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For: Li F, Zhou Y, Zhang Y, Yin J, Qiu Y, Gao J, Zhu F. POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability. Brief Bioinform 2022;23:6532538. [PMID: 35183059 DOI: 10.1093/bib/bbac040] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 12/17/2022]  Open
Number Cited by Other Article(s)
1
Singh S, Kaur N, Gehlot A. Application of artificial intelligence in drug design: A review. Comput Biol Med 2024;179:108810. [PMID: 38991316 DOI: 10.1016/j.compbiomed.2024.108810] [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: 03/18/2024] [Revised: 05/31/2024] [Accepted: 06/24/2024] [Indexed: 07/13/2024]
2
Zhao C, Su KJ, Wu C, Cao X, Sha Q, Li W, Luo Z, Qing T, Qiu C, Zhao LJ, Liu A, Jiang L, Zhang X, Shen H, Zhou W, Deng HW. Multi-scale variational autoencoder for imputation of missing values in untargeted metabolomics using whole-genome sequencing data. Comput Biol Med 2024;179:108813. [PMID: 38955127 PMCID: PMC11324385 DOI: 10.1016/j.compbiomed.2024.108813] [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: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
3
Raheel A. Emotion analysis and recognition in 3D space using classifier-dependent feature selection in response to tactile enhanced audio-visual content using EEG. Comput Biol Med 2024;179:108807. [PMID: 38970831 DOI: 10.1016/j.compbiomed.2024.108807] [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: 04/01/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
4
Ma S, Li R, Li G, Wei M, Li B, Li Y, Ha C. Identification of a G-protein coupled receptor-related gene signature through bioinformatics analysis to construct a risk model for ovarian cancer prognosis. Comput Biol Med 2024;178:108747. [PMID: 38897150 DOI: 10.1016/j.compbiomed.2024.108747] [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: 12/19/2023] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/21/2024]
5
Biswas B, Kumar N, Sugimoto M, Hoque MA. scHD4E: Novel ensemble learning-based differential expression analysis method for single-cell RNA-sequencing data. Comput Biol Med 2024;178:108769. [PMID: 38897145 DOI: 10.1016/j.compbiomed.2024.108769] [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: 04/01/2024] [Revised: 05/14/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
6
Islam MA, Majumder MZH, Miah MS, Jannaty S. Precision healthcare: A deep dive into machine learning algorithms and feature selection strategies for accurate heart disease prediction. Comput Biol Med 2024;176:108432. [PMID: 38744014 DOI: 10.1016/j.compbiomed.2024.108432] [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: 02/08/2024] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 05/16/2024]
7
Ameli A, Peña-Castillo L, Usefi H. Assessing the reproducibility of machine-learning-based biomarker discovery in Parkinson's disease. Comput Biol Med 2024;174:108407. [PMID: 38603902 DOI: 10.1016/j.compbiomed.2024.108407] [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: 09/21/2023] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024]
8
Fu Y, Wang C, Wu Z, Zhang X, Liu Y, Wang X, Liu F, Chen Y, Zhang Y, Zhao H, Wang Q. Discovery of the potential biomarkers for early diagnosis of endometrial cancer via integrating metabolomics and transcriptomics. Comput Biol Med 2024;173:108327. [PMID: 38552279 DOI: 10.1016/j.compbiomed.2024.108327] [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: 02/06/2024] [Revised: 03/07/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
9
Chen J, Wen B. Bi-level gene selection of cancer by combining clustering and sparse learning. Comput Biol Med 2024;172:108236. [PMID: 38471351 DOI: 10.1016/j.compbiomed.2024.108236] [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: 08/03/2023] [Revised: 02/07/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024]
10
