning

Li, J., Zheng, S., Chen, B., Butte, A. J., Swamidass, S. J., & Lu, Z. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv020 · Cited by 569

A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

Paulsen, R. D., Soni, D. V., Wollman, R., Hahn, A. T., Yee, M., Guan, A. S., Hesley, J., Miller, S. C., Cromwell, E. F., Solow-Cordero, D. E., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.06.021 · Cited by 564

Genome-wide Association of Hypoxia-inducible Factor (HIF)-1α and HIF-2α DNA Binding with Expression Profiling of Hypoxia-inducible Transcripts

Mole, D. R., Blancher, C., Copley, R. R., Pollard, P. J., Gleadle, J. M., Ragoussis, J., & Ratcliffe, P. J. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m901790200 · Cited by 552

Detecting shared pathogenesis from the shared genetics of immune-related diseases

Zhernakova, A., van Diemen, C. C., & Wijmenga, C. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2489 · Cited by 551

A map of open chromatin in human pancreatic islets

Gaulton, K. J., Nammo, T., Pasquali, L., Simon, J. M., Giresi, P. G., Fogarty, M. P., Panhuis, T. M., Mieczkowski, P. A., Secchi, A., Bosco, D., et al. (2010) · Nature Genetics · doi:10.1038/ng.530 · Cited by 540

Aberrant Overexpression of Satellite Repeats in Pancreatic and Other Epithelial Cancers

Ting, D. T., Lipson, D., Paul, S., Brannigan, B. W., Akhavanfard, S., Coffman, E. J., Contino, G., Deshpande, V., Iafrate, A. J., Letovsky, S., et al. (2011) · Science · doi:10.1126/science.1200801 · Cited by 540

Interaction of reactive astrocytes with type I collagen induces astrocytic scar formation through the integrin–N-cadherin pathway after spinal cord injury

Hara, M., Kobayakawa, K., Ohkawa, Y., Kumamaru, H., Yokota, K., Saito, T., Kijima, K., Yoshizaki, S., Harimaya, K., Nakashima, Y., et al. (2017) · Nature Medicine · doi:10.1038/nm.4354 · Cited by 555

Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling

Xu, G., Paige, J. S., & Jaffrey, S. R. (2010) · Nature Biotechnology · doi:10.1038/nbt.1654 · Cited by 537

Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling

Robbins, S. H., Walzer, T., Dembélé, D., Thibault-Carpentier, C., Defays, A., Bessou, G., Xu, H., Vivier, É., Sellars, M., Pierre, P., et al. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r17 · Cited by 582

Blastocyst-like structures generated solely from stem cells

Rivron, N. C., Frias-Aldeguer, J., Vrij, E., Boisset, J.-C., Korving, J., Vivié, J., Truckenmüller, R. K., van Oudenaarden, A., van Blitterswijk, C., & Geijsen, N. (2018) · Nature · doi:10.1038/s41586-018-0051-0 · Cited by 539

Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures

Plaisier, S. B., Taschereau, R., Wong, J. A., & Graeber, T. G. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq636 · Cited by 468

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

Mikkelsen, T. S., Zhao, X. D., Zhang, X., Wang, L., Gimble, J. M., Lander, E. S., & Rosen, E. D. (2010) · Cell · doi:10.1016/j.cell.2010.09.006 · Cited by 538

RNA-Seq analysis in MeV

Howe, E., Sinha, R., Schlauch, D., & Quackenbush, J. F. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr490 · Cited by 518

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinomaPreprint

Kan, Z., Zheng, H., Liu, X., Li, S., Barber, T. D., Gong, Z., Gao, H., Hao, K., Willard, M. D., Xu, J., et al. (2013) · Genome Research · doi:10.1101/gr.154492.113 · Cited by 530

Epigenetic and immune function profiles associated with posttraumatic stress disorder

Uddin, M., Aiello, A. E., Wildman, D. E., Koenen, K. C., Pawelec, G., de los Santos, R., Goldmann, E., & Galea, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910794107 · Cited by 518

Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesisPreprint

Nielsen, R., Pedersen, T. Å., Hagenbeek, D., Moulos, P., Siersbæk, R., Megens, E., Denissov, S., Børgesen, M., Françoijs, K., Mandrup, S., et al. (2008) · Genes & Development · doi:10.1101/gad.501108 · Cited by 520

A meta-analysis of nonsense mutations causing human genetic disease

Mort, M. E., Ivanov, D. K., Cooper, D. N., & Chuzhanova, N. A. (2008) · Human Mutation · doi:10.1002/humu.20763 · Cited by 518

Distinctive patterns of microRNA expression in primary muscular disorders

Eisenberg, I., Eran, A., Nishino, I., Moggio, M. G., Lamperti, C., Amato, A. A., Lidov, H. G. W., Kang, P. B., North, K. N., Mitrani‐Rosenbaum, S., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708115104 · Cited by 513

Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight

Ghazalpour, A., Doss, S., Zhang, B., Wang, S., Plaisier, C., Castellanos, R., Brozell, A., Schadt, E. E., Drake, T. A., Lusis, A. J., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020130 · Cited by 462

