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

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888

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

The control of the false discovery rate in multiple testing under dependency

Benjamini, Y., & Yekutieli, D. (2001) · The Annals of Statistics · doi:10.1214/aos/1013699998 · Cited by 10,490

GO::TermFinder–open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes

Boyle, E. I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J. M., & Sherlock, G. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth456 · Cited by 2,067

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

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw377 · Cited by 10,799

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw937 · Cited by 6,980

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

REVIGO summarizes and visualizes long lists of gene ontology terms

Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021800 · Cited by 6,264

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

Eden, E., Navon, R., Steinfeld, I., Lipson, D., & Yakhini, Z. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-48 · Cited by 3,356

agriGO: a GO analysis toolkit for the agricultural community

Du, Z., Zhou, X., Ling, Y., Zhang, Z., & Su, Z. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq310 · Cited by 2,396

Integration of biological networks and gene expression data using Cytoscape

Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., et al. (2007) · Nature Protocols · doi:10.1038/nprot.2007.324 · Cited by 2,507

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

Merico, D., Isserlin, R., Stueker, O., Emili, A., & Bader, G. D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013984 · Cited by 2,235

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

Reimand, J., Isserlin, R., Voisin, V., Kucera, M., Tannus-Lopes, C., Rostamianfar, A., Wadi, L., Meyer, M., Wong, J., Xu, C., et al. (2019) · Nature Protocols · doi:10.1038/s41596-018-0103-9 · Cited by 1,970

Precision mapping of the human O‐GalNAc glycoproteome through SimpleCell technology

Steentoft, C., Vakhrushev, S. Y., Joshi, H. J., Kong, Y., Vester‐Christensen, M. B., Schjoldager, K. T. G., Lavrsen, K., Dabelsteen, S., Pedersen, N. B., Marcos‐Silva, L., et al. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.79 · Cited by 1,408

Personal omics profiling reveals dynamic molecular and medical phenotypes

Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y. K., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.009 · Cited by 1,291

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

Reimand, J., Arak, T., Adler, P., Kolberg, L., Reisberg, S., Peterson, H., & Vilo, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw199 · Cited by 1,229

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

Van Hove, H., Martens, L., Scheyltjens, I., De Vlaminck, K., Pombo Antunes, A. R., De Prijck, S., Vandamme, N., De Schepper, S., Van Isterdael, G., Scott, C. L., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0393-4 · Cited by 1,074

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

Bojkova, D., Klann, K., Koch, B., Widera, M., Krause, D., Ciesek, S., Cinatl, J., & Münch, C. (2020) · Nature · doi:10.1038/s41586-020-2332-7 · Cited by 1,010

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

Janky, R., Verfaillie, A., Imrichová, H., Van de Sande, B., Standaert, L., Christiaens, V., Hulselmans, G., Herten, K., Naval Sanchez, M., Potier, D., et al. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003731 · Cited by 900

Application of a translational profiling approach for the comparative analysis of CNS cell types

Doyle, J. P., Dougherty, J. D., Heiman, M., Schmidt, E. F., Stevens, T. R., Ma, G., Bupp, S., Shrestha, P., Shah, R. D., Doughty, M. L., et al. (2008) · Cell · doi:10.1016/j.cell.2008.10.029 · Cited by 912

Efficiency of siRNA delivery by lipid nanoparticles is limited by endocytic recycling

Sahay, G., Querbes, W., Alabi, C., Eltoukhy, A., Sarkar, S., Zurenko, C., Karagiannis, E., Love, K., Chen, D., Zoncu, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2614 · Cited by 948

The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging

Cajigas, I. J., Tushev, G., Will, T. J., tom Dieck, S., Fuerst, N., & Schuman, E. M. (2012) · Neuron · doi:10.1016/j.neuron.2012.02.036 · Cited by 709

Microvesicles Derived from Adult Human Bone Marrow and Tissue Specific Mesenchymal Stem Cells Shuttle Selected Pattern of miRNAs

Collino, F., Deregibus, M. C., Bruno, S., Sterpone, L., Aghemo, G., Viltono, L., Tetta, C., & Camussi, G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011803 · Cited by 608

Therapeutic inhibition of inflammatory monocyte recruitment reduces steatohepatitis and liver fibrosis

Krenkel, O., Puengel, T., Govaere, O., Abdallah, A. T., Mossanen, J. C., Kohlhepp, M., Liepelt, A., Lefebvre, E., Luedde, T., Hellerbrand, C., et al. (2018) · Hepatology · doi:10.1002/hep.29544 · Cited by 557

Membrane Cholesterol Efflux Drives Tumor-Associated Macrophage Reprogramming and Tumor Progression

Goossens, P., Rodriguez-Vita, J., Etzerodt, A., Masse, M., Rastoin, O., Gouirand, V., Ulas, T., Papantonopoulou, O., Van Eck, M., Auphan-Anezin, N., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.02.016 · Cited by 502

PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression.

