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For: Wilson Sayres MA, Hauser C, Sierk M, Robic S, Rosenwald AG, Smith TM, Triplett EW, Williams JJ, Dinsdale E, Morgan WR, Burnette JM, Donovan SS, Drew JC, Elgin SCR, Fowlks ER, Galindo-Gonzalez S, Goodman AL, Grandgenett NF, Goller CC, Jungck JR, Newman JD, Pearson W, Ryder EF, Tosado-Acevedo R, Tapprich W, Tobin TC, Toro-Martínez A, Welch LR, Wright R, Barone L, Ebenbach D, McWilliams M, Olney KC, Pauley MA. Bioinformatics core competencies for undergraduate life sciences education. PLoS One 2018;13:e0196878. [PMID: 29870542 PMCID: PMC5988330 DOI: 10.1371/journal.pone.0196878] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/21/2018] [Indexed: 11/22/2022]  Open
Number Cited by Other Article(s)
1
Loyola Irizarry HG, Duarte H, Nakamura K, Benabentos R, McCartney M, Siltberg-Liberles J. A bioinformatics-driven CURE extension increases student self-efficacy and interest in biomedical research. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2025:e0023124. [PMID: 40207946 DOI: 10.1128/jmbe.00231-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Accepted: 03/05/2025] [Indexed: 04/11/2025]
2
Lee JS, Lowell JL, Whitewater K, Roane TM, Miller CS, Chan AP, Sylvester AW, Jackson D, Hunter LE. Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework. Mol Ecol Resour 2025;25:e13867. [PMID: 37702134 PMCID: PMC11696487 DOI: 10.1111/1755-0998.13867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 08/18/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
3
Reed LK, Kleinschmit AJ, Buonaccorsi V, Hunt AG, Chalker D, Williams J, Jones CJ, Martinez-Cruzado JC, Rosenwald A. A genomics learning framework for undergraduates. PLoS One 2025;20:e0313124. [PMID: 39787200 PMCID: PMC11717232 DOI: 10.1371/journal.pone.0313124] [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: 04/18/2024] [Accepted: 10/20/2024] [Indexed: 01/12/2025]  Open
4
Goclowski CL, Jakiela J, Collins T, Hiltemann S, Howells M, Loach M, Manning J, Moreno P, Ostrovsky A, Rasche H, Tekman M, Tyson G, Videm P, Bacon W. Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq. Gigascience 2025;14:giae107. [PMID: 39775842 PMCID: PMC11707610 DOI: 10.1093/gigascience/giae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 10/28/2024] [Accepted: 11/26/2024] [Indexed: 01/11/2025]  Open
5
Pandey S, Elliott SL, Liepkalns J, Taylor RT, Vanniasinkam T, Kleinschmit AJ, Justement LB, Lal A, Condry D, Bruns HA, Paustian T, Mixter PF, Sparks-Thissen RL, Sletten S, Wisenden BD. The ImmunoSkills Guide: Competencies for undergraduate immunology curricula. PLoS One 2024;19:e0313339. [PMID: 39527543 PMCID: PMC11554037 DOI: 10.1371/journal.pone.0313339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024]  Open
6
Plaisier SB, Alarid DO, Denning JA, Brownell SE, Buetow KH, Cooper KM, Wilson MA. Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics. PLoS Comput Biol 2024;20:e1012384. [PMID: 39264874 PMCID: PMC11392228 DOI: 10.1371/journal.pcbi.1012384] [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] [Indexed: 09/14/2024]  Open
7
Boland DJ, Ayres NM. Cracking AlphaFold2: Leveraging the power of artificial intelligence in undergraduate biochemistry curriculums. PLoS Comput Biol 2024;20:e1012123. [PMID: 38935611 PMCID: PMC11210786 DOI: 10.1371/journal.pcbi.1012123] [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] [Indexed: 06/29/2024]  Open
8
Yang MA, Korsnack K. Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom. Biol Methods Protoc 2024;9:bpae013. [PMID: 38463936 PMCID: PMC10924719 DOI: 10.1093/biomethods/bpae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/27/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024]  Open
9
