Bioinformatics

Search results

• Cleaned and pre-processed MS/MS datset (build from all positive ionmode spectra in GNPS) - zip file

  Huber, F. (Creator), Ridder, L. (Creator), Verhoeven, S. (Creator), Spaaks, J. H. (Creator), Diblen, F. (Creator), Rogers, S. (Creator) & van der Hooft, J. (Creator), 10 Aug 2020

  DOI: 10.5281/zenodo.3978118

  Dataset

• Data underlying the publication: "The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool"

  Jonkheer, E. (Creator), Smit, S. (Creator), van der Lee, T. (Creator), Brankovics, B. (Creator), van der Wolf, J. (Creator) & Vreeburg, R. (Creator), Wageningen University & Research, 23 Feb 2021

  DOI: 10.4121/14061122

  Dataset

• GNPS - Urine LC-MS/MS data used for Antihypertensive Drug Screening Validation Study

  van der Hooft, J. (Creator), Barrett, M. (Creator) & Padmanabhan, S. (Creator), Wageningen University, 2021

  DOI: 10.25345/c5ws0h

  Dataset

• Expression data from Arabidopsis root tips rRBr mutant

  Horvath, B. M. (Creator), Kourova, H. (Creator), Nagy, S. (Creator), Nemeth, E. (Creator), Magyar, Z. (Creator), Papdi, C. (Creator), Ahmad, Z. (Creator), Sanchez Perez, G. (Creator), Perilli, S. (Creator), Blilou, I. (Creator), Pettkó-Szandtner, A. (Creator), Darula, Z. (Creator), Meszaros, T. (Creator), Binarova, P. (Creator), Bogre, L. (Creator) & Scheres, B. (Creator), Wageningen University, 23 Dec 2015

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47715

  Dataset

• Ranunculales supplementary data

  Mutabdžija, L. (Creator), Myoli, A. (Creator), de Jonge, N. (Creator), Damiani, T. (Creator), Schmid, R. (Creator), van der Hooft, J. (Creator), Tugizimana, F. (Creator) & Pluskal, T. (Creator), Zenodo, 30 Mar 2023

  DOI: 10.5281/zenodo.7784920

  Dataset

• MS2Query case study files

  de Jonge, N. (Creator), Wageningen University & Research, 6 Jul 2022

  DOI: 10.5281/zenodo.6811539

  Dataset

• Tandem Mass Spectrometry Dataset for Machine Learning in Metabolomics

  Strobel, M. (Creator), de Jonge, N. (Creator), Gil de la Fuente, A. (Creator), Hecht, H. (Creator), van der Hooft, J. (Creator), Huber, F. (Creator) & Wang, M. (Creator), University of California, 5 Mar 2024

  DOI: 10.5281/zenodo.10724906

  Dataset

• BRANCHED1 Orchestrates an ABA Gene Regulatory Network to Promote axillary bud dormancy in Arabidopsis

  van Es, S. W. (Creator), Muñoz-Gasca, A. (Creator), Romero-Campero, F. J. (Creator), González-Grandío, E. (Creator), de los Reyes, P. (Creator), Tarancón, C. (Creator), van Dijk, A. (Creator), van Esse, W. (Creator), Pascual-García, A. (Creator), Angenent, G. (Creator), Immink, R. (Creator) & Cubas, P. (Creator), Wageningen University & Research, 24 Jul 2020

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155028

  Dataset

• sequencing data for Lactuca virosa assembly and annotation

  Xiong, W. (Creator), van Workum, D. M. (Creator), Berke, L. (Creator), Bakker, L. (Creator), Schijlen, E. (Creator), Becker, F. (Creator), van de Geest, H. (Creator), Peters, S. (Creator), Michelmore, R. (Creator), van Treuren, R. (Creator), Jeuken, M. (Creator), Smit, S. (Creator) & Schranz, E. (Creator), Wageningen University & Research, 25 May 2023

  https://www.ebi.ac.uk/ena/browser/view/PRJEB56289

  Dataset

• CCDC 1539193: Experimental Crystal Structure Determination

  Huang, A. C. (Creator), Kautsar, S. A. (Creator), Hong, Y. J. (Creator), Medema, M. (Creator), Bond, A. D. (Creator), Tantillo, D. J. (Creator) & Osbourn, A. (Creator), 20 Mar 2017