Zhou Y, Chen Z, Yang M, Chen F, Yin J, Zhang Y, Zhou X, Sun X, Ni Z, Chen L, Lv Q, Zhu F, Liu S. FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response. Brief Bioinform 2024;25:bbae223. [PMID: 38742521 PMCID: PMC11091744 DOI: 10.1093/bib/bbae223] [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: 10/17/2023] [Revised: 03/25/2024] [Accepted: 04/21/2024] [Indexed: 05/16/2024]  Open
11
Chen Y, Lu P, Wu S, Yang J, Liu W, Zhang Z, Xu Q. CD163-Mediated Small-Vessel Injury in Alzheimer's Disease: An Exploration from Neuroimaging to Transcriptomics. Int J Mol Sci 2024;25:2293. [PMID: 38396970 PMCID: PMC10888773 DOI: 10.3390/ijms25042293] [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: 01/10/2024] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024]  Open
12
Gao Y, Zhang G, Jiang S, Liu Y. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. IMETA 2024;3:e175. [PMID: 38868508 PMCID: PMC10989175 DOI: 10.1002/imt2.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 06/14/2024]
13
Yang Q, Chen S, Jiang W, Mi L, Liu J, Hu Y, Ji X, Wang J, Zhu F. MultiClassMetabo: A Superior Classification Model Constructed Using Metabolic Markers in Multiclass Metabolomics. Anal Chem 2024;96:1410-1418. [PMID: 38221713 DOI: 10.1021/acs.analchem.3c03212] [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: 01/16/2024]
14
Yin J, Chen Z, You N, Li F, Zhang H, Xue J, Ma H, Zhao Q, Yu L, Zeng S, Zhu F. VARIDT 3.0: the phenotypic and regulatory variability of drug transporter. Nucleic Acids Res 2024;52:D1490-D1502. [PMID: 37819041 PMCID: PMC10767864 DOI: 10.1093/nar/gkad818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/01/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]  Open
15
Zhou Y, Zhang Y, Zhao D, Yu X, Shen X, Zhou Y, Wang S, Qiu Y, Chen Y, Zhu F. TTD: Therapeutic Target Database describing target druggability information. Nucleic Acids Res 2024;52:D1465-D1477. [PMID: 37713619 PMCID: PMC10767903 DOI: 10.1093/nar/gkad751] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/31/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]  Open
16
Zhang Y, Zhou Y, Zhou Y, Yu X, Shen X, Hong Y, Zhang Y, Wang S, Mou M, Zhang J, Tao L, Gao J, Qiu Y, Chen Y, Zhu F. TheMarker: a comprehensive database of therapeutic biomarkers. Nucleic Acids Res 2024;52:D1450-D1464. [PMID: 37850638 PMCID: PMC10767989 DOI: 10.1093/nar/gkad862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/19/2023]  Open
17
Shen L, Sun X, Chen Z, Guo Y, Shen Z, Song Y, Xin W, Ding H, Ma X, Xu W, Zhou W, Che J, Tan L, Chen L, Chen S, Dong X, Fang L, Zhu F. ADCdb: the database of antibody-drug conjugates. Nucleic Acids Res 2024;52:D1097-D1109. [PMID: 37831118 PMCID: PMC10768060 DOI: 10.1093/nar/gkad831] [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] [Received: 08/14/2023] [Revised: 09/07/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]  Open
18
Wang J, Zhang L, Sun J, Yang X, Wu W, Chen W, Zhao Q. Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints. Methods 2024;221:18-26. [PMID: 38040204 DOI: 10.1016/j.ymeth.2023.11.014] [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: 10/21/2023] [Revised: 11/14/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]  Open
19
Zhou Q, Wang Y, Xin C, Wei X, Yao Y, Xia L. Identification of telomere-associated gene signatures to predict prognosis and drug sensitivity in glioma. Comput Biol Med 2024;168:107750. [PMID: 38029531 DOI: 10.1016/j.compbiomed.2023.107750] [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: 06/30/2023] [Revised: 11/11/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
20
Gong Y, Ding W, Wang P, Wu Q, Yao X, Yang Q. Evaluating Machine Learning Methods of Analyzing Multiclass Metabolomics. J Chem Inf Model 2023;63:7628-7641. [PMID: 38079572 DOI: 10.1021/acs.jcim.3c01525] [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: 12/26/2023]