Patel P, Pillai N, Toby I. No-boundary thinking for artificial intelligence in bioinformatics and education. FRONTIERS IN BIOINFORMATICS 2024;3:1332902. [PMID: 38259432 PMCID: PMC10800434 DOI: 10.3389/fbinf.2023.1332902] [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: 11/03/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]  Open
10
Samuel S, Mietchen D. Computational reproducibility of Jupyter notebooks from biomedical publications. Gigascience 2024;13:giad113. [PMID: 38206590 PMCID: PMC10783158 DOI: 10.1093/gigascience/giad113] [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: 10/05/2022] [Revised: 08/09/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]  Open
11
Piccolo SR, Denny P, Luxton-Reilly A, Payne SH, Ridge PG. Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course. PLoS Comput Biol 2023;19:e1011511. [PMID: 37769024 PMCID: PMC10564134 DOI: 10.1371/journal.pcbi.1011511] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 10/10/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023]  Open
12
Hargadon KM. A Bioinformatic Approach to Enhance Undergraduate Student Understanding of the Cancer-Immunity Cycle. JOURNAL OF CANCER EDUCATION : THE OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER EDUCATION 2023;38:991-999. [PMID: 36094725 PMCID: PMC9465667 DOI: 10.1007/s13187-022-02221-4] [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] [Accepted: 08/27/2022] [Indexed: 06/02/2023]
13
Karega P, Mwaura DK, Mwangi KW, Wanjiku M, Landi M, Kibet CK. Building awareness and capacity of bioinformatics and open science skills in Kenya: a sensitize, train, hack, and collaborate model. Front Res Metr Anal 2023;8:1070390. [PMID: 37324282 PMCID: PMC10267827 DOI: 10.3389/frma.2023.1070390] [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: 10/14/2022] [Accepted: 05/10/2023] [Indexed: 06/17/2023]  Open
14
Sano T, Sampad MJN, Gonzalez-Ferrer J, Hernandez S, Vera-Choqqueccota S, Vargas PA, Urcuyo R, Duran NM, Teodorescu M, Haussler D, Schmidt H, Mostajo-Radji MA. Open-loop lab-on-a-chip technology enables remote computer science training in Latinx life sciences students. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538776. [PMID: 37205466 PMCID: PMC10187215 DOI: 10.1101/2023.04.28.538776] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
15
Timpe LC. An online Google Colab project for exploring the SARS CoV-2 genome and mRNA vaccines. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023;51:209-211. [PMID: 36692038 DOI: 10.1002/bmb.21711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
16
Nanjala R, Nyasimi F, Masiga D, Kibet CK. A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya. PLoS Comput Biol 2023;19:e1010904. [PMID: 36862660 PMCID: PMC9980751 DOI: 10.1371/journal.pcbi.1010904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]  Open
17
Gao L, Guo M. A course-based undergraduate research experience for bioinformatics education in undergraduate students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023;51:189-199. [PMID: 36779350 DOI: 10.1002/bmb.21710] [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: 03/02/2022] [Revised: 11/30/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
18
Diversifying the genomic data science research community. Genome Res 2022;32:1231-1241. [PMID: 35858750 PMCID: PMC9341509 DOI: 10.1101/gr.276496.121] [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: 01/19/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
19
Reyes RJ, Hosmane N, Ihorn S, Johnson M, Kulkarni A, Nelson J, Savvides M, Ta D, Yoon I, Pennings PS. Ten simple rules for designing and running a computing minor for bio/chem students. PLoS Comput Biol 2022;18:e1010202. [PMID: 35834439 PMCID: PMC9282537 DOI: 10.1371/journal.pcbi.1010202] [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] [Indexed: 11/29/2022]  Open
