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For: Markowetz F. All biology is computational biology. PLoS Biol 2017;15:e2002050. [PMID: 28278152 PMCID: PMC5344307 DOI: 10.1371/journal.pbio.2002050] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Aguilera LU, Weber LM, Ron E, King CR, Öcal K, Popinga A, Cook J, May MP, Raymond WS, Fox ZR, Forero-Quintero LS, Forman JR, David A, Munsky B. Methods in quantitative biology-from analysis of single-cell microscopy images to inference of predictive models for stochastic gene expression. Phys Biol 2025;22:042001. [PMID: 40388970 DOI: 10.1088/1478-3975/adda85] [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: 03/23/2025] [Accepted: 05/19/2025] [Indexed: 05/21/2025]
2
Andreini C. Twenty years in metalloprotein bioinformatics: A short history of a long journey. J Inorg Biochem 2025;266:112854. [PMID: 39961171 DOI: 10.1016/j.jinorgbio.2025.112854] [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: 12/31/2024] [Revised: 01/31/2025] [Accepted: 02/07/2025] [Indexed: 03/01/2025]
3
Mougkogiannis P, Adamatzky A. On the Response of Proteinoid Ensembles to Fibonacci Sequences. ACS OMEGA 2025;10:10401-10424. [PMID: 40124033 PMCID: PMC11923683 DOI: 10.1021/acsomega.4c10571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 02/14/2025] [Accepted: 02/26/2025] [Indexed: 03/25/2025]
4
Hemel IMGM, Steen C, Denil SLIJ, Ertaylan G, Kutmon M, Adriaens M, Gerards M. The unusual suspect: A novel role for intermediate filament proteins in mitochondrial morphology. Mitochondrion 2025;81:102008. [PMID: 39909388 DOI: 10.1016/j.mito.2025.102008] [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: 12/20/2024] [Revised: 01/30/2025] [Accepted: 02/01/2025] [Indexed: 02/07/2025]
5
Ferenc K, Rauluseviciute I, Hovan L, Kumar V, Kuijjer ML, Mathelier A. Improving bioinformatics software quality through teamwork. Bioinformatics 2024;40:btae632. [PMID: 39436982 PMCID: PMC11537420 DOI: 10.1093/bioinformatics/btae632] [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: 08/07/2024] [Revised: 10/02/2024] [Accepted: 10/21/2024] [Indexed: 10/25/2024]  Open
6
Gallagher K, Creswell R, Lambert B, Robinson M, Lok Lei C, Mirams GR, Gavaghan DJ. Ten simple rules for training scientists to make better software. PLoS Comput Biol 2024;20:e1012410. [PMID: 39264985 PMCID: PMC11392269 DOI: 10.1371/journal.pcbi.1012410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]  Open
7
Matuszyńska A, Ebenhöh O, Zurbriggen MD, Ducat DC, Axmann IM. A new era of synthetic biology-microbial community design. Synth Biol (Oxf) 2024;9:ysae011. [PMID: 39086602 PMCID: PMC11290361 DOI: 10.1093/synbio/ysae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 06/21/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]  Open
8
Ouzounis CA. Biology's transformation: from observation through experiment to computation. BIOINFORMATICS ADVANCES 2024;4:vbae069. [PMID: 38799705 PMCID: PMC11127110 DOI: 10.1093/bioadv/vbae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
9
Wang X, Jenner AL, Salomone R, Warne DJ, Drovandi C. Calibration of agent based models for monophasic and biphasic tumour growth using approximate Bayesian computation. J Math Biol 2024;88:28. [PMID: 38358410 PMCID: PMC10869399 DOI: 10.1007/s00285-024-02045-4] [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: 06/28/2023] [Revised: 10/25/2023] [Accepted: 12/27/2023] [Indexed: 02/16/2024]
10
Berezin CT, Aguilera LU, Billerbeck S, Bourne PE, Densmore D, Freemont P, Gorochowski TE, Hernandez SI, Hillson NJ, King CR, Köpke M, Ma S, Miller KM, Moon TS, Moore JH, Munsky B, Myers CJ, Nicholas DA, Peccoud SJ, Zhou W, Peccoud J. Ten simple rules for managing laboratory information. PLoS Comput Biol 2023;19:e1011652. [PMID: 38060459 PMCID: PMC10703290 DOI: 10.1371/journal.pcbi.1011652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]  Open
11
