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For: Ryan MC, Stucky M, Wakefield C, Melott JM, Akbani R, Weinstein JN, Broom BM. Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. F1000Res 2019;8:ISCB Comm J-1750. [PMID: 32269754 PMCID: PMC7111501 DOI: 10.12688/f1000research.20590.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/12/2020] [Indexed: 11/15/2023]  Open
Number Cited by Other Article(s)
1
Wang H, Parker D. Improved humanized mouse model of Staphylococcus aureus infection. Mucosal Immunol 2025:S1933-0219(25)00048-0. [PMID: 40354999 DOI: 10.1016/j.mucimm.2025.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2025] [Revised: 05/05/2025] [Accepted: 05/06/2025] [Indexed: 05/14/2025]
2
Shao X, Zhao N, Li Y, Wang H, Xu X, Wang S. Quality Evaluation of Qingwei Huanglian Pills Based on Fingerprint and Quantitative Analysis of Multi-Index Components Combined with Chemical Pattern Recognition Analysis. J Chromatogr Sci 2025;63:bmaf018. [PMID: 40167512 DOI: 10.1093/chromsci/bmaf018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Indexed: 04/02/2025]
3
Pizzini L, Valle F, Osella M, Caselle M. Topic modeling analysis of the Allen Human Brain Atlas. Sci Rep 2025;15:6928. [PMID: 40011617 PMCID: PMC11865453 DOI: 10.1038/s41598-025-91079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Accepted: 02/18/2025] [Indexed: 02/28/2025]  Open
4
Soucy AM, Brune JE, Jayaraman A, Shenoy AT, Korkmaz FT, Etesami NS, Hiller BE, Martin IM, Goltry WN, Ha CT, Crossland NA, Campbell JD, Beach TG, Traber KE, Jones MR, Quinton LJ, Bosmann M, Frevert CW, Mizgerd JP. Transcriptomic responses of lung mesenchymal cells during pneumonia. JCI Insight 2025;10:e177084. [PMID: 39998887 PMCID: PMC11981624 DOI: 10.1172/jci.insight.177084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/18/2025] [Indexed: 02/27/2025]  Open
5
Yang CY, Chang TC, Lee YT, Shih TY, Li CW, Cheng CM. Exploring the Interplay Between Cervicovaginal Microbiome, HPV Infection, and Cervical Intraepithelial Neoplasia in Taiwanese Women. J Med Virol 2025;97:e70190. [PMID: 39868896 DOI: 10.1002/jmv.70190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 01/09/2025] [Accepted: 01/13/2025] [Indexed: 01/28/2025]
6
Sampson J, Ju HM, Zhang N, Yeoh S, Choi J, Bayliss R. Targeting ERBB3 and AKT to overcome adaptive resistance in EML4-ALK-driven non-small cell lung cancer. Cell Death Dis 2024;15:912. [PMID: 39695132 DOI: 10.1038/s41419-024-07272-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 11/22/2024] [Accepted: 11/29/2024] [Indexed: 12/20/2024]
7
Wang X, Wang Y, Bai B, Shaha A, Bao W, He L, Wang T, Kitange GJ, Kang N. PKMζ, a Brain-specific PKCζ Isoform, is Required for Glycolysis and Myofibroblastic Activation of Hepatic Stellate Cells. Cell Mol Gastroenterol Hepatol 2024;19:101429. [PMID: 39542399 PMCID: PMC11750446 DOI: 10.1016/j.jcmgh.2024.101429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 11/05/2024] [Accepted: 11/07/2024] [Indexed: 11/17/2024]
8
Onyango CO, Anyona SB, Hurwitz I, Raballah E, Wasena SA, Osata SW, Seidenberg P, McMahon BH, Lambert CG, Schneider KA, Ouma C, Cheng Q, Perkins DJ. Transcriptomic and Proteomic Insights into Host Immune Responses in Pediatric Severe Malarial Anemia: Dysregulation in HSP60-70-TLR2/4 Signaling and Altered Glutamine Metabolism. Pathogens 2024;13:867. [PMID: 39452740 PMCID: PMC11510049 DOI: 10.3390/pathogens13100867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 10/26/2024]  Open
