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For: Goh WWB, Wang W, Wong L. Why Batch Effects Matter in Omics Data, and How to Avoid Them. Trends Biotechnol 2017;35:498-507. [PMID: 28351613 DOI: 10.1016/j.tibtech.2017.02.012] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/16/2017] [Accepted: 02/28/2017] [Indexed: 12/23/2022]
Number Cited by Other Article(s)
1
Oliveira DVNP, Biskup E, O'Rourke CJ, Hentze JL, Andersen JB, Høgdall C, Høgdall EV. Developing a DNA Methylation Signature to Differentiate High-Grade Serous Ovarian Carcinomas from Benign Ovarian Tumors. Mol Diagn Ther 2024;28:821-834. [PMID: 39414761 PMCID: PMC11512855 DOI: 10.1007/s40291-024-00740-y] [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] [Accepted: 08/08/2024] [Indexed: 10/18/2024]
2
Yu Y, Mai Y, Zheng Y, Shi L. Assessing and mitigating batch effects in large-scale omics studies. Genome Biol 2024;25:254. [PMID: 39363244 PMCID: PMC11447944 DOI: 10.1186/s13059-024-03401-9] [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: 07/11/2023] [Accepted: 09/23/2024] [Indexed: 10/05/2024]  Open
3
Hanna MG, Olson NH, Zarella M, Dash RC, Herrmann MD, Furtado LV, Stram MN, Raciti PM, Hassell L, Mays A, Pantanowitz L, Sirintrapun JS, Krishnamurthy S, Parwani A, Lujan G, Evans A, Glassy EF, Bui MM, Singh R, Souers RJ, de Baca ME, Seheult JN. Recommendations for Performance Evaluation of Machine Learning in Pathology: A Concept Paper From the College of American Pathologists. Arch Pathol Lab Med 2024;148:e335-e361. [PMID: 38041522 DOI: 10.5858/arpa.2023-0042-cp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 12/03/2023]
4
Marín-Miret J, Pérez-Cobas AE, Domínguez-Santos R, Pérez-Rocher B, Latorre A, Moya A. Adaptability of the gut microbiota of the German cockroach Blattella germanica to a periodic antibiotic treatment. Microbiol Res 2024;287:127863. [PMID: 39106785 DOI: 10.1016/j.micres.2024.127863] [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: 01/26/2024] [Revised: 07/20/2024] [Accepted: 07/29/2024] [Indexed: 08/09/2024]
5
Shabani M, Eghbali M, Abiri A, Abiri M. Comprehensive microarray analysis of severe preeclampsia placenta to identify differentially expressed genes, biological pathways, hub genes, and their related non-coding RNAs. Placenta 2024;155:22-31. [PMID: 39121584 DOI: 10.1016/j.placenta.2024.08.003] [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: 04/30/2024] [Revised: 07/03/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
6
Hui HWH, Kong W, Goh WWB. Thinking points for effective batch correction on biomedical data. Brief Bioinform 2024;25:bbae515. [PMID: 39397427 PMCID: PMC11471903 DOI: 10.1093/bib/bbae515] [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: 06/19/2024] [Revised: 09/11/2024] [Accepted: 10/01/2024] [Indexed: 10/15/2024]  Open
7
Li Z, Katz S, Saccenti E, Fardo DW, Claes P, Martins dos Santos VAP, Van Steen K, Roshchupkin GV. Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping. Brief Bioinform 2024;25:bbae512. [PMID: 39413796 PMCID: PMC11483139 DOI: 10.1093/bib/bbae512] [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: 03/12/2024] [Revised: 09/20/2024] [Accepted: 09/25/2024] [Indexed: 10/18/2024]  Open
8
Weißbach S, Milkovits J, Pastore S, Heine M, Gerber S, Todorov H. Cortexa: a comprehensive resource for studying gene expression and alternative splicing in the murine brain. BMC Bioinformatics 2024;25:293. [PMID: 39237879 PMCID: PMC11378610 DOI: 10.1186/s12859-024-05919-y] [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: 06/06/2024] [Accepted: 08/28/2024] [Indexed: 09/07/2024]  Open
9