Kowalski TW, Feira MF, Lord VO, Gomes JDA, Giudicelli GC, Fraga LR, Sanseverino MTV, Recamonde-Mendoza M, Schuler-Faccini L, Vianna FSL. A New Strategy for the Old Challenge of Thalidomide: Systems Biology Prioritization of Potential Immunomodulatory Drug (IMiD)-Targeted Transcription Factors. Int J Mol Sci 2023;24:11515. [PMID: 37511270 PMCID: PMC10380514 DOI: 10.3390/ijms241411515] [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: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]  Open
12
Naha A, Antony S, Nath S, Sharma D, Mishra A, Biju DT, Madhavan A, Binod P, Varjani S, Sindhu R. A hypothetical model of multi-layered cost-effective wastewater treatment plant integrating microbial fuel cell and nanofiltration technology: A comprehensive review on wastewater treatment and sustainable remediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023;323:121274. [PMID: 36804140 DOI: 10.1016/j.envpol.2023.121274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
13
Sharma P, Dahiya S, Kaur P, Kapil A. Computational biology: Role and scope in taming antimicrobial resistance. Indian J Med Microbiol 2023;41:33-38. [PMID: 36870746 DOI: 10.1016/j.ijmmb.2022.12.005] [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: 05/20/2022] [Revised: 12/11/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023]
14
Sieow BFL, De Sotto R, Seet ZRD, Hwang IY, Chang MW. Synthetic Biology Meets Machine Learning. Methods Mol Biol 2023;2553:21-39. [PMID: 36227537 DOI: 10.1007/978-1-0716-2617-7_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
15
Rademaker DT, Xue LC, ‘t Hoen PAC, Vriend G. Entropy and Variability: A Second Opinion by Deep Learning. Biomolecules 2022;12:biom12121740. [PMID: 36551168 PMCID: PMC9775329 DOI: 10.3390/biom12121740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/13/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022]  Open
16
Cordier BA, Sawaya NPD, Guerreschi GG, McWeeney SK. Biology and medicine in the landscape of quantum advantages. J R Soc Interface 2022;19:20220541. [PMID: 36448288 PMCID: PMC9709576 DOI: 10.1098/rsif.2022.0541] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022]  Open
17
Topçu A, Kılıç S, Özgür E, Türkmen D, Denizli A. Inspirations of Biomimetic Affinity Ligands: A Review. ACS OMEGA 2022;7:32897-32907. [PMID: 36157742 PMCID: PMC9494661 DOI: 10.1021/acsomega.2c03530] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
18
Cohen‐Sasson O, Tur‐Sinai O. Facilitating open science without sacrificing IP rights. EMBO Rep 2022;23:e55841. [PMID: 35972193 PMCID: PMC9442283 DOI: 10.15252/embr.202255841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022]  Open
19
Caughman AM, Weigel EG. Biology Students' Math and Computer Science Task Values Are Closely Linked. CBE LIFE SCIENCES EDUCATION 2022;21:ar43. [PMID: 35759628 PMCID: PMC9582834 DOI: 10.1187/cbe.21-07-0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
20
Filazzola A, Lortie CJ. A call for clean code to effectively communicate science. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
21
Alser M, Lindegger J, Firtina C, Almadhoun N, Mao H, Singh G, Gomez-Luna J, Mutlu O. From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures. Comput Struct Biotechnol J 2022;20:4579-4599. [PMID: 36090814 PMCID: PMC9436709 DOI: 10.1016/j.csbj.2022.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 02/01/2023]  Open
22
Ren P, Yang X, Wang T, Hou Y, Zhang Z. Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. Comput Struct Biotechnol J 2022;20:2322-2331. [PMID: 35615014 PMCID: PMC9120227 DOI: 10.1016/j.csbj.2022.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/03/2022]  Open
23
Selvaggio G, Cristellon S, Marchetti L. A Novel Hybrid Logic-ODE Modeling Approach to Overcome Knowledge Gaps. Front Mol Biosci 2022;8:760077. [PMID: 34988115 PMCID: PMC8721169 DOI: 10.3389/fmolb.2021.760077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022]  Open
24
Sharma D, Sharma A, Singh B, Kumar S, Verma S. Neglected scrub typhus: An updated review with a focus on omics technologies. ASIAN PAC J TROP MED 2022. [DOI: 10.4103/1995-7645.364003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
25