Liu, W., Tanasa, B., Tyurina, O. V., Zhou, T. Y., Gassmann, R., Liu, W. T., Ohgi, K. A., Benner, C., Garcia-Bassets, I., Aggarwal, A. K., et al. (2010) · Nature · doi:10.1038/nature09272 · Cited by 441

Non-coding RNA regulatory networks

Panni, S., Lovering, R. C., Porras, P., & Orchard, S. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.194417 · Cited by 479

A Specificity Map for the PDZ Domain Family

Tonikian, R., Zhang, Y., Sazinsky, S. L., Currell, B., Yeh, J.-H., Reva, B., Held, H. A., Appleton, B. A., Evangelista, M., Wu, Y., et al. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060239 · Cited by 476

Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex

Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., Bartolini, G., Vitali, I., Cadilhac, C., Hippenmeyer, S., et al. (2019) · Science · doi:10.1126/science.aav2522 · Cited by 423

The IBD interactome: an integrated view of aetiology, pathogenesis and therapy

de Souza, H. S. P., Fiocchi, C., & Iliopoulos, D. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.110 · Cited by 447

Chemotherapy-induced antitumor immunity requires formyl peptide receptor 1

Vacchelli, E., Ma, Y., Baracco, E. E., Sistigu, A., Enot, D. P., Pietrocola, F., Yang, H., Adjemian, S., Chaba, K., Semeraro, M., et al. (2015) · Science · doi:10.1126/science.aad0779 · Cited by 452

Pathway and network-based analysis of genome-wide association studies in multiple sclerosis

Baranzini, S. E., Galwey, N. W., Wang, J., Khankhanian, P., Lindberg, R., Pelletier, D., Wu, W., Uitdehaag, B. M. J., Kappos, L., GeneMSA Consortium, et al. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddp120 · Cited by 383

The unfolded protein response governs integrity of the haematopoietic stem-cell pool during stress

van Galen, P., Kreso, A., Mbong, N., Kent, D. G., Fitzmaurice, T., Chambers, J. E., Xie, S., Laurenti, E., Hermans, K., Eppert, K., et al. (2014) · Nature · doi:10.1038/nature13228 · Cited by 363

Global Proteome Analysis of the NCI-60 Cell Line Panel

Gholami, A. M., Hahne, H., Wu, Z., Auer, F. J., Meng, C., Wilhelm, M., & Kuster, B. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.07.018 · Cited by 302

Chemokine (C‐C motif) receptor 2–positive monocytes aggravate the early phase of acetaminophen‐induced acute liver injury

Mossanen, J. C., Krenkel, O., Ergen, C., Govaere, O., Liepelt, A., Puengel, T., Heymann, F., Kalthoff, S., Lefebvre, E., Eulberg, D., et al. (2016) · Hepatology · doi:10.1002/hep.28682 · Cited by 325

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Proteome Quantitation of Mouse Embryonic Stem Cells to a Depth of 5,111 Proteins

Graumann, J., Hubner, N. C., Kim, J. B., Ko, K., Moser, M., Kumar, C., Cox, J., Schöler, H., & Mann, M. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700460-mcp200 · Cited by 275

IFNs Modify the Proteome of Legionella-Containing Vacuoles and Restrict Infection Via IRG1-Derived Itaconic Acid

Naujoks, J., Tabeling, C., Dill, B. D., Hoffmann, C., Brown, A. S., Kunze, M., Kempa, S., Peter, A., Mollenkopf, H.-J., Dorhoi, A., et al. (2016) · PLOS Pathogens · doi:10.1371/journal.ppat.1005408 · Cited by 261

Mechanism of adrenergic CaV1.2 stimulation revealed by proximity proteomics

Liu, G., Papa, A., Katchman, A. N., Zakharov, S. I., Roybal, D., Hennessey, J. A., Kushner, J., Yang, L., Chen, B.-X., Kushnir, A., et al. (2020) · Nature · doi:10.1038/s41586-020-1947-z · Cited by 243