Jiang P, Zhang Z, Yu Q, Wang Z, Diao L, Li D. ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation. Int J Mol Sci 2024;25:9544. [PMID: 39273492 PMCID: PMC11394870 DOI: 10.3390/ijms25179544] [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: 07/21/2024] [Revised: 08/26/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]  Open
10
Goh WWB, Kabir MN, Yoo S, Wong L. Ten quick tips for ensuring machine learning model validity. PLoS Comput Biol 2024;20:e1012402. [PMID: 39298376 DOI: 10.1371/journal.pcbi.1012402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]  Open
11
Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024;4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
12
Moral-Turón C, Asencio-Cortés G, Rodriguez-Diaz F, Rubio A, Navarro AG, Brokate-Llanos AM, Garzón A, Muñoz MJ, Pérez-Pulido AJ. ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing. Brief Funct Genomics 2024;23:484-494. [PMID: 38422352 DOI: 10.1093/bfgp/elae006] [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: 09/07/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024]  Open
13
Regueira-Iglesias A, Suárez-Rodríguez B, Blanco-Pintos T, Relvas M, Alonso-Sampedro M, Balsa-Castro C, Tomás I. The salivary microbiome as a diagnostic biomarker of periodontitis: a 16S multi-batch study before and after the removal of batch effects. Front Cell Infect Microbiol 2024;14:1405699. [PMID: 39071165 PMCID: PMC11272481 DOI: 10.3389/fcimb.2024.1405699] [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: 03/23/2024] [Accepted: 06/17/2024] [Indexed: 07/30/2024]  Open
14
Nitz AA, Giraldez Chavez JH, Eliason ZG, Payne SH. Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses. J Proteome Res 2024. [PMID: 38981598 DOI: 10.1021/acs.jproteome.4c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
15
Yu Y, Hou W, Liu Y, Wang H, Dong L, Mai Y, Chen Q, Li Z, Sun S, Yang J, Cao Z, Zhang P, Zi Y, Liu R, Gao J, Zhang N, Li J, Ren L, Jiang H, Shang J, Zhu S, Wang X, Qing T, Bao D, Li B, Li B, Suo C, Pi Y, Wang X, Dai F, Scherer A, Mattila P, Han J, Zhang L, Jiang H, Thierry-Mieg D, Thierry-Mieg J, Xiao W, Hong H, Tong W, Wang J, Li J, Fang X, Jin L, Xu J, Qian F, Zhang R, Shi L, Zheng Y. Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling. Nat Biotechnol 2024;42:1118-1132. [PMID: 37679545 PMCID: PMC11251996 DOI: 10.1038/s41587-023-01867-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/15/2023] [Indexed: 09/09/2023]
16
Zheng Y, Liu Y, Yang J, Dong L, Zhang R, Tian S, Yu Y, Ren L, Hou W, Zhu F, Mai Y, Han J, Zhang L, Jiang H, Lin L, Lou J, Li R, Lin J, Liu H, Kong Z, Wang D, Dai F, Bao D, Cao Z, Chen Q, Chen Q, Chen X, Gao Y, Jiang H, Li B, Li B, Li J, Liu R, Qing T, Shang E, Shang J, Sun S, Wang H, Wang X, Zhang N, Zhang P, Zhang R, Zhu S, Scherer A, Wang J, Wang J, Huo Y, Liu G, Cao C, Shao L, Xu J, Hong H, Xiao W, Liang X, Lu D, Jin L, Tong W, Ding C, Li J, Fang X, Shi L. Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials. Nat Biotechnol 2024;42:1133-1149. [PMID: 37679543 PMCID: PMC11252085 DOI: 10.1038/s41587-023-01934-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 09/09/2023]
17
Takemoto Y, Ito D, Komori S, Kishimoto Y, Yamada S, Hashizume A, Katsuno M, Nakatochi M. Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs. BMC Bioinformatics 2024;25:221. [PMID: 38902629 PMCID: PMC11188187 DOI: 10.1186/s12859-024-05840-4] [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: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]  Open
18
Xue Y, Friedl V, Ding H, Wong CK, Stuart JM. Single-cell signatures identify microenvironment factors in tumors associated with patient outcomes. CELL REPORTS METHODS 2024;4:100799. [PMID: 38889686 PMCID: PMC11228369 DOI: 10.1016/j.crmeth.2024.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
19
Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024;25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [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: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024]  Open
