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For: Ma S, Dai Y. Principal component analysis based methods in bioinformatics studies. Brief Bioinform 2011;12:714-22. [PMID: 21242203 DOI: 10.1093/bib/bbq090] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Haghayegh F, Norouziazad A, Haghani E, Feygin AA, Rahimi RH, Ghavamabadi HA, Sadighbayan D, Madhoun F, Papagelis M, Felfeli T, Salahandish R. Revolutionary Point-of-Care Wearable Diagnostics for Early Disease Detection and Biomarker Discovery through Intelligent Technologies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400595. [PMID: 38958517 DOI: 10.1002/advs.202400595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/19/2024] [Indexed: 07/04/2024]
2
Tsukamoto M, Hishida A, Tamura T, Nagayoshi M, Okada R, Kubo Y, Kato Y, Hamajima N, Nishida Y, Shimanoe C, Ibusuki R, Shibuya K, Takashima N, Nakamura Y, Kusakabe M, Nakamura Y, Koyanagi YN, Oze I, Nishiyama T, Suzuki S, Watanabe I, Matsui D, Otonari J, Ikezaki H, Katsuura-Kamano S, Arisawa K, Kuriki K, Nakatochi M, Momozawa Y, Takeuchi K, Wakai K, Matsuo K. GWAS of Folate Metabolism With Gene-environment Interaction Analysis Revealed the Possible Role of Lifestyles in the Control of Blood Folate Metabolites in Japanese: The J-MICC Study. J Epidemiol 2024;34:228-237. [PMID: 37517992 PMCID: PMC10999522 DOI: 10.2188/jea.je20220341] [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: 01/09/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]  Open
3
Hozumi Y, Tanemura KA, Wei GW. Preprocessing of Single Cell RNA Sequencing Data Using Correlated Clustering and Projection. J Chem Inf Model 2024;64:2829-2838. [PMID: 37402705 PMCID: PMC11009150 DOI: 10.1021/acs.jcim.3c00674] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
4
Li T, Yao J. Unveiling the hub genes in the SIGLECs family in colon adenocarcinoma with machine learning. Front Genet 2024;15:1375100. [PMID: 38650859 PMCID: PMC11033367 DOI: 10.3389/fgene.2024.1375100] [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: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024]  Open
5
He X, Yang Z, Wang L, Sun Y, Cao H, Liang Y. NeuTox: A weighted ensemble model for screening potential neuronal cytotoxicity of chemicals based on various types of molecular representations. JOURNAL OF HAZARDOUS MATERIALS 2024;465:133443. [PMID: 38198870 DOI: 10.1016/j.jhazmat.2024.133443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
6
Nagayoshi M, Hishida A, Shimizu T, Kato Y, Kubo Y, Okada R, Tamura T, Otonari J, Ikezaki H, Hara M, Nishida Y, Oze I, Koyanagi YN, Nakamura Y, Kusakabe M, Ibusuki R, Shibuya K, Suzuki S, Nishiyama T, Koyama T, Ozaki E, Kuriki K, Takashima N, Nakamura Y, Katsuura-Kamano S, Arisawa K, Nakatochi M, Momozawa Y, Takeuchi K, Wakai K. BMI and Cardiometabolic Traits in Japanese: A Mendelian Randomization Study. J Epidemiol 2024;34:51-62. [PMID: 36709979 PMCID: PMC10751192 DOI: 10.2188/jea.je20220154] [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: 05/26/2022] [Accepted: 12/28/2022] [Indexed: 01/28/2023]  Open
7
Palarea-Albaladejo J, McNeilly TN, Nisbet AJ. A curated multivariate approach to study efficacy and optimisation of a prototype vaccine against teladorsagiasis in sheep. Vet Res Commun 2024;48:367-379. [PMID: 37707655 PMCID: PMC10810991 DOI: 10.1007/s11259-023-10208-9] [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: 05/17/2023] [Accepted: 08/25/2023] [Indexed: 09/15/2023]
8
Wang Y, Yu X, Gu Y, Li W, Zhu K, Chen L, Tang Y, Liu G. XGraphCDS: An explainable deep learning model for predicting drug sensitivity from gene pathways and chemical structures. Comput Biol Med 2024;168:107746. [PMID: 38039896 DOI: 10.1016/j.compbiomed.2023.107746] [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: 08/12/2023] [Revised: 10/29/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023]
9
Carhuaricra-Huaman D, Setubal JC. Step-by-Step Bacterial Genome Comparison. Methods Mol Biol 2024;2802:107-134. [PMID: 38819558 DOI: 10.1007/978-1-0716-3838-5_5] [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: 06/01/2024]
10
Swarup N, Cheng J, Choi I, Heo YJ, Kordi M, Aziz M, Arora A, Li F, Chia D, Wei F, Elashoff D, Zhang L, Kim S, Kim Y, Wong DTW. Multi-faceted attributes of salivary cell-free DNA as liquid biopsy biomarkers for gastric cancer detection. Biomark Res 2023;11:90. [PMID: 37817261 PMCID: PMC10566128 DOI: 10.1186/s40364-023-00524-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023]  Open