20
Forrester C, Schwikert S, Foster J, Corwin L. Undergraduate R Programming Anxiety in Ecology: Persistent Gender Gaps and Coping Strategies. CBE LIFE SCIENCES EDUCATION 2022;21:ar29. [PMID: 35426729 PMCID: PMC9508917 DOI: 10.1187/cbe.21-05-0133] [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: 05/24/2021] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
21
Chen A, Phillips KA, Schaefer JE, Sonner PM. The Development of Core Concepts for Neuroscience Higher Education: From Beginning to Summer Virtual Meeting Satellite Session. JOURNAL OF UNDERGRADUATE NEUROSCIENCE EDUCATION : JUNE : A PUBLICATION OF FUN, FACULTY FOR UNDERGRADUATE NEUROSCIENCE 2022;20:A161-A165. [PMID: 38323056 PMCID: PMC10653233 DOI: 10.59390/ghor4737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 02/08/2024]
22
Garzón A, Rubio A, Pérez-Pulido AJ. E-learning strategies from a bioinformatics postgraduate programme to improve student engagement and completion rate. BIOINFORMATICS ADVANCES 2022;2:vbac031. [PMID: 36699370 PMCID: PMC9710613 DOI: 10.1093/bioadv/vbac031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/16/2022] [Accepted: 04/29/2022] [Indexed: 01/28/2023]
23
Parks ST, Taylor C. Development of a Remote, Course-Based Undergraduate Experience to Facilitate In Silico Study of Microbial Metabolic Pathways. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2022;23:jmbe00318-21. [PMID: 35340445 PMCID: PMC8941885 DOI: 10.1128/jmbe.00318-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 05/09/2023]
24
Emery NC, Crispo E, Supp SR, Farrell KJ, Kerkhoff AJ, Bledsoe EK, O'Donnell KL, McCall AC, Aiello-Lammens ME. Data Science in Undergraduate Life Science Education: A Need for Instructor Skills Training. Bioscience 2021;71:1274-1287. [PMID: 34867087 PMCID: PMC8634500 DOI: 10.1093/biosci/biab107] [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] [Indexed: 12/05/2022]  Open
25
Drew JC, Grandgenett N, Dinsdale EA, Vázquez Quiñones LE, Galindo S, Morgan WR, Pauley M, Rosenwald A, Triplett EW, Tapprich W, Kleinschmit AJ. There Is More than Multiple Choice: Crowd-Sourced Assessment Tips for Online, Hybrid, and Face-to-Face Environments. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021;22:e00205-21. [PMID: 34970386 PMCID: PMC8673258 DOI: 10.1128/jmbe.00205-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/12/2021] [Indexed: 06/14/2023]
26
Stinziano JR, Roback C, Sargent D, Murphy BK, Hudson PJ, Muir CD. Principles of resilient coding for plant ecophysiologists. AOB PLANTS 2021;13:plab059. [PMID: 34646435 PMCID: PMC8501907 DOI: 10.1093/aobpla/plab059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 09/15/2021] [Indexed: 06/02/2023]
27
Yang L, Zheng S, Xu X, Sun Y, Wang X, Li J. Medical Data Mining Course Development in Postgraduate Medical Education: Web-Based Survey and Case Study. JMIR MEDICAL EDUCATION 2021;7:e24027. [PMID: 34596575 PMCID: PMC8520135 DOI: 10.2196/24027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/16/2020] [Accepted: 08/08/2021] [Indexed: 06/13/2023]
28
Community development, implementation, and assessment of a NIBLSE bioinformatics sequence similarity learning resource. PLoS One 2021;16:e0257404. [PMID: 34506617 PMCID: PMC8432852 DOI: 10.1371/journal.pone.0257404] [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: 03/10/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022]  Open
29
da Silva AL, Abreu APD, Mariano D, Caixeta F, Santos FB, Lage FSD, Quintanilha-Peixoto G, Hilário HO, Xavier JS, Queiroz LR, de Toledo NE, Tavares R, Kato RB, dos Santos RG, Soares S, Goes WM, Nogueira WG, Batista TM, Ortega JM, De Carvalho VAA, Franco GR, Melo-Minardi RCD, Góes-Neto A. From In-Person to the Online World: Insights Into Organizing Events in Bioinformatics. FRONTIERS IN BIOINFORMATICS 2021;1:711463. [DOI: 10.3389/fbinf.2021.711463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022]  Open
