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For: Fillbrunn A, Dietz C, Pfeuffer J, Rahn R, Landrum GA, Berthold MR. KNIME for reproducible cross-domain analysis of life science data. J Biotechnol 2017;261:149-156. [DOI: 10.1016/j.jbiotec.2017.07.028] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
1
Ballweg T, Liu M, Mama A, Wenzel W, Franzreb M. Molecular insights into chromatography: Automated workflows for the virtual design of methacrylate-based chromatography resins. J Chromatogr A 2025;1754:466027. [PMID: 40367847 DOI: 10.1016/j.chroma.2025.466027] [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: 02/08/2025] [Revised: 04/14/2025] [Accepted: 05/06/2025] [Indexed: 05/16/2025]
2
Kurz NS, Kornrumpf K, Tucholski T, Drofenik K, König A, Beißbarth T, Dönitz J. Onkopus: precise interpretation and prioritization of sequence variants for biomedical research and precision medicine. Nucleic Acids Res 2025:gkaf376. [PMID: 40377094 DOI: 10.1093/nar/gkaf376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Revised: 04/14/2025] [Accepted: 04/25/2025] [Indexed: 05/18/2025]  Open
3
Schimunek J, Luukkonen S, Klambauer G. MHNfs: Prompting In-Context Bioactivity Predictions for Low-Data Drug Discovery. J Chem Inf Model 2025;65:4243-4250. [PMID: 40302701 PMCID: PMC12076497 DOI: 10.1021/acs.jcim.4c02373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 04/09/2025] [Accepted: 04/10/2025] [Indexed: 05/02/2025]
4
Astolfi A, Cernicchi G, Primavera E, Rocchi M, Manfroni G, Sabatini S, Letizia Barreca M. Addressing Data Point Homogeneity and Annotation Challenges to Enhance Data-Driven Approaches: The S. aureus NorA Efflux Pump Case Study. ChemMedChem 2025;20:e202400927. [PMID: 39843395 DOI: 10.1002/cmdc.202400927] [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: 11/16/2024] [Revised: 01/15/2025] [Accepted: 01/20/2025] [Indexed: 01/24/2025]
5
Zhao Y, Cao LY, Zhao YX, Zhao D, Huang YF, Wang F, Wang Q. Harnessing Risk Assessment for Thrombosis and Bleeding to Optimize Anticoagulation Strategy in Nonvalvular Atrial Fibrillation. Thromb Haemost 2025;125:492-504. [PMID: 39137902 PMCID: PMC12040435 DOI: 10.1055/a-2385-1452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/04/2024] [Indexed: 08/15/2024]
6
Steinbeck C. The evolution of open science in cheminformatics: a journey from closed systems to collaborative innovation. J Cheminform 2025;17:44. [PMID: 40181430 PMCID: PMC11969984 DOI: 10.1186/s13321-025-00990-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Accepted: 03/19/2025] [Indexed: 04/05/2025]  Open
7
Ge W, De Silva R, Fan Y, Sisson SA, Stenzel MH. Machine Learning in Polymer Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2025;37:e2413695. [PMID: 39924835 PMCID: PMC11923530 DOI: 10.1002/adma.202413695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 12/21/2024] [Indexed: 02/11/2025]
8
Malashin I, Tynchenko V, Gantimurov A, Nelyub V, Borodulin A. Support Vector Machines in Polymer Science: A Review. Polymers (Basel) 2025;17:491. [PMID: 40006153 PMCID: PMC11859395 DOI: 10.3390/polym17040491] [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: 01/06/2025] [Revised: 02/06/2025] [Accepted: 02/11/2025] [Indexed: 02/27/2025]  Open
9
Zhang D, Deacon BN, Li W, Lian G, Chen T. A computational workflow for end-to-end simulation of percutaneous absorption. Int J Pharm 2025;670:125084. [PMID: 39681219 DOI: 10.1016/j.ijpharm.2024.125084] [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: 08/02/2024] [Revised: 11/29/2024] [Accepted: 12/11/2024] [Indexed: 12/18/2024]
10
