Reports

A number of reports have been produced by the transPLANT project for public discussion.

Project publications

DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species.
Alter S, Bader KC, Spannagl M, Wang Y, Bauer E, Schön CC, Mayer KF
Database (Oxford) 2015;2015:bav046
PMID:
25979979
DOI:
10.1093/database/bav046
Triticeae resources in Ensembl Plants.
Bolser DM, Kerhornou A, Walts B, Kersey P
Plant Cell Physiol. 2015;56:e3
PMID:
25432969
DOI:
10.1093/pcp/pcu183
Towards recommendations for metadata and data handling in plant phenotyping.
Krajewski P, Chen D, Ćwiek H, van Dijk AD, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S
J. Exp. Bot. 2015;:
PMID:
26044092
DOI:
10.1093/jxb/erv271
The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining
Szakonyi, D. et al.
Current Plant Biology 2015;:
DOI:
10.1016/j.cpb.2014.12.002
LAILAPS: The Plant Science Search Engine.
Esch M, Chen J, Colmsee C, Klapperstück M, Grafahrend-Belau E, Scholz U, Lange M
Plant Cell Physiol. 2015;56:e8
PMID:
25480116
DOI:
10.1093/pcp/pcu185
Prioritization of candidate genes in QTL regions based on associations between traits and biological processes
Joachim W. Bargsten, Jan-Peter Nap, Gabino F. Sanchez-Perez and Aalt D.J. van Dijk
BMC Plant Biology 2014;14:330
PMID:
25492368
DOI:
10.1186/s12870-014-0330-3
Ensembl Genomes 2013: scaling up access to genome-wide data.
Kersey, P.J. et al.
Nucleic Acids Res. 2014;42:D546-52
PMID:
24163254
DOI:
10.1093/nar/gkt979
Gramene 2013: comparative plant genomics resources.
Monaco, M.K. et al.
Nucleic Acids Res. 2014;42:D1193-9
PMID:
24217918
DOI:
10.1093/nar/gkt1110
De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P
PLoS ONE 2014;9:e96855
PMID:
24821410
DOI:
10.1371/journal.pone.0096855
Biological Process Annotation of Proteins across the Plant Kingdom
Edouard I. Severing, Jan-Peter Nap, Gabino F. Sanchez-Perez, Aalt D.J. van Dijk
Current Plant Biology (in press) 2014;:
DOI:
10.1016/j.cpb.2014.07.001
Genome interplay in the grain transcriptome of hexaploid bread wheat.
Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, IWGSC, Mayer KF, Olsen OA
Science 2014;345:1250091
PMID:
25035498
DOI:
10.1126/science.1250091
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.
IWGSC
Science 2014;345:1251788
PMID:
25035500
DOI:
10.1126/science.1251788
Ancient hybridizations among the ancestral genomes of bread wheat.
Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, IWGSC, Jakobsen KS, Wulff BB, Steuernagel B, Mayer KF, Olsen OA
Science 2014;345:1250092
PMID:
25035499
DOI:
10.1126/science.1250092
A Query Suggestion Workflow for Life Science IR-Systems
Esch M, Chen J, Weise S, Hassani-Pak K, Scholz U, Lange M
J Integr Bioinform 2014;11:237
PMID:
24953306
DOI:
10.2390/biecoll-jib-2014-237
e!DAL - a framework to store, share and publish research data
Matthias Lange, Jinbo Chen, Christian Colmsee, Steffen Flemming, Denny Hecht and Uwe Scholz
BMC Bioinformatics 2014;15:214
PMID:
24958009
DOI:
10.1186/1471-2105-15-214
NextClip: an analysis and read preparation tool for Nextera long mate pair libraries.
Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M
Bioinformatics 2013;:
PMID:
24297520
Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes.
Kourmpetis YA, van Dijk ADj, Ter Braak CJ
Algorithms Mol Biol 2013;8:10
PMID:
23531338
DOI:
10.1186/1748-7188-8-10
Information Retrieval in Life Sciences: a programmatic survey
Lange M, Henkel R, Müller W, Waltemath D, Weise S
Springer: Approaches in Integrative Bioinformatics – Towards Virtual Cell 2013;Chen M, Hofestädt R (Eds.):
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden.
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren Ü, Hellmann I, Nordborg M
Nat. Genet. 2013;45:884-890
PMID:
23793030
DOI:
10.1038/ng.2678
GnpIS: an information system to integrate genetic and genomic data from plants and fungi
Steinbach D, Alaux M, Amselem J, Choisne N, Durand S, Flores R, Keliet AO, Kimmel E, Lapalu N, Luyten I, Michotey C, Mohellibi N, Pommier C, Reboux S, Valdenaire D, Verdelet D, Quesneville H
Database (Oxford) 2013;2013:bat058
PMID:
23959375
DOI:
10.1093/database/bat058
Extraction and prediction of biomedical database identifier using neural networks towards data network construction
H. Mehlhorn, M. Lange, U. Scholz, and F. Schreiber.
Cases on Open-Linked Data and Semantic Web Applications 2013;Information Science Reference (an imprint of IGI Global). Editors: P. Ordez de Pablos, M. D. Lytras, and R. Tennyson.:58–83
ISBN:
781466628274
A large-scale evaluation of computational protein function prediction.
Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I
Nat. Methods 2013;10:221-227
PMID:
23353650
DOI:
10.1038/nmeth.2340
GWAPP: a web application for genome-wide association mapping in Arabidopsis.
Seren Ü, Vilhjálmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M
Plant Cell 2012;24:4793-4805
PMID:
23277364
DOI:
10.1105/tpc.112.108068
MIPS PlantsDB: a database framework for comparative plant genome research.
Nussbaumer T, Martis MM, Roessner SK, Pfeifer M, Bader KC, Sharma S, Gundlach H, Spannagl M
Nucleic Acids Res. 2013;41:D1144-51
PMID:
23203886
DOI:
10.1093/nar/gks1153
Analysis of the bread wheat genome using whole-genome shotgun sequencing.
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N
Nature 2012;491:705-710
PMID:
23192148
DOI:
10.1038/nature11650
The e!DAL JAVA-API: Store, Share and Cite Primary Data in Life Sciences
Arend, D. and Lange, M. and Colmsee, C. and Flemming, S. and Chen, J. and Scholz, U
IEEE International Conference on Bioinformatics and Biomedicine 2012;:511-515
DOI:
10.5447/IPK/2012/13
A mixed-model approach for genome-wide association studies of correlated traits in structured populations.
Korte A, Vilhjálmsson BJ, Segura V, Platt A, Long Q, Nordborg M
Nat. Genet. 2012;44:1066-1071
PMID:
22902788
DOI:
10.1038/ng.2376
IDPredictor: predict database links in biomedical database
Mehlhorn H, Lange M, Scholz U, Schreiber F
Journal of Integrative Bioinformatics 2012;9:190
PMID:
22736059
DOI:
10.2390/biecoll-jib-2012-190
An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations.
Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, Nordborg M
Nat. Genet. 2012;44:825-830
PMID:
22706313
DOI:
10.1038/ng.2314
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E
Nucleic Acids Res. 2012;40:D91-97
PMID:
22067447
DOI:
10.1093/nar/gkr895