30
Taylor MD, Mendenhall B, Woods CS, Rasband ME, Vallejo MC, Bailey EG, Payne SH. Online Tools for Teaching Cancer Bioinformatics. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021;22:jmbe00167-21. [PMID: 34594439 PMCID: PMC8442005 DOI: 10.1128/jmbe.00167-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/19/2021] [Indexed: 06/02/2023]
31
Zeng H, Zhang J, Preising GA, Rubel T, Singh P, Ritz A. Graphery: interactive tutorials for biological network algorithms. Nucleic Acids Res 2021;49:W257-W262. [PMID: 34037782 PMCID: PMC8262715 DOI: 10.1093/nar/gkab420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/19/2021] [Accepted: 05/03/2021] [Indexed: 11/14/2022]  Open
32
Melendrez MC, Shaw S, Brown CT, Goodner BW, Kvaal C. Editorial: Curriculum Applications in Microbiology: Bioinformatics in the Classroom. Front Microbiol 2021;12:705233. [PMID: 34276638 PMCID: PMC8281245 DOI: 10.3389/fmicb.2021.705233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022]  Open
33
Goller CC, Srougi MC, Chen SH, Schenkman LR, Kelly RM. Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules. FRONTIERS IN EDUCATION 2021;6:711403. [PMID: 35036827 PMCID: PMC8758113 DOI: 10.3389/feduc.2021.711403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
34
Niepielko MG, Shumskaya M. Early Requirement for Bioinformatics in Undergraduate Biology Curricula. FRONTIERS IN BIOINFORMATICS 2021;1:656531. [PMID: 36303737 PMCID: PMC9581004 DOI: 10.3389/fbinf.2021.656531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/08/2021] [Indexed: 11/13/2022]  Open
35
Robinson SL, Biernath T, Rosenthal C, Young D, Wackett LP, Martinez-Vaz BM. Development of the Organonitrogen Biodegradation Database: Teaching Bioinformatics and Collaborative Skills to Undergraduates during a Pandemic. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021;22:jmbe-22-49. [PMID: 33884084 PMCID: PMC8046652 DOI: 10.1128/jmbe.v22i1.2351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/09/2020] [Indexed: 05/24/2023]
36
Petrie KL, Xie R. Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics. Front Microbiol 2021;12:578859. [PMID: 33796082 PMCID: PMC8008064 DOI: 10.3389/fmicb.2021.578859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/16/2021] [Indexed: 11/23/2022]  Open
37
Tapprich WE, Reichart L, Simon DM, Duncan G, McClung W, Grandgenett N, Pauley MA. An instructional definition and assessment rubric for bioinformatics instruction. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021;49:38-45. [PMID: 32744803 DOI: 10.1002/bmb.21361] [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: 01/31/2019] [Revised: 02/06/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
38
Lyles JK, Oli M. The student-centered classroom: the new gut feeling. FEMS Microbiol Lett 2020;367:6000213. [PMID: 33232449 DOI: 10.1093/femsle/fnaa191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022]  Open
39
Clemmons AW, Timbrook J, Herron JC, Crowe AJ. BioSkills Guide: Development and National Validation of a Tool for Interpreting the Vision and Change Core Competencies. CBE LIFE SCIENCES EDUCATION 2020;19:ar53. [PMID: 33001766 PMCID: PMC8693931 DOI: 10.1187/cbe.19-11-0259] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 05/24/2023]
40
Muth TR, Caplan AJ. Microbiomes for All. Front Microbiol 2020;11:593472. [PMID: 33281791 PMCID: PMC7688743 DOI: 10.3389/fmicb.2020.593472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/19/2020] [Indexed: 01/15/2023]  Open
