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

An eight‐long noncoding RNA expression signature for colorectal cancer patients’ prognosis

Zhang, L., Chen, S., Wang, B., Su, Y., Li, S., Liu, G., & Zhang, X. (2018) · Journal of Cellular Biochemistry · doi:10.1002/jcb.27847 · Cited by 39

Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes

Basnet, R. K., Moreno-Pachon, N. M., Lin, K., Bucher, J., Visser, R. G. F., Maliepaard, C. A., & Bonnema, G. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-840 · Cited by 39

Proteasomal Inhibition by Ixazomib Induces CHK1 and MYC-Dependent Cell Death in T-cell and Hodgkin Lymphoma

Ravi, D., Beheshti, A., Abermil, N., Passero, F. C., Sharma, J., Coyle, M., Kritharis, A., Kandela, I. K., Hlatky, L., Sitkovsky, M. V., et al. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-2477 · Cited by 39

A potential prognostic lncRNA signature for predicting survival in patients with bladder urothelial carcinoma

Bao, Z., Zhang, W., & Dong, D. (2017) · Oncotarget · doi:10.18632/oncotarget.14441 · Cited by 39

A Potential Prognostic Long Noncoding RNA Signature to Predict Recurrence among ER-positive Breast Cancer Patients Treated with Tamoxifen

Wang, K., Li, J., Xiong, Y.-F., Zeng, Z., Zhang, X., & Li, H. (2018) · Scientific Reports · doi:10.1038/s41598-018-21581-w · Cited by 39

Transcriptome signatures associated with meningioma progression

Viaene, A. N., Zhang, B., Martinez‐Lage, M., Xiang, C., Tosi, U., Thawani, J. P., Gungor, B., Zhu, Y., Roccograndi, L., Zhang, L., et al. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0690-x · Cited by 39

Transcriptional Signature Derived from Murine Tumor-Associated Macrophages Correlates with Poor Outcome in Breast Cancer Patients

Tuit, S., Salvagno, C., Kapellos, T. S., Hau, C., Seep, L., Oestreich, M., Klee, K., de Visser, K. E., Ulas, T., & Schultze, J. L. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.09.067 · Cited by 40

A 3-D human model of complex cardiac arrhythmias

Williams, K., Liang, T., Massé, S., Khan, S. T., Hatkar, R., Keller, G. M., Nanthakumar, K., & Nunes, S. S. (2021) · Acta Biomaterialia · doi:10.1016/j.actbio.2021.03.004 · Cited by 39

Colonization of distant organs by tumor cells generating circulating homotypic clusters adaptive to fluid shear stress

Maeshiro, M., Shinriki, S., Liu, R., Nakachi, Y., Komohara, Y., Fujiwara, Y., Ohtsubo, K., Yoshida, R., Iwamoto, K., Nakayama, H., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-85743-z · Cited by 39

Tissue-specific transcriptomics reveal functional differences in floral development

Yang, H., Nukunya, K., Ding, Q., & Thompson, B. E. (2021) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiab557 · Cited by 39

ISL1 is necessary for auditory neuron development and contributes toward tonotopic organization

Filová, I., Pysanenko, K., Tavakoli, M., Vochyánová, S., Dvořáková, M., Bohuslavová, R., Smolík, O., Fabriciova, V., Hrabalova, P., Benesova, S., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2207433119 · Cited by 39

Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues

Diamanti, K., Cavalli, M., Pereira, M. J., Pan, G., Castillejo-López, C., Kumar, C., Mundt, F., Komorowski, J., Deshmukh, A. S., Mann, M., et al. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100763 · Cited by 40

UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma

Kostyrko, K., Román, M., Lee, A. G., Simpson, D. R., Dinh, P., Leung, S. G., Marini, K. D., Kelly, M. R., Broyde, J., Califano, A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39591-2 · Cited by 41

Determination of an Angiotensin II-regulated Proteome in Primary Human Kidney Cells by Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC)