Camci M, Şenol H, Kose A, Karaman Mayack B, Alayoubi MM, Karali N, Gezginci MH. Bioisosteric replacement of the carboxylic acid group in Hepatitis-C virus NS5B thumb site II inhibitors: phenylalanine derivatives. Eur J Med Chem 2024;279:116832. [PMID: 39288595 DOI: 10.1016/j.ejmech.2024.116832] [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: 07/11/2023] [Revised: 11/03/2023] [Accepted: 09/01/2024] [Indexed: 09/19/2024]
11
Luo Y, Zhao C, Chen F. Multiomics Research: Principles and Challenges in Integrated Analysis. BIODESIGN RESEARCH 2024;6:0059. [PMID: 39990095 PMCID: PMC11844812 DOI: 10.34133/bdr.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/24/2024] [Accepted: 10/28/2024] [Indexed: 02/25/2025]  Open
12
Pekdas IG, Uflaz E, Tornacı F, Arslan O, Turan O. Developing a machine learning-based evaluation system for the recruitment of maritime professionals. OCEAN ENGINEERING 2024;313:119406. [DOI: 10.1016/j.oceaneng.2024.119406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2025]
13
Henkel M, Fillbrunn A, Marchand V, Raghunathan G, Berthold MR, Motorin Y, Marx A. A DNA Polymerase Variant Senses the Epigenetic Marker 5-Methylcytosine by Increased Misincorporation. Angew Chem Int Ed Engl 2024;63:e202413304. [PMID: 39449390 DOI: 10.1002/anie.202413304] [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: 07/15/2024] [Indexed: 10/26/2024]
14
Aksenova A, Johny A, Adams T, Gribbon P, Jacobs M, Hofmann-Apitius M. Current state of data stewardship tools in life science. Front Big Data 2024;7:1428568. [PMID: 39351001 PMCID: PMC11439729 DOI: 10.3389/fdata.2024.1428568] [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: 05/06/2024] [Accepted: 08/23/2024] [Indexed: 10/04/2024]  Open
15
Keikhosravi A, Almansour F, Bohrer CH, Fursova NA, Guin K, Sood V, Misteli T, Larson DR, Pegoraro G. High-throughput image processing software for the study of nuclear architecture and gene expression. Sci Rep 2024;14:18426. [PMID: 39117696 PMCID: PMC11310328 DOI: 10.1038/s41598-024-66600-1] [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: 10/27/2023] [Accepted: 07/02/2024] [Indexed: 08/10/2024]  Open
16
Goyzueta-Mamani LD, Barazorda-Ccahuana HL, Candia-Puma MA, Galdino AS, Machado-de-Avila RA, Giunchetti RC, Medina-Franco JL, Florin-Christensen M, Ferraz Coelho EA, Chávez-Fumagalli MA. Targeting Leishmania infantum Mannosyl-oligosaccharide glucosidase with natural products: potential pH-dependent inhibition explored through computer-aided drug design. Front Pharmacol 2024;15:1403203. [PMID: 38873424 PMCID: PMC11169604 DOI: 10.3389/fphar.2024.1403203] [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: 03/19/2024] [Accepted: 04/25/2024] [Indexed: 06/15/2024]  Open
17
Long TZ, Jiang DJ, Shi SH, Deng YC, Wang WX, Cao DS. Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence. J Chem Inf Model 2024;64:3222-3236. [PMID: 38498003 DOI: 10.1021/acs.jcim.4c00159] [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: 03/19/2024]
18
von Lersner A, Fernandes F, Ozawa PM, Jackson M, Masureel M, Ho H, Lima SM, Vagner T, Sung BH, Wehbe M, Franze K, Pua H, Wilson JT, Irish JM, Weaver AM, Di Vizio D, Zijlstra A. Multiparametric Single-Vesicle Flow Cytometry Resolves Extracellular Vesicle Heterogeneity and Reveals Selective Regulation of Biogenesis and Cargo Distribution. ACS NANO 2024;18:10464-10484. [PMID: 38578701 PMCID: PMC11025123 DOI: 10.1021/acsnano.3c11561] [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: 11/20/2023] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
19
Mansouri K, Moreira-Filho JT, Lowe CN, Charest N, Martin T, Tkachenko V, Judson R, Conway M, Kleinstreuer NC, Williams AJ. Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling. J Cheminform 2024;16:19. [PMID: 38378618 PMCID: PMC10880251 DOI: 10.1186/s13321-024-00814-3] [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: 11/29/2023] [Accepted: 02/10/2024] [Indexed: 02/22/2024]  Open
