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For: Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2010;39:D691-7. [PMID: 21067998 PMCID: PMC3013646 DOI: 10.1093/nar/gkq1018] [Citation(s) in RCA: 1092] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Li W, Ballard J, Zhao Y, Long Q. Knowledge-guided learning methods for integrative analysis of multi-omics data. Comput Struct Biotechnol J 2024;23:1945-1950. [PMID: 38736693 PMCID: PMC11087912 DOI: 10.1016/j.csbj.2024.04.053] [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: 02/15/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024]  Open
2
Picard M, Scott-Boyer MP, Bodein A, Leclercq M, Prunier J, Périn O, Droit A. Target repositioning using multi-layer networks and machine learning: The case of prostate cancer. Comput Struct Biotechnol J 2024;24:464-475. [PMID: 38983753 PMCID: PMC11231507 DOI: 10.1016/j.csbj.2024.06.012] [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: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]  Open
3
Kunes RZ, Walle T, Land M, Nawy T, Pe'er D. Supervised discovery of interpretable gene programs from single-cell data. Nat Biotechnol 2024;42:1084-1095. [PMID: 37735262 PMCID: PMC10958532 DOI: 10.1038/s41587-023-01940-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 08/09/2023] [Indexed: 09/23/2023]
4
Singh A, Verma A, Dutta G, Gowane GR, Ludri A, Alex R. Functional transcriptome analysis revealed major changes in pathways affecting systems biology of Tharparkar cattle under seasonal heat stress. 3 Biotech 2024;14:177. [PMID: 38855148 PMCID: PMC11156831 DOI: 10.1007/s13205-024-04018-2] [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: 12/11/2023] [Accepted: 05/26/2024] [Indexed: 06/11/2024]  Open
5
Al-Odat OS, Nelson E, Budak-Alpdogan T, Jonnalagadda SC, Desai D, Pandey MK. Discovering Potential in Non-Cancer Medications: A Promising Breakthrough for Multiple Myeloma Patients. Cancers (Basel) 2024;16:2381. [PMID: 39001443 PMCID: PMC11240591 DOI: 10.3390/cancers16132381] [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: 05/24/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024]  Open
6
Teppert K, Yonezawa Ogusuku IE, Brandes C, Herbel V, Winter N, Werchau N, Khorkova S, Wöhle C, Jelveh N, Bisdorf K, Engels B, Schaser T, Anders K, Künkele A, Lock D. CAR'TCR-T cells co-expressing CD33-CAR and dNPM1-TCR as superior dual-targeting approach for AML treatment. MOLECULAR THERAPY. ONCOLOGY 2024;32:200797. [PMID: 38601972 PMCID: PMC11004219 DOI: 10.1016/j.omton.2024.200797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024]
7
Robertson H, Kim HJ, Li J, Robertson N, Robertson P, Jimenez-Vera E, Ameen F, Tran A, Trinh K, O'Connell PJ, Yang JYH, Rogers NM, Patrick E. Decoding the hallmarks of allograft dysfunction with a comprehensive pan-organ transcriptomic atlas. Nat Med 2024:10.1038/s41591-024-03030-6. [PMID: 38890530 DOI: 10.1038/s41591-024-03030-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
8
Seth S, Chen R, Liu Y, Fujimoto J, Hong L, Reuben A, Varghese S, Behrens C, McDowell T, Soto LS, Haymaker C, Weissferdt A, Kalhor N, Wu J, Le X, Vokes NI, Cheng C, Heymach JV, Gibbons DL, Futreal PA, Wistuba II, Kadara H, Zhang J, Moran C, Zhang J. Integrative genomic and transcriptomic profiling of pulmonary sarcomatoid carcinoma identifies molecular subtypes associated with distinct immune features and clinical outcomes. CANCER INNOVATION 2024;3:e112. [PMID: 38947760 PMCID: PMC11212327 DOI: 10.1002/cai2.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/25/2023] [Accepted: 01/05/2024] [Indexed: 07/02/2024]
9
Cossarini F, Shang J, Krek A, Al-Taie Z, Hou R, Canales-Herrerias P, Tokuyama M, Tankelevich M, Tillowiz A, Jha D, Livanos AE, Leyre L, Uzzan M, Martinez-Delgado G, Tylor M, Sharma K, Bourgonje AR, Cruz M, Ioannou G, Dawson T, D'Souza D, Kim-Schulze S, Akm A, Aberg JA, Chen BK, Gnjatic S, Polydorides AD, Cerutti A, Argmann C, Vujkovic-Cvijin I, Suarez-Farinas M, Petralia F, Faith JJ, Mehandru S. HIV-1 infection is associated with depletion of germinal center B cells and a decrease in IgA + plasma cells in the GI tract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.590425. [PMID: 38826293 PMCID: PMC11142040 DOI: 10.1101/2024.05.17.590425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