Konvalinka, A., Zhou, J., Dimitromanolakis, A., Drabovich, A. P., Fang, F., Gurley, S. B., Coffman, T. M., John, R., Zhang, S., Diamandis, E. P., et al. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.485326 · Cited by 39

Analysis of proteins that rapidly change upon mechanistic/mammalian target of rapamycin complex 1 (mTORC1) repression identifies parkinson protein 7 (PARK7) as a novel protein aberrantly expressed in tuberous sclerosis complex (TSC)

Niere, F., Namjoshi, S., Song, E., Dilly, G. A., Schoenhard, G., Zemelman, B. V., Mechref, Y., & Raab-Graham, K. F. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.055079 · Cited by 38

WWP2 Regulates Renal Fibrosis and the Metabolic Reprogramming of Profibrotic Myofibroblasts

Chen, H., You, R., Guo, J., Zhou, W., Chew, G., Devapragash, N., Loh, J. Z., Gesualdo, L., Li, Y., Jiang, Y., et al. (2024) · Journal of the American Society of Nephrology · doi:10.1681/asn.0000000000000328 · Cited by 41

Dormancy-inducing 3D engineered matrix uncovers mechanosensitive and drug-protective FHL2-p21 signaling axis

Bakhshandeh, S., Heras, U., Taïeb, H. M., Varadarajan, A. R., Lissek, S. M., Hücker, S. M., Lu, X., Garske, D. S., Young, S. A. E., Abaurrea, A., et al. (2024) · Science Advances · doi:10.1126/sciadv.adr3997 · Cited by 40

Detection of Convergent Genome-Wide Signals of Adaptation to Tropical Forests in Humans

Amorim, C. E. G., Daub, J. T., Salzano, F. M., Foll, M., & Excoffier, L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0121557 · Cited by 41

A quantitative proteomic analysis of cellular responses to high glucose media in Chinese hamster ovary cells

Liu, Z., Dai, S., Bones, J., Ray, S., Cha, S., Karger, B. L., Li, J. J., Wilson, L., Hinkle, G., & Rossomando, A. J. (2015) · Biotechnology Progress · doi:10.1002/btpr.2090 · Cited by 39

Host-parasite interaction: changes in human placental gene expression induced by Trypanosoma cruzi

Castillo, C., Carrillo, I., Libisch, G., Juiz, N. A., Schijman, A. G., Robello, C., & Kemmerling, U. (2018) · Parasites & Vectors · doi:10.1186/s13071-018-2988-0 · Cited by 38

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury

Squair, J. W., Tigchelaar, S., Moon, K., Liu, J., Tetzlaff, W., Kwon, B. K., Krassioukov, A. V., West, C. R., Foster, L. J., & Skinnider, M. A. (2018) · eLife · doi:10.7554/elife.39188 · Cited by 38

Systems pharmacology uncover the mechanism of anti-non-small cell lung cancer for Hedyotis diffusa Willd

Su, X., Li, Y., Jiang, M., Zhu, J., Zheng, C., Chen, X., Zhou, J., Li, Y., Xiao, W., & Wang, Y. (2018) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2018.10.162 · Cited by 38

Bioinformatics analysis of vascular RNA-seq data revealed hub genes and pathways in a novel Tibetan minipig atherosclerosis model induced by a high fat/cholesterol diet

Pan, Y., Yu, C., Huang, J., Rong, Y., Chen, J., & Chen, M. (2020) · Lipids in Health and Disease · doi:10.1186/s12944-020-01222-w · Cited by 38

Profiling the Course of Resolving vs. Persistent Inflammation in Human Monocytes: The Role of IL-1 Family Molecules

Italiani, P., Mosca, E., Camera, G. D., Melillo, D., Migliorini, P., Milanesi, L., & Boraschi, D. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.01426 · Cited by 38

