| Autoren |
Titel |
| 2019 |
| Beier S, Ulpinnis C, Schwalbe M, Münch T, Hoffie R, Koeppel I, Hertig C, Budhagatapalli N, Hiekel S, Pathi K M, Hensel G, Grosse M, Chamas S, Gerasimova S, Kumlehn J, Scholz U, Schmutzer T |
Kmasker plants - a tool for assessing complex sequence space in plant species. Plant J. (2019) accepted. dx.doi.org/10.1111/tpj.14645 |
| Bolger A M, Poorter H, Dumschott K, Bolger M E, Arend D, Osorio S, Gundlach H, Mayer K F, Lange M, Scholz U, Usadel B |
Computational aspects underlying genome to phenome analysis in plants. Plant J. 97 (2019) 182-198. dx.doi.org/10.1111/tpj.14179 |
| Boudichevskaia A, Houben A, Fiebig A, Prochazkova K, Pecinka A, Lermontova I |
Depletion of KNL2 results in altered expression of genes involved in regulation of the cell cycle, transcription, and development in Arabidopsis. Int. J. Mol. Sci. 20 (2019) 5726. dx.doi.org/10.3390/ijms20225726 |
| Brown P, RELISH Consortium (including IPK author M. Lange), Zhou Y |
Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database 2019 (2019) baz085. doi.org/10.1093/database/baz085 |
| Drozdova P, Rivarola-Duarte L, Bedulina D, Axenov-Gribanov D, Schreiber S, Gurkov A, Shatilina Z, Vereshchagina K, Lubyaga Y, Madyarova E, Otto C, Jühling F, Busch W, Jakob L, Lucassen M, Sartoris F J, Hackermuller J, Hoffmann S, Portner H O, Luckenbach T, Timofeyev M, Stadler P F |
Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods. BMC Genomics 20 (2019) 712. dx.doi.org/10.1186/s12864-019-6024-3 |
| Ghaffar M, Schüler D, König P, Arend D, Junker A, Scholz U, Lange M |
Programmatic access to FAIRified digital plant genetic resources. J. Integr. Bioinform. 16 (2019) 20190060. dx.doi.org/10.1515/jib-2019-0060 |
| Keilwagen J, Lehnert H, Berner T, Beier S, Scholz U, Himmelbach A, Stein N, Badaeva E D, Lang D, Kilian B, Hackauf B, Perovic D |
Detecting large chromosomal modifications using short read data from genotyping-by-sequencing. Front. Plant Sci. 10 (2019) 1133. dx.doi.org/10.3389/fpls.2019.01133 |
| Li M, Hensel G, Mascher M, Melzer M, Budhagatapalli N, Rutten T, Himmelbach A, Beier S, Korzun V, Kumlehn J, Boerner T, Stein N |
Leaf variegation and impaired chloroplast development caused by a truncated CCT domain gene in albostrians barley. Plant Cell 31 (2019) 1430-1445. dx.doi.org/10.1105/tpc.19.00132 |
| Liu F |
Aufbau einer effizienten API zu der Generierung semantischer Metadaten am Beispiel von Pflanzenphänotypisierungsdaten. (Master Thesis) Köthen, Hochschule Anhalt, Fachbereich 5 „Informatik und Sprachen“ (2019) 75 pp. |
| Liu F, Zhao Y, Beier S, Jiang Y, Thorwarth P, Longin C F H, Ganal M, Himmelbach A, Reif J C, Schulthess A W |
Exome association analysis sheds light onto leaf rust (Puccinia triticina) resistance genes currently used in wheat breeding (Triticum aestivum L.). Plant Biotechnol. J. (2019) accepted. dx.doi.org/10.1111/pbi.13303 |
| Mascher M, Schreiber M, Scholz U, Graner A, Reif J C, Stein N |
Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding. Nat. Genet. 51 (2019) 1076-1081. dx.doi.org/10.1038/s41588-019-0443-6 |
| Mayer G, Quast C, Felden J, Lange M, Prinz M, Pühler A, Lawerenz C, Scholz U, Glöckner F O, Müller W, Marcus K, Eisenacher M |
A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects. Brief. Bioinform. 20 (2019) 1215-1221. dx.doi.org/10.1093/bib/bbx140 |
| Milner S G, Jost M, Taketa S, Mazón E R, Himmelbach A, Oppermann M, Weise S, Knüpffer H, Basterrechea M, König P, Schüler D, Sharma R, Pasam R K, Rutten T, Guo G, Xu D, Zhang J, Herren G, Müller T, Krattinger S G, Keller B, Jiang Y, González M Y, Zhao Y, Habekuß A, Färber S, Ordon F, Lange M, Börner A, Graner A, Reif J C, Scholz U, Mascher M, Stein N |