20
Ma Y, Pei Y. NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data. J Bioinform Comput Biol 2024;22:2450015. [PMID: 39036845 DOI: 10.1142/s021972002450015x] [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: 07/23/2024]
21
Liu L, Jia R, Hou R, Huang C. Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state. Methods 2024;226:151-160. [PMID: 38670416 DOI: 10.1016/j.ymeth.2024.04.014] [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: 03/02/2024] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]  Open
22
Goldstein Y, Cohen OT, Wald O, Bavli D, Kaplan T, Benny O. Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning. SCIENCE ADVANCES 2024;10:eadj4370. [PMID: 38809990 PMCID: PMC11314625 DOI: 10.1126/sciadv.adj4370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
23
Ma C, Zhang Y, Ding R, Chen H, Wu X, Xu L, Yu C. In search of the ratio of miRNA expression as robust biomarkers for constructing stable diagnostic models among multi-center data. Front Genet 2024;15:1381917. [PMID: 38746057 PMCID: PMC11091382 DOI: 10.3389/fgene.2024.1381917] [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: 02/04/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]  Open
24
Zhang T, Zhang Z, Li L, Ren J, Wu Z, Gao B, Wang G. GTADC: A Graph-Based Method for Inferring Cell Spatial Distribution in Cancer Tissues. Biomolecules 2024;14:436. [PMID: 38672453 PMCID: PMC11048052 DOI: 10.3390/biom14040436] [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: 03/13/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]  Open
25
Marmarelis MG, Littman R, Battaglin F, Niedzwiecki D, Venook A, Ambite JL, Galstyan A, Lenz HJ, Ver Steeg G. q-Diffusion leverages the full dimensionality of gene coexpression in single-cell transcriptomics. Commun Biol 2024;7:400. [PMID: 38565955 PMCID: PMC11255321 DOI: 10.1038/s42003-024-06104-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: 06/23/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024]  Open
26
Orcel E, Hage H, Taha M, Boucher N, Chautard E, Courtois V, Saliou A. A single workflow for multi-species blood transcriptomics. BMC Genomics 2024;25:282. [PMID: 38493105 PMCID: PMC10944614 DOI: 10.1186/s12864-024-10208-2] [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: 12/15/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024]  Open
27
Lin H, Zhang M, Hu M, Zhang Y, Jiang W, Tang W, Ouyang Y, Jiang L, Mi Y, Chen Z, He P, Zhao G, Ouyang X. Emerging applications of single-cell profiling in precision medicine of atherosclerosis. J Transl Med 2024;22:97. [PMID: 38263066 PMCID: PMC10804726 DOI: 10.1186/s12967-023-04629-y] [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: 06/12/2023] [Accepted: 10/14/2023] [Indexed: 01/25/2024]  Open
28
Bai L, Wu Y, Li G, Zhang W, Zhang H, Su J. AI-enabled organoids: Construction, analysis, and application. Bioact Mater 2024;31:525-548. [PMID: 37746662 PMCID: PMC10511344 DOI: 10.1016/j.bioactmat.2023.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/09/2023] [Accepted: 09/09/2023] [Indexed: 09/26/2023]  Open
29
Gruntenko NE, Deryuzhenko MA, Andreenkova OV, Shishkina OD, Bobrovskikh MA, Shatskaya NV, Vasiliev GV. Drosophila melanogaster Transcriptome Response to Different Wolbachia Strains. Int J Mol Sci 2023;24:17411. [PMID: 38139239 PMCID: PMC10743526 DOI: 10.3390/ijms242417411] [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] [Revised: 11/26/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023]  Open
30
Wang H, Lim KP, Kong W, Gao H, Wong BJH, Phua SX, Guo T, Goh WWB. MultiPro: DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects. Sci Data 2023;10:858. [PMID: 38042886 PMCID: PMC10693559 DOI: 10.1038/s41597-023-02779-8] [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: 04/11/2023] [Accepted: 11/23/2023] [Indexed: 12/04/2023]  Open