CB1-receptor-mediated inhibitory LTD triggers presynaptic remodeling via protein synthesis and ubiquitination

Monday, H. R., Bourdenx, M., Jordan, B. A., & Castillo, P. E. (2020) · eLife · doi:10.7554/elife.54812 · Cited by 39

Proteomic analysis of ubiquitination substrates reveals a CTLH E3 ligase complex‐dependent regulation of glycolysis

Maitland, M. E. R., Kuljanin, M., Wang, X., Lajoie, G., & Schild‐Poulter, C. (2021) · The FASEB Journal · doi:10.1096/fj.202100664r · Cited by 38

Inhibition of Protein Geranylgeranylation Specifically Interferes with CD40-Dependent B Cell Activation, Resulting in a Reduced Capacity To Induce T Cell Immunity

Shimabukuro‐Vornhagen, A., Zoghi, S., Liebig, T. M., Wennhold, K., Chemitz, J., Draube, A., Kochanek, M., Blaschke, F., Pallasch, C. P., Holtick, U., et al. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1203436 · Cited by 38

Annexin 2A sustains glioblastoma cell dissemination and proliferation

Maule, F., Bresolin, S., Rampazzo, E., Boso, D., Puppa, A. D., Esposito, G., Porcù, E., Mitola, S. M. F., Lombardi, G., Accordi, B., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.10565 · Cited by 38

Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules

Bersanelli, M., Mosca, E., Remondini, D., Castellani, G., & Milanesi, L. (2016) · Scientific Reports · doi:10.1038/srep34841 · Cited by 40

Differences between Platelets Derived from Neonatal Cord Blood and Adult Peripheral Blood Assessed by Mass Spectrometry

Stokhuijzen, E., Koornneef, J. M., Nota, B., van den Eshof, B. L., van Alphen, F. P. J., van den Biggelaar, M., van der Zwaan, C., Kuijk, C., Mertens, K., Fijnvandraat, K., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00298 · Cited by 38

Tissue-Specific Transcriptome Analysis Reveals Multiple Responses to Salt Stress in Populus euphratica Seedlings

Yu, L., Ma, J., Niu, Z., Bai, X., Lei, W., Shao, X., Chen, N., Zhou, F., & Wan, D. (2017) · Genes · doi:10.3390/genes8120372 · Cited by 38

Egr1 regulates regenerative senescence and cardiac repair

Zhang, L., Elkahal, J., Wang, T., Rimmer, R., Genzelinakh, A., Bassat, E., Wang, J., Perez, D. E., Kain, D., Lendengolts, D., et al. (2024) · Nature Cardiovascular Research · doi:10.1038/s44161-024-00493-1 · Cited by 37

Early rhombic lip Protogenin+ve stem cells in a human-specific neurovascular niche initiate and maintain group 3 medulloblastoma

Visvanathan, A., Saulnier, O., Chen, C., Haldipur, P., Orisme, W., Delaidelli, A., Shin, S., Millman, J., Bryant, A., Abeysundara, N., et al. (2024) · Cell · doi:10.1016/j.cell.2024.06.011 · Cited by 37

TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity

Chymkowitch, P., Aurélie Nguéa, P., Aanes, H., Robertson, J. M., Klungland, A., & Enserink, J. M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1615093114 · Cited by 37

Expression Profiling in Pinus pinaster in Response to Infection with the Pine Wood Nematode Bursaphelenchus xylophilus

Gaspar, D., Trindade, C. S., Usié, A., Meireles, B., Barbosa, P., Fortes, A. M., Pesquita, C., Costa, R. M. L., & Ramos, A. M. (2017) · Forests · doi:10.3390/f8080279 · Cited by 37

GLI2 Modulated by SUFU and SPOP Induces Intestinal Stem Cell Niche Signals in Development and Tumorigenesis

Coquenlorge, S., Yin, W.-C., Yung, T. M., Pan, J., Zhang, X., Mo, R., Belik, J., Hui, C., & Kim, T.-H. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.05.016 · Cited by 37