9
Schultz DF, Davies BA, Payne JA, Martin CP, Minard AY, Childs BG, Zhang C, Jeganathan KB, Sturmlechner I, White TA, de Bruin A, Harkema L, Chen H, Davies MA, Jachim S, LeBrasseur NK, Piper RC, Li H, Baker DJ, van Deursen J, Billadeau DD, Katzmann DJ. Loss of HD-PTP function results in lipodystrophy, defective cellular signaling and altered lipid homeostasis. J Cell Sci 2024;137:jcs262032. [PMID: 39155850 PMCID: PMC11449442 DOI: 10.1242/jcs.262032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024]  Open
10
Dias C, Mo A, Cai C, Sun L, Cabral K, Brownstein CA, Rockowitz S, Walsh CA. Cell-type-specific effects of autism-associated 15q duplication syndrome in the human brain. Am J Hum Genet 2024;111:1544-1558. [PMID: 39079538 PMCID: PMC11339625 DOI: 10.1016/j.ajhg.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 08/11/2024]  Open
11
Lépine M, Robert MC, Sleno L. Discovery and Verification of Sjögren's Syndrome Protein Biomarkers in Tears by Targeted LC-MRM. J Proteome Res 2024;23:2219-2229. [PMID: 38682820 DOI: 10.1021/acs.jproteome.4c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
12
Ke CH, Wu HY, Wang YS, Huang WH, Lin CS. Tumors Established in a Defective Immune Environment Reprogram the Oncogenic Signaling Pathways to Escalate Tumor Antigenicity. Biomedicines 2024;12:846. [PMID: 38672200 PMCID: PMC11047836 DOI: 10.3390/biomedicines12040846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]  Open
13
Bertolo A, Valido E, Stoyanov J. Optimized bacterial community characterization through full-length 16S rRNA gene sequencing utilizing MinION nanopore technology. BMC Microbiol 2024;24:58. [PMID: 38365589 PMCID: PMC10870487 DOI: 10.1186/s12866-024-03208-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/28/2024] [Indexed: 02/18/2024]  Open
14
Feng F, Duan Q, Jiang X, Kao X, Zhang D. DendroX: multi-level multi-cluster selection in dendrograms. BMC Genomics 2024;25:134. [PMID: 38308243 PMCID: PMC10835886 DOI: 10.1186/s12864-024-10048-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 02/04/2024]  Open
15
Ratanasereeprasert N, Hsu LF, Wang SK, Jane Yao CC. Orthodontically induced changes to the genetic profile in periodontal ligament tissue and cytokine release in gingival crevicular fluid - A pilot investigation. J Dent Sci 2024;19:387-396. [PMID: 38303827 PMCID: PMC10829649 DOI: 10.1016/j.jds.2023.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 07/31/2023] [Indexed: 02/03/2024]  Open
16
Jain D, Schmidt W. Protein Phosphorylation Orchestrates Acclimations of Arabidopsis Plants to Environmental pH. Mol Cell Proteomics 2024;23:100685. [PMID: 38000714 PMCID: PMC10837763 DOI: 10.1016/j.mcpro.2023.100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 10/18/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]  Open
17
Cui W, Fiore N, Figueroa F, Rubilar C, Pizarro L, Pinto M, Pérez S, Beltrán MF, Carreras C, Pimentel P, Zamorano A. Transcriptome Analysis of Sweet Cherry (Prunus avium L.) Cultivar 'Lapins' upon Infection of Pseudomonas syringae pv. syringae. PLANTS (BASEL, SWITZERLAND) 2023;12:3718. [PMID: 37960074 PMCID: PMC10647540 DOI: 10.3390/plants12213718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
18
Martins ÁM, Lopes TM, Diniz F, Pires J, Osório H, Pinto F, Freitas D, Reis CA. Differential Protein and Glycan Packaging into Extracellular Vesicles in Response to 3D Gastric Cancer Cellular Organization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023;10:e2300588. [PMID: 37340602 PMCID: PMC10460857 DOI: 10.1002/advs.202300588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/26/2023] [Indexed: 06/22/2023]