20
Barazorda-Ccahuana HL, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Galdino AS, Machado-de-Ávila RA, Giunchetti RC, Coelho EAF, Chávez-Fumagalli MA. Targeting with Structural Analogs of Natural Products the Purine Salvage Pathway in Leishmania (Leishmania) infantum by Computer-Aided Drug-Design Approaches. Trop Med Infect Dis 2024;9:41. [PMID: 38393130 PMCID: PMC10891554 DOI: 10.3390/tropicalmed9020041] [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: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024]  Open
21
Jan M, Spangaro A, Lenartowicz M, Mattiazzi Usaj M. From pixels to insights: Machine learning and deep learning for bioimage analysis. Bioessays 2024;46:e2300114. [PMID: 38058114 DOI: 10.1002/bies.202300114] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 12/08/2023]
22
Gogoberidze N, Cimini BA. Defining the boundaries: challenges and advances in identifying cells in microscopy images. Curr Opin Biotechnol 2024;85:103055. [PMID: 38142646 PMCID: PMC11170924 DOI: 10.1016/j.copbio.2023.103055] [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: 10/07/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/26/2023]
23
Mikutis S, Lawrinowitz S, Kretzer C, Dunsmore L, Sketeris L, Rodrigues T, Werz O, Bernardes GJL. Machine Learning Uncovers Natural Product Modulators of the 5-Lipoxygenase Pathway and Facilitates the Elucidation of Their Biological Mechanisms. ACS Chem Biol 2024;19:217-229. [PMID: 38149598 PMCID: PMC10804367 DOI: 10.1021/acschembio.3c00725] [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: 11/28/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
24
Zhan C, Tang T, Wu E, Zhang Y, He M, Wu R, Bi C, Wang J, Zhang Y, Shen B. From multi-omics approaches to personalized medicine in myocardial infarction. Front Cardiovasc Med 2023;10:1250340. [PMID: 37965091 PMCID: PMC10642346 DOI: 10.3389/fcvm.2023.1250340] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]  Open
25
Donisi L, Jacob D, Guerrini L, Prisco G, Esposito F, Cesarelli M, Amato F, Gargiulo P. sEMG Spectral Analysis and Machine Learning Algorithms Are Able to Discriminate Biomechanical Risk Classes Associated with Manual Material Liftings. Bioengineering (Basel) 2023;10:1103. [PMID: 37760205 PMCID: PMC10525808 DOI: 10.3390/bioengineering10091103] [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: 07/24/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]  Open
26
Barazorda-Ccahuana HL, Ranilla LG, Candia-Puma MA, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Davila-Del-Carpio G, Medina-Franco JL, Chávez-Fumagalli MA. PeruNPDB: the Peruvian Natural Products Database for in silico drug screening. Sci Rep 2023;13:7577. [PMID: 37165197 PMCID: PMC10170056 DOI: 10.1038/s41598-023-34729-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023]  Open
27
Lei Y, Chen X, Shi J, Liu Y, Xu YJ. Development and application of a data processing method for food metabolomics analysis. Mol Omics 2023. [PMID: 37139637 DOI: 10.1039/d2mo00338d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
28
Romero S, Unchwaniwala N, Evans EL, Eliceiri KW, Loeb DD, Sherer NM. Live Cell Imaging Reveals HBV Capsid Translocation from the Nucleus To the Cytoplasm Enabled by Cell Division. mBio 2023;14:e0330322. [PMID: 36809075 PMCID: PMC10127671 DOI: 10.1128/mbio.03303-22] [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: 11/29/2022] [Accepted: 01/17/2023] [Indexed: 02/23/2023]  Open
29
Lignieres L, Sénécaut N, Dang T, Bellutti L, Hamon M, Terrier S, Legros V, Chevreux G, Lelandais G, Mège RM, Dumont J, Camadro JM. Extending the Range of SLIM-Labeling Applications: From Human Cell Lines in Culture to Caenorhabditis elegans Whole-Organism Labeling. J Proteome Res 2023;22:996-1002. [PMID: 36748112 PMCID: PMC9990122 DOI: 10.1021/acs.jproteome.2c00699] [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: 02/08/2023]