10
Shlapakova PS, Dobrynina LA, Kalashnikova LA, Gubanova MV, Danilova MS, Gnedovskaya EV, Grigorenko AP, Gusev FE, Manakhov AD, Rogaev EI. Peripheral Blood Gene Expression Profiling Reveals Molecular Pathways Associated with Cervical Artery Dissection. Int J Mol Sci 2024;25:5205. [PMID: 38791244 PMCID: PMC11121660 DOI: 10.3390/ijms25105205] [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: 03/26/2024] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024]  Open
11
Liu X, Tao Y, Cai Z, Bao P, Ma H, Li K, Li M, Zhu Y, Lu ZJ. Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data. Bioinformatics 2024;40:btae316. [PMID: 38741230 PMCID: PMC11139513 DOI: 10.1093/bioinformatics/btae316] [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: 12/20/2023] [Revised: 03/29/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]  Open
12
Kumar N, Acharya V. Advances in machine intelligence-driven virtual screening approaches for big-data. Med Res Rev 2024;44:939-974. [PMID: 38129992 DOI: 10.1002/med.21995] [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: 09/12/2022] [Revised: 07/15/2023] [Accepted: 10/29/2023] [Indexed: 12/23/2023]
13
James DW, Quintela M, Lucini L, Alkafri NK, Healey GD, Younas K, Bunkheila A, Margarit L, Francis LW, Gonzalez D, Conlan RS. Homeobox regulator Wilms Tumour 1 is displaced by androgen receptor at cis-regulatory elements in the endometrium of PCOS patients. Front Endocrinol (Lausanne) 2024;15:1368494. [PMID: 38745948 PMCID: PMC11091321 DOI: 10.3389/fendo.2024.1368494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024]  Open
14
Xia Y, Sun M, Huang H, Jin WL. Drug repurposing for cancer therapy. Signal Transduct Target Ther 2024;9:92. [PMID: 38637540 PMCID: PMC11026526 DOI: 10.1038/s41392-024-01808-1] [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: 02/06/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/20/2024]  Open
15
Mukherjee A, Abraham S, Singh A, Balaji S, Mukunthan KS. From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies. Mol Biotechnol 2024:10.1007/s12033-024-01133-6. [PMID: 38565775 DOI: 10.1007/s12033-024-01133-6] [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: 12/27/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
16
Hart M, Kern F, Fecher-Trost C, Krammes L, Aparicio E, Engel A, Hirsch P, Wagner V, Keller V, Schmartz GP, Rheinheimer S, Diener C, Fischer U, Mayer J, Meyer MR, Flockerzi V, Keller A, Meese E. Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease. Exp Mol Med 2024;56:935-945. [PMID: 38556547 PMCID: PMC11059366 DOI: 10.1038/s12276-024-01202-5] [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: 08/21/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 04/02/2024]  Open
17
Xu B, Hwangbo DS, Saurabh S, Rosensweig C, Allada R, Kath WL, Braun R. Temperature-driven coordination of circadian transcriptional regulation. PLoS Comput Biol 2024;20:e1012029. [PMID: 38648221 PMCID: PMC11108206 DOI: 10.1371/journal.pcbi.1012029] [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: 12/01/2023] [Revised: 05/21/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024]  Open
18
Colombo PC, Castagna F, Onat D, Wong KY, Harxhi A, Hayashi Y, Friedman RA, Pinsino A, Ladanyi A, Mebazaa A, Jelic S, Arrigo M, Lejemtel TH, Papapanou P, Sabbah HN, Schmidt AM, Yuzefpolskaya M, Demmer RT. Experimentally Induced Peripheral Venous Congestion Exacerbates Inflammation, Oxidative Stress, and Neurohormonal and Endothelial Cell Activation in Patients With Systolic Heart Failure. J Card Fail 2024;30:580-591. [PMID: 37625581 PMCID: PMC10884348 DOI: 10.1016/j.cardfail.2023.07.016] [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: 05/09/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
19
