Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

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

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625

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

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

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890

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

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

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108

Bioconductor: open software development for computational biology and bioinformatics

Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,082

DAVID: Database for Annotation, Visualization, and Integrated Discovery

Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W.-H., Pagès, F., Trajanoski, Z., & Galon, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp101 · Cited by 6,280

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Maere, S., Heymans, K., & Kuiper, M. T. R. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti551 · Cited by 4,093

On the Interpretation of χ 2 from Contingency Tables, and the Calculation of P

Fisher, R. A. (1922) · Journal Of The Royal Statistical Society · doi:10.2307/2340521 · Cited by 2,975

Natural Variation in RNA m 6 A Methylation and Its Relationship with Translational Status

Luo, J. L., Wang, Y., Wang, M., Zhang, L., Peng, H., Zhou, Y., Jia, G., & He, Y. (2019) · PLANT PHYSIOLOGY · doi:10.1104/pp.19.00987 · Cited by 129

Microglial PD-1 stimulation by astrocytic PD-L1 suppresses neuroinflammation and Alzheimer’s disease pathology

Kummer, M. P., Ising, C., Kummer, C., Sarlus, H., Griep, A., Vieira‐Saecker, A., Schwartz, S., Halle, A., Brückner, M., Händler, K., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2021108662 · Cited by 127

Rapid 3D Bioprinting of Glioblastoma Model Mimicking Native Biophysical Heterogeneity

Tang, M., Tiwari, S. K., Agrawal, K., Tan, M. L., Dang, J. W., Tam, T., Tian, J., Wan, X., Schimelman, J. B., You, S., et al. (2021) · Small · doi:10.1002/smll.202006050 · Cited by 126

Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns

Barutcu, A. R., Wu, M., Braunschweig, U., Dyakov, B. J. A., Luo, Z. D., Turner, K. M., Durbic, T., Lin, Z., Weatheritt, R. J., Maass, P. G., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2021.12.010 · Cited by 132

Retinal and circulating mi RNA expression patterns in diabetic retinopathy: An in silico and in vivo approach

Platania, C. B. M., Maisto, R., Trotta, M. C., D’Amico, M., Rossi, S., Gesualdo, C., D’Amico, G., Baltă, C., Herman, H., Hermenean, A. O., et al. (2019) · British Journal of Pharmacology · doi:10.1111/bph.14665 · Cited by 125

Comprehensive analysis of lncRNA expression profiles reveals a novel lncRNA signature to discriminate nonequivalent outcomes in patients with ovarian cancer

Zhou, M., Sun, Y., Sun, Y., Xu, W., Zhang, Z., Zhao, H., Zhong, Z., & Sun, J. (2016) · Oncotarget · doi:10.18632/oncotarget.8653 · Cited by 125

Rapid Inflammasome Activation following Mucosal SIV Infection of Rhesus Monkeys

Barouch, D. H., Ghneim, K., Bosche, W. J., Li, Y., Berkemeier, B., Hull, M. J., Bhattacharyya, S., Cameron, M. J., Liu, J., Smith, K. M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.03.021 · Cited by 124

SIRT1 regulates macrophage self‐renewal

Imperatore, F., Maurizio, J., Aguilar, S. V., Busch, C. J., Favret, J., Kowenz‐Leutz, E., Cathou, W., Gentek, R., Perrin, P., Leutz, A., et al. (2017) · The EMBO Journal · doi:10.15252/embj.201695737 · Cited by 127

Lung γδ T Cells Mediate Protective Responses during Neonatal Influenza Infection that Are Associated with Type 2 Immunity

Guo, X.-Z. J., Dash, P., Crawford, J. C., Allen, E. K., Zamora, A. E., Boyd, D. F., Duan, S., Bajracharya, R., Awad, W., Apiwattanakul, N., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.07.011 · Cited by 128

Multiscale Analysis of Extracellular Matrix Remodeling in the Failing Heart

Perestrelo, A. R., Silva, A. C., Cruz, J. O. L., Martino, F. D., Horváth, V., Caluori, G., Polanský, O., Vinarský, V., Azzato, G., de Marco, G., et al. (2020) · Circulation Research · doi:10.1161/circresaha.120.317685 · Cited by 131

Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications

Zhao, W., Luo, J., & Jiao, S. (2014) · Scientific Reports · doi:10.1038/srep06591 · Cited by 123

Inhibition of Cancer Cell Proliferation by PPARγ Is Mediated by a Metabolic Switch that Increases Reactive Oxygen Species Levels

Srivastava, N., Kollipara, R. K., Singh, D. K., Sudderth, J., Hu, Z., Nguyen, H. P., Wang, S., Humphries, C. G., Carstens, R. M., Huffman, K. E., et al. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.08.003 · Cited by 125

PLK1 inhibition exhibits strong anti-tumoral activity in CCND1-driven breast cancer metastases with acquired palbociclib resistance

Montaudon, É., Nikitorowicz-Buniak, J., Sourd, L., Morisset, L., Botty, R. E., Huguet, L., Dahmani, A., Painsec, P., Némati, F., Vacher, S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17697-1 · Cited by 124

Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes

Ehx, G., Larouche, J., Durette, C., Laverdure, J., Hesnard, L., Vincent, K., Hardy, M., Thériault, C., Rulleau, C., Lanoix, J., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.03.001 · Cited by 129

High expression of SMARCA4 or SMARCA2 is frequently associated with an opposite prognosis in cancer

Guerrero-Martinez, J. A., & Reyes, J. C. (2018) · Scientific Reports · doi:10.1038/s41598-018-20217-3 · Cited by 126

Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

Davidsson, P. R., Broberg, M. E., Kariola, T., Sipari, N., Pirhonen, M., & Palva, E. T. (2017) · BMC Plant Biology · doi:10.1186/s12870-016-0959-1 · Cited by 120

Peri-Infarct Upregulation of the Oxytocin Receptor in Vascular Dementia

McKay, E. C., Beck, J. S., Khoo, S. K., Dykema, K. J., Cottingham, S. L., Winn, M. E., Paulson, H. L., Lieberman, A. P., & Counts, S. (2019) · Journal of Neuropathology & Experimental Neurology · doi:10.1093/jnen/nlz023 · Cited by 121

Myc targeted CDK18 promotes ATR and homologous recombination to mediate PARP inhibitor resistance in glioblastoma

Ning, J.-F., Stanciu, M., Humphrey, M. R., Gorham, J., Wakimoto, H., Nishihara, R., Lees, J. A., Zou, L., Martuza, R. L., Wakimoto, H., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10993-5 · Cited by 120

CD8+ T Cell Priming in Established Chronic Viral Infection Preferentially Directs Differentiation of Memory-like Cells for Sustained Immunity

Snell, L. M., MacLeod, B. L., Law, J. C., Osokine, I., Elsaesser, H. J., Hezaveh, K., Dickson, R. J., Gavin, M. A., Guidos, C. J., McGaha, T. L., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.08.002 · Cited by 122

De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders

Qi, H., Yu, L., Zhou, X., Wynn, J., Zhao, H., Guo, Y., Zhu, N., Kitaygorodsky, A., Hernan, R., Aspelund, G., et al. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007822 · Cited by 122

Ontogeny and Vulnerabilities of Drug-Tolerant Persisters in HER2+ Breast Cancer

Chang, C. A., Jen, J., Jiang, S., Sayad, A., Mer, A. S., Brown, K. R., Nixon, A. M. L., Dhabaria, A., Tang, K. H., Venet, D., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-1265 · Cited by 119

Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain

Androvic, P., Kirdajova, D., Tureckova, J., Zucha, D., Rohlova, E., Abaffy, P., Kriska, J., Valny, M., Anderova, M., Kubista, M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107777 · Cited by 118

RCy3: Network biology using Cytoscape from within R

Gustavsen, J., Pai, S., Isserlin, R., Demchak, B., & Pico, A. R. (2019) · F1000Research · doi:10.12688/f1000research.20887.1 · Cited by 118

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

Leavey, K., Bainbridge, S. A., & Cox, B. (2015) · PLoS ONE · doi:10.1371/journal.pone.0116508 · Cited by 122

aPEAR : an R package for autonomous visualization of pathway enrichment networks

Kerševičiūtė, I., & Gordevičius, J. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad672 · Cited by 117