MicroRNA-125b Promotes Neuronal Differentiation in Human Cells by Repressing Multiple Targets

Le, M. T. N., Xie, H., Zhou, B., Chia, P. H., Rizk, P., Um, M., Udolph, G., Yang, H., Lim, B., & Lodish, H. F. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01694-08 · Cited by 253

Huntington’s Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits

Lim, R. G., Quan, C., Reyes-Ortiz, A. M., Lutz, S. E., Kedaigle, A. J., Gipson, T. A., Wu, J., Vatine, G. D., Stocksdale, J., Casale, M. S., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.04.021 · Cited by 253

A Systems Biology Approach for the Investigation of the Heparin/Heparan Sulfate Interactome

Ori, A., Wilkinson, M. C., & Fernig, D. G. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.228114 · Cited by 251

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

Li, X., Gianoulis, T. A., Yip, K. Y., Gerstein, M., & Snyder, M. (2010) · Cell · doi:10.1016/j.cell.2010.09.048 · Cited by 237

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

Kar, G., Gursoy, A., & Keskin, O. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000601 · Cited by 235

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

Imrichová, H., Hulselmans, G., Kalender Atak, Z., Potier, D., & Aerts, S. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv395 · Cited by 202

Integrated Genome-Wide Association Study Findings: Identification of a Neurodevelopmental Network for Attention Deficit Hyperactivity Disorder

Poelmans, G., Pauls, D. L., Buitelaar, J. K., & Franke, B. (2011) · American Journal of Psychiatry · doi:10.1176/appi.ajp.2010.10070948 · Cited by 223

Insecticide resistance mechanisms associated with different environments in the malaria vector Anopheles gambiae: a case study in Tanzania

Nkya, T. E., Akhouayri, I., Poupardin, R., Batengana, B., Mosha, F., Magesa, S., Kisinza, W., & David, J.-P. (2014) · Malaria Journal · doi:10.1186/1475-2875-13-28 · Cited by 195

Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis)

Li, C.-F., Zhu, Y., Yu, Y., Zhao, Q.-Y., Wang, S.-J., Wang, X.-C., Yao, M.-Z., Luo, D., Li, X., Chen, L., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1773-0 · Cited by 180

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

Minty, J. J., Lesnefsky, A. A., Lin, F., Chen, Y., Zaroff, T. A., Veloso, A. B., Xie, B., McConnell, C. A., Ward, R. J., Schwartz, D. R., et al. (2011) · Microbial Cell Factories · doi:10.1186/1475-2859-10-18 · Cited by 185

Data Integration Challenges for Machine Learning in Precision Medicine

Martínez-García, M., & Hernández-Lemus, E. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2021.784455 · Cited by 185

A Physical Interaction Network of Dengue Virus and Human Proteins

Khadka, S., Vangeloff, A. D., Zhang, C., Siddavatam, P., Heaton, N. S., Wang, L., Sengupta, R., Sahasrabudhe, S., Randall, G., Gribskov, M., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.012187 · Cited by 175

Fish and chips: functional genomics of social plasticity in an African cichlid fish

Renn, S. C. P., Aubin-Horth, N., & Hofmann, H. A. (2008) · Journal of Experimental Biology · doi:10.1242/jeb.018242 · Cited by 169

A Regulated Response to Impaired Respiration Slows Behavioral Rates and Increases Lifespan in Caenorhabditis elegans

Cristina, D., Cary, M., Lunceford, A., Clarke, C., & Kenyon, C. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000450 · Cited by 166

PD-1 axis expression in musculoskeletal tumors and antitumor effect of nivolumab in osteosarcoma model of humanized mouse

Zheng, B., Ren, T., Huang, Y., Sun, K., Wang, S., Bao, X., Liu, K., & Guo, W. (2018) · Journal of Hematology & Oncology · doi:10.1186/s13045-018-0560-1 · Cited by 151

Identification of the Arabidopsis dry2/sqe1‐5 mutant reveals a central role for sterols in drought tolerance and regulation of reactive oxygen species

Posé, D., Castanedo, I., Borsani, O., Nieto, B., Rosado, A., Taconnat, L., Ferrer, A., Dolan, L., Valpuesta, V., & Botella, M. A. (2009) · The Plant Journal · doi:10.1111/j.1365-313x.2009.03849.x · Cited by 145