30
Zhao Y, Cao LY, Zhao YX, Wang F, Xie LL, Xing HY, Wang Q. Medical record data-enabled machine learning can enhance prediction of left atrial appendage thrombosis in nonvalvular atrial fibrillation. Thromb Res 2023;223:174-183. [PMID: 36764084 DOI: 10.1016/j.thromres.2023.01.001] [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: 10/11/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
31
Su Y, Huang C, Yin W, Lyu X, Ma L, Tao Z. Diabetes Mellitus risk prediction using age adaptation models. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2022.104381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
32
Long TZ, Shi SH, Liu S, Lu AP, Liu ZQ, Li M, Hou TJ, Cao DS. Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. J Chem Inf Model 2023;63:111-125. [PMID: 36472475 DOI: 10.1021/acs.jcim.2c01088] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
33
Griess K, Rieck M, Müller N, Karsai G, Hartwig S, Pelligra A, Hardt R, Schlegel C, Kuboth J, Uhlemeyer C, Trenkamp S, Jeruschke K, Weiss J, Peifer-Weiss L, Xu W, Cames S, Yi X, Cnop M, Beller M, Stark H, Kondadi AK, Reichert AS, Markgraf D, Wammers M, Häussinger D, Kuss O, Lehr S, Eizirik D, Lickert H, Lammert E, Roden M, Winter D, Al-Hasani H, Höglinger D, Hornemann T, Brüning JC, Belgardt BF. Sphingolipid subtypes differentially control proinsulin processing and systemic glucose homeostasis. Nat Cell Biol 2023;25:20-29. [PMID: 36543979 PMCID: PMC9859757 DOI: 10.1038/s41556-022-01027-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 10/11/2022] [Indexed: 12/24/2022]
34
Sharma C, Sakhuja S, Nijjer S. Recent trends of green human resource management: Text mining and network analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022;29:84916-84935. [PMID: 35790632 PMCID: PMC9255839 DOI: 10.1007/s11356-022-21471-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
35
Chicco D, Oneto L, Tavazzi E. Eleven quick tips for data cleaning and feature engineering. PLoS Comput Biol 2022;18:e1010718. [PMID: 36520712 PMCID: PMC9754225 DOI: 10.1371/journal.pcbi.1010718] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
36
Morger A, Garcia de Lomana M, Norinder U, Svensson F, Kirchmair J, Mathea M, Volkamer A. Studying and mitigating the effects of data drifts on ML model performance at the example of chemical toxicity data. Sci Rep 2022;12:7244. [PMID: 35508546 PMCID: PMC9068909 DOI: 10.1038/s41598-022-09309-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022]  Open
37
R Packages for Data Quality Assessments and Data Monitoring: A Software Scoping Review with Recommendations for Future Developments. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
38
Alka O, Shanthamoorthy P, Witting M, Kleigrewe K, Kohlbacher O, Röst HL. DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics. Nat Commun 2022;13:1347. [PMID: 35292629 PMCID: PMC8924252 DOI: 10.1038/s41467-022-29006-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/18/2022] [Indexed: 11/09/2022]  Open
39
Soiland-Reyes S, Bayarri G, Andrio P, Long R, Lowe D, Niewielska A, Hospital A, Groth P. Making Canonical Workflow Building Blocks Interoperable across Workflow Languages. DATA INTELLIGENCE 2022. [DOI: 10.1162/dint_a_00135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]  Open
40
Watson ER, Taherian Fard A, Mar JC. Computational Methods for Single-Cell Imaging and Omics Data Integration. Front Mol Biosci 2022;8:768106. [PMID: 35111809 PMCID: PMC8801747 DOI: 10.3389/fmolb.2021.768106] [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: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]  Open
