{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T02:27:30Z","timestamp":1778552850443,"version":"3.51.4"},"reference-count":34,"publisher":"Walter de Gruyter GmbH","issue":"3","license":[{"start":{"date-parts":[[2019,5,30]],"date-time":"2019-05-30T00:00:00Z","timestamp":1559174400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand of scientists with a combined background in both fields, the education of dry and wet lab subjects are often still separated. This work describes an example of integrated education with a focus on genomics and transcriptomics. Participants learned computational and molecular biology methods in the same practical course. Peer-review was applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. The positive evaluation results indicate that this approach was accepted by the participants and would likely be suitable for wider scale application.<\/jats:p>","DOI":"10.1515\/jib-2019-0005","type":"journal-article","created":{"date-parts":[[2019,5,30]],"date-time":"2019-05-30T05:02:52Z","timestamp":1559192572000},"source":"Crossref","is-referenced-by-count":31,"title":["Integrating Molecular Biology and Bioinformatics Education"],"prefix":"10.1515","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3321-7471","authenticated-orcid":false,"given":"Boas","family":"Pucker","sequence":"first","affiliation":[{"name":"Genetics and Genomics of Plants, CeBiTec and Faculty of Biology , Bielefeld University , Bielefeld , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0474-7753","authenticated-orcid":false,"given":"Hanna Marie","family":"Schilbert","sequence":"additional","affiliation":[{"name":"Genetics and Genomics of Plants, CeBiTec and Faculty of Biology , Bielefeld University , Bielefeld , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1471-1287","authenticated-orcid":false,"given":"Sina Franziska","family":"Schumacher","sequence":"additional","affiliation":[{"name":"Bielefeld University , Bielefeld , Germany"}]}],"member":"374","published-online":{"date-parts":[[2019,5,30]]},"reference":[{"key":"2023033120074885990_j_jib-2019-0005_ref_001_w2aab3b7b3b1b6b1ab1b5b1Aa","doi-asserted-by":"crossref","unstructured":"Spotlight on Bioinformatics. NatureJobs 2016. doi: 10.1038\/nj0478.","DOI":"10.1038\/nj0478"},{"key":"2023033120074885990_j_jib-2019-0005_ref_002_w2aab3b7b3b1b6b1ab1b5b2Aa","doi-asserted-by":"crossref","unstructured":"Attwood TK, Blackford S, Brazas MD, Davies A, Schneider MV. A global perspective on evolving bioinformatics and data science training needs. Briefings in Bioinformatics. 2017;20(2):398\u2013404. DOI:  10.1093\/bib\/bbx100 .","DOI":"10.1093\/bib\/bbx100"},{"key":"2023033120074885990_j_jib-2019-0005_ref_003_w2aab3b7b3b1b6b1ab1b5b3Aa","doi-asserted-by":"crossref","unstructured":"Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV. Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies. PLoS Computational Biology. 2014;10(3):e1003496\u2013e1003496. DOI:  10.1371\/journal.pcbi.1003496.","DOI":"10.1371\/journal.pcbi.1003496"},{"key":"2023033120074885990_j_jib-2019-0005_ref_004_w2aab3b7b3b1b6b1ab1b5b4Aa","doi-asserted-by":"crossref","unstructured":"Ranganathan S. Bioinformatics Education\u2014Perspectives and Challenges. PLoS Computational Biology. 