Bioinformatics

Search results

• Comprehensive Genome Analysis of Halolamina pelagica CDK2: Insights into Abiotic Stress Tolerance Genes

  Gaba, S. (Creator), Naitam, M. G. (Creator), Kumari, A. (Creator), Medema, M. (Creator) & Kaushik, R. (Creator), 1 Oct 2021

  DOI: 10.5281/zenodo.5543458

  Dataset

• Comparison of tomato fruit gene expression data obtained by microarray analysis and by treatment of degradome sequencing data as an RNAseq experiment

  de Maagd, R. (Creator), Plant Research International, 12 Nov 2013

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42784

  Dataset

• Transcriptome data from a mix of flower, bud, leaf and root tissues of sexual diploid Taraxacum officinale (common dandelion; accession FCh72, France)

  Xiong, W. (Creator), Risse, J. (Creator), Berke, L. (Creator), Zhao, T. (Creator), van de Geest, H. (Creator), Oplaat, C. (Creator), Busscher, M. (Creator), Ferreira de Carvalho, J. (Creator), van der Meer, I. (Creator), Verhoeven, K. J. F. (Creator), Schranz, E. (Creator) & Vijverberg, K. (Creator), Wageningen University & Research, 11 Jun 2023

  https://www.ebi.ac.uk/ena/browser/view/PRJEB58886

  Dataset

• Transcription Factor-Mediated Control of Anthocyanin Biosynthesis in Vegetative Tissues of Tomato

  Outchkourov, N. S. (Creator), Karlova, R. (Creator), Hölscher, M. (Creator), Schrama, X. (Creator), Blilou, I. (Creator), Jongedijk, E. (Creator), Diez Simon, C. (Creator), van Dijk, A. (Creator), Bosch, D. (Creator), Hall, R. (Creator) & Beekwilder, M. J. (Creator), Wageningen University & Research, 29 Jan 2018

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109772

  Dataset

• Whole genome shotgun sequencing in a Solanum tuberosum interspecific backcross genotype

  Xu, X. (Creator), Pan, S. K. (Creator), Cheng, S. F. (Creator), Zhang, B. (Creator), Bachem, C. (Creator), de Boer, J. (Creator), Borm, T. (Creator), Kloosterman, B. (Creator), van Eck, H. (Creator), Datema, E. (Creator), Goverse, A. (Creator), van Ham, R. (Creator) & Visser, R. (Creator), Wageningen University and Research Centre, 11 Jul 2011

  https://www.ebi.ac.uk/ena/data/view/PRJEB2504

  Dataset

• P starvation in tomato

  Wang, Y. (Creator), Suarez Duran, H. (Creator), van Haarst, J. (Creator), Schijlen, E. (Creator), Ruyter-Spira, C. (Creator), Medema, M. (Creator), Dong, L. (Creator) & Bouwmeester, H. J. (Creator), University of Amsterdam, 18 Nov 2020

  https://www.ncbi.nlm.nih.gov/bioproject/PRJNA679261

  Dataset

• 84 tomato accessions - Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

  Aflitos, S. (Creator), Schijlen, E. (Creator), de Jong, H. (Creator), de Ridder, D. (Creator), Smit, S. (Creator), Finkers, R. (Creator), Bakker, F. (Creator), van de Geest, H. (Creator), te Lintel Hekkert, B. (Creator), van Haarst, J. (Creator), Smits, L. (Creator), Koops, A. (Creator), Sanchez-Perez, M. J. (Creator), van Heusden, S. (Creator), Visser, R. (Creator), Schranz, E. (Creator) & Peters, S. (Creator), Plant Research International, 29 Jan 2014

  https://www.ebi.ac.uk/ena/browser/view/PRJEB5235

  Dataset

• Operophtera brumata RefSeq Genome

  Derks, M. (Creator), Smit, S. (Creator), Salis, L. (Creator), Schijlen, E. (Creator), Bossers, A. (Creator), Mateman, C. (Creator), Pijl, A. S. (Creator), de Ridder, D. (Creator), Groenen, M. A. M. (Creator), Visser, M. E. (Creator) & Megens, H. (Creator), Wageningen University & Research, 17 Aug 2015

  https://www.ncbi.nlm.nih.gov/bioproject/293072

  Dataset

• Comparative genomics including the basal pathogen Peronospora belbahrii reveal common evolutionary patterns and the monophyly of downy mildews in a paraphyletic Phytophthora