31
Zhang T, Zhang Z, Li L, Dong B, Wang G, Zhang D. GTAD: a graph-based approach for cell spatial composition inference from integrated scRNA-seq and ST-seq data. Brief Bioinform 2023;25:bbad469. [PMID: 38127088 PMCID: PMC10734610 DOI: 10.1093/bib/bbad469] [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: 10/21/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]  Open
32
Zhou R, Ng SK, Sung JJY, Goh WWB, Wong SH. Data pre-processing for analyzing microbiome data - A mini review. Comput Struct Biotechnol J 2023;21:4804-4815. [PMID: 37841330 PMCID: PMC10569954 DOI: 10.1016/j.csbj.2023.10.001] [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: 07/14/2023] [Revised: 10/01/2023] [Accepted: 10/01/2023] [Indexed: 10/17/2023]  Open
33
Ng S, Masarone S, Watson D, Barnes MR. The benefits and pitfalls of machine learning for biomarker discovery. Cell Tissue Res 2023;394:17-31. [PMID: 37498390 PMCID: PMC10558383 DOI: 10.1007/s00441-023-03816-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
34
Regueira-Iglesias A, Balsa-Castro C, Blanco-Pintos T, Tomás I. Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis. Mol Oral Microbiol 2023;38:347-399. [PMID: 37804481 DOI: 10.1111/omi.12434] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
35
Alchahin AM, Tsea I, Baryawno N. Recent Advances in Single-Cell RNA-Sequencing of Primary and Metastatic Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2023;15:4734. [PMID: 37835428 PMCID: PMC10571653 DOI: 10.3390/cancers15194734] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]  Open
36
Zhang Z, Mathew D, Lim T, Mason K, Martinez CM, Huang S, Wherry EJ, Susztak K, Minn AJ, Ma Z, Zhang NR. Signal recovery in single cell batch integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539614. [PMID: 37215021 PMCID: PMC10197537 DOI: 10.1101/2023.05.05.539614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
37
Papoutsoglou G, Tarazona S, Lopes MB, Klammsteiner T, Ibrahimi E, Eckenberger J, Novielli P, Tonda A, Simeon A, Shigdel R, Béreux S, Vitali G, Tangaro S, Lahti L, Temko A, Claesson MJ, Berland M. Machine learning approaches in microbiome research: challenges and best practices. Front Microbiol 2023;14:1261889. [PMID: 37808286 PMCID: PMC10556866 DOI: 10.3389/fmicb.2023.1261889] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]  Open
38
Wang P, Paquet ÉR, Robert C. Comprehensive transcriptomic analysis of long non-coding RNAs in bovine ovarian follicles and early embryos. PLoS One 2023;18:e0291761. [PMID: 37725621 PMCID: PMC10508637 DOI: 10.1371/journal.pone.0291761] [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: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023]  Open
39
Edwards JM, Andrews MC, Burridge H, Smith R, Owens C, Edinger M, Pilkington K, Desfrancois J, Shackleton M, Senthi S, van Zelm MC. Design, optimisation and standardisation of a high-dimensional spectral flow cytometry workflow assessing T-cell immunophenotype in patients with melanoma. Clin Transl Immunology 2023;12:e1466. [PMID: 37692904 PMCID: PMC10484688 DOI: 10.1002/cti2.1466] [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: 03/30/2023] [Revised: 06/26/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023]  Open
40
Yu Y, Zhang N, Mai Y, Ren L, Chen Q, Cao Z, Chen Q, Liu Y, Hou W, Yang J, Hong H, Xu J, Tong W, Dong L, Shi L, Fang X, Zheng Y. Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method. Genome Biol 2023;24:201. [PMID: 37674217 PMCID: PMC10483871 DOI: 10.1186/s13059-023-03047-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/18/2023] [Indexed: 09/08/2023]  Open
41