Leventhal MJ, Zanella CA, Kang B, Peng J, Gritsch D, Liao Z, Bukhari H, Wang T, Pao PC, Danquah S, Benetatos J, Nehme R, Farhi S, Tsai LH, Dong X, Scherzer CR, Feany MB, Fraenkel E. A systems-biology approach connects aging mechanisms with Alzheimer's disease pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585262. [PMID: 38559190 PMCID: PMC10980014 DOI: 10.1101/2024.03.17.585262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
20
Hwang AS, Kechter JA, Li X, Hughes A, Severson KJ, Boudreaux B, Bhullar P, Nassir S, Yousif M, Zhang N, Butterfield RJ, Nelson S, Xing X, Tsoi LC, Zunich S, Sekulic A, Pittelkow M, Gudjonsson JE, Mangold A. Topical Ruxolitinib in the Treatment of Necrobiosis Lipoidica: A Prospective, Open-Label Study. J Invest Dermatol 2024:S0022-202X(24)00159-3. [PMID: 38417541 DOI: 10.1016/j.jid.2023.11.027] [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: 10/10/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 03/01/2024]
21
Gobena S, Admassu B, Kinde MZ, Gessese AT. Proteomics and Its Current Application in Biomedical Area: Concise Review. ScientificWorldJournal 2024;2024:4454744. [PMID: 38404932 PMCID: PMC10894052 DOI: 10.1155/2024/4454744] [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: 12/07/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]  Open
22
Li Z, Liu G, Yang X, Shu M, Jin W, Tong Y, Liu X, Wang Y, Yuan J, Yang Y. An atlas of cell-type-specific interactome networks across 44 human tumor types. Genome Med 2024;16:30. [PMID: 38347596 PMCID: PMC10860273 DOI: 10.1186/s13073-024-01303-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024]  Open
23
Rawal P, Tripathi DM, Hemati H, Kumar J, Tyagi P, Sarin SK, Nain V, Kaur S. Targeted HBx gene editing by CRISPR/Cas9 system effectively reduces epithelial to mesenchymal transition and HBV replication in hepatoma cells. Liver Int 2024;44:614-624. [PMID: 38105495 DOI: 10.1111/liv.15805] [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: 08/03/2022] [Revised: 10/28/2023] [Accepted: 11/12/2023] [Indexed: 12/19/2023]
24
Liu PW, Lin J, Hou R, Cai Z, Gong Y, He PA, Yang J. Single-cell RNA-seq reveals the metabolic status of immune cells response to immunotherapy in triple-negative breast cancer. Comput Biol Med 2024;169:107926. [PMID: 38183706 DOI: 10.1016/j.compbiomed.2024.107926] [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: 10/02/2023] [Revised: 12/09/2023] [Accepted: 01/01/2024] [Indexed: 01/08/2024]
25
Buzzao D, Castresana-Aguirre M, Guala D, Sonnhammer ELL. Benchmarking enrichment analysis methods with the disease pathway network. Brief Bioinform 2024;25:bbae069. [PMID: 38436561 PMCID: PMC10939300 DOI: 10.1093/bib/bbae069] [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: 09/29/2023] [Revised: 01/10/2024] [Accepted: 02/03/2024] [Indexed: 03/05/2024]  Open
26
Iwata K, Ferdousi F, Arai Y, Isoda H. Modulation of mitochondrial activity by sugarcane (Saccharum officinarum L.) top extract and its bioactive polyphenols: a comprehensive transcriptomics analysis in C2C12 myotubes and HepG2 hepatocytes. NATURAL PRODUCTS AND BIOPROSPECTING 2024;14:2. [PMID: 38177614 PMCID: PMC10766937 DOI: 10.1007/s13659-023-00423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024]
27
Li Z, Guo Z, Xiao H, Chen X, Liu W, Zhou H. Simulating neuronal development: exploring potential mechanisms for central nervous system metastasis in acute lymphoblastic leukemia. Front Oncol 2024;13:1331802. [PMID: 38239636 PMCID: PMC10794646 DOI: 10.3389/fonc.2023.1331802] [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: 11/01/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024]  Open
28
Onarman Umu ÖC, Mydland LT, Chen C, de Nanclares MP, Shurson GC, Urriola PE, Sørum H, Øverland M. Integrated multi-omics approach reveals novel associations in the rapeseed diet-microbiota-host axis in pigs. ISME COMMUNICATIONS 2024;4:ycae061. [PMID: 38800131 PMCID: PMC11128262 DOI: 10.1093/ismeco/ycae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024]
29
