Bioinformatics

Search results

• 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

• data

  Farooq, M. (Creator), Wageningen University & Research, 1 Jul 2022

  DOI: 10.6084/m9.figshare.20209700

  Dataset

• Dataset: 295,416 RiPP BGCs from BiG-FAM version 1.0

  Kautsar, S. (Creator), Wageningen University & Research, 19 Oct 2020

  DOI: 10.5281/zenodo.4106679, https://bigfam.bioinformatics.nl

  Dataset

• 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), Wageningen University, 24 May 2018

  https://www.ebi.ac.uk/ena/data/view/PRJEB26502

  Dataset

• Data from: Heritable gene expression differences between apomictic clone members in Taraxacum officinale: insights into early stages of evolutionary divergence in asexual plants

  Ferreira de Carvalho, J. (Creator), Oplaat, C. (Creator), de Ridder, D. (Creator) & Verhoeven, K. J. F. (Creator), Wageningen University & Research, 2016

  DOI: 10.5061/dryad.6p2n6

  Dataset

• Data underlying the publication: "PanTools v3: functional annotation, classification, and phylogenomics "

  Jonkheer, E. (Creator) & Smit, S. (Creator), Wageningen University & Research, 4 Jul 2022

  DOI: 10.4121/19874485

  Dataset

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

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

  DOI: 10.25345/c5zd70

  Dataset

• From mass spectral features to molecules in molecular networks: MolNotator LDB dataset.

  Olivier-Jimenez, D. (Creator), Bouchouireb, Z. (Creator), Ollivier, S. (Creator), Mocquard, J. (Creator), Allard, P. (Creator), Bernadat, G. (Creator), Chollet-Krugler, M. (Creator), Rondeau, D. (Creator), Boustie, J. (Creator), van der Hooft, J. (Creator) & Wolfender, J. (Creator), 16 Dec 2021

  DOI: 10.5281/zenodo.5785844

  Dataset

• Collection of fragmentation mass spectra (all from GNPS, accessed on 2020-05-11)

  Huber, F. (Creator), Ridder, L. (Creator), Verhoeven, S. (Creator), Spaaks, J. H. (Creator), Diblen, F. (Creator), Rogers, S. (Creator) & van der Hooft, J. (Creator), 11 Aug 2020

  DOI: 10.5281/zenodo.3979010

  Dataset

• Cleaned libraries and settings matchms library cleaning pipeline

  de Jonge, N. (Creator), Hecht, H. (Creator), van der Hooft, J. (Creator) & Huber, F. (Creator), Wageningen University & Research, 20 Nov 2023

  DOI: 10.5281/zenodo.10036538

  Dataset

• Whole-genome amplification (WGA) create specific chimeric fragments, which consist mainly of palindrome sequences. We developed the tool Pacasus to detect and correct these palindromic sequences in long reads, for example from PacBio and Nanopore

  Warris, S. (Creator), Schijlen, E. (Creator), van de Geest, H. C. (Creator), Vegesna, R. (Creator), Hesselink, T. (Creator), te Lintel Hekkert, B. (Creator), Sanchez Perez, G. F. (Creator), Medvedev, P. (Creator), Makova, K. D. (Creator) & de Ridder, D. (Creator), Wageningen UR, 31 Jul 2017

  https://www.ebi.ac.uk/ena/data/view/PRJEB21791

  Dataset

• MS2Query pre-trained embeddings and models 15-12-2021

  de Jonge, N. (Creator), Zenodo, 17 Feb 2022

  DOI: 10.5281/zenodo.6124553

  Dataset

• Cleaned and split GNPS dataset for training MS2Query of 24-11-2021

  de Jonge, N. (Creator), Wageningen University & Research, 1 Dec 2021

  DOI: 10.5281/zenodo.5746934

  Dataset

• MS2Query negative mode model and library 15_12_21

  de Jonge, N. (Creator), Wageningen University & Research, 22 Sept 2022

  DOI: 10.5281/zenodo.7104184

  Dataset

• Salvia dorisiana

  Jongedijk, E. (Creator), Müller, S. (Creator), van Dijk, A. (Creator), Schijlen, E. (Creator), Champagne, A. (Creator), Boutry, M. (Creator), Levisson, M. (Creator), Van Der Krol, S. (Creator), Bouwmeester, H. (Creator) & Beekwilder, J. (Creator), Wageningen University & Research, 13 Dec 2019

  https://www.ncbi.nlm.nih.gov/bioproject/595496

  Dataset

• Beauveria bassiana Genome sequencing and assembly

  Valero Jimenez, C. A. (Creator), Faino, L. (Creator), Spring in 'T Veld, D. (Creator), Smit, S. (Creator), Zwaan, B. (Creator) & van Kan, J. (Creator), Wageningen University, 8 Jul 2016

  https://www.ncbi.nlm.nih.gov/bioproject/PRJNA260878/

  Dataset

• CCDC 1535306: 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.cc1njm0t

  Dataset

• Reliable genomic strategies for species classification of plant genetic resources

  van Bemmelen van der Plaat, A. (Creator), van Treuren, R. (Creator) & van Hintum, T. (Creator), Wageningen University & Research, 16 Apr 2021

  DOI: 10.6084/m9.figshare.c.5362234

  Dataset

• CCDC 1539192: 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.cc1nnncb

  Dataset

• Data for iPRESTO: automated discovery of biosynthetic sub-clusters linked to specific natural product substructures

  Louwen, J. J. R. (Creator), Kautsar, S. A. (Creator), van der Burg, S. (Creator), Medema, M. (Creator) & van der Hooft, J. (Creator), Wageningen University & Research, 2 Aug 2022

  DOI: 10.5281/zenodo.6953656

  Dataset

• CCDC 1535307: 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.cc1njm1v

  Dataset

• Supporting data for "BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters"

  Kautsar, S. (Creator), van der Hooft, J. (Creator), de Ridder, D. (Creator) & Medema, M. (Creator), Wageningen University & Research, 24 Nov 2020

  DOI: 10.5524/100826

  Dataset

• Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

  Ceniceros, A. (Creator), Dijkhuizen, L. (Creator), Petrusma, M. (Creator) & Medema, M. (Creator), University of Groningen, 9 Aug 2017

  DOI: 10.6084/m9.figshare.c.3849541

  Dataset

• Paired omics Data Platform projects

  Verhoeven, S. (Creator), Schorn, M. (Contributor), Medema, M. (Contributor), Dorrestein, P. C. (Creator) & van der Hooft, J. (Creator), 1 Apr 2020

  DOI: 10.5281/zenodo.3736430

  Dataset

• Databases for exploratory mode of RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery

  Kloosterman, A. M. (Creator), Shelton, K. E. (Creator), van Wezel, G. P. (Creator), Medema, M. (Creator) & Mitchell, D. A. (Creator), Leiden University, 30 Mar 2020

  DOI: 10.5281/zenodo.3733240

  Dataset