21
Moslemi A, Ahmadian A. Dual regularized subspace learning using adaptive graph learning and rank constraint: Unsupervised feature selection on gene expression microarray datasets. Comput Biol Med 2023;167:107659. [PMID: 37950946 DOI: 10.1016/j.compbiomed.2023.107659] [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: 06/05/2023] [Revised: 10/13/2023] [Accepted: 10/31/2023] [Indexed: 11/13/2023]
22
Wu Z, Wang Z, Wu H, Zheng N, Huang D, Huang Z, Han H, Bao J, Xu H, Zhang R, Du Z, Wu D. The pan-cancer multi-omics landscape of key genes of sialylation combined with RNA-sequencing validation. Comput Biol Med 2023;166:107556. [PMID: 37801920 DOI: 10.1016/j.compbiomed.2023.107556] [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: 03/28/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023]
23
Liang S, Zhao Y, Jin J, Qiao J, Wang D, Wang Y, Wei L. Rm-LR: A long-range-based deep learning model for predicting multiple types of RNA modifications. Comput Biol Med 2023;164:107238. [PMID: 37515874 DOI: 10.1016/j.compbiomed.2023.107238] [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: 05/24/2023] [Revised: 06/16/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
24
Alkady W, ElBahnasy K, Gad W. A diagnostic model for COVID-19 based on proteomics analysis. Comput Biol Med 2023;162:107109. [PMID: 37276752 PMCID: PMC10232940 DOI: 10.1016/j.compbiomed.2023.107109] [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: 08/31/2022] [Revised: 05/21/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
25
Xu PH, Chen S, Wang Y, Jin S, Wang J, Ye D, Zhu X, Shen Y. FGFR3 mutation characterization identifies prognostic and immune-related gene signatures in bladder cancer. Comput Biol Med 2023;162:106976. [PMID: 37301098 DOI: 10.1016/j.compbiomed.2023.106976] [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: 10/11/2022] [Revised: 03/31/2023] [Accepted: 04/22/2023] [Indexed: 06/12/2023]
26
Luo X, Wang Y, Zou Q, Xu L. Recall DNA methylation levels at low coverage sites using a CNN model in WGBS. PLoS Comput Biol 2023;19:e1011205. [PMID: 37315069 DOI: 10.1371/journal.pcbi.1011205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/22/2023] [Indexed: 06/16/2023]  Open
27
Vahabzadeh V, Moattar MH. Robust microarray data feature selection using a correntropy based distance metric learning approach. Comput Biol Med 2023;161:107056. [PMID: 37235945 DOI: 10.1016/j.compbiomed.2023.107056] [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: 12/09/2022] [Revised: 04/18/2023] [Accepted: 05/20/2023] [Indexed: 05/28/2023]
28
Walakira A, Skubic C, Nadižar N, Rozman D, Režen T, Mraz M, Moškon M. Integrative computational modeling to unravel novel potential biomarkers in hepatocellular carcinoma. Comput Biol Med 2023;159:106957. [PMID: 37116239 DOI: 10.1016/j.compbiomed.2023.106957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/17/2023] [Accepted: 04/16/2023] [Indexed: 04/30/2023]
29
Zhou Y, Liu C, Zhang Z, Chen J, Zhao D, Li L, Tong M, Zhang G. Identification and validation of diagnostic biomarkers of coronary artery disease progression in type 1 diabetes via integrated computational and bioinformatics strategies. Comput Biol Med 2023;159:106940. [PMID: 37075605 DOI: 10.1016/j.compbiomed.2023.106940] [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: 12/11/2022] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023]
30
Fajarda O, Almeida JR, Duarte-Pereira S, Silva RM, Oliveira JL. Methodology to identify a gene expression signature by merging microarray datasets. Comput Biol Med 2023;159:106867. [PMID: 37060770 DOI: 10.1016/j.compbiomed.2023.106867] [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: 10/19/2022] [Revised: 03/01/2023] [Accepted: 03/30/2023] [Indexed: 04/17/2023]
31