Sub-region-Specific Optic Nerve Head Glial Activation in Glaucoma

Oikawa, K., Hoeve, J. N. V., Teixeira, L. B. C., Snyder, K. C., Kiland, J. A., Ellinwood, N. M., & McLellan, G. J. (2020) · Molecular Neurobiology · doi:10.1007/s12035-020-01910-9 · Cited by 38

Modeling germline mutations in pineoblastoma uncovers lysosome disruption-based therapy

Chung, P. E. D., Gendoo, D. M. A., Ghanbari-Azarnier, R., Liu, J. C., Jiang, Z., Tsui, J., Wang, D., Xiao, X., Li, B. K., Dubuc, A. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15585-2 · Cited by 38

Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy

Housley, S. N., Nardelli, P., Carrasco, D. I., Rotterman, T. M., Pfahl, E., Matyunina, L. V., McDonald, J. F., & Cope, T. C. (2020) · Cancer Research · doi:10.1158/0008-5472.can-19-2331 · Cited by 38

Genome-Wide Association Study in Asians Identifies Novel Loci for High Myopia and Highlights a Nervous System Role in Its Pathogenesis

Meguro, A., Yamane, T., Takeuchi, M., Miyake, M., Fan, Q., Zhao, W., Wang, I., Mizuki, Y., Yamada, N., Nomura, N., et al. (2020) · Ophthalmology · doi:10.1016/j.ophtha.2020.05.014 · Cited by 38

Dynamic rewiring of the human interactome by interferon signaling

Kerr, C. H., Skinnider, M. A., Madero, A. M., Andrews, D. D. T., Stacey, R. G., Chan, Q. W. T., Stoynov, N., Jan, E., & Foster, L. J. (2020) · Genome biology · doi:10.1186/s13059-020-02050-y · Cited by 38

Presynaptic dysfunction in CASK-related neurodevelopmental disorders

Becker, M., Mastropasqua, F., Reising, J. P., Maier, S. J., Ho, M., Rabkina, I., Li, D., Neufeld, J., Ballenberger, L., Myers, L., et al. (2020) · Translational Psychiatry · doi:10.1038/s41398-020-00994-0 · Cited by 40

Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis

Xu, R., Guo, Y., Peng, S., Liu, J., Li, P., Jia, W., & Zhao, J. (2021) · Biomolecules · doi:10.3390/biom11050688 · Cited by 37

Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder

Nishioka, M., Kazuno, A., Nakamura, T., Sakai, N., Hayama, T., Fujii, K., Matsuo, K., Komori, A., Ishiwata, M., Watanabe, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23453-w · Cited by 38

Epicardial and endothelial cell activation concurs with extracellular matrix remodeling in atrial fibrillation

van den Berg, N. W. E., Kawasaki, M., Fabrizi, B., Nariswari, F. A., Verduijn, A. C., Neefs, J., Wesselink, R., Al‐Shama, R., van der Wal, A. C., de Boer, O. J., et al. (2021) · Clinical and Translational Medicine · doi:10.1002/ctm2.558 · Cited by 37

Epigenetic regulation of lncRNA connects ubiquitin-proteasome system with infection-inflammation in preterm births and preterm premature rupture of membranes

Luo, X., Pan, J., Wang, L., Wang, P., Zhang, M., Liu, M., Dong, Z., Meng, Q., Tao, X., Zhao, X., et al. (2015) · BMC Pregnancy and Childbirth · doi:10.1186/s12884-015-0460-0 · Cited by 37

Metabolic Adaptation to Chronic Inhibition of Mitochondrial Protein Synthesis in Acute Myeloid Leukemia Cells

Jhas, B., Sriskanthadevan, S., Škrtić, M., Sukhai, M. A., Voisin, V., Jitkova, Y., Gronda, M., Hurren, R., Laister, R. C., Bader, G. D., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058367 · Cited by 39