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

Functional Analysis and Transcriptomic Profiling of iPSC-Derived Macrophages and Their Application in Modeling Mendelian Disease

Zhang, H., Xue, C., Shah, R., Bermingham, K., Hinkle, C. C., Li, W., Rodrigues, A., Tabita-Martinez, J., Millar, J. S., Cuchel, M., et al. (2015) · Circulation Research · doi:10.1161/circresaha.117.305860 · Cited by 126

Cap2-HAP complex is a critical transcriptional regulator that has dual but contrasting roles in regulation of iron homeostasis in Candida albicans

Singh, R. P., Prasad, H. K., Sinha, I., Agarwal, N., & Natarajan, K. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.233569 · Cited by 113

Microbial-Host Co-metabolites Are Prodromal Markers Predicting Phenotypic Heterogeneity in Behavior, Obesity, and Impaired Glucose Tolerance

Dumas, M.-E., Rothwell, A. R., Hoyles, L., Aranias, T., Chilloux, J., Calderari, S., Noll, E. M., Péan, N., Boulangé, C. L., Blancher, C., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.039 · Cited by 114

Contrasting cadmium resistance strategies in two metallicolous populations of Arabidopsis halleri

Corso, M., Schvartzman, M. S., Guzzo, F., Souard, F., Malkowski, E., Hanikenne, M., & Verbruggen, N. (2018) · New Phytologist · doi:10.1111/nph.14948 · Cited by 110

Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell

Magtanong, L., Ho, C. H., Barker, S. L., Jiao, W., Baryshnikova, A., Bahr, S., Smith, A. M., Heisler, L. E., Choy, J. S., Kuzmin, E., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1855 · Cited by 108

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Applied to Quantitative Proteomics of Bacillus subtilis

Soufi, B., Kumar, C., Gnad, F., Mann, M., Mijakovic, I., & Macek, B. (2010) · Journal of Proteome Research · doi:10.1021/pr100150w · Cited by 107

Proteomics-Based Methods for Discovery, Quantification, and Validation of Protein–Protein Interactions

Miteva, Y. V., Budayeva, H. G., & Cristea, I. M. (2013) · Analytical Chemistry · doi:10.1021/ac3033257 · Cited by 105

Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles

Mankoo, P. K., Shen, R., Schultz, N., Levine, D. A., & Sander, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024709 · Cited by 104

Integrative multi-omics module network inference with lemon-tree

Bonnet, E., Calzone, L., & Michoel, T. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003983 · Cited by 98

Epigenetic reprogramming of melanoma cells by vitamin C treatment

Gustafson, C. B., Yang, C., Dickson, K. M., Shao, H., Van Booven, D., Harbour, J. W., Liu, Z.-J., & Wang, G. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0087-z · Cited by 90

Delicate metabolic control and coordinated stress response critically determine antifungal tolerance of Candida albicans biofilm persisters

Li, P., Seneviratne, C. J., Alpi, E., Vizcaino, J. A., & Jin, L. (2015) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00543-15 · Cited by 95

BLBP-expression in astrocytes during experimental demyelination and in human multiple sclerosis lesions

Kipp, M., Gingele, S., Pott, F., Clarner, T., van der Valk, P., Denecke, B., Gan, L., Siffrin, V., Zipp, F., Dreher, W., et al. (2011) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2011.05.003 · Cited by 83

Proteomic Plasma Membrane Profiling Reveals an Essential Role for gp96 in the Cell Surface Expression of LDLR Family Members, Including the LDL Receptor and LRP6

Weekes, M. P., Antrobus, R., Talbot, S., Hör, S., Simecek, N., Smith, D. L., Bloor, S., Randow, F., & Lehner, P. J. (2012) · Journal of Proteome Research · doi:10.1021/pr201135e · Cited by 82

Calcineurin Orchestrates Lateral Transfer of Aspergillus fumigatus during Macrophage Cell Death

Shah, A., Kannambath, S., Herbst, S., Rogers, A., Soresi, S., Carby, M., Reed, A., Mostowy, S., Fisher, M. C., Shaunak, S., et al. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201601-0070oc · Cited by 71

Adipose mesenchymal extracellular vesicles as Alpha-1-antitrypsin physiological delivery systems for lung regeneration