11
Boigenzahn H, González LD, Thompson JC, Zavala VM, Yin J. Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network. J Mol Evol 2023;91:730-744. [PMID: 37796316 DOI: 10.1007/s00239-023-10132-1] [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: 05/24/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023]
12
Le NQK, Li W, Cao Y. Sequence-based prediction model of protein crystallization propensity using machine learning and two-level feature selection. Brief Bioinform 2023;24:bbad319. [PMID: 37649385 DOI: 10.1093/bib/bbad319] [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: 03/09/2023] [Revised: 07/09/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]  Open
13
Swarup N, Cheng J, Choi I, Heo YJ, Kordi M, Li F, Aziz M, Chia D, Wei F, Elashoff D, Zhang L, Kim S, Kim Y, Wong DT. Multi-Faceted Attributes of Salivary Cell-free DNA as Liquid Biopsy Biomarkers for Gastric Cancer Detection. RESEARCH SQUARE 2023:rs.3.rs-3154388. [PMID: 37503289 PMCID: PMC10371094 DOI: 10.21203/rs.3.rs-3154388/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
14
Watts J, Allen E, Mitoubsi A, Khojandi A, Eales J, Papamarkou T. Towards Faster Gene Expression Prediction via Dimensionality Reduction and Feature Selection. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023;2023:1-4. [PMID: 38083578 DOI: 10.1109/embc40787.2023.10340962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
15
Qian X, Dai X, Luo L, Lin M, Xu Y, Zhao Y, Huang D, Qiu H, Liang L, Liu H, Liu Y, Gu L, Lu T, Chen Y, Zhang Y. An Interpretable Multitask Framework BiLAT Enables Accurate Prediction of Cyclin-Dependent Protein Kinase Inhibitors. J Chem Inf Model 2023. [PMID: 37171216 DOI: 10.1021/acs.jcim.3c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
16
Wang Y, Huang M, Deng H, Li W, Wu Z, Tang Y, Liu G. Identification of vital chemical information via visualization of graph neural networks. Brief Bioinform 2023;24:6936421. [PMID: 36537081 DOI: 10.1093/bib/bbac577] [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: 09/01/2022] [Revised: 11/02/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]  Open
17
Revealing genetic links of Type 2 diabetes that lead to the development of Alzheimer's disease. Heliyon 2022;9:e12202. [PMID: 36711310 PMCID: PMC9876837 DOI: 10.1016/j.heliyon.2022.e12202] [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: 05/27/2022] [Revised: 11/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]  Open
18
Shu Z, Long Q, Zhang L, Yu Z, Wu XJ. Robust Graph Regularized NMF with Dissimilarity and Similarity Constraints for ScRNA-seq Data Clustering. J Chem Inf Model 2022;62:6271-6286. [PMID: 36459053 DOI: 10.1021/acs.jcim.2c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
19
Chen T, Pubu D, Zhang W, Meng S, Yu C, Yin X, Liu J, Zhang Y. Optimization of the extraction process and metabonomics analysis of uric acid-reducing active substances from Gymnadenia R.Br. and its protective effect on hyperuricemia zebrafish. Front Nutr 2022;9:1054294. [PMID: 36545468 PMCID: PMC9760756 DOI: 10.3389/fnut.2022.1054294] [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: 09/26/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]  Open
20
Li P, Luo H, Ji B, Nielsen J. Machine learning for data integration in human gut microbiome. Microb Cell Fact 2022;21:241. [PMID: 36419034 PMCID: PMC9685977 DOI: 10.1186/s12934-022-01973-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022]  Open
21
Single and Combined Associations of Plasma and Urine Essential Trace Elements (Zn, Cu, Se, and Mn) with Cardiovascular Risk Factors in a Mediterranean Population. Antioxidants (Basel) 2022;11:antiox11101991. [PMID: 36290714 PMCID: PMC9598127 DOI: 10.3390/antiox11101991] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]  Open
22
Gamage HN, Chetty M, Shatte A, Hallinan J. Filter feature selection based Boolean Modelling for Genetic Network Inference. Biosystems 2022;221:104757. [PMID: 36007675 DOI: 10.1016/j.biosystems.2022.104757] [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: 02/24/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/02/2022]
23