Pten in stromal fibroblasts suppresses mammary epithelial tumours

Trimboli, A. J., Cantemir-Stone, C. Z., Li, F., Wallace, J. A., Merchant, A. S., Creasap, N., Thompson, J. C., Caserta, E., Wang, H., Chong, J.-L., et al. (2009) · Nature · doi:10.1038/nature08486 · Cited by 507

Genome-wide analysis of a long-term evolution experiment with Drosophila

Burke, M. K., Dunham, J. P., Shahrestani, P., Thornton, K. R., Rose, M. R., & Long, A. D. (2010) · Nature · doi:10.1038/nature09352 · Cited by 448

Systems genetics of complex traits in Drosophila melanogaster

Ayroles, J. F., Carbone, M. A., Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., et al. (2009) · Nature Genetics · doi:10.1038/ng.332 · Cited by 499

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

Deng, J., Shoemaker, R., Xie, B., Gore, A., LeProust, E. M., Antosiewicz‐Bourget, J., Egli, D. M., Maherali, N., Park, I., Yu, J., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1530 · Cited by 502

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

Lokk, K., Modhukur, V., Rajashekar, B., Märtens, K., Mägi, R., Kolde, R., Koltšina, M., Nilsson, T. K., Vilo, J., Salumets, A., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-4-r54 · Cited by 444

LincRNA-p21 Regulates Neointima Formation, Vascular Smooth Muscle Cell Proliferation, Apoptosis, and Atherosclerosis by Enhancing p53 Activity

Wu, G., Cai, J., Han, Y., Chen, J., Huang, Z., Chen, C., Cai, Y., Huang, H., Yang, Y., Liu, Y., et al. (2014) · Circulation · doi:10.1161/circulationaha.114.011675 · Cited by 486

Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq

Karaayvaz, M., Cristea, S., Gillespie, S. M., Patel, A. P., Mylvaganam, R., Luo, C. C., Specht, M. C., Bernstein, B., Michor, F., & Ellisen, L. W. (2018) · Nature Communications · doi:10.1038/s41467-018-06052-0 · Cited by 481

Loss of p53 drives neuron reprogramming in head and neck cancer

Amit, M., Takahashi, H., Dragomir, M. P., Lindemann, A., Gleber-Netto, F. O., Pickering, C. R., Anfossi, S., Osman, A. A., Cai, Y., Wang, R., et al. (2020) · Nature · doi:10.1038/s41586-020-1996-3 · Cited by 483

Wnt5a Potentiates TGF-β Signaling to Promote Colonic Crypt Regeneration After Tissue Injury

Miyoshi, H., Ajima, R., Luo, C. T., Yamaguchi, T. P., & Stappenbeck, T. S. (2012) · Science · doi:10.1126/science.1223821 · Cited by 487

Molecular Dissection of Mesenchymal–Epithelial Interactions in the Hair Follicle

Rendl, M., Lewis, L. E., & Fuchs, E. V. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030331 · Cited by 476

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

Rey, G., Cesbron, F., Rougemont, J., Reinke, H., Brunner, M., & Naef, F. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000595 · Cited by 490

The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines

Eizirik, D. L., Sammeth, M., Bouckenooghe, T., Bottu, G., Sisino, G., Igoillo-Esteve, M., Ortis, F., Santin, I., Colli, M. L., Barthson, J., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002552 · Cited by 465

Mitochondrial and Nuclear Accumulation of the Transcription Factor ATFS-1 Promotes OXPHOS Recovery during the UPRmt

Nargund, A. M., Fiorese, C. J., Pellegrino, M. W., Deng, P., & Haynes, C. M. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.008 · Cited by 464

Cyclin D activates the Rb tumor suppressor by mono-phosphorylation

Narasimha, A. M., Kaulich, M., Shapiro, G. S., Choi, Y. J., Siciński, P., & Dowdy, S. F. (2014) · eLife · doi:10.7554/elife.02872 · Cited by 496

Identification of Molecular Subtypes of Gastric Cancer With Different Responses to PI3-Kinase Inhibitors and 5-Fluorouracil

Lei, Z., Tan, I. B., Das, K., Deng, N., Zouridis, H., Pattison, S. T., Chua, C., Feng, Z., Guan, Y. K., Ooi, C.-H., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.05.010 · Cited by 468

MicroRNA 29b functions in acute myeloid leukemia

Garzon, R., Heaphy, C. E. A., Havelange, V., Fabbri, M., Volinia, S., Tsao, T., Zanesi, N., Kornblau, S. M., Marcucci, G., Calin, G. A., et al. (2009) · Blood · doi:10.1182/blood-2009-03-211938 · Cited by 473

Extracting Biological Meaning from Large Gene Lists with DAVID

Huang, D. W., Sherman, B. T., Zheng, X. M., Yang, J., Imamichi, T., Stephens, R. M., & Lempicki, R. A. (2009) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1311s27 · Cited by 457

