Bioinformatics

Search results

• Parental Effects on Seed Transcriptome-Metabolome

  He, H. (Creator), Willems, L. (Creator), Batushansky, A. (Creator), Fait, A. (Creator), Hanson, J. (Creator), Nijveen, H. (Creator), Hilhorst, H. (Creator) & Bentsink, L. (Creator), Wageningen University, 1 Jan 2016

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75837

  Dataset

• Indexed pPHRED summary scores

  Gross, C. (Creator), Derks, M. (Creator), Megens, H. (Creator), Bosse, M. (Creator), Groenen, M. A. M. (Creator), Reinders, M. (Creator) & de Ridder, D. (Creator), Wageningen University & Research, 2020

  http://www.bioinformatics.nl/pCADD/indexed_pPHRED-summary-scores/

  Dataset

• Data from: Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus

  Singh, K. (Creator), De-Kayne, R. (Creator), Omufwoko, K. S. (Creator), Martins, D. (Creator), Bass, C. (Creator), Ffrench-Constant, R. (Creator) & Martin, S. H. (Creator), Wageningen University, 27 Nov 2021

  DOI: 10.5281/zenodo.5731560

  Dataset

• Picochlorum sp. BPE23 genome assembly

  Barten, R. J. P. (Creator), van Workum, D. M. (Creator), de Bakker, E. (Creator), Risse, J. (Creator), Kleisman, M. (Creator), Correia Navalho, S. A. (Creator), Smit, S. (Creator), Wijffels, R. (Creator), Nijveen, H. (Creator) & Barbosa, M. (Creator), Wageningen University & Research, 23 Aug 2022

  https://www.ncbi.nlm.nih.gov/bioproject/872549

  Dataset

• Wolbachia endosymbiont of Operophtera brumata strain:Ob_Wba Genome sequencing and assembly

  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, 11 Aug 2015

  https://www.ncbi.nlm.nih.gov/bioproject/276497

  Dataset

• Operophtera brumata isolate:WM2013NL Genome sequencing and assembly

  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, 11 Aug 2015

  https://www.ncbi.nlm.nih.gov/bioproject/263715

  Dataset

• NPLinker eScience Workshop on Natural Product Genome & Metabolome Mining Materials

  van der Hooft, J. (Creator), Medema, M. (Creator), Weber, T. (Creator), Leao, T. (Creator), Navarro Munoz, J. (Creator), Schmid, R. (Creator), Brungs, C. (Creator), Zdouc, M. (Creator), Terlouw, B. (Creator), Barona-Gómez, P. (Creator) & Geng, C. (Creator), Wageningen University & Research, 5 Apr 2023

  DOI: 10.5281/zenodo.7801712

  Dataset

• Hirschfeldia incana isolate:HINC_NIJ6 Genome sequencing and assembly

  Garassino, F. (Creator), Wijfjes, R. Y. (Creator), Boesten, R. (Creator), Reyes Marquez, F. (Creator), Becker, F. (Creator), Clapero, V. (Creator), van den Hatert, I. (Creator), Holmer, R. (Creator), Schranz, E. (Creator), Harbinson, J. (Creator), de Ridder, D. (Creator), Smit, S. (Creator) & Aarts, M. (Creator), Wageningen University & Research, 21 Nov 2022

  https://www.ncbi.nlm.nih.gov/bioproject/612790

  Dataset

• This study contains the re-sequencing data of 100 Lactuca accessions derived from the CGN (Centre for Genetic Resources, the Netherlands) collection.

  Xiong, W. (Creator), Berke, L. (Creator), Michelmore, R. (Creator), van Workum, D. M. (Creator), Becker, F. (Creator), Schijlen, E. (Creator), Bakker, L. V. (Creator), Peters, S. (Creator), van Treuren, R. (Creator), Jeuken, M. (Creator), Bouwmeester, K. (Creator) & Schranz, E. (Creator), Wageningen University & Research, 29 Jun 2020

  https://www.ebi.ac.uk/ena/browser/view/PRJEB36060

  Dataset

• NPOmix 1: antiSMASH results from 1,040 PoDP paired samples

  Leao, T. F. (Creator), Wang, M. (Creator), Silva, R. (Creator), Gurevich, A. (Creator), Bauermeister, A. (Creator), Gomes, P. W. P. (Creator), Brejnrod, A. (Creator), Glukhov, E. (Creator), Aron, A. T. (Creator), Louwen, J. (Creator), Kim, H. W. (Creator), Reher, R. (Creator), Fiore, M. F. (Creator), van der Hooft, J. (Creator), Gerwick, L. (Creator), Gerwick, W. H. (Creator), Bandeira, N. (Creator) & Dorrestein, P. C. (Creator), University of California, 13 Jun 2022