Helmy M, Agrawal R, Ali J, Soudy M, Bui TT, Selvarajoo K. GeneCloudOmics: A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis. FRONTIERS IN BIOINFORMATICS 2021;1:693836. [PMID: 36303746 PMCID: PMC9581002 DOI: 10.3389/fbinf.2021.693836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/14/2021] [Indexed: 11/18/2022]  Open
26
Liu L, Gao H, Zaikin A, Chen S. Unraveling Aβ-Mediated Multi-Pathway Calcium Dynamics in Astrocytes: Implications for Alzheimer's Disease Treatment From Simulations. Front Physiol 2021;12:767892. [PMID: 34777023 PMCID: PMC8581622 DOI: 10.3389/fphys.2021.767892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/02/2023]  Open
27
Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley SD, Gosline SJC, Lȇ Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, Fertig EJ. A field guide to cultivating computational biology. PLoS Biol 2021;19:e3001419. [PMID: 34618807 PMCID: PMC8525744 DOI: 10.1371/journal.pbio.3001419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/19/2021] [Indexed: 11/18/2022]  Open
28
Padhi AK, Rath SL, Tripathi T. Accelerating COVID-19 Research Using Molecular Dynamics Simulation. J Phys Chem B 2021;125:9078-9091. [PMID: 34319118 PMCID: PMC8340580 DOI: 10.1021/acs.jpcb.1c04556] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/12/2021] [Indexed: 12/14/2022]
29
Lortie CJ. The early bird gets the return: The benefits of publishing your data sooner. Ecol Evol 2021;11:10736-10740. [PMID: 34429876 PMCID: PMC8366834 DOI: 10.1002/ece3.7853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/02/2022]  Open
30
Chen Q, Leaman R, Allot A, Luo L, Wei CH, Yan S, Lu Z. Artificial Intelligence in Action: Addressing the COVID-19 Pandemic with Natural Language Processing. Annu Rev Biomed Data Sci 2021;4:313-339. [PMID: 34465169 DOI: 10.1146/annurev-biodatasci-021821-061045] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
31
Lydic R, Baghdoyan HA. Prefrontal Cortex Metabolome Is Modified by Opioids, Anesthesia, and Sleep. Physiology (Bethesda) 2021;36:203-219. [PMID: 34159803 DOI: 10.1152/physiol.00043.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
32
Schweizer RM, Saarman N, Ramstad KM, Forester BR, Kelley JL, Hand BK, Malison RL, Ackiss AS, Watsa M, Nelson TC, Beja-Pereira A, Waples RS, Funk WC, Luikart G. Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field. J Hered 2021;112:313-327. [PMID: 33860294 DOI: 10.1093/jhered/esab019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/13/2021] [Indexed: 02/07/2023]  Open
33
Driscoll MK, Zaritsky A. Data science in cell imaging. J Cell Sci 2021;134:jcs254292. [PMID: 33795377 PMCID: PMC8034880 DOI: 10.1242/jcs.254292] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
34
Lawlor B, Sleator RD. The roles of code in biology. Sci Prog 2021;104:368504211010570. [PMID: 33856939 PMCID: PMC10454959 DOI: 10.1177/00368504211010570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
35
Richter CF, Lortie CJ, Kelly TL, Filazzola A, Nunes KA, Sarkar R. Online but not remote: Adapting field-based ecology laboratories for online learning. Ecol Evol 2021;11:3616-3624. [PMID: 33898014 PMCID: PMC8057323 DOI: 10.1002/ece3.7008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/14/2020] [Accepted: 10/16/2020] [Indexed: 11/06/2022]  Open
36
Thessen AE, Bogdan P, Patterson DJ, Casey TM, Hinojo-Hinojo C, de Lange O, Haendel MA. From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences. PLoS Biol 2021;19:e3001129. [PMID: 33770077 PMCID: PMC7997011 DOI: 10.1371/journal.pbio.3001129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
37
Bourne PE. Is "bioinformatics" dead? PLoS Biol 2021;19:e3001165. [PMID: 33735179 PMCID: PMC7984605 DOI: 10.1371/journal.pbio.3001165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/22/2021] [Indexed: 11/18/2022]  Open
38
Jafari M, Guan Y, Wedge DC, Ansari-Pour N. Re-evaluating experimental validation in the Big Data Era: a conceptual argument. Genome Biol 2021;22:71. [PMID: 33627141 PMCID: PMC7903713 DOI: 10.1186/s13059-021-02292-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
39