Liu Y, Ma J, Wang X, Liu P, Cai C, Han Y, Zeng S, Feng Z, Shen H. Lipophagy-related gene RAB7A is involved in immune regulation and malignant progression in hepatocellular carcinoma. Comput Biol Med 2023;158:106862. [PMID: 37044053 DOI: 10.1016/j.compbiomed.2023.106862] [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: 11/16/2022] [Revised: 02/05/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023]
32
Pan J, Gao Y, Han H, Pan T, Guo J, Li S, Xu J, Li Y. Multi-omics characterization of RNA binding proteins reveals disease comorbidities and potential drugs in COVID-19. Comput Biol Med 2023;155:106651. [PMID: 36805221 PMCID: PMC9916187 DOI: 10.1016/j.compbiomed.2023.106651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
33
Nalepa J, Kotowski K, Machura B, Adamski S, Bozek O, Eksner B, Kokoszka B, Pekala T, Radom M, Strzelczak M, Zarudzki L, Krason A, Arcadu F, Tessier J. Deep learning automates bidimensional and volumetric tumor burden measurement from MRI in pre- and post-operative glioblastoma patients. Comput Biol Med 2023;154:106603. [PMID: 36738710 DOI: 10.1016/j.compbiomed.2023.106603] [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: 10/19/2022] [Revised: 01/11/2023] [Accepted: 01/22/2023] [Indexed: 02/05/2023]
34
Yang Y, Cao Y, Han X, Ma X, Li R, Wang R, Xiao L, Xie L. Revealing EXPH5 as a potential diagnostic gene biomarker of the late stage of COPD based on machine learning analysis. Comput Biol Med 2023;154:106621. [PMID: 36746116 DOI: 10.1016/j.compbiomed.2023.106621] [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: 09/16/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/01/2023]
35
Baran Y, Doğan B. scMAGS: Marker gene selection from scRNA-seq data for spatial transcriptomics studies. Comput Biol Med 2023;155:106634. [PMID: 36774895 DOI: 10.1016/j.compbiomed.2023.106634] [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: 11/05/2022] [Revised: 01/28/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
36
Moon S, Kim HJ, Lee Y, Lee YJ, Jung S, Lee JS, Hahn SH, Kim K, Roh JY, Nam S. Oncogenic signaling pathways and hallmarks of cancer in Korean patients with acral melanoma. Comput Biol Med 2023;154:106602. [PMID: 36716688 DOI: 10.1016/j.compbiomed.2023.106602] [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: 06/20/2022] [Revised: 12/23/2022] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
37
Huang H, Cai X, Lin J, Wu Q, Zhang K, Lin Y, Liu B, Lin J. A novel five-gene metabolism-related risk signature for predicting prognosis and immune infiltration in endometrial cancer: A TCGA data mining. Comput Biol Med 2023;155:106632. [PMID: 36805217 DOI: 10.1016/j.compbiomed.2023.106632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/01/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023]
38
Marjit S, Bhattacharyya T, Chatterjee B, Sarkar R. Simulated annealing aided genetic algorithm for gene selection from microarray data. Comput Biol Med 2023;158:106854. [PMID: 37023541 DOI: 10.1016/j.compbiomed.2023.106854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/26/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023]
39
Rather AA, Chachoo MA. Robust correlation estimation and UMAP assisted topological analysis of omics data for disease subtyping. Comput Biol Med 2023;155:106640. [PMID: 36774889 DOI: 10.1016/j.compbiomed.2023.106640] [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: 11/07/2022] [Revised: 01/08/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023]
40
Zafari N, Bathaei P, Velayati M, Khojasteh-Leylakoohi F, Khazaei M, Fiuji H, Nassiri M, Hassanian SM, Ferns GA, Nazari E, Avan A. Integrated analysis of multi-omics data for the discovery of biomarkers and therapeutic targets for colorectal cancer. Comput Biol Med 2023;155:106639. [PMID: 36805214 DOI: 10.1016/j.compbiomed.2023.106639] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/14/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