Genomic Profiling of Human Leishmania braziliensis Lesions Identifies Transcriptional Modules Associated with Cutaneous Immunopathology

Novais, F. O., Carvalho, L. P., Passos, S., Roos, D. S., Carvalho, E. M., Scott, P., & Beiting, D. P. (2014) · Journal of Investigative Dermatology · doi:10.1038/jid.2014.305 · Cited by 118

Insights into Diabetic Kidney Disease Using Urinary Proteomics and Bioinformatics

Van, J. A. D., Scholey, J. W., & Konvalinka, A. (2017) · Journal of the American Society of Nephrology · doi:10.1681/asn.2016091018 · Cited by 117

Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

Cohen, A. J., Saiakhova, A., Corradin, O., Luppino, J. M., Lovrenert, K., Bartels, C. F., Morrow, J. J., Mack, S. C., Dhillon, G. K., Beard, L., et al. (2017) · Nature Communications · doi:10.1038/ncomms14400 · Cited by 118

Identification of Therapeutic Targets for Amyotrophic Lateral Sclerosis Using PandaOmics – An AI-Enabled Biological Target Discovery Platform

Pun, F. W., Liu, B. H. M., Long, X., Leung, H. W., Leung, G. H. D., Mewborne, Q. T., Gao, J., Shneyderman, A., Ozerov, I. V., Wang, J., et al. (2022) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.914017 · Cited by 115

Transcriptome Association Identifies Regulators of Wheat Spike Architecture

Wang, Y., Yu, H., Tian, C., Sajjad, M., Gao, C., Tong, Y., Wang, X., & Jiao, Y. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.00694 · Cited by 115

Comprehensive Proteomics Analysis of Stressed Human Islets Identifies GDF15 as a Target for Type 1 Diabetes Intervention

Nakayasu, E. S., Syed, F., Tersey, S. A., Gritsenko, M. A., Mitchell, H. D., Chan, C. Y., Dirice, E., Turatsinze, J., Cui, Y., Kulkarni, R., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2019.12.005 · Cited by 116

Persistent or Transient Human β Cell Dysfunction Induced by Metabolic Stress: Specific Signatures and Shared Gene Expression with Type 2 Diabetes

Marselli, L., Piron, A., Suleiman, M., Colli, M. L., Yi, X., Khamis, A., Carrat, G., Rutter, G. A., Bugliani, M., Giusti, L., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108466 · Cited by 126

Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases

Emmert‐Streib, F., & Glazko, G. V. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002053 · Cited by 114

Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome

Johnson, B. S., Zhao, Y.-T., Fasolino, M., Lamonica, J. M., Kim, Y. J., Georgakilas, G. K., Wood, K. H., Bu, D. D., Cui, Y., Goffin, D., et al. (2017) · Nature Medicine · doi:10.1038/nm.4406 · Cited by 120

Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2

Hekman, R. M., Hume, A. J., Goel, R. K., Abo, K. M., Huang, J., Blum, B. C., Werder, R. B., Suder, E. L., Paul, I., Phanse, S., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.11.028 · Cited by 115

The creatine kinase pathway is a metabolic vulnerability in EVI1-positive acute myeloid leukemia

Fenouille, N., Bassil, C. F., Ben‐Sahra, I., Benajiba, L., Alexe, G., Ramos, A., Pikman, Y., Conway, A. S., Burgess, M. R., Li, Q., et al. (2017) · Nature Medicine · doi:10.1038/nm.4283 · Cited by 112

Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing

Grive, K. J., Hu, Y., Shu, E., Grimson, A., Elemento, O., Grenier, J. K., & Cohen, P. E. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1007810 · Cited by 117

Combined deletion of Pten and p53 in mammary epithelium accelerates triple‐negative breast cancer with dependency on eEF2K

Liu, J. C., Voisin, V., Wang, S., Wang, D., Jones, R. A., Datti, A., Uehling, D., Al‐awar, R., Egan, S. E., Bader, G. D., et al. (2014) · EMBO Molecular Medicine · doi:10.15252/emmm.201404402 · Cited by 110

Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

Utsunomiya, Y. T., O’Brien, A. M. P., Sonstegard, T. S., Tassell, C. P. V., do Carmo, A. S., Mészáros, G., Sölkner, J., & Garcia, J. F. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064280 · Cited by 110

Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Balasubramanian, M. N., Panserat, S., Dupont‐Nivet, M., Quillet, E., Montfort, J., Cam, A. L., Médale, F., Kaushik, S., & Geurden, I. (2016) · BMC Genomics · doi:10.1186/s12864-016-2804-1 · Cited by 108

Molecular-Subtype-Specific Biomarkers Improve Prediction of Prognosis in Colorectal Cancer

Bramsen, J. B., Rasmussen, M. H., Ongen, H., Mattesen, T. B., Ørntoft, M. W., Árnadóttir, S. S., Sandoval, J., Laguna, T., Vang, S., Øster, B., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.04.045 · Cited by 110

Conserved gene regulation during acute inflammation between zebrafish and mammals

Forn‐Cuní, G., Varela, M., Pereiro, P., Novoa, B., & Figueras, A. J. (2017) · Scientific Reports · doi:10.1038/srep41905 · Cited by 107

Crosstalk with lung epithelial cells regulates Sfrp2-mediated latency in breast cancer dissemination

Montagner, M., Bhome, R., Hooper, S., Chakravarty, P., Qin, X., Sufi, J., Bhargava, A., Ratcliffe, C. D. H., Naito, Y., Pocaterra, A., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0474-3 · Cited by 113

Identification of a gut microbiota member that ameliorates DSS-induced colitis in intestinal barrier enhanced Dusp6-deficient mice

Chang, C., Liao, Y.-C., Huang, C., Lin, C.-M., Cheung, C. H. Y., Ruan, J., Yu, W.-H., Tsai, Y.-T., Lin, I.-J., Huang, C., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110016 · Cited by 108

Essential and non-overlapping IL-2Rα-dependent processes for thymic development and peripheral homeostasis of regulatory T cells

Toomer, K. H., Lui, J. B., Altman, N. H., Ban, Y. J., Chen, X. X., & Malek, T. R. (2019) · Nature Communications · doi:10.1038/s41467-019-08960-1 · Cited by 111

Tomato MYB21 Acts in Ovules to Mediate Jasmonate-Regulated Fertility

Schubert, R., Dobritzsch, S., Gruber, C., Hause, G., Athmer, B., Schreiber, T., Marillonnet, S., Okabe, Y., Ezura, H., Acosta, I. F., et al. (2019) · The Plant Cell · doi:10.1105/tpc.18.00978 · Cited by 105

IL-2/CD25: A Long-Acting Fusion Protein That Promotes Immune Tolerance by Selectively Targeting the IL-2 Receptor on Regulatory T Cells

Ward, N. C., Yu, A., Moro, A., Ban, Y. J., Chen, X., Hsiung, S., Keegan, J., Arbanas, J. M., Loubeau, M., Thankappan, A., et al. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1800907 · Cited by 106

Gain-of-function mutation of microRNA-140 in human skeletal dysplasia

Grigelioniene, G., Suzuki, H. I., Taylan, F., Mirzamohammadi, F., Borochowitz, Z. U., Ayturk, U. M., Tzur, S., Horemuzova, E., Lindstrand, A., Weis, M. A., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0353-2 · Cited by 103

The Psychiatric Risk Gene Transcription Factor 4 (TCF4) Regulates Neurodevelopmental Pathways Associated With Schizophrenia, Autism, and Intellectual Disability

Forrest, M. P., Hill, M., Kavanagh, D. H., Tansey, K. E., Waite, A. J., & Blake, D. J. (2017) · Schizophrenia Bulletin · doi:10.1093/schbul/sbx164 · Cited by 107

Single cell and genetic analyses reveal conserved populations and signaling mechanisms of gastrointestinal stromal niches

Kim, J., Fei, L., Yin, W.-C., Coquenlorge, S., Rao‐Bhatia, A., Zhang, X., Shi, S. S. W., Lee, J. H., Hahn, N. A., Rizvi, W., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14058-5 · Cited by 111

A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression

Liu, J., Ottaviani, D., Sefta, M., Desbrousses, C., Chapeaublanc, E., Aschero, R., Sirab, N., Lubieniecki, F. J., Lamas, G., Tonon, L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25792-0 · Cited by 103