Rohan P, dos Santos EC, Abdelhay E, Binato R. High Expression of THY1 in Intestinal Gastric Cancer as a Key Factor in Tumor Biology: A Poor Prognosis-Independent Marker Related to the Epithelial-Mesenchymal Transition Profile. Genes (Basel) 2023;15:28. [PMID: 38254918 PMCID: PMC10815053 DOI: 10.3390/genes15010028] [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: 12/03/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]  Open
30
Rade M, Böhlen S, Neuhaus V, Löffler D, Blumert C, Merz M, Köhl U, Dehmel S, Sewald K, Reiche K. A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation. Genome Biol 2023;24:287. [PMID: 38098113 PMCID: PMC10722659 DOI: 10.1186/s13059-023-03120-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/22/2023] [Indexed: 12/17/2023]  Open
31
Soleymani S, Gravel N, Huang LC, Yeung W, Bozorgi E, Bendzunas NG, Kochut KJ, Kannan N. Dark kinase annotation, mining, and visualization using the Protein Kinase Ontology. PeerJ 2023;11:e16087. [PMID: 38077442 PMCID: PMC10704995 DOI: 10.7717/peerj.16087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/22/2023] [Indexed: 12/18/2023]  Open
32
Comertpay B, Gov E. Immune cell-specific and common molecular signatures in rheumatoid arthritis through molecular network approaches. Biosystems 2023;234:105063. [PMID: 37852410 DOI: 10.1016/j.biosystems.2023.105063] [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: 02/19/2023] [Revised: 09/20/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
33
Denis AA, Toledo D, Hakim QA, Quintana AA, Escobar CR, Oluwole SA, Costa A, Garcia EG, Hill AR, Agatemor C. Ligand-Independent Activation of Aryl Hydrocarbon Receptor and Attenuation of Glutamine Levels by Natural Deep Eutectic Solvent. Chembiochem 2023;24:e202300540. [PMID: 37615422 DOI: 10.1002/cbic.202300540] [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: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 08/25/2023]
34
Bowley TY, Merkley SD, Lagutina IV, Ortiz MC, Lee M, Tawfik B, Marchetti D. Targeting Translation and the Cell Cycle Inversely Affects CTC Metabolism but Not Metastasis. Cancers (Basel) 2023;15:5263. [PMID: 37958436 PMCID: PMC10650766 DOI: 10.3390/cancers15215263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]  Open
35
Xu B, Hwangbo DS, Saurabh S, Rosensweig C, Allada R, Kath WL, Braun R. Temperature-driven coordination of circadian transcriptome regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.563979. [PMID: 37961403 PMCID: PMC10634908 DOI: 10.1101/2023.10.27.563979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
36
Fu L, Li M, Lv J, Yang C, Zhang Z, Qin S, Li W, Wang X, Chen L. Deep neural network for discovering metabolism-related biomarkers for lung adenocarcinoma. Front Endocrinol (Lausanne) 2023;14:1270772. [PMID: 37955007 PMCID: PMC10634586 DOI: 10.3389/fendo.2023.1270772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]  Open
37
Gao J, Yi X, Wang Z. The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Comput Struct Biotechnol J 2023;21:4933-4943. [PMID: 37867968 PMCID: PMC10585227 DOI: 10.1016/j.csbj.2023.10.016] [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: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023]  Open
38
Jain SS, McNamara ME, Varghese RS, Ressom HW. Deconvolution of immune cell composition and biological age of hepatocellular carcinoma using DNA methylation. Methods 2023;218:125-132. [PMID: 37574160 PMCID: PMC10529003 DOI: 10.1016/j.ymeth.2023.08.004] [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: 04/21/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]  Open
39
Yoshimura Y, Muto Y, Omachi K, Miner JH, Humphreys BD. Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids. J Am Soc Nephrol 2023;34:1672-1686. [PMID: 37488681 PMCID: PMC10561821 DOI: 10.1681/asn.0000000000000197] [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: 03/07/2023] [Accepted: 07/08/2023] [Indexed: 07/26/2023]  Open
40
Sharma A, Kumar R, Varadwaj P. Developing human olfactory network and exploring olfactory receptor-odorant interaction. J Biomol Struct Dyn 2023;41:8941-8960. [PMID: 36310099 DOI: 10.1080/07391102.2022.2138976] [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: 07/26/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