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He H, Duo H, Hao Y, Zhang X, Zhou X, Zeng Y, Li Y, Li B. Computational drug repurposing by exploiting large-scale gene expression data: Strategy, methods and applications. Comput Biol Med 2023;155:106671. [PMID: 36805225 DOI: 10.1016/j.compbiomed.2023.106671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
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Yan TC, Yue ZX, Xu HQ, Liu YH, Hong YF, Chen GX, Tao L, Xie T. A systematic review of state-of-the-art strategies for machine learning-based protein function prediction. Comput Biol Med 2023;154:106446. [PMID: 36680931 DOI: 10.1016/j.compbiomed.2022.106446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
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Wang T, Sun J, Zhao Q. Investigating cardiotoxicity related with hERG channel blockers using molecular fingerprints and graph attention mechanism. Comput Biol Med 2023;153:106464. [PMID: 36584603 DOI: 10.1016/j.compbiomed.2022.106464] [Citation(s) in RCA: 110] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
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Cheng N, Liu J, Chen C, Zheng T, Li C, Huang J. Prediction of lung cancer metastasis by gene expression. Comput Biol Med 2023;153:106490. [PMID: 36638618 DOI: 10.1016/j.compbiomed.2022.106490] [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: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
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Huang P, Yan L, Li Z, Zhao S, Feng Y, Zeng J, Chen L, Huang A, Chen Y, Lei S, Huang X, Deng Y, Xie D, Guan H, Peng W, Yu L, Chen B. Potential shared gene signatures and molecular mechanisms between atherosclerosis and depression: Evidence from transcriptome data. Comput Biol Med 2023;152:106450. [PMID: 36565484 DOI: 10.1016/j.compbiomed.2022.106450] [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: 10/18/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
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Xiang J, Wang X, Wang X, Zhang J, Yang S, Yang W, Han X, Liu Y. Automatic diagnosis and grading of Prostate Cancer with weakly supervised learning on whole slide images. Comput Biol Med 2023;152:106340. [PMID: 36481762 DOI: 10.1016/j.compbiomed.2022.106340] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/02/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
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Zhao Y, Zhang L, Hu Q, Zhu D, Xie Z. Identification and analysis of C17orf53 as a prognostic signature for hepatocellular carcinoma. Comput Biol Med 2023;152:106348. [PMID: 36470143 DOI: 10.1016/j.compbiomed.2022.106348] [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: 06/11/2022] [Revised: 10/28/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
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Liu C, Zhou Y, Zhou Y, Tang X, Tang L, Wang J. Identification of crucial genes for predicting the risk of atherosclerosis with system lupus erythematosus based on comprehensive bioinformatics analysis and machine learning. Comput Biol Med 2023;152:106388. [PMID: 36470144 DOI: 10.1016/j.compbiomed.2022.106388] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
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Yue ZX, Yan TC, Xu HQ, Liu YH, Hong YF, Chen GX, Xie T, Tao L. A systematic review on the state-of-the-art strategies for protein representation. Comput Biol Med 2023;152:106440. [PMID: 36543002 DOI: 10.1016/j.compbiomed.2022.106440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
50
Zhou Y, Zhang Y, Li F, Lian X, Zhu Q, Zhu F, Qiu Y. SISPRO: signature identification for spatial proteomics. J Mol Biol 2023. [DOI: 10.1016/j.jmb.2022.167944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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