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For: Yang Y, Sun H, Zhang Y, Zhang T, Gong J, Wei Y, Duan YG, Shu M, Yang Y, Wu D, Yu D. Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data. Cell Rep 2021;36:109442. [PMID: 34320340 DOI: 10.1016/j.celrep.2021.109442] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/01/2021] [Accepted: 07/01/2021] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Sweet-Jones J, Martin AC. An antibody developability triaging pipeline exploiting protein language models. MAbs 2025;17:2472009. [PMID: 40038849 PMCID: PMC11901365 DOI: 10.1080/19420862.2025.2472009] [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: 10/31/2024] [Revised: 02/17/2025] [Accepted: 02/20/2025] [Indexed: 03/06/2025]  Open
2
Fuellen G, Palmer D, Fruijtier C, Avelar RA. In-silico Evaluation of Aging-Related Interventions Using Omics Data and Predictive Modeling. Ageing Res Rev 2025:102777. [PMID: 40414362 DOI: 10.1016/j.arr.2025.102777] [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: 01/25/2025] [Revised: 03/12/2025] [Accepted: 05/16/2025] [Indexed: 05/27/2025]
3
Pavel A, Grønberg MG, Clemmensen LH. The impact of dropouts in scRNAseq dense neighborhood analysis. Comput Struct Biotechnol J 2025;27:1278-1285. [PMID: 40225837 PMCID: PMC11992407 DOI: 10.1016/j.csbj.2025.03.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 03/19/2025] [Accepted: 03/20/2025] [Indexed: 04/15/2025]  Open
4
Wu CH, Zhou X, Chen M. Exploring and mitigating shortcomings in single-cell differential expression analysis with a new statistical paradigm. Genome Biol 2025;26:58. [PMID: 40098192 PMCID: PMC11912664 DOI: 10.1186/s13059-025-03525-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/05/2025] [Indexed: 03/19/2025]  Open
5
Wang YJ, Choo WC, Ng KY, Bi R, Wang PW. Evolution of AI enabled healthcare systems using textual data with a pretrained BERT deep learning model. Sci Rep 2025;15:7540. [PMID: 40038367 PMCID: PMC11880528 DOI: 10.1038/s41598-025-91622-8] [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: 10/30/2024] [Accepted: 02/21/2025] [Indexed: 03/06/2025]  Open
6
Golob J, Rao K, Berinstein JA, Singh P, Chey WD, Owyang C, Kamada N, Higgins PDR, Young V, Bishu S, Lee AA. Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways. Inflamm Bowel Dis 2025;31:763-776. [PMID: 39541261 PMCID: PMC11879174 DOI: 10.1093/ibd/izae238] [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: 07/12/2024] [Indexed: 11/16/2024]
7
Xie Z, Li L, Hou W, Fan Z, Zeng L, He L, Ji Y, Zhang J, Wang F, Xing Z, Wang Y, Ye Y. Critical role of Oas1g and STAT1 pathways in neuroinflammation: insights for Alzheimer's disease therapeutics. J Transl Med 2025;23:182. [PMID: 39953505 PMCID: PMC11829366 DOI: 10.1186/s12967-025-06112-2] [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: 05/24/2024] [Accepted: 01/08/2025] [Indexed: 02/17/2025]  Open
8
Joosse HJ, Chumsaeng-Reijers C, Huisman A, Hoefer IE, van Solinge WW, Haitjema S, van Es B. Haematology dimension reduction, a large scale application to regular care haematology data. BMC Med Inform Decis Mak 2025;25:75. [PMID: 39939843 PMCID: PMC11823074 DOI: 10.1186/s12911-025-02899-8] [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: 10/24/2023] [Accepted: 01/28/2025] [Indexed: 02/14/2025]  Open
9
Denkert C, Rachakonda S, Karn T, Weber K, Martin M, Marmé F, Untch M, Bonnefoi H, Kim SB, Seiler S, Bear HD, Witkiewicz AK, Im SA, DeMichele A, Pehl A, Van't Veer L, McCarthy N, Stiewe T, Jank P, Gelmon KA, García-Sáenz JA, Westhoff CC, Kelly CM, Reimer T, Felder B, Olivé MM, Knudsen ES, Turner N, Rojo F, Schmitt WD, Fasching PA, Teply-Szymanski J, Zhang Z, Toi M, Rugo HS, Gnant M, Makris A, Holtschmidt J, Nekljudova V, Loibl S. Dynamics of molecular heterogeneity in high-risk luminal breast cancer-From intrinsic to adaptive subtyping. Cancer Cell 2025;43:232-247.e4. [PMID: 39933898 DOI: 10.1016/j.ccell.2025.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 01/09/2025] [Accepted: 01/09/2025] [Indexed: 02/13/2025]
10