2005;1(6):e52\u2013e52. DOI:  10.1371\/journal.pcbi.0010052.16322761","DOI":"10.1371\/journal.pcbi.0010052"},{"key":"2023033120074885990_j_jib-2019-0005_ref_005_w2aab3b7b3b1b6b1ab1b5b5Aa","doi-asserted-by":"crossref","unstructured":"Bialek W. Introductory Science and Mathematics Education for 21st-Century Biologists. Science. 2004;303(5659):788\u2013790. DOI: 10.1126\/science.1095480.14764865","DOI":"10.1126\/science.1095480"},{"key":"2023033120074885990_j_jib-2019-0005_ref_006_w2aab3b7b3b1b6b1ab1b5b6Aa","doi-asserted-by":"crossref","unstructured":"Abeln S, Molenaar D, Feenstra KA, Hoefsloot HCJ, Teusink B, Heringa J. Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. Briefings in Bioinformatics. 2013;14(5):589\u2013598. DOI:  10.1093\/bib\/bbt023.23603092","DOI":"10.1093\/bib\/bbt023"},{"key":"2023033120074885990_j_jib-2019-0005_ref_007_w2aab3b7b3b1b6b1ab1b5b7Aa","doi-asserted-by":"crossref","unstructured":"Rubinstein A, Chor B. Computational Thinking in Life Science Education. PLoS Computational Biology. 2014;10(11):e1003897\u2013e1003897. DOI:  10.1371\/journal.pcbi.1003897.25411839","DOI":"10.1371\/journal.pcbi.1003897"},{"key":"2023033120074885990_j_jib-2019-0005_ref_008_w2aab3b7b3b1b6b1ab1b5b8Aa","doi-asserted-by":"crossref","unstructured":"Goodman AL, Dekhtyar A. Teaching bioinformatics in concert. PLoS Comput Biol 2014;10:e1003896.10.1371\/journal.pcbi.100389625411792","DOI":"10.1371\/journal.pcbi.1003896"},{"key":"2023033120074885990_j_jib-2019-0005_ref_009_w2aab3b7b3b1b6b1ab1b5b9Aa","doi-asserted-by":"crossref","unstructured":"Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, et al. Best practices in bioinformatics training for life scientists. Brief Bioinform 2013;14:528\u201337.2380330110.1093\/bib\/bbt043","DOI":"10.1093\/bib\/bbt043"},{"key":"2023033120074885990_j_jib-2019-0005_ref_010_w2aab3b7b3b1b6b1ab1b5c10Aa","doi-asserted-by":"crossref","unstructured":"Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, et al. The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS Comput Biol 2018;14:e1005772.29390004","DOI":"10.1371\/journal.pcbi.1005772"},{"key":"2023033120074885990_j_jib-2019-0005_ref_011_w2aab3b7b3b1b6b1ab1b5c11Aa","doi-asserted-by":"crossref","unstructured":"Pucker B, Holtgr\u00e4we D, Rosleff S\u00f6rensen T, Stracke R, Vieh\u00f6ver P, Weisshaar B. A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence\/Absence Variation and Strong Synteny. PLOS ONE. 2016;11(10):e0164321\u2013e0164321. DOI:  10.1371\/journal.pone.0164321.","DOI":"10.1371\/journal.pone.0164321"},{"key":"2023033120074885990_j_jib-2019-0005_ref_012_w2aab3b7b3b1b6b1ab1b5c12Aa","doi-asserted-by":"crossref","unstructured":"Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res 2011;39:D19\u201321.10.1093\/nar\/gkq101921062823","DOI":"10.1093\/nar\/gkq1019"},{"key":"2023033120074885990_j_jib-2019-0005_ref_013_w2aab3b7b3b1b6b1ab1b5c13Aa","doi-asserted-by":"crossref","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114\u20132120. DOI:  10.1093\/bioinformatics\/btu170.24695404","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"2023033120074885990_j_jib-2019-0005_ref_014_w2aab3b7b3b1b6b1ab1b5c14Aa","unstructured":"Andrews S. FastQC A Quality Control tool for High Throughput Sequence Data [Internet]. 