  DOI: 10.5281/zenodo.6637082

  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

• 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

• 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

• Reciprocal cybrids reveal how organellar genomes affect plant phenotypes

  Theeuwen, T. (Creator), Flood, P. (Creator), Schneeberger, K. (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 & Research, 19 Dec 2019

  DOI: 10.5061/dryad.cz8w9gj05

  Dataset

• Maternal environment dependent expression-QTLs of Tomato seeds

  Sterken, M. (Creator), Nijveen, H. (Creator), Van zanten, M. (Creator), Jiménez-Gómez, J. M. (Creator), Geshnizjani, N. (Creator), Willems, L. (Creator), Rienstra, J. (Creator), Hilhorst, H. W. M. (Creator), Ligterink, W. (Creator) & Snoek, B. L. (Creator), Wageningen University & Research, 25 Feb 2021

  https://www.ncbi.nlm.nih.gov/bioproject/704909

  Dataset

• Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

  van Velzen, R. (Creator), Holmer, R. (Creator), Bu, F. (Creator), Rutten, L. J. J. (Creator), van Zeijl, A. L. (Creator), Liu, W. (Creator), Santuari, L. (Creator), Cao, Q. (Creator), Sharma, T. (Creator), Shen, D. (Creator), Roswanjaya, Y. (Creator), Wardhani, T. (Creator), Seifi Kalhor, M. (Creator), Jansen, J. (Creator), van den Hoogen, D. J. (Creator), Gungor, B. (Creator), Hartog, M. (Creator), Hontelez, J. (Creator), Verver, J. W. G. (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 & Research, 3 May 2018

  DOI: 10.5061/dryad.fq7gv88

  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

• Supplemental Dataset for Automated genome mining predicts combinatorial diversity and taxonomic distribution of peptide metallophore structures

  Reitz, Z. (Creator), Wageningen University & Research, 14 Dec 2022

  DOI: 10.5281/zenodo.7439476

  Dataset

• Transposon insertion polymorphisms in tomato cultivars: Supporting Information

  Demirci, S. (Creator), Wageningen University & Research, 13 Jun 2021

  DOI: 10.5281/zenodo.4939935

  Dataset

• Data and reproducible scripts for "Distribution of Putative Self-resistance Genes for Antibiotic Biosynthetic Gene Cluster in Actinobacteria"

  Kautsar, S. (Creator), Wageningen University & Research, 16 Sept 2020

  DOI: 10.5281/zenodo.4032306

  Dataset

• Constraint based modeling in R using metabolic reconstruction databases

  Gavai, A. K. (Creator), Hettinga, H. (Creator) & Leunissen, J. A. M. (Creator), Wageningen UR, 14 Jul 2015

  http://bioconductor.org/packages/release/bioc/html/BiGGR.html

  Dataset

• Data from: Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes

  Moran, P. A. (Creator), Pascoal, S. (Creator), Cezard, T. (Creator), Risse, J. (Creator), Ritchie, M. G. (Creator) & Bailey, N. W. (Creator), 17 May 2018

  DOI: 10.5061/dryad.573531d

  Dataset

• Genomics of Rapid Evolution in Field Crickets

  Pascoal, S. (Creator), Risse, J. (Creator), Zhang, X. (Creator), Blaxter, M. (Creator), Cezard, T. (Creator), Challis, R. J. (Creator), Gharbi, K. (Creator), Hunt, J. (Creator), Kumar, S. (Creator), Langan, E. (Creator), Liu, X. (Creator), Rayner, J. G. (Creator), Ritchie, M. G. (Creator), Snoek, B. (Creator), Trivedi, U. (Creator) & Bailey, N. W. (Creator), University of Edinburgh, 22 Jan 2020

  https://www.ebi.ac.uk/ena/data/view/PRJEB24786

  Dataset

• Analysis results of the paper baseLess: Lightweight detection of sequences in raw MinION data

  Noordijk, B. (Creator), Nijland, R. (Creator), Carrion, V. J. (Creator), Raaijmakers, J. (Creator), de Ridder, D. (Creator) & de Lannoy, C. (Creator), Wageningen University & Research, 18 Jul 2022

  DOI: 10.4121/20261392

  Dataset

• GNPS - Stool (fecal) HILIC LC-MS/MS and LC-MS NEG mode data from clinical cohort - used for MS2LDA substructure discovery

  van der Hooft, J. (Creator), Wageningen University, 2020

  DOI: 10.25345/c5tq4q

  Dataset