Ramanan S, Akarca D, Henderson SK, Rouse MA, Allinson K, Patterson K, Rowe JB, Lambon Ralph MA. The graded multidimensional geometry of phenotypic variation and progression in neurodegenerative syndromes. Brain 2025;148:448-466. [PMID: 39018014 PMCID: PMC11788217 DOI: 10.1093/brain/awae233] [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: 01/03/2024] [Revised: 05/29/2024] [Accepted: 06/17/2024] [Indexed: 07/18/2024]  Open
11
Lichtarge J, Cappuccio G, Pati S, Dei-Ampeh AK, Sing S, Ma L, Liu Z, Maletic-Savatic M. MetaboLINK is a novel algorithm for unveiling cell-specific metabolic pathways in longitudinal datasets. Front Neurosci 2025;18:1520982. [PMID: 39872998 PMCID: PMC11769959 DOI: 10.3389/fnins.2024.1520982] [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: 11/01/2024] [Accepted: 12/20/2024] [Indexed: 01/30/2025]  Open
12
Vial L, Descotes F, Lopez J, Alsugair Z, Céruse P, Philouze P, Fieux M, Wassef M, Baglin AC, Onea M, Castain C, Delvenne P, Fromont-Hankard G, Gilles H, Monnien F, Mauvais O, Lépine C, Le Gall F, Rousselet MC, Sudaka A, Uro-Coste E, Casiraghi O, Costes-Martineau V, Benzerdjeb N. Reappraisal of Oncocytic Adenocarcinoma: Unveiling Its Connection to Oncocytic Variants of Salivary Duct Carcinoma and Mucoepidermoid Carcinoma Through ImmunoHisto-Molecular Perspectives. Am J Surg Pathol 2025;49:73-82. [PMID: 39513520 PMCID: PMC11634103 DOI: 10.1097/pas.0000000000002324] [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: 11/15/2024]
13
Che Y, Zhao M, Gao Y, Zhang Z, Zhang X. Application of machine learning for mass spectrometry-based multi-omics in thyroid diseases. Front Mol Biosci 2024;11:1483326. [PMID: 39741929 PMCID: PMC11685090 DOI: 10.3389/fmolb.2024.1483326] [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: 08/23/2024] [Accepted: 12/02/2024] [Indexed: 01/03/2025]  Open
14
Shao Y, Lv X, Ying S, Guo Q. Artificial Intelligence-Driven Precision Medicine: Multi-Omics and Spatial Multi-Omics Approaches in Diffuse Large B-Cell Lymphoma (DLBCL). FRONT BIOSCI-LANDMRK 2024;29:404. [PMID: 39735973 DOI: 10.31083/j.fbl2912404] [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: 05/16/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 12/31/2024]
15
Kittke V, Zhao C, Lam DD, Harrer P, Krezel W, Schormair B, Oexle K, Winkelmann J. RLS-associated MEIS transcription factors control distinct processes in human neural stem cells. Sci Rep 2024;14:28986. [PMID: 39578497 PMCID: PMC11584712 DOI: 10.1038/s41598-024-80266-9] [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: 06/24/2024] [Accepted: 11/18/2024] [Indexed: 11/24/2024]  Open
16
Lara-Ramírez EE, Rivera G, Oliva-Hernández AA, Bocanegra-Garcia V, López JA, Guo X. Unsupervised learning analysis on the proteomes of Zika virus. PeerJ Comput Sci 2024;10:e2443. [PMID: 39650519 PMCID: PMC11623125 DOI: 10.7717/peerj-cs.2443] [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: 05/18/2024] [Accepted: 10/01/2024] [Indexed: 12/11/2024]
17
Jin H, Park SY, Lee JE, Park H, Jeong M, Lee H, Cho J, Lee YS. GTSE1-driven ZEB1 stabilization promotes pulmonary fibrosis through the epithelial-to-mesenchymal transition. Mol Ther 2024;32:4138-4157. [PMID: 39342428 PMCID: PMC11573610 DOI: 10.1016/j.ymthe.2024.09.029] [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: 04/14/2024] [Revised: 08/06/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024]  Open
18
Park LM, Lannigan J, Low Q, Jaimes MC, Bonilla DL. OMIP-069 version 2: Update to the 40-color full Spectrum flow cytometry panel for deep immunophenotyping of major cell subsets in human peripheral blood. Cytometry A 2024;105:791-799. [PMID: 39268753 DOI: 10.1002/cyto.a.24898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/12/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024]
19
Liu D, Wei C, Guan L, Ju W, Xiang S, Lian F. Combining single-cell RNA sequencing and network pharmacology to explore the target of cangfu daotan decoction in the treatment of obese polycystic ovary syndrome from an immune perspective. Front Pharmacol 2024;15:1451300. [PMID: 39539629 PMCID: PMC11557475 DOI: 10.3389/fphar.2024.1451300] [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: 06/19/2024] [Accepted: 09/26/2024] [Indexed: 11/16/2024]  Open