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Rosen GL, Hammrich P. Teaching Microbiome Analysis: From Design to Computation Through Inquiry. Front Microbiol 2020;11:528051. [PMID: 33193120 PMCID: PMC7658192 DOI: 10.3389/fmicb.2020.528051] [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: 01/18/2020] [Accepted: 09/09/2020] [Indexed: 11/23/2022]  Open
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Mitchell K, Ronas J, Dao C, Freise AC, Mangul S, Shapiro C, Moberg Parker J. PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom. Front Microbiol 2020;11:584699. [PMID: 33123113 PMCID: PMC7573227 DOI: 10.3389/fmicb.2020.584699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022]  Open
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Martinez-Vaz BM, Mickelson MM. In silico Phage Hunting: Bioinformatics Exercises to Identify and Explore Bacteriophage Genomes. Front Microbiol 2020;11:577634. [PMID: 33072043 PMCID: PMC7533560 DOI: 10.3389/fmicb.2020.577634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]  Open
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Kruchten AE. A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R. Front Microbiol 2020;11:578600. [PMID: 33013816 PMCID: PMC7511545 DOI: 10.3389/fmicb.2020.578600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/12/2020] [Indexed: 01/06/2023]  Open
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Davies A, Mueller J, Moulton G. Core competencies for clinical informaticians: A systematic review. Int J Med Inform 2020;141:104237. [PMID: 32771960 DOI: 10.1016/j.ijmedinf.2020.104237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022]
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Bennett JA. The CURE for the Typical Bioinformatics Classroom. Front Microbiol 2020;11:1728. [PMID: 32903295 PMCID: PMC7434937 DOI: 10.3389/fmicb.2020.01728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/02/2020] [Indexed: 11/19/2022]  Open
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Ryder EF, Morgan WR, Sierk M, Donovan SS, Robertson SD, Orndorf HC, Rosenwald AG, Triplett EW, Dinsdale E, Pauley MA, Tapprich WE. Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020;48:381-390. [PMID: 32585745 PMCID: PMC7496352 DOI: 10.1002/bmb.21387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/02/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
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Tractenberg RE, Lindvall JM, Attwood TK, Via A. The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training. PLoS One 2019;14:e0225256. [PMID: 31770418 PMCID: PMC6879125 DOI: 10.1371/journal.pone.0225256] [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] [Received: 06/06/2019] [Accepted: 10/24/2019] [Indexed: 11/18/2022]  Open
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Williams JJ, Drew JC, Galindo-Gonzalez S, Robic S, Dinsdale E, Morgan WR, Triplett EW, Burnette JM, Donovan SS, Fowlks ER, Goodman AL, Grandgenett NF, Goller CC, Hauser C, Jungck JR, Newman JD, Pearson WR, Ryder EF, Sierk M, Smith TM, Tosado-Acevedo R, Tapprich W, Tobin TC, Toro-Martínez A, Welch LR, Wilson MA, Ebenbach D, McWilliams M, Rosenwald AG, Pauley MA. Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. PLoS One 2019;14:e0224288. [PMID: 31738797 PMCID: PMC6860448 DOI: 10.1371/journal.pone.0224288] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/09/2019] [Indexed: 01/27/2023]  Open
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Wright AM, Schwartz RS, Oaks JR, Newman CE, Flanagan SP. The why, when, and how of computing in biology classrooms. F1000Res 2019;8:1854. [PMID: 32025290 PMCID: PMC6971840 DOI: 10.12688/f1000research.20873.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/18/2019] [Indexed: 03/29/2024]  Open
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