A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC

Darragh, L. B., Knitz, M. W., Hu, J., Clambey, E. T., Backus, J., Dumit, A., Samedi, V., Bubak, A. N., Greene, C. S., Waxweiler, T. V., et al. (2022) · Nature Cancer · doi:10.1038/s43018-022-00450-6 · Cited by 106

A potential prognostic long non-coding RNA signature to predict metastasis-free survival of breast cancer patients

Sun, J., Chen, X., Wang, Z., Guo, M., Shi, H., Wang, X., Cheng, L., & Zhou, M. (2015) · Scientific Reports · doi:10.1038/srep16553 · Cited by 104

Transcriptome Sequencing Revealed Significant Alteration of Cortical Promoter Usage and Splicing in Schizophrenia

Wu, J. Q., Wang, X., Beveridge, N. J., Tooney, P. A., Scott, R. J., Carr, V. J., & Cairns, M. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036351 · Cited by 103

Toll-like receptor 4 senses oxidative stress mediated by the oxidation of phospholipids in extracellular vesicles

Manček‐Keber, M., Frank‐Bertoncelj, M., Hafner‐Bratkovič, I., Smole, A., Zorko, M. S., Pirher, N., Hayer, S., Kralj‐Iglič, V., Rozman, B., Ilc, N., et al. (2015) · Science Signaling · doi:10.1126/scisignal.2005860 · Cited by 104

Biomechanical forces promote blood development through prostaglandin E2 and the cAMP–PKA signaling axis

Diaz, M. F., Li, N., Lee, H. J., Adamo, L., Evans, S. M., Willey, H. E., Arora, N., Torisawa, Y., Vickers, D. A. L., Morris, S. A., et al. (2015) · The Journal of Experimental Medicine · doi:10.1084/jem.20142235 · Cited by 101

Identification of a five-long non-coding RNA signature to improve the prognosis prediction for patients with hepatocellular carcinoma

Zhao, Q.-J., Zhang, J., Xu, L., & Liu, F. (2018) · World Journal of Gastroenterology · doi:10.3748/wjg.v24.i30.3426 · Cited by 100

Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities

Oh, S., Yeom, J., Cho, H. J., Kim, J.-H., Yoon, S., Kim, H.-D., Sa, J. K., Ju, S., Lee, H., Oh, M. J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17139-y · Cited by 100

Genome‐wide analysis of DNA methylation in relation to socioeconomic status during development and early adulthood

McDade, T. W., Ryan, C. P., Jones, M. J., Hoke, M. K., Borja, J. B., Miller, G. E., Kuzawa, C. W., & Kobor, M. S. (2019) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23800 · Cited by 106

Patient-specific data fusion defines prognostic cancer subtypes

Yuan, Y., Savage, R. S., & Markowetz, F. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002227 · Cited by 97

Magnesium transporter 1 (MAGT1) deficiency causes selective defects in N-linked glycosylation and expression of immune-response genes

Matsuda‐Lennikov, M., Biancalana, M., Zou, J., Ravell, J. C., Zheng, L., Kanellopoulou, C., Jiang, P. D., Notarangelo, G., Jing, H., Masutani, E., et al. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.008903 · Cited by 99

ARG1-expressing microglia show a distinct molecular signature and modulate postnatal development and function of the mouse brain

Stratoulias, V., Ruiz, R., Kanatani, S., Osman, A. M., Keane, L., Armengol, J. A., Rodríguez-Moreno, A., Murgoci, A.-N., García-Domínguez, I., Alonso-Bellido, I., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01326-3 · Cited by 96

Cycling CD4+ T cells in HIV-infected immune nonresponders have mitochondrial dysfunction

Younes, S., Talla, A., Ribeiro, S. P., Сайдакова, Е. В., Korolevskaya, L. B., Владимирович, Ш. К., Shive, C. L., Freeman, M. L., Panigrahi, S., Zweig, S. A., et al. (2018) · Journal of Clinical Investigation · doi:10.1172/jci120245 · Cited by 99

Shared Molecular Genetic Mechanisms Underlie Endometriosis and Migraine Comorbidity