Human Papillomavirus 16 E6 and E7 Oncoproteins Alter the Abundance of Proteins Associated with DNA Damage Response, Immune Signaling and Epidermal Differentiation. Viruses 2022;14:v14081764. [PMID: 36016386 PMCID: PMC9415472 DOI: 10.3390/v14081764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]  Open
24
Min W, Wan X, Chang TH, Zhang S. A Novel Sparse Graph-Regularized Singular Value Decomposition Model and Its Application to Genomic Data Analysis. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022;33:3842-3856. [PMID: 33556027 DOI: 10.1109/tnnls.2021.3054635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
25
Virtual reality for the observation of oncology models (VROOM): immersive analytics for oncology patient cohorts. Sci Rep 2022;12:11337. [PMID: 35790803 PMCID: PMC9256599 DOI: 10.1038/s41598-022-15548-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/24/2022] [Indexed: 11/08/2022]  Open
26
Prediction of Lithium-Ion Battery Capacity by Functional Principal Component Analysis of Monitoring Data. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
27
Exploratory Analysis of Associations Between Whole Blood Mitochondrial Gene Expression and Cancer-Related Fatigue Among Breast Cancer Survivors. Nurs Res 2022;71:411-417. [PMID: 35416182 PMCID: PMC9420746 DOI: 10.1097/nnr.0000000000000598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
28
pH-degradable, bisphosphonate-loaded nanogels attenuate liver fibrosis by repolarization of M2-type macrophages. Proc Natl Acad Sci U S A 2022;119:e2122310119. [PMID: 35290110 PMCID: PMC8944276 DOI: 10.1073/pnas.2122310119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
29
Wang Y, Gu Y, Lou C, Gong Y, Wu Z, Li W, Tang Y, Liu G. A multitask GNN-based interpretable model for discovery of selective JAK inhibitors. J Cheminform 2022;14:16. [PMID: 35292114 PMCID: PMC8922399 DOI: 10.1186/s13321-022-00593-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/26/2022] [Indexed: 11/10/2022]  Open
30
Nguyen L, Nguyen Vo TH, Trinh QH, Nguyen BH, Nguyen-Hoang PU, Le L, Nguyen BP. iANP-EC: Identifying Anticancer Natural Products Using Ensemble Learning Incorporated with Evolutionary Computation. J Chem Inf Model 2022;62:5080-5089. [PMID: 35157472 DOI: 10.1021/acs.jcim.1c00920] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
31
Shahraki MF, Atanaki FF, Ariaeenejad S, Ghaffari MR, Norouzi‐Beirami MH, Maleki M, Salekdeh GH, Kavousi K. A computational learning paradigm to targeted discovery of biocatalysts from metagenomic data: a case study of lipase identification. Biotechnol Bioeng 2022;119:1115-1128. [DOI: 10.1002/bit.28037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/18/2021] [Accepted: 12/01/2021] [Indexed: 11/09/2022]
32
Ma C, Wu M, Ma S. Analysis of cancer omics data: a selective review of statistical techniques. Brief Bioinform 2022;23:6510158. [PMID: 35039832 DOI: 10.1093/bib/bbab585] [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: 09/20/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022]  Open
33
Xia Y, Zhang H, Wang H, Wang Q, Zhu P, Gu Y, Yang H, Geng D. Identification and validation of ferroptosis key genes in bone mesenchymal stromal cells of primary osteoporosis based on bioinformatics analysis. Front Endocrinol (Lausanne) 2022;13:980867. [PMID: 36093072 PMCID: PMC9452779 DOI: 10.3389/fendo.2022.980867] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022]  Open
34
Liu Z, Chen Z, Song K. SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications. BMC Bioinformatics 2021;22:581. [PMID: 34875998 PMCID: PMC8650269 DOI: 10.1186/s12859-021-04492-y] [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: 06/04/2021] [Accepted: 11/24/2021] [Indexed: 12/02/2022]  Open
35
Nijs M, Smets T, Waelkens E, De Moor B. A mathematical comparison of non-negative matrix factorization related methods with practical implications for the analysis of mass spectrometry imaging data. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021;35:e9181. [PMID: 34374141 PMCID: PMC9285509 DOI: 10.1002/rcm.9181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 05/25/2023]
36
Frost HR. Eigenvectors from Eigenvalues Sparse Principal Component Analysis (EESPCA). J Comput Graph Stat 2021;31:486-501. [PMID: 35693984 PMCID: PMC9187050 DOI: 10.1080/10618600.2021.1987254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/13/2021] [Accepted: 09/22/2021] [Indexed: 01/03/2023]
37