  Thines, M. (Creator), Sharma, R. (Creator), Rodenburg, Y. A. (Creator), Gogleva, A. (Creator), Judelson, H. S. (Creator), Xia, X. (Creator), van den Hoogen, D. J. (Creator), Kitner, M. (Creator), Klein, J. (Creator), de Ridder, D. (Creator), Seidl, M. F. (Creator), van den Ackerveken, G. (Creator), Govers, F. (Creator), Schornack, S. (Creator) & Studholme, D. J. (Creator), 10 Aug 2018

  https://www.ebi.ac.uk/ena/browser/view/PRJEB15119

  Dataset

• Microarray analysis of Bay-0 x Sha recombinant inbred lines at four seed germination stages

  Nijveen, H. (Creator) & Hartanto, M. (Creator), Wageningen University & Research, 24 Jun 2020

  https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9080/

  Dataset

• CyLineUp

  Dias Costa, M. C. (Creator), Slijkhuis, T. (Creator) & Nijveen, H. (Creator), Wageningen University & Research, 2016

  DOI: 10.5281/zenodo.48135

  Dataset

• Xerophyta viscosa Genome sequencing and assembly

  Dias Costa, M. C. (Creator), Silva Artur, M. (Creator), Maia de Oliveira, J. (Creator), Jonkheer, E. (Creator), Derks, M. (Creator), Nijveen, H. (Creator), Williams, B. (Creator), Mundree, S. (Creator), Jiménez-Gómez, J. M. (Creator), Hesselink, T. (Creator), Schijlen, E. (Creator), Ligterink, W. (Creator), Oliver, M. J. (Creator), Farrant, J. M. (Creator) & Hilhorst, H. W. M. (Creator), Wageningen University & Research, 31 Mar 2017

  https://www.ncbi.nlm.nih.gov/bioproject/291133

  Dataset

• NPClassifier predictions of COCONUT compounds

  Nollen, L. (Creator), Meijer, D. (Creator), Sorokina, M. (Creator) & van der Hooft, J. (Creator), Wageningen University & Research, 7 Feb 2024

  DOI: 10.5281/zenodo.10629837

  Dataset

• Trema orientale Genome sequencing and assembly

  van Velzen, R. (Creator), Holmer, R. (Creator), Bu, F. (Creator), Rutten, L. (Creator), van Zeijl, A. (Creator), Liu, W. (Creator), Santuari, L. (Creator), Cao, Q. (Creator), Sharma, T. (Creator), Shen, D. (Creator), Purwana Roswanjaya, Y. (Creator), Wardhani, T. (Creator), Seifi Kalhor, M. (Creator), Jansen, J. (Creator), van den Hoogen, J. (Creator), Güngör, B. (Creator), Hartog, M. (Creator), Hontelez, J. (Creator), Verver, J. (Creator), Yang, W. (Creator), Schijlen, E. (Creator), Repin, R. (Creator), Schilthuizen, M. (Creator), Schranz, E. (Creator), Heidstra, R. (Creator), Miyata, K. (Creator), Fedorova, E. (Creator), Kohlen, W. (Creator), Bisseling, T. (Creator), Smit, S. (Creator) & Geurts, R. (Creator), Wageningen University, 2 Feb 2018

  https://www.ncbi.nlm.nih.gov/bioproject/PRJNA272482/

  Dataset

• Data underlying the publication: "A mammalian commensal of the oropharyngeal cavity produces antibiotic and antiviral valinomycin in vivo"

  Gaiser, R. (Creator), Ferrando, L. (Creator), Oddo, A. (Creator), Pereira, M. (Creator), Boekhorst, J. (Creator), Guan, X. (Creator), Molist, F. (Creator), Fernandez Gutierrez, M. (Creator), Fredriksen, S. (Creator), Bryant, C. E. (Creator), Petras, D. (Creator), Dorrestein, P. C. (Creator), Boeren, S. (Creator), Medema, M. (Creator), Hill, C. (Creator), Kleerebezem, M. (Creator), van Baarlen, P. (Creator) & Wells, J. (Creator), Wageningen University & Research, 28 Sept 2023

  DOI: 10.17026/dans-zf3-7tt4

  Dataset

• Rothia nasimurium strain:PT-32 Genome sequencing and assembly

  Gaiser, R. A. (Creator), Medema, M. (Creator), Kleerebezem, M. (Creator), van Baarlen, P. (Creator) & Wells, J. (Creator), Wageningen University, 3 Sept 2016

  http://www.ebi.ac.uk/ena/data/view/PRJNA321506

  Dataset

• Reciprocal cybrids reveal how organellar genomes affect plant phenotypes - RNA Sequencing