B cells sustain inflammation and predict response to immune checkpoint blockade in human melanomaPreprint

Griss, J., Bauer, W. M., Wagner, C., Maurer‐Granofszky, M., Simon, M., Chen, M., Steinberger, P., Grabmeier‐Pfistershammer, K., Roka, F., Penz, T., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/478735 · Cited by 37

The transcriptional landscape of glycosylation-related genes in cancer

Rodríguez, E., Lindijer, D., van Vliet, S. J., García-Vallejo, J. J., & van Kooyk, Y. (2024) · iScience · doi:10.1016/j.isci.2024.109037 · Cited by 36

Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes

Robinson, W., Stone, J. K., Schischlik, F., Gasmi, B., Kelly, M. C., Seibert, C., Dadkhah, K., Gertz, E. M., Lee, J. S., Zhu, K., et al. (2024) · Science Advances · doi:10.1126/sciadv.adj7402 · Cited by 37

A Genome-Wide Longitudinal Transcriptome Analysis of the Aging Model Podospora anserine

Philipp, O., Hamann, A., Servos, J., Werner, A., Koch, I., & Osiewacz, H. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083109 · Cited by 36

Network2Canvas: network visualization on a canvas with enrichment analysis

Tan, C. M., Chen, E. Y., Dannenfelser, R., Clark, N. R., & Ma’ayan, A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt319 · Cited by 36

IQGAP1 is a key node within the small GTPase network

Jacquemet, G., & Humphries, M. J. (2013) · Small GTPases · doi:10.4161/sgtp.27451 · Cited by 37

Employing artificial neural networks for constructing metadata-based model to automatically select an appropriate data visualization technique

Tufail, M., & Halim, Z. (2016) · Applied Soft Computing · doi:10.1016/j.asoc.2016.08.039 · Cited by 36

Golgi stress–induced transcriptional changes mediated by MAPK signaling and three ETS transcription factors regulate MCL1 splicing

Baumann, J., Ignashkova, T. I., Chirasani, S. R., Ramírez‐Peinado, S., Alborzinia, H., Gendarme, M., Kuhnigk, K., Kramer, V., Lindemann, R. K., & Reiling, J. H. (2017) · Molecular Biology of the Cell · doi:10.1091/mbc.e17-06-0418 · Cited by 39

Long non-coding RNA GAS5 and ZFAS1 are prognostic markers involved in translation targeted by miR-940 in prostate cancer

Chen, X., Yang, C., Xie, S., & Cheung, E. C. W. (2017) · Oncotarget · doi:10.18632/oncotarget.23254 · Cited by 36

Inflammatory genes are novel prognostic biomarkers for colorectal cancer

Jiang, H., Li, D., Gong, F., Gu, Y., Zhang, H., Fan, D., & Sun, Z. (2018) · International Journal of Molecular Medicine · doi:10.3892/ijmm.2018.3631 · Cited by 36

Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

Winterbottom, E. F., Ban, Y. J., Sun, X., Capobianco, A. J., Marsit, C. J., Chen, X., Wang, L., Karagas, M. R., & Robbins, D. J. (2019) · Environmental Health · doi:10.1186/s12940-019-0535-x · Cited by 36

Human Milk Oligosaccharides Protect against Necrotizing Enterocolitis by Activating Intestinal Cell Differentiation

Li, B., Wu, R., Horne, R. G., Ahmed, A., Lee, D., Robinson, S. C., Zhu, H., Lee, C. M., Cadete, M., Johnson‐Henry, K. C., et al. (2020) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.202000519 · Cited by 36

Epigenetic Lens to Visualize the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Infection in COVID-19 Pandemic

Saksena, N. K., Bonam, S. R., & Saksena, M. M. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.581726 · Cited by 36

Common virulence gene expression in adult first-time infected malaria patients and severe cases