20
Chinni BK, Manlhiot C. Emerging Analytical Approaches for Personalized Medicine Using Machine Learning In Pediatric and Congenital Heart Disease. Can J Cardiol 2024;40:1880-1896. [PMID: 39097187 DOI: 10.1016/j.cjca.2024.07.026] [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: 05/31/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/05/2024]  Open
21
Golob J, Rao K, Berinstein JA, Singh P, Chey WD, Owyang C, Kamada N, Higgins PDR, Young V, Bishu S, Lee AA. Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.08.24313266. [PMID: 39314983 PMCID: PMC11419226 DOI: 10.1101/2024.09.08.24313266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
22
de Back TR, van Hooff SR, Sommeijer DW, Vermeulen L. Transcriptomic subtyping of gastrointestinal malignancies. Trends Cancer 2024;10:842-856. [PMID: 39019673 DOI: 10.1016/j.trecan.2024.06.007] [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: 04/25/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/19/2024]
23
Verma R, Alban TJ, Parthasarathy P, Mokhtari M, Toro Castano P, Cohen ML, Lathia JD, Ahluwalia M, Tiwari P. Sexually dimorphic computational histopathological signatures prognostic of overall survival in high-grade gliomas via deep learning. SCIENCE ADVANCES 2024;10:eadi0302. [PMID: 39178259 PMCID: PMC11343024 DOI: 10.1126/sciadv.adi0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/16/2024] [Indexed: 08/25/2024]
24
Moreira-Filho JT, Ranganath D, Conway M, Schmitt C, Kleinstreuer N, Mansouri K. Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow. J Cheminform 2024;16:101. [PMID: 39152469 PMCID: PMC11330086 DOI: 10.1186/s13321-024-00894-1] [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: 03/28/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]  Open
25
Colombo F, Calesella F, Bravi B, Fortaner-Uyà L, Monopoli C, Tassi E, Carminati M, Zanardi R, Bollettini I, Poletti S, Lorenzi C, Spadini S, Brambilla P, Serretti A, Maggioni E, Fabbri C, Benedetti F, Vai B. Multimodal brain-derived subtypes of Major depressive disorder differentiate patients for anergic symptoms, immune-inflammatory markers, history of childhood trauma and treatment-resistance. Eur Neuropsychopharmacol 2024;85:45-57. [PMID: 38936143 DOI: 10.1016/j.euroneuro.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/29/2024]
26
Bayones L, Zainos A, Alvarez M, Romo R, Franci A, Rossi-Pool R. Orthogonality of sensory and contextual categorical dynamics embedded in a continuum of responses from the second somatosensory cortex. Proc Natl Acad Sci U S A 2024;121:e2316765121. [PMID: 38990946 PMCID: PMC11260089 DOI: 10.1073/pnas.2316765121] [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: 09/26/2023] [Accepted: 06/12/2024] [Indexed: 07/13/2024]  Open
27
Smith BJ, Guest PC, Martins-de-Souza D. Maximizing Analytical Performance in Biomolecular Discovery with LC-MS: Focus on Psychiatric Disorders. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024;17:25-46. [PMID: 38424029 DOI: 10.1146/annurev-anchem-061522-041154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
28
Qing X, Lu G, Zhang X, Chen Q, Zhou X, He W, Xu L, Zhang J. Essential spectral pixels-based improvement of UMAP classifying hyperspectral imaging data to identify minor compounds in food matrix. Talanta 2024;273:125845. [PMID: 38442566 DOI: 10.1016/j.talanta.2024.125845] [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: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
29
Li L, Momma H, Chen H, Nawrin SS, Xu Y, Inada H, Nagatomi R. Dietary patterns associated with the incidence of hypertension among adult Japanese males: application of machine learning to a cohort study. Eur J Nutr 2024;63:1293-1314. [PMID: 38403812 PMCID: PMC11139695 DOI: 10.1007/s00394-024-03342-w] [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: 05/15/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
30