Bari, E., Ferrarotti, I., Di Silvestre, D., Grisoli, P., Barzon, V., Balderacchi, A., Torre, M. L., Rossi, R., Mauri, P., Corsico, A. G., et al. (2019) · Cells · doi:10.3390/cells8090965 · Cited by 70

Cilia interactome with predicted protein-protein interactions reveals connections to Alzheimer’s disease, aging and other neuropsychiatric processes

Karunakaran, K. B., Chaparala, S., Lo, C. W., & Ganapathiraju, M. K. (2020) · Scientific Reports · doi:10.1038/s41598-020-72024-4 · Cited by 56

An LaeA- and BrlA-Dependent Cellular Network Governs Tissue-Specific Secondary Metabolism in the Human Pathogen Aspergillus fumigatus

Lind, A. L., Lim, F. Y., Soukup, A. A., Keller, N. P., & Rokas, A. (2018) · mSphere · doi:10.1128/msphere.00050-18 · Cited by 64

Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks

Stevens, A., Hanson, D., Whatmore, A., Destenaves, B., Chatelain, P., & Clayton, P. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-547 · Cited by 65

Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps

Isserlin, R., Merico, D., Alikhani‐Koupaei, R., Gramolini, A., Bader, G. D., & Emili, A. (2010) · PROTEOMICS · doi:10.1002/pmic.200900412 · Cited by 63

A practical data processing workflow for multi-OMICS projects

Kohl, M., Megger, D. A., Trippler, M., Meckel, H., Ahrens, M., Bracht, T., Weber, F., Hoffmann, A.-C., Baba, H. A., Sitek, B., et al. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2013.02.029 · Cited by 60

Protein S -Nitrosylation Controls Glycogen Synthase Kinase 3β Function Independent of Its Phosphorylation State

Wang, S.-B., Venkatraman, V., Crowgey, E. L., Liu, T., Fu, Z., Holewinski, R., Ranek, M., Kass, D. A., O’Rourke, B., & Van Eyk, J. E. (2018) · Circulation Research · doi:10.1161/circresaha.118.312789 · Cited by 54

Functional Genome-wide Screen Identifies Pathways Restricting Central Nervous System Axonal Regeneration

Sekine, Y., Lin-Moore, A., Chenette, D. M., Wang, X., Jiang, Z., Cafferty, W. B., Hammarlund, M., & Strittmatter, S. M. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.058 · Cited by 52

In silico assessment of adverse drug reactions and associated mechanisms

Ivanov, S. M., Lagunin, A. A., & Poroikov, V. V. (2016) · Drug Discovery Today · doi:10.1016/j.drudis.2015.07.018 · Cited by 49

Brain glucose induces tolerance of Cryptococcus neoformans to amphotericin B during meningitis

Chen, L., Tian, X., Zhang, L., Wang, W., Hu, P., Ma, Z., Li, Y., Li, S., Shen, Z., Fan, X., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01561-1 · Cited by 46

Construction of a polycystic ovarian syndrome (PCOS) pathway based on the interactions of PCOS-related proteins retrieved from bibliomic data

Mohamed-Hussein, Z.-A., & Harun, S. (2009) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-6-18 · Cited by 46

Comparative Ploidy Proteomics of Candida albicans Biofilms Unraveled the Role of the AHP1 Gene in the Biofilm Persistence Against Amphotericin B

Truong, T., Zeng, G., Qingsong, L., Kwang, L. T., Tong, C., Chan, F. Y., Wang, Y., & Seneviratne, C. J. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.061523 · Cited by 45

Pogo-like Transposases Have Been Repeatedly Domesticated into CENP-B-Related Proteins

Mateo, L., & González, J. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu153 · Cited by 44

The Osteocyte Transcriptome Is Extensively Dysregulated in Mouse Models of Osteogenesis Imperfecta

Zimmerman, S. M., Dimori, M., Heard‐Lipsmeyer, M. E., & Morello, R. (2019) · JBMR Plus · doi:10.1002/jbm4.10171 · Cited by 41

A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation

Valverde, J. M., Dubra, G., Phillips, M., Haider, A., Elena-Real, C., Fournet, A., Alghoul, E., Chahar, D., Andrés-Sanchez, N., Paloni, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42049-0 · Cited by 33

Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease

Brooks, L. R. K., & Mias, G. I. (2019) · Frontiers in Neuroscience · doi:10.3389/fnins.2019.00392 · Cited by 32