Gene Expression Profiles Distinguish Idiopathic Pulmonary Fibrosis from Hypersensitivity Pneumonitis

Selman, M., Pardo, A., Barrera, L., Estrada, A., Watson, S. R., Wilson, K., Aziz, N. A., Kaminski, N., & Zlotnik, A. (2005) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.200504-644oc · Cited by 455

Statistical analysis strategies for association studies involving rare variants

Bansal, V., Libiger, O., Torkamani, A., & Schork, N. J. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2867 · Cited by 455

Understanding network concepts in modules

Dong, J., & Horvath, S. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-24 · Cited by 455

Network visualization and analysis of gene expression data using BioLayout Express3D

Theocharidis, A., van Dongen, S., Enright, A. J., & Freeman, T. C. (2009) · Nature Protocols · doi:10.1038/nprot.2009.177 · Cited by 455

Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells

Yıldırım, Ö., Li, R., Hung, J., Chen, P. B., Dong, X., Ee, L.-S., Weng, Z., Rando, O. J., & Fazzio, T. G. (2011) · Cell · doi:10.1016/j.cell.2011.11.054 · Cited by 463

Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies

Bushman, F. D., Malani, N., Fernandes, J. D., D’Orso, I., Cagney, G., Diamond, T. L., Zhou, H., Hazuda, D. J., Espeseth, A. S., König, R., et al. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000437 · Cited by 464

Cardiac fibrosis in mice with hypertrophic cardiomyopathy is mediated by non-myocyte proliferation and requires Tgf-β

Teekakirikul, P., Eminaga, S., Toka, O., Alcalai, R., Wang, L., Wakimoto, H., Nayor, M. G., Konno, T., Gorham, J., Wolf, C. M., et al. (2010) · Journal of Clinical Investigation · doi:10.1172/jci42028 · Cited by 456

Promoter features related to tissue specificity as measured by Shannon entropy

Schug, J., Winfried-Paul, S., Kappen, C., Salbaum, J. M., Bućan, M., & Stoeckert, C. J. (2005) · Genome biology · doi:10.1186/gb-2005-6-4-r33 · Cited by 455

Nucleoporins Directly Stimulate Expression of Developmental and Cell-Cycle Genes Inside the Nucleoplasm

Kalverda, B., Pickersgill, H., Shloma, V. V., & Fornerod, M. W. J. (2010) · Cell · doi:10.1016/j.cell.2010.01.011 · Cited by 459

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

Nogales‐Cadenas, R., Carmona‐Sáez, P., Vázquez, M., Vicente, C., Yang, X., Tirado, F., Carazo, J. M., & Pascual-Montano, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp416 · Cited by 446

Iron regulates phosphorylation of Smad1/5/8 and gene expression of Bmp6, Smad7, Id1, and Atoh8 in the mouse liver

Kautz, L., Meynard, D., Monnier, A., Darnaud, V., Bouvet, R., Wang, R.-H., Deng, C., Vaulont, S., Mosser, J., Coppin, H., et al. (2008) · Blood · doi:10.1182/blood-2008-03-143354 · Cited by 437

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

Feng, J., Meyer, C. A., Wang, Q., Liu, J. S., Liu, X. S., & Zhang, Y. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts515 · Cited by 433

RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay

Yang, Y., Wang, L., Han, X., Yang, W.-L., Zhang, M., Ma, H., Sun, B., Li, A., Xia, J., Chen, J., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.06.033 · Cited by 437

Schizophrenia is associated with an increase in cortical microRNA biogenesis

Beveridge, N. J., Gardiner, E. J., Carroll, A. P., Tooney, P. A., & Cairns, M. J. (2009) · Molecular Psychiatry · doi:10.1038/mp.2009.84 · Cited by 435

A Genome-wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells

Zhang, E. E., Liu, A. C., Hirota, T., Miraglia, L. J., Welch, G. L., Pongsawakul, P. Y., Liu, X., Atwood, A., Huss, J. W., Janes, J. O., et al. (2009) · Cell · doi:10.1016/j.cell.2009.08.031 · Cited by 437

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data

Karnovsky, A., Weymouth, T. E., Hull, T., Tarcea, V. G., Scardoni, G., Laudanna, C., Sartor, M. A., Stringer, K. A., Jagadish, H. V., Burant, C., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr661 · Cited by 421

A critical developmental switch defines the kinetics of kidney cyst formation after loss of Pkd1

Piontek, K., Menezes, L. F., García-González, M. Á., Huso, D. L., & Germino, G. G. (2007) · Nature Medicine · doi:10.1038/nm1675 · Cited by 433

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Systemic Delivery of Synthetic MicroRNA-16 Inhibits the Growth of Metastatic Prostate Tumors via Downregulation of Multiple Cell-cycle Genes

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Ascorbate Peroxidase 1 Plays a Key Role in the Response of Arabidopsis thaliana to Stress Combination

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N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells

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Therapeutic potential of Bifidobacterium breve strain A1 for preventing cognitive impairment in Alzheimer’s disease

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Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence

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A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

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