Park SY, Bae H, Jeong HY, Lee JY, Kwon YK, Kim CE. Identifying Novel Subtypes of Functional Gastrointestinal Disorder by Analyzing Nonlinear Structure in Integrative Biopsychosocial Questionnaire Data. J Clin Med 2024;13:2821. [PMID: 38792363 PMCID: PMC11122158 DOI: 10.3390/jcm13102821] [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: 03/26/2024] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]  Open
31
Srivastava A, Manchel A, Waters J, Ambelil M, Barnhart BK, Hoek JB, Shah AP, Vadigepalli R. Integrated transcriptomics and histopathology approach identifies a subset of rejected donor livers with potential suitability for transplantation. BMC Genomics 2024;25:437. [PMID: 38698335 PMCID: PMC11067109 DOI: 10.1186/s12864-024-10362-7] [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: 03/01/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]  Open
32
Lechner K, Kia S, von Korn P, Dinges SM, Mueller S, Tjønna AE, Wisløff U, Van Craenenbroeck EM, Pieske B, Adams V, Pressler A, Landmesser U, Halle M, Kränkel N. Cardiometabolic and immune response to exercise training in patients with metabolic syndrome: retrospective analysis of two randomized clinical trials. Front Cardiovasc Med 2024;11:1329633. [PMID: 38638882 PMCID: PMC11025358 DOI: 10.3389/fcvm.2024.1329633] [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: 10/29/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024]  Open
33
Walsh JR, Sun G, Balan J, Hardcastle J, Vollenweider J, Jerde C, Rumilla K, Koellner C, Koleilat A, Hasadsri L, Kipp B, Jenkinson G, Klee E. A supervised learning method for classifying methylation disorders. BMC Bioinformatics 2024;25:66. [PMID: 38347515 PMCID: PMC10863277 DOI: 10.1186/s12859-024-05673-1] [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: 09/20/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024]  Open
34
Wu S, Wagner G. Computational inference of eIF4F complex function and structure in human cancers. Proc Natl Acad Sci U S A 2024;121:e2313589121. [PMID: 38266053 PMCID: PMC10835048 DOI: 10.1073/pnas.2313589121] [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: 08/10/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024]  Open
35
Guo Z, Zhang J, Sun J, Dong H, Huang J, Geng L, Li S, Jing X, Guo Y, Sun X. A multivariate algorithm for identifying contaminated peanut using visible and near-infrared hyperspectral imaging. Talanta 2024;267:125187. [PMID: 37722342 DOI: 10.1016/j.talanta.2023.125187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023]
36
Xiang Q, Tao JS, Fu CJ, Liao LX, Liu LN, Deng J, Li XH. The integrated analysis and underlying mechanisms of FNDC5 on diabetic induced cognitive deficits. Int J Geriatr Psychiatry 2024;39:e6047. [PMID: 38161286 DOI: 10.1002/gps.6047] [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: 05/25/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
37
Filippa M, Benis D, Adam-Darque A, Grandjean D, Hüppi PS. Preterm infants show an atypical processing of the mother's voice. Brain Cogn 2023;173:106104. [PMID: 37949001 DOI: 10.1016/j.bandc.2023.106104] [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: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
38
Xi Z, Yang T, Huang T, Zhou J, Yang P. Identification and Preliminary Clinical Validation of Key Extracellular Proteins as the Potential Biomarkers in Hashimoto's Thyroiditis by Comprehensive Analysis. Biomedicines 2023;11:3127. [PMID: 38137348 PMCID: PMC10740579 DOI: 10.3390/biomedicines11123127] [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: 10/10/2023] [Revised: 11/04/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]  Open
39
Golob J, Rao K, Berinstein JA, Chey WD, Owyang C, Kamada N, Higgins PD, Young V, Bishu S, Lee AA. The Microbiome in Quiescent Crohn's Disease With Persistent Symptoms Show Disruptions in Microbial Sulfur and Tryptophan Pathways. GASTRO HEP ADVANCES 2023;3:167-177. [PMID: 39129952 PMCID: PMC11307550 DOI: 10.1016/j.gastha.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/09/2023] [Indexed: 08/13/2024]
40