19
Pirone A, Ciregia F, Lazzarini G, Miragliotta V, Ronci M, Zuccarini M, Zallocco L, Beghelli D, Mazzoni MR, Lucacchini A, Giusti L. Proteomic Profiling Reveals Specific Molecular Hallmarks of the Pig Claustrum. Mol Neurobiol 2023;60:4336-4358. [PMID: 37095366 PMCID: PMC10293365 DOI: 10.1007/s12035-023-03347-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
20
Alkim C, Farias D, Fredonnet J, Serrano-Bataille H, Herviou P, Picot M, Slama N, Dejean S, Morin N, Enjalbert B, François JM. Toxic effect and inability of L-homoserine to be a nitrogen source for growth of Escherichia coli resolved by a combination of in vivo evolution engineering and omics analyses. Front Microbiol 2022;13:1051425. [PMID: 36583047 PMCID: PMC9792984 DOI: 10.3389/fmicb.2022.1051425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]  Open
21
Diwa RR, Elvira MV, Deocaris CC, Fukuyama M, Belo LP. Transport of toxic metals in the bottom sediments and health risk assessment of Corbicula fluminea (Asiatic clam) collected from Laguna de Bay, Philippines. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022;838:156522. [PMID: 35679944 DOI: 10.1016/j.scitotenv.2022.156522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
22
Ke CH, Wang YS, Chiang HC, Wu HY, Liu WJ, Huang CC, Huang YC, Lin CS. Xenograft cancer vaccines prepared from immunodeficient mice increase tumor antigen diversity and host T cell efficiency against colorectal cancers. Cancer Lett 2022;526:66-75. [PMID: 34808284 DOI: 10.1016/j.canlet.2021.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
23
Martins LJ, Szaniawski MA, Williams ESCP, Coiras M, Hanley TM, Planelles V. HIV-1 Accessory Proteins Impart a Modest Interferon Response and Upregulate Cell Cycle-Related Genes in Macrophages. Pathogens 2022;11:163. [PMID: 35215107 PMCID: PMC8878269 DOI: 10.3390/pathogens11020163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/18/2021] [Accepted: 01/23/2022] [Indexed: 12/10/2022]  Open
24
Roles of Close Homologues SigB and SigD in Heat and High Light Acclimation of the Cyanobacterium Synechocystis sp. PCC 6803. Life (Basel) 2022;12:life12020162. [PMID: 35207450 PMCID: PMC8875361 DOI: 10.3390/life12020162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 11/18/2022]  Open
25
Gu Z, Hübschmann D. Make Interactive Complex Heatmaps in R. Bioinformatics 2021;38:1460-1462. [PMID: 34864868 PMCID: PMC8826183 DOI: 10.1093/bioinformatics/btab806] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/29/2021] [Accepted: 11/27/2021] [Indexed: 01/05/2023]  Open
26
Webb JL, Moe SM, Bolstad AK, McNeill EM. Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive. PLoS One 2021;16:e0255085. [PMID: 34379632 PMCID: PMC8357136 DOI: 10.1371/journal.pone.0255085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 07/09/2021] [Indexed: 11/19/2022]  Open
27
He Y, Zhang R, Quan Z, He B, Xu Y, Chen Z, Ren Y, Liu X. Synthesis, Characterization, and Specific Localization of Mitochondrial-Targeted Antioxidant Peptide SS31 Probe. BIOMED RESEARCH INTERNATIONAL 2021;2021:9915699. [PMID: 34056004 PMCID: PMC8142804 DOI: 10.1155/2021/9915699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/07/2021] [Indexed: 11/23/2022]
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