Cardiopoietic stem cell therapy restores infarction-altered cardiac proteome

Arrell, D. K., Rosenow, C. S., Yamada, S., Behfar, A., & Terzic, A. (2020) · npj Regenerative Medicine · doi:10.1038/s41536-020-0091-6 · Cited by 30

Placental proteome abnormalities in women with gestational diabetes and large-for-gestational-age newborns

Assi, E., D'Addio, F., Mandò, C., Maestroni, A., Loretelli, C., Ben Nasr, M., Usuelli, V., Abdelsalam, A., Seelam, A. J., Pastore, I., et al. (2020) · BMJ Open Diabetes Research & Care · doi:10.1136/bmjdrc-2020-001586 · Cited by 30

A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

Sawyer, E. B., Phelan, J. E., Clark, T. G., & Cortes, T. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108695 · Cited by 25

Dysregulation of Neuronal Cholesterol Homeostasis upon Exposure to HIV-1 Tat and Cocaine Revealed by RNA-Sequencing

Mohseni Ahooyi, T., Shekarabi, M., Torkzaban, B., Langford, T. D., Burdo, T. H., Gordon, J., Datta, P. K., Amini, S., & Khalili, K. (2018) · Scientific Reports · doi:10.1038/s41598-018-34539-9 · Cited by 29

Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches

Onisiforou, A., & Spyrou, G. M. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab141 · Cited by 23

RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells

Durand, S., Bruelle, M., Bourdelais, F., Bennychen, B., Blin-Gonthier, J., Isaac, C., Huyghe, A., Martel, S., Seyve, A., Vanbelle, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36037-7 · Cited by 21

Temporal and Fluoride Control of Secondary Metabolism Regulates Cellular Organofluorine Biosynthesis

Walker, M. C., Wen, M., Weeks, A. M., & Chang, M. C. Y. (2012) · ACS Chemical Biology · doi:10.1021/cb3002057 · Cited by 21

ADAMTS12 acts as a tumor microenvironment related cancer promoter in gastric cancer

Hou, Y., Xu, Y., & Wu, D. (2021) · Scientific Reports · doi:10.1038/s41598-021-90330-3 · Cited by 19

Induction of an Alternative mRNA 5′ Leader Enhances Translation of the Ciliopathy Gene Inpp5e and Resistance to Oncolytic Virus Infection

Hoang, H.-D., Graber, T. E., Jia, J.-J., Vaidya, N., Gilchrist, V. H., Xiang, X., Li, W., Cowan, K. N., Gkogkas, C. G., Jaramillo, M., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.072 · Cited by 18

Use of Haploid Model of Candida albicans to Uncover Mechanism of Action of a Novel Antifungal Agent

Truong, T., Suriyanarayanan, T., Zeng, G., Le, T. D., Liu, L., Li, J., Tong, C., Wang, Y., & Seneviratne, C. J. (2018) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2018.00164 · Cited by 16

Chaotic aging: intrinsically disordered proteins in aging-related processes

Manyilov, V. D., Ilyinsky, N. S., Nesterov, S. V., Saqr, B. M. G. A., Dayhoff, G. W., Zinovev, E. V., Matrenok, S. S., Fonin, A. V., Kuznetsova, I. M., Turoverov, K. K., et al. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04897-3 · Cited by 14

Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines

Crowgey, E. L., Matlock, A., Venkatraman, V., Fert-Bober, J., & Van Eyk, J. E. (2017) · Methods in Molecular Biology · doi:10.1007/978-1-4939-6783-4_19 · Cited by 9

A Comparative Cross-Platform Analysis to Identify Potential Biomarker Genes for Evaluation of Teratozoospermia and Azoospermia

Das, S., Guha, P., Nath, M., Das, S., Sen, S., Sahu, J., Kopanska, M., Dutta, S., Jamal, Q. M. S., Kesari, K. K., et al. (2022) · Genes · doi:10.3390/genes13101721 · Cited by 9

Human Adult Astrocyte Extracellular Vesicle Transcriptomics Study Identifies Specific RNAs Which Are Preferentially Secreted as EV Luminal Cargo

Shanthi, K., Fischer, D., Sharma, A., Kiviniemi, A., Kaakinen, M., Vainio, S., & Bart, G. (2023) · Genes · doi:10.3390/genes14040853 · Cited by 5

Network integration and protein structural binding analysis of neurodegeneration-related interactome

Chen, H., Zhou, Y., Liu, Y., Zhang, P., & Chen, M. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad237 · Cited by 5