  Flood, P. (Creator), Theeuwen, T. (Creator), Schneeberger, K. (Creator), Keizer, P. (Creator), Kruijer, W. (Creator), Severing, E. (Creator), Kouklas, E. (Creator), Hageman, J. (Creator), Wijfjes, R. (Creator), Calvo Baltanas, V. (Creator), Becker, F. (Creator), Schnabel, S. (Creator), Willems, L. (Creator), Ligterink, W. (Creator), van Arkel, J. (Creator), Mumm, R. (Creator), Gualberto, J. M. (Creator), Savage, L. (Creator), Kramer, D. M. (Creator), Keurentjes, J. (Creator), van Eeuwijk, F. (Creator), Koornneef, M. (Creator), Harbinson, J. (Creator), Aarts, M. (Creator) & Wijnker, E. (Creator), Wageningen University, 12 Nov 2019

  https://www.ebi.ac.uk/ena/data/view/PRJEB35324

  Dataset

• Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

  Thompson, O. A. (Creator), Snoek, B. (Creator), Nijveen, H. (Creator), Sterken, M. (Creator), Volkers, R. (Creator), Brenchley, R. (Creator), van 't Hof, A. (Creator), Bevers, R. (Creator), Cossins, A. R. (Creator), Yanai, I. (Creator), Hajnal, A. (Creator), Schmid, T. (Creator), Perkins, J. D. (Creator), Spencer, D. (Creator), Kruglyak, L. (Creator), Andersen, E. C. (Creator), Moerman, D. G. (Creator), Hillier, L. W. (Creator), Kammenga, J. (Creator) & Waterston, R. H. (Creator), University of Washington, 20 May 2016

  DOI: 10.5061/dryad.1k8kq

  Dataset

• A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits

  Snoek, B. (Creator), Volkers, R. (Creator), Nijveen, H. (Creator), Petersen, C. (Creator), Dirksen, P. (Creator), Sterken, M. (Creator), Nakad, R. (Creator), Riksen, J. (Creator), Rosenstiel, P. C. (Creator), Stastna, J. J. (Creator), Braekman, B. P. (Creator), Harvey, S. C. (Creator), Schulenburg, H. (Creator) & Kammenga, J. (Creator), Wageningen University & Research, 12 Mar 2019

  DOI: 10.6084/m9.figshare.c.4433543

  Dataset

• Rhizophagus irregularis C3 genome assembly and analysis

  van Creij, J. (Creator), Auxier, B. (Creator), An, J. (Creator), Wijfjes, R. (Creator), Bergin, C. (Creator), Rosling, A. (Creator), Bisseling, T. (Creator), Pan, Z. (Creator) & Limpens, E. (Creator), Wageningen University & Research, 17 Jul 2021

  https://www.ncbi.nlm.nih.gov/bioproject/PRJNA747641

  Dataset

• Reciprocal cybrids reveal how organellar genomes affect plant phenotypes - Whole Genome Sequencing

  Flood, P. (Creator), Theeuwen, T. (Creator), Schneeberger, K. (Creator), Keizer, P. (Creator), Kruijer, W. (Creator), Severing, E. (Creator), Kouklas, E. (Creator), Hageman, J. (Creator), Wijfjes, R. (Creator), Calvo Baltanas, V. (Creator), Becker, F. (Creator), Schnabel, S. (Creator), Willems, L. (Creator), Ligterink, W. (Creator), van Arkel, J. (Creator), Mumm, R. (Creator), Gualberto, J. M. (Creator), Savage, L. (Creator), Kramer, D. M. (Creator), Keurentjes, J. (Creator), van Eeuwijk, F. (Creator), Koornneef, M. (Creator), Harbinson, J. (Creator), Aarts, M. (Creator) & Wijnker, E. (Creator), Wageningen University, 11 Nov 2019

  https://www.ebi.ac.uk/ena/data/view/PRJEB29654

  Dataset

• Supplemental Material for Hartanto et al., 2020

  Hartanto, M. (Creator), Joosen, R. (Creator), Snoek, B. L. (Creator), Willems, L. (Creator), Sterken, M. (Creator), de Ridder, D. (Creator), Hilhorst, H. (Creator), Ligterink, W. (Creator) & Nijveen, H. (Creator), Wageningen University & Research, 22 Sept 2020

  DOI: 10.25387/g3.12844358

  Dataset