  DOI: 10.5517/ccdc.csd.cc1nnndc

  Dataset

• CCDC 1539191: Experimental Crystal Structure Determination

  Huang, A. C. (Creator), Kautsar, S. A. (Creator), Hong, Y. J. (Creator), Medema, M. (Creator), Bond, A. D. (Creator), Tantillo, D. J. (Creator) & Osbourn, A. (Creator), 20 Mar 2017

  DOI: 10.5517/ccdc.csd.cc1nnnb9

  Dataset

• Pectobacterium genome sequencing for pangenomics

  Jonkheer, E. (Creator), Brankovics, B. (Creator), Houwers, I. (Creator), van der Wolf, J. (Creator), Bonants, P. (Creator), Vreeburg, R. A. M. (Creator), Bollema, R. (Creator), de Haan, J. R. (Creator), Berke, L. (Creator), Smit, S. (Creator), de Ridder, D. (Creator) & van der Lee, T. (Creator), Wageningen Plant Research, 28 Jul 2020

  https://www.ncbi.nlm.nih.gov/bioproject/PRJNA649220

  Dataset

• The Natural Products Atlas - data download

  Van Santen, J. A. (Creator), Jacob, G. (Creator), Singh, A. L. (Creator), Aniebok, V. (Creator), Balunas, M. J. (Creator), Bunsko, D. (Creator), Neto, F. C. (Creator), Castaño-Espriu, L. (Creator), Chang, C. (Creator), Clark, T. N. (Creator), Cleary Little, J. L. (Creator), Delgadillo, D. A. (Creator), Dorrestein, P. C. (Creator), Duncan, K. R. (Creator), Egan, J. M. (Creator), Galey, M. M. (Creator), Haeckl, J. (Creator), Hua, A. (Creator), Hughes, A. H. (Creator), Iskakova, D. (Creator), Khadilkar, A. (Creator), Lee, J. H. (Creator), Lee, S. (Creator), Legrow, N. (Creator), Liu, D. Y. (Creator), Macho, J. M. (Creator), McCaughey, C. S. (Creator), Medema, M. (Creator), Neupane, R. P. (Creator), O'Donnell, T. J. (Creator), Paula, J. S. (Creator), Sanchez, L. M. (Creator), Shaikh, A. F. (Creator), Soldatou, S. (Creator), Terlouw, B. R. (Creator), Tran, T. A. (Creator), Valentine, M. (Creator), van der Hooft, J. (Creator), Vo, D. A. (Creator), Wang, M. (Creator), Wilson, D. (Creator), Zink, K. E. (Creator) & Linington, R. G. (Creator), Wageningen University, 19 May 2021

  DOI: 10.5281/zenodo.3530792

  Dataset

• Pre-computed MGCs from human microbiome reference genomes

  Andreu, V. P. (Creator), Augustijn, H. (Creator), van den Berg, K. (Creator), van der Hooft, J. (Creator), Fischbach, M. A. (Creator) & Medema, M. (Creator), Wageningen University, 26 Oct 2022

  DOI: 10.5281/zenodo.7252624

  Dataset

• CCDC 1535308: Experimental Crystal Structure Determination

  Huang, A. C. (Creator), Kautsar, S. A. (Creator), Hong, Y. J. (Creator), Medema, M. (Creator), Bond, A. D. (Creator), Tantillo, D. J. (Creator) & Osbourn, A. (Creator), 28 Feb 2017

  DOI: 10.5517/ccdc.csd.cc1njm2w

  Dataset

• Pentapetalae cytochrome P450 mRNA, complete cds.