41
Jamal M, Lei Y, He H, Zeng X, Bangash HI, Xiao D, Shao L, Zhou F, Zhang Q. CCR9 overexpression promotes T-ALL progression by enhancing cholesterol biosynthesis. Front Pharmacol 2023;14:1257289. [PMID: 37745085 PMCID: PMC10512069 DOI: 10.3389/fphar.2023.1257289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023]  Open
42
Guthrie J, Ko¨stel Bal S, Lombardo SD, Mu¨ller F, Sin C, Hu¨tter CV, Menche J, Boztug K. AutoCore: A network-based definition of the core module of human autoimmunity and autoinflammation. SCIENCE ADVANCES 2023;9:eadg6375. [PMID: 37656781 PMCID: PMC10848965 DOI: 10.1126/sciadv.adg6375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
43
Zhang H, Steele JR, Kahrood HV, Lucas DD, Shah AD, Schittenhelm RB. Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data. J Proteome Res 2023;22:2890-2899. [PMID: 37584946 DOI: 10.1021/acs.jproteome.3c00186] [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: 08/17/2023]
44
Shin E, Han SH, Park IS, Wee JH, Lee JS, Kim H. Does the Necrotic Portion of Metastatic Lymphadenopathy from Squamous Cell Carcinoma Still Have Tumoral Oncologic Information? Differential Diagnosis of Benign Necrotic Lymphadenopathy Using microRNA. Biomedicines 2023;11:2407. [PMID: 37760848 PMCID: PMC10525664 DOI: 10.3390/biomedicines11092407] [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: 07/28/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023]  Open
45
Wang Y, Yu Y, Li L, Zheng M, Zhou J, Gong H, Feng B, Wang X, Meng X, Cui Y, Xia Y, Chu S, Lin L, Chang H, Zhou R, Ma M, Li Z, Ji R, Lu M, Yang X, Zuo X, Li S, Li Y. Bile acid-dependent transcription factors and chromatin accessibility determine regional heterogeneity of intestinal antimicrobial peptides. Nat Commun 2023;14:5093. [PMID: 37607912 PMCID: PMC10444805 DOI: 10.1038/s41467-023-40565-7] [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: 10/26/2022] [Accepted: 08/01/2023] [Indexed: 08/24/2023]  Open
46
Ribarski-Chorev I, Schudy G, Strauss C, Schlesinger S. Short heat shock has a long-term effect on mesenchymal stem cells' transcriptome. iScience 2023;26:107305. [PMID: 37529103 PMCID: PMC10387575 DOI: 10.1016/j.isci.2023.107305] [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: 12/22/2022] [Revised: 05/23/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023]  Open
47
Weeks EM, Ulirsch JC, Cheng NY, Trippe BL, Fine RS, Miao J, Patwardhan TA, Kanai M, Nasser J, Fulco CP, Tashman KC, Aguet F, Li T, Ordovas-Montanes J, Smillie CS, Biton M, Shalek AK, Ananthakrishnan AN, Xavier RJ, Regev A, Gupta RM, Lage K, Ardlie KG, Hirschhorn JN, Lander ES, Engreitz JM, Finucane HK. Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases. Nat Genet 2023;55:1267-1276. [PMID: 37443254 PMCID: PMC10836580 DOI: 10.1038/s41588-023-01443-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 06/09/2023] [Indexed: 07/15/2023]
48
Yap JYY, Goh LSH, Lim AJW, Chong SS, Lim LJ, Lee CG. Machine Learning Identifies a Signature of Nine Exosomal RNAs That Predicts Hepatocellular Carcinoma. Cancers (Basel) 2023;15:3749. [PMID: 37509410 PMCID: PMC10377993 DOI: 10.3390/cancers15143749] [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: 06/16/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023]  Open
49
Roverso M, Dogra R, Visentin S, Pettenuzzo S, Cappellin L, Pastore P, Bogialli S. Mass spectrometry-based "omics" technologies for the study of gestational diabetes and the discovery of new biomarkers. MASS SPECTROMETRY REVIEWS 2023;42:1424-1461. [PMID: 35474466 DOI: 10.1002/mas.21777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/15/2021] [Accepted: 04/04/2022] [Indexed: 06/07/2023]
50
Chatterjee B, Thakur SS. Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein-metabolite interactomes are its potential biomarkers. Proteomics 2023;23:e2200257. [PMID: 36919629 DOI: 10.1002/pmic.202200257] [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: 06/14/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023]
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