Adewuyi, E. O., Sapkota, Y., Auta, A., Yoshihara, K., Nyegaard, M., Griffiths, L. R., Montgomery, G. W., Chasman, D. I., & Nyholt, D. R. (2020) · Genes · doi:10.3390/genes11030268 · Cited by 99

The estrous cycle surpasses sex differences in regulating the transcriptome in the rat medial prefrontal cortex and reveals an underlying role of early growth response 1

Duclot, F., & Kabbaj, M. (2015) · Genome biology · doi:10.1186/s13059-015-0815-x · Cited by 98

Highly proliferative primitive fetal liver hematopoietic stem cells are fueled by oxidative metabolic pathways

Manesia, J. K., Xu, Z., Broekaert, D., Boon, R., van Vliet, A. R., Eelen, G., Vanwelden, T., Stegen, S., van Gastel, N., Pascual-Montano, A., et al. (2015) · Stem Cell Research · doi:10.1016/j.scr.2015.11.001 · Cited by 99

Functional Translatome Proteomics Reveal Converging and Dose-Dependent Regulation by mTORC1 and eIF2α

Klann, K., Tascher, G., & Münch, C. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.11.010 · Cited by 98

Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma

Gwynne, W. D., Suk, Y., Custers, S., Mikolajewicz, N., Chan, J. K., Zador, Z. E., Chafe, S. C., Zhai, K., Escudero, L., Zhang, C., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.10.009 · Cited by 95

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

Singh, K., Chen, Y., Hassanzadeh, S., Han, K., Judy, J., Seifuddin, F., Tunc, I., Sack, M. N., & Pirooznia, M. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.599261 · Cited by 99

Concerted Perturbation Observed in a Hub Network in Alzheimer’s Disease

Liang, D., Han, G., Feng, X., Sun, J., Duan, Y., & Lei, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040498 · Cited by 93

Expansion of Human Mesenchymal Stromal Cells from Fresh Bone Marrow in a 3D Scaffold-Based System under Direct Perfusion

Papadimitropoulos, A., Piccinini, E., Brachat, S., Braccini, A., Wendt, D. J., Barbero, A., Jacobi, C., & Martín, I. (2014) · PLoS ONE · doi:10.1371/journal.pone.0102359 · Cited by 93

Endothelial deletion of Ino80 disrupts coronary angiogenesis and causes congenital heart disease

Rhee, S., Chung, J. I., King, D. A., D’Amato, G., Paik, D. T., Duan, A., Chang, A. H., Nagelberg, D., Sharma, B., Jeong, Y., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02796-3 · Cited by 98

EAG2 potassium channel with evolutionarily conserved function as a brain tumor target

Huang, X., He, Y., Dubuc, A. M., Hashizume, R., Zhang, W., Reimand, J., Yang, H., Wang, T. A., Stehbens, S. J., Younger, S. H., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4088 · Cited by 93

Changes in the Excitability of Neocortical Neurons in a Mouse Model of Amyotrophic Lateral Sclerosis Are Not Specific to Corticospinal Neurons and Are Modulated by Advancing Disease

Kim, J., Hughes, E. G., Shetty, A. S., Arlotta, P., Goff, L. A., Bergles, D. E., & Brown, S. P. (2017) · Journal of Neuroscience · doi:10.1523/jneurosci.0811-17.2017 · Cited by 99

Environmental temperature variation affects brain protein expression and cognitive abilities in adult zebrafish (Danio rerio): A proteomic and behavioural study

Toni, M., Angiulli, E., Miccoli, G., Cioni, C., Alleva, E., Frabetti, F., Pizzetti, F., Scalvini, F. G., Nonnis, S., Negri, A. L., et al. (2019) · Journal of Proteomics · doi:10.1016/j.jprot.2019.103396 · Cited by 95

GOsummaries: an R Package for Visual Functional Annotation of Experimental Data

Kolde, R., & Vilo, J. (2015) · F1000Research · doi:10.12688/f1000research.6925.1 · Cited by 94

Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver

Beheshti, A., Chakravarty, K., Fogle, H., Fazelinia, H., Silveira, W. A. D., Boyko, V., Polo, S.-H. L., Saravia-Butler, A. M., Hardiman, G., Taylor, D., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-55869-2 · 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 transcriptional landscape of Shh medulloblastoma

Skowron, P., Farooq, H., Cavalli, F. M. G., Morrissy, A. S., Ly, M., Hendrikse, L. D., Wang, E. Y., Djambazian, H. H. V., Zhu, H., Mungall, K. L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21883-0 · Cited by 89

Interactions between antibiotics and heavy metals determine their combined toxicity to Synechocystis sp.