  Wang, Y. (Creator), Durairaj, J. (Creator), Suarez Duran, H. (Creator), van Velzen, R. (Creator), Flokova, K. (Creator), Liao, C. Y. (Creator), Chojnacka, A. (Creator), Macfarlane, S. (Creator), Schranz, E. (Creator), Medema, M. (Creator), van Dijk, A. (Creator), Dong, L. (Creator) & Bouwmeester, H. (Creator), Wageningen University & Research, 1 Jul 2022

  https://www.ncbi.nlm.nih.gov/popset/2251331960

  Dataset

• Genomic basis of divergence of modern cultivated potatoes

  Li, H. (Creator), Brouwer, M. (Creator), del Pup, E. (Creator), van Lieshout, N. (Creator), Finkers, R. (Creator), Bachem, C. (Creator) & Visser, R. (Creator), Wageningen University & Research, 14 Mar 2023

  https://www.ncbi.nlm.nih.gov/bioproject/944441

  Dataset

• Transcription profiling by array of Arabidopsis thaliana wild type (Col-0) and flowering time mutants to investigate synchronized induction of flowering

  Valentim, F. L. (Creator), van Mourik, S. (Creator), Posé, D. (Creator), Kim, M. C. (Creator), Schmid, M. (Creator), van Ham, R. C. H. J. (Creator), Busscher, M. (Creator), Sanchez Perez, G. F. (Creator), Immink, R. (Creator) & van Dijk, A. (Creator), Wageningen UR, 1 Nov 2013

  https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-4001/

  Dataset

• Study of Arabidopsis thaliana seeds during dormancy cycling

  Buijs, G. (Creator), Vogelzang, A. (Creator), Nijveen, H. (Creator) & Bentsink, L. (Creator), Wageningen University & Research, 13 Jul 2019

  https://www.ncbi.nlm.nih.gov/bioproject/554414

  Dataset

• A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

  Witjes, L. (Creator), Kooke, R. (Creator), van der Hooft, J. (Creator), de Vos, R. (Creator), Keurentjes, J. (Creator), Medema, M. (Creator) & Nijveen, H. (Creator), Wageningen University & Research, 2 Apr 2019

  DOI: 10.6084/m9.figshare.c.4456952

  Dataset

• Reverse genetics using CRISPR-Cas9 in the tropical tree Parasponia andersonii revealed a promotive role for PanNODULE ROOT1 in stem secondary growth

  Shen, D. (Creator), Holmer, R. (Creator), Kulikova, O. (Creator), Mannapperuma, C. (Creator), Street, N. R. (Creator), Yan, Z. (Creator), van der Maden, T. (Creator), Bu, F. (Creator), Zhang, Y. (Creator), Geurts, R. (Creator) & Magne, K. (Creator), Wageningen University, 3 May 2021

  https://www.ebi.ac.uk/ena/browser/view/PRJEB37036

  Dataset

• Indexed pPHRED scores

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

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

  Dataset

• D.chry2.2 assembly

  Singh, K. (Creator), De-Kayne, R. (Creator), Omufwoko, K. S. (Creator), Martins, D. J. (Creator), Bass, C. (Creator), Ffrench-Constant, R. (Creator) & Martin, S. H. (Creator), University of Edinburgh, 2 Oct 2021

  https://www.ncbi.nlm.nih.gov/bioproject/PRJEB47812

  Dataset

• Accelerated discovery of functional variation in pigs

  Derks, M. (Creator), Gross, C. (Creator), Lopes, M. S. (Creator), Reinders, M. J. T. (Creator), Bosse, M. (Creator), Gjuvsland, A. B. (Creator), Harlizius, B. (Creator), de Ridder, D. (Creator), Megens, H. (Creator) & Groenen, M. A. M. (Creator), Wageningen University & Research, 4 Apr 2021

  https://www.ebi.ac.uk/ena/browser/view/PRJEB44082

  Dataset

• Parasponia andersonii isolate:WU1-14

  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/PRJNA272473/

  Dataset