Goh WWB, Hui HWH, Wong L. How missing value imputation is confounded with batch effects and what you can do about it. Drug Discov Today 2023;28:103661. [PMID: 37301250 DOI: 10.1016/j.drudis.2023.103661] [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: 02/08/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
42
Chen C, Wang J, Pan D, Wang X, Xu Y, Yan J, Wang L, Yang X, Yang M, Liu G. Applications of multi-omics analysis in human diseases. MedComm (Beijing) 2023;4:e315. [PMID: 37533767 PMCID: PMC10390758 DOI: 10.1002/mco2.315] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 08/04/2023]  Open
43
Ye H, Zhang X, Wang C, Goode EL, Chen J. Batch-effect correction with sample remeasurement in highly confounded case-control studies. NATURE COMPUTATIONAL SCIENCE 2023;3:709-719. [PMID: 38177326 PMCID: PMC10993308 DOI: 10.1038/s43588-023-00500-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 07/11/2023] [Indexed: 01/06/2024]
44
Zhong L, Bacher R. Leveraging remeasured samples in biomedical studies. NATURE COMPUTATIONAL SCIENCE 2023;3:669-670. [PMID: 38177325 DOI: 10.1038/s43588-023-00491-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
45
Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, Rathi KS, Zhu Y, Egolf LE, Farrow BK, Miller DP, Yang Y, Koganti T, Noureen N, Koptyra MP, Duong N, Santi M, Kim J, Robins S, Storm PB, Mack SC, Lilly JV, Xie HM, Jain P, Raman P, Rood BR, Lulla RR, Nazarian J, Kraya AA, Vaksman Z, Heath AP, Kline C, Scolaro L, Viaene AN, Huang X, Way GP, Foltz SM, Zhang B, Poetsch AR, Mueller S, Ennis BM, Prados M, Diskin SJ, Zheng S, Guo Y, Kannan S, Waanders AJ, Margol AS, Kim MC, Hanson D, Van Kuren N, Wong J, Kaufman RS, Coleman N, Blackden C, Cole KA, Mason JL, Madsen PJ, Koschmann CJ, Stewart DR, Wafula E, Brown MA, Resnick AC, Greene CS, Rokita JL, Taroni JN. OpenPBTA: The Open Pediatric Brain Tumor Atlas. CELL GENOMICS 2023;3:100340. [PMID: 37492101 PMCID: PMC10363844 DOI: 10.1016/j.xgen.2023.100340] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/28/2023] [Accepted: 05/04/2023] [Indexed: 07/27/2023]
46
Zhao Y, Wang X, Sun T, Shan P, Zhan Z, Zhao Z, Jiang Y, Qu M, Lv Q, Wang Y, Liu P, Chen S. Artificial intelligence-driven electrochemical immunosensing biochips in multi-component detection. BIOMICROFLUIDICS 2023;17:041301. [PMID: 37614678 PMCID: PMC10444200 DOI: 10.1063/5.0160808] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023]
47
Maqueda JJ, Giovanazzi A, Rocha AM, Rocha S, Silva I, Saraiva N, Bonito N, Carvalho J, Maia L, Wauben MHM, Oliveira C. Adapter dimer contamination in sRNA-sequencing datasets predicts sequencing failure and batch effects and hampers extracellular vesicle-sRNA analysis. JOURNAL OF EXTRACELLULAR BIOLOGY 2023;2:e91. [PMID: 38938917 PMCID: PMC11080836 DOI: 10.1002/jex2.91] [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: 02/17/2023] [Revised: 04/21/2023] [Accepted: 05/10/2023] [Indexed: 06/29/2024]
48
Maxwell CB, Sandhu JK, Cao TH, McCann GP, Ng LL, Jones DJL. The Edge Effect in High-Throughput Proteomics: A Cautionary Tale. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37155737 DOI: 10.1021/jasms.3c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
49
Olbrich M, Künstner A, Busch H. MBECS: Microbiome Batch Effects Correction Suite. BMC Bioinformatics 2023;24:182. [PMID: 37138207 PMCID: PMC10155362 DOI: 10.1186/s12859-023-05252-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/20/2023] [Indexed: 05/05/2023]  Open
50
Guo F, Lin G, Dong L, Cheng KK, Deng L, Xu X, Raftery D, Dong J. Concordance-Based Batch Effect Correction for Large-Scale Metabolomics. Anal Chem 2023;95:7220-7228. [PMID: 37115661 DOI: 10.1021/acs.analchem.2c05748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
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