Genebank genomics highlights the diversity of a global barley collection. Nat. Genet. 51 (2019) 319-326. doi.org/10.1038/s41588-018-0266-x |
| Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer G J, Schulman A H, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer K F X, Spannagl M, Stein N, Mascher M |
TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol. 20 (2019) 284. dx.doi.org/10.1186/s13059-019-1899-5 |
| Philipp N, Weise S, Oppermann M, Börner A, Keilwagen J, Kilian B, Arend D, Zhao Y, Graner A, Reif J C, Schulthess A W |
Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection. Sci. Data 6 (2019) 137. dx.doi.org/10.1038/s41597-019-0146-y |
| Selby P, Abbeloos R, Backlund J E, Basterrechea Salido M, Bauchet G, Benites-Alfaro O E, Birkett C, Calaminos V C, Carceller P, Cornut G, Vasques Costa B, Edwards J D, Finkers R, Yanxin Gao S, Ghaffar M, Glaser P, Guignon V, Hok P, Kilian A, König P, Lagare J E B, Lange M, Laporte M-A, Larmande P, LeBauer D S, Lyon D A, Marshall D S, Matthews D, Milne I, Mistry N, Morales N, Mueller L A, Neveu P, Papoutsoglou E, Pearce B, Perez-Masias I, Pommier C, Ramírez-González R H, Rathore A, Raquel A M, Raubach S, Rife T, Robbins K, Rouard M, Sarma C, Scholz U, Sempéré G, Shaw P D, Simon R, Soldevilla N, Stephen G, Sun Q, Tovar C, Uszynski G, Verouden M, The BrAPI consortium |
BrAPI—an application programming interface for plant breeding applications. Bioinformatics 35 (2019) 4147-4155. dx.doi.org/10.1093/bioinformatics/btz190 |
| Stöbe E |
Konzeption und Implementierung einer nachrichtenorientierten Sensorikinfrastruktur für eine Pflanzenphänotypisierung und einer adaptiven Bewässerungssteuerung. (Master Thesis) Mittweida, Hochschule Mittweida, University of Applied Sciences, Fakultät: Angewandte Computer- und Biowissenschaften (2019) 65 pp. |
| Wibberg D, Batut B, Belmann P, Blom J, Glöckner F, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, Kohlbacher O |
The de.NBI / ELIXIR-DE training platform ‒ Bioinformatics training in Germany and across Europe within ELIXIR [version 1; peer review: awaiting peer review]. F1000Research 8 (2019) dx.doi.org/10.12688/f1000research.20244.1 |
| 2018 |
| Arend D |
Nachhaltige Infrastruktur zur Forschungsdatenpublikation am Beispiel von Hochdurchsatz-Pflanzenphänotypisierungsdaten. (PhD Thesis) Magdeburg, Otto-von-Guericke-Universität Magdeburg, Fakultät für Informatik (2018) 146 pp. |
| Beier S, Bolser D M, Scholz U, Spannagl M, Kersey P J |
Databases and tools for the analysis of the barley genome. In: Stein N, Muehlbauer G J (Eds.): The Barley Genome, 1st ed. (Series: Kole, C (Ed.): Compendium of Plant Genomes) Cham: Springer (2018) 377-394. dx.doi.org/10.1007/978-3-319-92528-8_21 ISBN 978-3-319-92528-8 |
| Braumann I, Dockter C, Beier S, Himmelbach A, Lok F, Lundqvist U, Skadhauge B, Stein N, Zakhrabekova S, Zhou R, Hansson M |
Mutations in the gene of the Gα subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding. Hereditas 155 (2018) 10. dx.doi.org/10.1186/s41065-017-0045-1 |
| Chen D, Shi R, Pape J-M, Neumann K, Arend D, Graner A, Chen M, Klukas C |
Predicting plant biomass accumulation from image-derived parameters. GigaScience 7 (2018) 1-13. dx.doi.org/10.1093/gigascience/giy001 |
| Chen J, Scholz U, Zhou R, Lange M |
LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions. PLoS Comput. Biol. 14 (2018) e1006058. dx.doi.org/10.1371/journal.pcbi.1006058 |