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Noor A. Improving bioinformatics software quality through incorporation of software engineering practices. PeerJ Comput Sci 2022;8:e839. [PMID: 35111923 PMCID: PMC8771759 DOI: 10.7717/peerj-cs.839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
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Jukič M, Kores K, Janežič D, Bren U. Repurposing of Drugs for SARS-CoV-2 Using Inverse Docking Fingerprints. Front Chem 2021;9:757826. [PMID: 35028304 PMCID: PMC8748264 DOI: 10.3389/fchem.2021.757826] [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: 08/12/2021] [Accepted: 11/12/2021] [Indexed: 01/08/2023]  Open
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Samuel ELG, Holmes SL, Young DW. Processing binding data using an open-source workflow. J Cheminform 2021;13:99. [PMID: 34895330 PMCID: PMC8666039 DOI: 10.1186/s13321-021-00577-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022]  Open
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Phanchana M, Harnvoravongchai P, Wongkuna S, Phetruen T, Phothichaisri W, Panturat S, Pipatthana M, Charoensutthivarakul S, Chankhamhaengdecha S, Janvilisri T. Frontiers in antibiotic alternatives for Clostridioides difficile infection. World J Gastroenterol 2021;27:7210-7232. [PMID: 34876784 PMCID: PMC8611198 DOI: 10.3748/wjg.v27.i42.7210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/12/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023]  Open
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Yang ZY, Fu L, Lu AP, Liu S, Hou TJ, Cao DS. Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion. J Cheminform 2021;13:86. [PMID: 34774096 PMCID: PMC8590336 DOI: 10.1186/s13321-021-00564-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/30/2021] [Indexed: 12/01/2022]  Open
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Kolar K, Dondorp D, Zwiggelaar JC, Høyer J, Chatzigeorgiou M. Mesmerize is a dynamically adaptable user-friendly analysis platform for 2D and 3D calcium imaging data. Nat Commun 2021;12:6569. [PMID: 34772921 PMCID: PMC8589933 DOI: 10.1038/s41467-021-26550-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 10/13/2021] [Indexed: 01/09/2023]  Open
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Wang M, Hou S, Liu Y, Li D, Lin J. Identification of Novel Antagonists Targeting Cannabinoid Receptor 2 Using a Multi-Step Virtual Screening Strategy. Molecules 2021;26:molecules26216679. [PMID: 34771087 PMCID: PMC8587544 DOI: 10.3390/molecules26216679] [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: 09/23/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]  Open
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Balluet M, Sizaire F, El Habouz Y, Walter T, Pont J, Giroux B, Bouchareb O, Tramier M, Pecreaux J. Neural network fast-classifies biological images through features selecting to power automated microscopy. J Microsc 2021;285:3-19. [PMID: 34623634 DOI: 10.1111/jmi.13062] [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: 03/15/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022]
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Wratten L, Wilm A, Göke J. Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nat Methods 2021;18:1161-1168. [PMID: 34556866 DOI: 10.1038/s41592-021-01254-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 07/29/2021] [Indexed: 02/08/2023]
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Dobson ETA, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW. ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Curr Protoc 2021;1:e89. [PMID: 34038030 DOI: 10.1002/cpz1.89] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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