You, X., Li, H., Pan, B., You, M., & Sun, W. (2021) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2021.127707 · Cited by 89

Skeletal muscle characteristics are preserved in hTERT/cdk4 human myogenic cell lines

Thorley, M., Duguez, S., Mazza, E. M. C., Valsoni, S., Bigot, A., Mamchaoui, K., Harmon, B. T., Voït, T., Mouly, V., & Duddy, W. J. (2016) · Skeletal Muscle · doi:10.1186/s13395-016-0115-5 · Cited by 88

A Systems Biology Approach Reveals that Tissue Tropism to West Nile Virus Is Regulated by Antiviral Genes and Innate Immune Cellular Processes

Suthar, M. S., Brassil, M. M., Blahnik, G., McMillan, A., Ramos, H. J., Proll, S. C., Belisle, S. E., Katze, M. G., & Gale, M. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003168 · Cited by 87

Nine quick tips for pathway enrichment analysis

Chicco, D., & Agapito, G. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010348 · Cited by 99

Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis

Pai, S., Li, P., Killinger, B. A., Marshall, L. L., Jia, P., Liao, J., Petronis, A., Szabó, P. E., & Labrie, V. (2019) · Nature Communications · doi:10.1038/s41467-019-09786-7 · Cited by 86

Phosphoproteomic Analysis of Neonatal Regenerative Myocardium Revealed Important Roles of Checkpoint Kinase 1 via Activating Mammalian Target of Rapamycin C1/Ribosomal Protein S6 Kinase b-1 Pathway

Fan, Y., Cheng, Y., Li, Y., Chen, B., Wang, Z., Wei, T., Zhang, H., Guo, Y., Wang, Q., Wei, Y., et al. (2020) · Circulation · doi:10.1161/circulationaha.119.040747 · Cited by 86

Direct reprogramming of fibroblasts into neural stem cells by single non-neural progenitor transcription factor Ptf1a

Xiao, D., Liu, X., Zhang, M., Zou, M., Deng, Q., Sun, D., Bian, X., Cai, Y., Guo, Y., Liu, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05209-1 · Cited by 88

Long noncoding RNA expression signature to predict platinum-based chemotherapeutic sensitivity of ovarian cancer patients

Liu, R., Zeng, Y., Zhou, C., Wang, Y., Li, X., Liu, Z., Chen, X., Zhang, W., & Zhou, H. (2017) · Scientific Reports · doi:10.1038/s41598-017-00050-w · Cited by 85

Methylation and transcription patterns are distinct in IDH mutant gliomas compared to other IDH mutant cancers

Unruh, D. J., Zewde, M. G., Buss, A., Drumm, M. R., Tran, A. N., Scholtens, D. M., & Horbinski, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-45346-1 · Cited by 91

Transcriptome analysis of human adipocytes implicates the NOD-like receptor pathway in obesity-induced adipose inflammation

Yin, Z., Deng, T., Peterson, L. E., Yu, R., Lin, J., Hamilton, D. J., Reardon, P. R., Sherman, V., Winnier, G. E., Zhan, M., et al. (2014) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2014.06.018 · Cited by 88

Genomic and Clinical Effects Associated with a Relaxation Response Mind-Body Intervention in Patients with Irritable Bowel Syndrome and Inflammatory Bowel Disease

Kuo, B., Bhasin, M., Jacquart, J., Scult, M. A., Slipp, L. E., Riklin, E. I. K., Lepoutre, V., Comosa, N., Norton, B.-A., Dassatti, A., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0123861 · Cited by 85

A C19MC-LIN28A-MYCN Oncogenic Circuit Driven by Hijacked Super-enhancers Is a Distinct Therapeutic Vulnerability in ETMRs: A Lethal Brain Tumor