2010 [cited 14 Dec 2017]. Available from: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"2023033120074885990_j_jib-2019-0005_ref_015_w2aab3b7b3b1b6b1ab1b5c15Aa","doi-asserted-by":"crossref","unstructured":"Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012;1:18.2358711810.1186\/2047-217X-1-18","DOI":"10.1186\/2047-217X-1-18"},{"key":"2023033120074885990_j_jib-2019-0005_ref_016_w2aab3b7b3b1b6b1ab1b5c16Aa","doi-asserted-by":"crossref","unstructured":"Hoff KJ, Stanke M. WebAUGUSTUS \u2013 a web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Res 2013;41:W123\u20138.2370030710.1093\/nar\/gkt418","DOI":"10.1093\/nar\/gkt418"},{"key":"2023033120074885990_j_jib-2019-0005_ref_017_w2aab3b7b3b1b6b1ab1b5c17Aa","doi-asserted-by":"crossref","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403\u201310.10.1016\/S0022-2836(05)80360-22231712","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"2023033120074885990_j_jib-2019-0005_ref_018_w2aab3b7b3b1b6b1ab1b5c18Aa","doi-asserted-by":"crossref","unstructured":"Poland JA, Rife TW. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 2012;5:92\u2013102.10.3835\/plantgenome2012.05.0005","DOI":"10.3835\/plantgenome2012.05.0005"},{"key":"2023033120074885990_j_jib-2019-0005_ref_019_w2aab3b7b3b1b6b1ab1b5c19Aa","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv13033997 Q-Bio. 2013; Available from: http:\/\/arxiv.org\/abs\/1303.3997."},{"key":"2023033120074885990_j_jib-2019-0005_ref_020_w2aab3b7b3b1b6b1ab1b5c20Aa","doi-asserted-by":"crossref","unstructured":"Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 2012;40:D1202\u201310.2214010910.1093\/nar\/gkr1090","DOI":"10.1093\/nar\/gkr1090"},{"key":"2023033120074885990_j_jib-2019-0005_ref_021_w2aab3b7b3b1b6b1ab1b5c21Aa","doi-asserted-by":"crossref","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297\u2013303.2064419910.1101\/gr.107524.110","DOI":"10.1101\/gr.107524.110"},{"key":"2023033120074885990_j_jib-2019-0005_ref_022_w2aab3b7b3b1b6b1ab1b5c22Aa","doi-asserted-by":"crossref","unstructured":"Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly (Austin) 2012;6:80\u201392.2272867210.4161\/fly.19695","DOI":"10.4161\/fly.19695"},{"key":"2023033120074885990_j_jib-2019-0005_ref_023_w2aab3b7b3b1b6b1ab1b5c23Aa","doi-asserted-by":"crossref","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29:15\u201321.10.1093\/bioinformatics\/bts63523104886","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2023033120074885990_j_jib-2019-0005_ref_024_w2aab3b7b3b1b6b1ab1b5c24Aa","doi-asserted-by":"crossref","unstructured":"Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinforma Oxf Engl 2014;30:923\u201330.10.1093\/bioinformatics\/btt656","DOI":"10.1093\/bioinformatics\/btt656"},{"key":"2023033120074885990_j_jib-2019-0005_ref_025_w2aab3b7b3b1b6b1ab1b5c25Aa","doi-asserted-by":"crossref","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014;15(12). DOI:  10.1186\/s13059-014-0550-8.25516281","DOI":"10.1186\/s13059-014-0550-8"},{"key":"2023033120074885990_j_jib-2019-0005_ref_026_w2aab3b7b3b1b6b1ab1b5c26Aa","doi-asserted-by":"crossref","unstructured":"Haak M, Vinke S, Keller W, Droste J, R\u00fcckert C, Kalinowski J, Pucker B. High Quality de Novo Transcriptome Assembly of Croton tiglium. Frontiers in Molecular Biosciences. 2018;5. DOI:  10.3389\/fmolb.2018.00062.30027092","DOI":"10.3389\/fmolb.2018.00062"},{"key":"2023033120074885990_j_jib-2019-0005_ref_027_w2aab3b7b3b1b6b1ab1b5c27Aa","unstructured":"Friedrich A, Pucker B. Peer-review as a teaching method. 