Chen L, Qing Y, Li R, Li C, Li H, Feng X, Li SC. Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics. Brief Bioinform 2021;23:6406714. [PMID: 34671807 DOI: 10.1093/bib/bbab452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/15/2022]  Open
38
Vilor-Tejedor N, Garrido-Martín D, Rodriguez-Fernandez B, Lamballais S, Guigó R, Gispert JD. Multivariate Analysis and Modelling of multiple Brain endOphenotypes: Let's MAMBO! Comput Struct Biotechnol J 2021;19:5800-5810. [PMID: 34765095 PMCID: PMC8567328 DOI: 10.1016/j.csbj.2021.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/01/2022]  Open
39
Dimension-reduction simplifies the analysis of signal crosstalk in a bacterial quorum sensing pathway. Sci Rep 2021;11:19719. [PMID: 34611201 PMCID: PMC8492804 DOI: 10.1038/s41598-021-99169-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022]  Open
40
Wang M, Chen D, Zheng H, Zhao L, Xue X, Yu F, Zhang Y, Cheng C, Niu Q, Wang S, Zhang Y, Wu L. Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs. Front Cell Dev Biol 2021;9:690167. [PMID: 34422813 PMCID: PMC8377728 DOI: 10.3389/fcell.2021.690167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022]  Open
41
Schlieben LD, Prokisch H, Yépez VA. How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data. Front Mol Biosci 2021;8:647277. [PMID: 34141720 PMCID: PMC8204083 DOI: 10.3389/fmolb.2021.647277] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022]  Open
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Dong Z, Alterovitz G. netAE: semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling. Bioinformatics 2021;37:43-49. [PMID: 32726427 DOI: 10.1093/bioinformatics/btaa669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 06/07/2020] [Accepted: 07/17/2020] [Indexed: 01/03/2023]  Open
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Guo L, Hu Z, Zhao C, Xu X, Wang S, Xu J, Dong J, Cai Z. Data Filtering and Its Prioritization in Pipelines for Spatial Segmentation of Mass Spectrometry Imaging. Anal Chem 2021;93:4788-4793. [PMID: 33683863 DOI: 10.1021/acs.analchem.0c05242] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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VIRMOTIF: A User-Friendly Tool for Viral Sequence Analysis. Genes (Basel) 2021;12:genes12020186. [PMID: 33514039 PMCID: PMC7911170 DOI: 10.3390/genes12020186] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/10/2021] [Accepted: 01/19/2021] [Indexed: 12/16/2022]  Open
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Wu M, Jiang Y, Ma S. Integration of Proteomics and Other Omics Data. Methods Mol Biol 2021;2361:307-324. [PMID: 34236669 DOI: 10.1007/978-1-0716-1641-3_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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Wang X, Gao M, Ye J, Jiang Q, Yang Q, Zhang C, Wang S, Zhang J, Wang L, Wu J, Zhan H, Hou X, Han D, Zhao S. An Immune Gene-Related Five-lncRNA Signature for to Predict Glioma Prognosis. Front Genet 2020;11:612037. [PMID: 33391355 PMCID: PMC7772413 DOI: 10.3389/fgene.2020.612037] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022]  Open
47
Li X, Liang B, Xu D, Wu C, Li J, Zheng Y. Antimicrobial Resistance Risk Assessment Models and Database System for Animal-Derived Pathogens. Antibiotics (Basel) 2020;9:E829. [PMID: 33228076 PMCID: PMC7699434 DOI: 10.3390/antibiotics9110829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/01/2020] [Accepted: 11/17/2020] [Indexed: 01/06/2023]  Open
48
Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A. Assessing reproducibility of matrix factorization methods in independent transcriptomes. Bioinformatics 2020;35:4307-4313. [PMID: 30938767 PMCID: PMC6821374 DOI: 10.1093/bioinformatics/btz225] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 03/20/2019] [Accepted: 04/01/2019] [Indexed: 12/26/2022]  Open
49
Vinga S. Structured sparsity regularization for analyzing high-dimensional omics data. Brief Bioinform 2020;22:77-87. [PMID: 32597465 DOI: 10.1093/bib/bbaa122] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022]  Open
50
Cieslak MC, Castelfranco AM, Roncalli V, Lenz PH, Hartline DK. t-Distributed Stochastic Neighbor Embedding (t-SNE): A tool for eco-physiological transcriptomic analysis. Mar Genomics 2020;51:100723. [DOI: 10.1016/j.margen.2019.100723] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/20/2019] [Accepted: 11/01/2019] [Indexed: 01/19/2023]
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