Sin‐Chan, P., Mumal, I., Suwal, T., Ho, B., Fan, X., Singh, I., Du, Y., Lu, M., Patel, N., Torchia, J., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.06.002 · Cited by 84

A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals

Lázaro, J., Costanzo, M., Sanaki-Matsumiya, M., Girardot, C., Hayashi, M., Hayashi, K., Diecke, S., Hildebrandt, T. B., Lazzari, G., Wu, J., et al. (2023) · Cell stem cell · doi:10.1016/j.stem.2023.05.014 · Cited by 87

Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity

Udyavar, A. R., Wooten, D. J., Hoeksema, M., Bansal, M., Califano, A., Estrada, L., Schnell, S. D., Irish, J. M., Massion, P. P., & Quaranta, V. (2016) · Cancer Research · doi:10.1158/0008-5472.can-16-1467 · Cited by 83

GKAP Acts as a Genetic Modulator of NMDAR Signaling to Govern Invasive Tumor Growth

Li, L., Zeng, Q., Bhutkar, A. J., Galván, J. A., Karamitopoulou, E., Noordermeer, D., Peng, M.-W., Piersigilli, A., Perren, A. A., Zlobec, I., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.02.011 · Cited by 84

Leukemic stem cell signatures identify novel therapeutics targeting acute myeloid leukemia

Laverdière, I., Boileau, M., Neumann, A. L., Frison, H., Mitchell, A., Ng, S., Wang, J. C. Y., Minden, M. D., & Eppert, K. (2018) · Blood Cancer Journal · doi:10.1038/s41408-018-0087-2 · Cited by 90

Bassoon proteinopathy drives neurodegeneration in multiple sclerosis

Schattling, B., Engler, J. B., Volkmann, C., Rothammer, N., Woo, M. S., Petersen, M., Winkler, I., Kaufmann, M., Rosenkranz, S. C., Fejtova, A., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0385-4 · Cited by 86

Combined Cohesin–RUNX1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes

Ochi, Y., Kon, A., Sakata, T., Nakagawa, M. M., Nakazawa, N., Kakuta, M., Kataoka, K., Koseki, H., Nakayama, M., Morishita, D., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0982 · Cited by 86

Human plasma proteomic profiles indicative of cardiorespiratory fitness

Robbins, J., Peterson, B. D., Schranner, D., Tahir, U. A., Rienmüller, T. M., Deng, S., Keyes, M. J., Katz, D. H., Beltran, P. M. J., Barber, J. L., et al. (2021) · Nature Metabolism · doi:10.1038/s42255-021-00400-z · Cited by 86

De novo copy number variants are associated with congenital diaphragmatic hernia

Yu, L., Wynn, J., Ma, L., Guha, S., Mychaliska, G. B., Crombleholme, T. M., Azarow, K. S., Lim, F. Y., Chung, D. H., Potoka, D. A., et al. (2012) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2012-101135 · Cited by 83

The WASH complex, an endosomal Arp2/3 activator, interacts with the Hermansky–Pudlak syndrome complex BLOC-1 and its cargo phosphatidylinositol-4-kinase type IIα

Ryder, P. V., Vistein, R., Gokhale, A., Seaman, M. N., Puthenveedu, M. A., & Faundez, V. (2013) · Molecular Biology of the Cell · doi:10.1091/mbc.e13-02-0088 · Cited by 87

Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map

Merico, D., Isserlin, R., & Bader, G. D. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-276-2_12 · Cited by 76

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

Geistlinger, L., Csaba, G., & Zimmer, R. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0884-1 · Cited by 93

EnrichNet: network-based gene set enrichment analysis

Glaab, E., Baudot, A., Krasnogor, N., Schneider, R., & Valencia, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts389 · Cited by 311

Constellation Map: Downstream visualization and interpretation of gene set enrichment results

Tan, Y. Q., Wu, F., Tamayo, P., Haining, W. N., & Mesirov, J. P. (2015) · F1000Research · doi:10.12688/f1000research.6644.1 · Cited by 4

GSPlot: Visualizing gene set similarity in enrichment resultsPreprint

Le, T. C., Espinoza, C. G., Courtois, J., & Babur, Ö. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.11.731691