Wichers-Misterek, J. S., Tonkin‐Hill, G. Q., Thye, T., Krumkamp, R., Kreuels, B., Strauss, J., von Thien, H., Scholz, J. A. M., Hansson, H. S., Jensen, R. W., et al. (2021) · eLife · doi:10.7554/elife.69040 · Cited by 38

Systems Biology and Bioinformatics approach to Identify blood based signatures molecules and drug targets of patient with COVID-19

Hasan, M. I., Rahman, M. H., Islam, M. B., Islam, M. Z., Hossain, M. A., & Moni, M. A. (2021) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2021.100840 · Cited by 36

Glioblastoma stem cells reprogram chromatin in vivo to generate selective therapeutic dependencies on DPY30 and phosphodiesterases

Dixit, D., Prager, B. C., Gimple, R. C., Miller, T. E., Wu, Q., Yomtoubian, S., Kidwell, R. L., Lv, D., Zhao, L., Qiu, Z., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abf3917 · Cited by 36

Diverging metabolic effects of 2 energy-restricted diets differing in nutrient quality: a 12-week randomized controlled trial in subjects with abdominal obesity

Schutte, S., Esser, D., Siebelink, E., Michielsen, C. C. J. R., Daanje, M., Matualatupauw, J. C., Boshuizen, H. C., Mensink, M., & Afman, L. A. (2022) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/nqac025 · Cited by 36

Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognitionPreprint

Dumas, G., Malesys, S., & Bourgeron, T. (2021) · Genome Research · doi:10.1101/gr.262113.120 · Cited by 38

Prognostic value of an autophagy-related gene expression signature for endometrial cancer patients

Wang, H., Ma, X., Liu, J., Wan, Y., Jiang, Y., Xia, Y., & Cheng, W. (2020) · Cancer Cell International · doi:10.1186/s12935-020-01413-6 · Cited by 35

Transciptome Analysis of the Gill and Swimbladder of Takifugu rubripes by RNA-Seq

Cui, J., Liu, S., Zhang, B., Wang, H., Sun, H., Song, S., Qiu, X., Liu, Y., Wang, X., Jiang, Z., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085505 · Cited by 35

shRNA Kinome Screen Identifies TBK1 as a Therapeutic Target for HER2+ Breast Cancer

Deng, T., Liu, J. C., Chung, P. E. D., Uehling, D., Aman, A. M., Joseph, B., Ketela, T. W., Jiang, Z., Schachter, N. F., Rottapel, R. K., et al. (2014) · Cancer Research · doi:10.1158/0008-5472.can-13-2138 · Cited by 38

Motility and stem cell properties induced by the epithelial-mesenchymal transition require destabilization of lipid rafts

Tisza, M. J., Zhao, W., Fuentes, J. S. R., Prijic, S., Chen, X., Levental, I., & Chang, J. T. (2016) · Oncotarget · doi:10.18632/oncotarget.9928 · Cited by 35

Gogadget: An R Package for Interpretation and Visualization of GO Enrichment Results

Nota, B. (2016) · Molecular Informatics · doi:10.1002/minf.201600132 · Cited by 35

Regulation of mycobacterial infection by macrophage Gch1 and tetrahydrobiopterin

McNeill, E., Stylianou, E., Crabtree, M. J., Harrington-Kandt, R., Kolb, A.-L., Diotallevi, M., Hale, A., Bettencourt, P. J. G., Tanner, R., O’Shea, M. K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07714-9 · Cited by 35

Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures

Reyes, M., Vickers, D. A. L., Billman, K., Eisenhaure, T., Hoover, P., Browne, E. P., Rao, D. A., Hacohen, N., & Blainey, P. C. (2019) · Science Advances · doi:10.1126/sciadv.aau9223 · Cited by 35

Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock

Castelo-Szekely, V., Matos, M. D., Tusup, M., Pascolo, S., Ule, J., & Gatfield, D. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz261 · Cited by 35