Chitoiu L, Dobranici A, Gherghiceanu M, Dinescu S, Costache M. Multi-Omics Data Integration in Extracellular Vesicle Biology-Utopia or Future Reality? Int J Mol Sci 2020;21:ijms21228550. [PMID: 33202771 PMCID: PMC7697477 DOI: 10.3390/ijms21228550] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]  Open
40
Lortie CJ. Online conferences for better learning. Ecol Evol 2020;10:12442-12449. [PMID: 33250984 PMCID: PMC7679531 DOI: 10.1002/ece3.6923] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 02/01/2023]  Open
41
Li B, Cao Y, Westhof E, Miao Z. Advances in RNA 3D Structure Modeling Using Experimental Data. Front Genet 2020;11:574485. [PMID: 33193680 PMCID: PMC7649352 DOI: 10.3389/fgene.2020.574485] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/02/2020] [Indexed: 12/26/2022]  Open
42
Leaman R, Wei CH, Allot A, Lu Z. Ten tips for a text-mining-ready article: How to improve automated discoverability and interpretability. PLoS Biol 2020;18:e3000716. [PMID: 32479517 PMCID: PMC7289435 DOI: 10.1371/journal.pbio.3000716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/11/2020] [Indexed: 12/22/2022]  Open
43
Lortie CJ, Braun J, Filazzola A, Miguel F. A checklist for choosing between R packages in ecology and evolution. Ecol Evol 2020;10:1098-1105. [PMID: 32076500 PMCID: PMC7029065 DOI: 10.1002/ece3.5970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/18/2019] [Accepted: 12/05/2019] [Indexed: 11/12/2022]  Open
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Brito JJ, Mosqueiro T, Rotman J, Xue V, Chapski DJ, la Hoz JD, Matias P, Martin LS, Zelikovsky A, Pellegrini M, Mangul S. Telescope: an interactive tool for managing large-scale analysis from mobile devices. Gigascience 2020;9:giz163. [PMID: 31972019 PMCID: PMC6977584 DOI: 10.1093/gigascience/giz163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/26/2019] [Accepted: 12/19/2019] [Indexed: 11/27/2022]  Open
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Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AKM, Dayama G, Grieneisen L, Martin LS, Flint J, Eskin E, Blekhman R. Challenges and recommendations to improve the installability and archival stability of omics computational tools. PLoS Biol 2019;17:e3000333. [PMID: 31220077 PMCID: PMC6605654 DOI: 10.1371/journal.pbio.3000333] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/02/2019] [Indexed: 01/07/2023]  Open
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Lemos A, Lynce I, Monteiro PT. Repairing Boolean logical models from time-series data using Answer Set Programming. Algorithms Mol Biol 2019;14:9. [PMID: 30962813 PMCID: PMC6434824 DOI: 10.1186/s13015-019-0145-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/14/2019] [Indexed: 11/20/2022]  Open
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Mangul S, Martin LS, Eskin E, Blekhman R. Improving the usability and archival stability of bioinformatics software. Genome Biol 2019;20:47. [PMID: 30813962 PMCID: PMC6391762 DOI: 10.1186/s13059-019-1649-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
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Guerfali FZ, Laouini D, Boudabous A, Tekaia F. Designing and running an advanced Bioinformatics and genome analyses course in Tunisia. PLoS Comput Biol 2019;15:e1006373. [PMID: 30689625 PMCID: PMC6349305 DOI: 10.1371/journal.pcbi.1006373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
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In-Silico Selection of Aptamer: A Review on the Revolutionary Approach to Understand the Aptamer Design and Interaction Through Computational Chemistry. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.matpr.2019.11.185] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Zaritsky A. Sharing and reusing cell image data. Mol Biol Cell 2018;29:1274-1280. [PMID: 29851565 PMCID: PMC5994892 DOI: 10.1091/mbc.e17-10-0606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/02/2018] [Accepted: 04/06/2018] [Indexed: 01/19/2023]  Open
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