2018. Available from: https:\/\/pub.uni-bielefeld.de\/record\/2920633."},{"key":"2023033120074885990_j_jib-2019-0005_ref_028_w2aab3b7b3b1b6b1ab1b5c28Aa","doi-asserted-by":"crossref","unstructured":"Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 2005;3:e196.1590715510.1371\/journal.pbio.0030196","DOI":"10.1371\/journal.pbio.0030196"},{"key":"2023033120074885990_j_jib-2019-0005_ref_029_w2aab3b7b3b1b6b1ab1b5c29Aa","doi-asserted-by":"crossref","unstructured":"Vuka\u0161inovi\u0107 N, Cvr\u010dkov\u00e1 F, Eli\u00e1\u0161 M, Cole R, Fowler JE, \u017d\u00e1rsk\u00fd V, et al. Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus. PloS One 2014;9:e94077.24728280","DOI":"10.1371\/journal.pone.0094077"},{"key":"2023033120074885990_j_jib-2019-0005_ref_030_w2aab3b7b3b1b6b1ab1b5c30Aa","doi-asserted-by":"crossref","unstructured":"Zapata L, Ding J, Willing E-M, Hartwig B, Bezdan D, Jiao W-B, et al. Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proc Natl Acad Sci 2016;113:E4052\u201360.10.1073\/pnas.1607532113","DOI":"10.1073\/pnas.1607532113"},{"key":"2023033120074885990_j_jib-2019-0005_ref_031_w2aab3b7b3b1b6b1ab1b5c31Aa","doi-asserted-by":"crossref","unstructured":"Pucker B, Holtgr\u00e4we D, Stadermann KB, Frey K, Huettel B, Reinhardt R, Weisshaar B. A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set. bioRxiv. 2018. DOI:  10.1101\/407627.","DOI":"10.1101\/407627"},{"key":"2023033120074885990_j_jib-2019-0005_ref_032_w2aab3b7b3b1b6b1ab1b5c32Aa","doi-asserted-by":"crossref","unstructured":"Tennant JP. The state of the art in peer review. FEMS Microbiology Letters. 2018;365(19). DOI:  10.1093\/femsle\/fny204.30137294","DOI":"10.1093\/femsle\/fny204"},{"key":"2023033120074885990_j_jib-2019-0005_ref_033_w2aab3b7b3b1b6b1ab1b5c33Aa","unstructured":"Williams KC, Williams CC. Five key ingredients for improving student motivation. Res High Educ J 2011:121\u20133. Available: https:\/\/scholarsarchive.library.albany.edu\/cgi\/viewcontent.cgi?article=1000&context=math_fac_scholar."},{"key":"2023033120074885990_j_jib-2019-0005_ref_034_w2aab3b7b3b1b6b1ab1b5c34Aa","doi-asserted-by":"crossref","unstructured":"Parker K, Chao J. Wiki as a teaching tool. Interdiscip J E-Learn Learn Objects 2007;3:57\u201372.","DOI":"10.28945\/3131"}],"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyter.com\/view\/journals\/jib\/16\/3\/article-20190005.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2019-0005\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2019-0005\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T04:26:25Z","timestamp":1680323185000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2019-0005\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,30]]},"references-count":34,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2019,7,13]]},"published-print":{"date-parts":[[2019,9,25]]}},"alternative-id":["10.1515\/jib-2019-0005"],"URL":"https:\/\/doi.org\/10.1515\/jib-2019-0005","relation":{"has-preprint":[{"id-type":"doi","id":"10.20944\/preprints201811.0183.v1","asserted-by":"object"},{"id-type":"doi","id":"10.20944\/preprints201811.0183.v2","asserted-by":"object"}]},"ISSN":["1613-4516"],"issn-type":[{"value":"1613-4516","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,30]]},"article-number":"20190005"}}