Transcriptomic and functional analyses of 3D placental extravillous trophoblast spheroids

Wong, M. K., Wahed, M., Shawky, S. A., Dvorkin‐Gheva, A., & Raha, S. (2019) · Scientific Reports · doi:10.1038/s41598-019-48816-8 · Cited by 36

5-Hydroxymethylcytosine Profiles in Circulating Cell-Free DNA Associate with Disease Burden in Children with Neuroblastoma

Applebaum, M. A., Barr, E. K., Karpus, J., West-Szymanski, D. C., Oliva, M., Sokol, E., Zhang, S., Zhang, Z., Zhang, W., Chlenski, A., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-2829 · Cited by 35

TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation

Marini, F., Scherzinger, D., & Danckwardt, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa722 · Cited by 35

Mitochondrial Fragmentation Triggers Ineffective Hematopoiesis in Myelodysplastic Syndromes

Aoyagi, Y., Hayashi, Y., Harada, Y., Choi, K., Matsunuma, N., Sadato, D., Maemoto, Y., Ito, A., Yanagi, S., Starczynowski, D. T., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0032 · Cited by 35

Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function

Mayneris‐Perxachs, J., Arnoriaga‐Rodríguez, M., Garre‐Olmo, J., Puig, J., Ramos, R., Trelis, M., Burokas, A., Coll, C., Zapata-Tona, C., Pedraza, S., et al. (2022) · The ISME Journal · doi:10.1038/s41396-022-01262-3 · Cited by 35

Changes in mammary histology and transcriptome profiles by low-dose exposure to environmental phenols at critical windows of development

Gopalakrishnan, K., Teitelbaum, S. L., Lambertini, L., Wetmur, J. G., Manservisi, F., Falcioni, L., Panzacchi, S., Belpoggi, F., & Chen, J. (2016) · Environmental Research · doi:10.1016/j.envres.2016.10.021 · Cited by 35

Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker

Brown, L. A., Williams, J. A., Taylor, L., Thomson, R. J., Nolan, P. M., Foster, F., & Peirson, S. N. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx714 · Cited by 36

Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues

Ferreira, M., Francisco, S., Soares, A. R., Nobre, A., Pinheiro, M. M., Reis, A., Neto, S. C., Rodrigues, A. J., Sousa, N., Moura, G. R., et al. (2021) · Aging · doi:10.18632/aging.203379 · Cited by 34

Carbon ion irradiation of the human prostate cancer cell line PC3: A whole genome microarray study

Suetens, A., Moreels, M., Quintens, R., Chiriotti, S., Tabury, K., Michaux, A., Grégoire, V., & Baatout, S. (2014) · International Journal of Oncology · doi:10.3892/ijo.2014.2287 · Cited by 34

Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1

Driessen, T. M., Lee, J. S., & Lim, J. (2018) · eLife · doi:10.7554/elife.39981 · Cited by 34

Loss of the dystonia geneThap1leads to transcriptional deficits that converge on common pathogenic pathways in dystonic syndromes

Frederick, N. M., Shah, P., Didonna, A., Langley, M. R., Kanthasamy, A. G., & Opal, P. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy433 · Cited by 35

The p38/HOG stress-activated protein kinase network couples growth to division in Candida albicans

Sellam, A., Chaillot, J., Mallick, J., Tebbji, F., Albert, J. R., Cook, M. A., & Tyers, M. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008052 · Cited by 38

Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results

Savage, S. R., Shi, Z., Liao, Y., & Zhang, B. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.001263 · Cited by 34

Network vulnerability‐based and knowledge‐guided identification of microRNA biomarkers indicating platinum resistance in high‐grade serous ovarian cancer

Qi, X., Yu, C., Wang, Y., Lin, Y., & Shen, B. (2019) · Clinical and Translational Medicine · doi:10.1186/s40169-019-0245-6 · Cited by 34

Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1

Martin, K. B., Williams, I. M., Cluzeau, C. V. M., Cougnoux, A., Dale, R., Iben, J., Cawley, N. X., Wassif, C. A., & Porter, F. D. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms21010292 · Cited by 34

The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation

Boyko, A. V., Girich, A. S., Tkacheva, E. S., & Dolmatov, I. Y. (2020) · Scientific Reports · doi:10.1038/s41598-020-58470-0 · Cited by 34

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons

Hahn, A., Bayer, C., Pensold, D., Tittelmeier, J., Marx-Blümel, L., González-Bermúdez, L., Linde, J., Groß, J., Salinas, G., Lingner, T., et al. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00639 · Cited by 36

Topography of transcriptionally active chromatin in glioblastoma

Xu, L., Chen, Y., Huang, Y., Sandanaraj, E., Yu, J. S., Lin, R. Y., Dakle, P., Ke, X., Chong, Y. K., Koh, L., et al. (2021) · Science Advances · doi:10.1126/sciadv.abd4676 · Cited by 35

Quantifying the role of transcript levels in mediating DNA methylation effects on complex traits and diseases

Sadler, M. C., Auwerx, C., Lepik, K., Porcu, E., & Kutalik, Z. (2022) · Nature Communications · doi:10.1038/s41467-022-35196-3 · Cited by 35

Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer

Bedard, M. C., Chihanga, T., Carlile, A., Jackson, R., Brusadelli, M. G., Lee, D., VonHandorf, A., Rochman, M., Dexheimer, P. J., Chalmers, J. J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37377-0 · Cited by 34

Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining

Jessulat, M., Malty, R. H., Nguyen‐Tran, D., Deineko, V., Aoki, H., Vlasblom, J., Omidi, K., Jin, K., Minić, Z., Hooshyar, M., et al. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.00007-15 · Cited by 34

Ets-1 global gene expression profile reveals associations with metabolism and oxidative stress in ovarian and breast cancers

Verschoor, M. L., Verschoor, C. P., & Singh, G. (2013) · Cancer & Metabolism · doi:10.1186/2049-3002-1-17 · Cited by 35

A systematic analysis of human lipocalin family and its expression in esophageal carcinoma

Du, Z., Wu, B., Wu, X., Lin, X., Qiu, X., Zhan, X.-F., Wang, S., Shen, J., Zheng, C.-P., Wu, Z., et al. (2015) · Scientific Reports · doi:10.1038/srep12010 · Cited by 34

MYRF haploinsufficiency causes 46,XY and 46,XX disorders of sex development: bioinformatics consideration

Hamanaka, K., Takata, A., Uchiyama, Y., Miyatake, S., Miyake, N., Mitsuhashi, S., Iwama, K., Fujita, A., Imagawa, E., Alkanaq, A. N., et al. (2019) · Human Molecular Genetics · doi:10.1093/hmg/ddz066 · Cited by 34

Co-methylation analysis in lung tissue identifies pathways for fetal origins of COPD

Kachroo, P., Morrow, J. D., Kho, A. T., Vyhlidal, C. A., Silverman, E. K., Weiss, S. T., Tantisira, K. G., & DeMeo, D. L. (2020) · European Respiratory Journal · doi:10.1183/13993003.02347-2019 · Cited by 38

Aberrant T follicular helper cells generated by TH17 cell plasticity in the gut promote extraintestinal autoimmunity

Fan, T., Tai, C., Sleiman, K. C., Cutcliffe, M. P., Kim, H., Liu, Y., Li, J., Xin, G., Grashel, M., Baert, L., et al. (2025) · Nature Immunology · doi:10.1038/s41590-025-02125-7 · Cited by 33

Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration

Wu, Y., Wu, B. Z., Ellenbogen, Y., Kant, J. A., Yu, P., Li, X., Caloren, L. C., Sotov, V., Tran, C. N., Restrepo, M., et al. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.04.022 · Cited by 35

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