Sekita A, Kawasaki H, Fukushima-Nomura A, Yashiro K, Tanese K, Toshima S, Ashizaki K, Miyai T, Yazaki J, Kobayashi A, Namba S, Naito T, Wang QS, Kawakami E, Seita J, Ohara O, Sakurada K, Okada Y, Amagai M, Koseki H. Multifaceted analysis of cross-tissue transcriptomes reveals phenotype-endotype associations in atopic dermatitis. Nat Commun 2023;14:6133. [PMID: 37783685 PMCID: PMC10545679 DOI: 10.1038/s41467-023-41857-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/19/2023] [Indexed: 10/04/2023]  Open
41
Higginbotham L, Carter EK, Dammer EB, Haque RU, Johnson ECB, Duong DM, Yin L, De Jager PL, Bennett DA, Felsky D, Tio ES, Lah JJ, Levey AI, Seyfried NT. Unbiased classification of the elderly human brain proteome resolves distinct clinical and pathophysiological subtypes of cognitive impairment. Neurobiol Dis 2023;186:106286. [PMID: 37689213 PMCID: PMC10750427 DOI: 10.1016/j.nbd.2023.106286] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/24/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]  Open
42
Liu J, Huang T, Yao J, Zhao T, Zhang Y, Zhang R. Epitranscriptomic subtyping, visualization, and denoising by global motif visualization. Nat Commun 2023;14:5944. [PMID: 37741827 PMCID: PMC10517956 DOI: 10.1038/s41467-023-41653-4] [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: 01/01/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]  Open
43
Kang H, Sun H, Yang Y, Tuong ZK, Shu M, Wei Y, Zhang Y, Yu D, Tao Y. Autoimmune uveitis in Behçet's disease and Vogt-Koyanagi-Harada disease differ in tissue immune infiltration and T cell clonality. Clin Transl Immunology 2023;12:e1461. [PMID: 37720629 PMCID: PMC10503407 DOI: 10.1002/cti2.1461] [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: 01/06/2023] [Revised: 06/16/2023] [Accepted: 08/04/2023] [Indexed: 09/19/2023]  Open
44
Wu S, Wagner G. Computational inference of eIF4F complex function and structure in human cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552450. [PMID: 37609226 PMCID: PMC10441403 DOI: 10.1101/2023.08.10.552450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
45
Chari T, Pachter L. The specious art of single-cell genomics. PLoS Comput Biol 2023;19:e1011288. [PMID: 37590228 PMCID: PMC10434946 DOI: 10.1371/journal.pcbi.1011288] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]  Open
46
Luo M, Miao YR, Ke YJ, Guo AY, Zhang Q. A comprehensive landscape of transcription profiles and data resources for human leukemia. Blood Adv 2023;7:3435-3449. [PMID: 36595475 PMCID: PMC10362280 DOI: 10.1182/bloodadvances.2022008410] [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: 06/27/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023]  Open
47
Coria-Rodríguez H, Ochoa S, de Anda-Jáuregui G, Hernández-Lemus E. Drug repurposing for Basal breast cancer subpopulations using modular network signatures. Comput Biol Chem 2023;105:107902. [PMID: 37348299 DOI: 10.1016/j.compbiolchem.2023.107902] [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: 07/20/2022] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
48
Cai C, Yue Y, Yue B. Single-cell RNA sequencing in skeletal muscle developmental biology. Biomed Pharmacother 2023;162:114631. [PMID: 37003036 DOI: 10.1016/j.biopha.2023.114631] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/01/2023]  Open
49
Chandra R, Bansal C, Kang M, Blau T, Agarwal V, Singh P, Wilson LOW, Vasan S. Unsupervised machine learning framework for discriminating major variants of concern during COVID-19. PLoS One 2023;18:e0285719. [PMID: 37200352 PMCID: PMC10194860 DOI: 10.1371/journal.pone.0285719] [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: 12/23/2022] [Accepted: 04/28/2023] [Indexed: 05/20/2023]  Open
50
Smith RN, Rosales IA, Tomaszewski KT, Mahowald GT, Araujo-Medina M, Acheampong E, Bruce A, Rios A, Otsuka T, Tsuji T, Hotta K, Colvin R. Utility of Banff Human Organ Transplant Gene Panel in Human Kidney Transplant Biopsies. Transplantation 2023;107:1188-1199. [PMID: 36525551 PMCID: PMC10132999 DOI: 10.1097/tp.0000000000004389] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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