| Ghaffar M, Biere N, Jäger D, Klein K, Schreiber F, Kruse O, Sommer B |
3D modelling and visualisation of heterogeneous cell membranes in blender. In: Proceedings of the 11th International Symposium on Visual Information Communication and Interaction, August 13-15 2018, Växjö, Sweden. New York: ACM (2018) 64-71. dx.doi.org/10.1145/3231622.3231639 ISBN: 9781450365017 |
| Gonzalez M Y, Weise S, Zhao Y, Philipp N, Arend D, Börner A, Oppermann M, Graner A, Reif J C, Schulthess A W |
Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection. Sci. Data 5 (2018) 180278. dx.doi.org/10.1038/sdata.2018.278 |
| Rajaraman J, Douchkov D, Lück S, Hensel G, Nowara D, Pogoda M, Rutten T, Meitzel T, Brassac J, Höfle C, Hückelhoven R, Klinkenberg J, Trujillo M, Bauer E, Schmutzer T, Himmelbach A, Mascher M, Lazzari B, Stein N, Kumlehn J, Schweizer P |
Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance. Genome Biol. 19 (2018) 116. dx.doi.org/10.1186/s13059-018-1472-7 |
| Schilling F |
Analyse des Pan-Transkriptoms von Weizen und Erstellung von PAV Markern zur Vorhersage der Hybridleistung. (Master Thesis) Köthen, Hochschule Anhalt (FH) (2018) 50 pp. |
| Schorderet M, Duvvuru Muni R R, Fiebig A, Reinhardt D |
Deregulation of MADS-box transcription factor genes in a mutant defective in the WUSCHEL-LIKE HOMEOBOX gene EVERGREEN of Petunia hybrida. Plant Signal. Behav. 13 (2018) e1471299. dx.doi.org/10.1080/15592324.2018.1471299 |
| Schwalbe M |
Erstellung eines Tools zur Vorhersage von CRISPR/Cas Transformationseffizienzen und Off-Target Effekten. (Bachelor Thesis) Mittweida, Hochschule Mittweida, University of Applied Sciences, Fakultät: Angewandte Computer- und Biowissenschaften (2018) 45 pp. |
| Stöbe E |
Entwicklung eines webbasierten Informationssystems und einem programmatischen Interface zur Integration von Sensorikdaten aus Pflanzenphänotypisierungsanlagen. (Bachelor Thesis) Mittweida, Hochschule Mittweida, University of Applied Sciences, Fakultät: Angewandte Computer- und Biowissenschaften (2018) 72 pp. |
| 2017 |
| Basterrechea M |
Web-Interface to browse, filter and visualize plant genotyping data. (Master Thesis) Sweden, Lund University, Faculty of Science (2017) 17 pp. |
| Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis M M, Twardziok S O, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer K F X, Schmid K, Schön C-C, Scholz U |
Towards a whole-genome sequence for rye (Secale cereale L.). Plant J. 89 (2017) 853-869. dx.doi.org/10.1111/tpj.13436 |
| Beier S |
Engineering of a semi-automatic pipeline for the construction of a reference genome sequence for barley (Hordeum vulgare L.) and evaluation of assembly quality. (PhD Thesis) Bielefeld, Universität Bielefeld, Biologische Fakultät (2017) 107 pp. |
| Beier S, Himmelbach A, Colmsee C, Zhang X-Q, Barrero R A, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke J K, Tan C, Wang S, Yin S, Zhou G, Poland J A, Bellgard M I, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer G J, Kersey P, Clark M D, Caccamo M, Schulman A H, Platzer M, Close T J, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M |
Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci. Data 4 (2017) 170044. dx.doi.org/10.1038/sdata.2017.44 |
| Beier S, Thiel T, Münch T, Scholz U, Mascher M |
MISA-web: a web server for microsatellite prediction. Bioinformatics 33 (2017) 2583–2585. dx.doi.org/10.1093/bioinformatics/btx198 |
| Bolger M, Schwacke R, Gundlach H, Schmutzer T, Chen J, Arend D, Oppermann M, Weise S, Lange M, Fiorani F, Spannagl M, Scholz U, Mayer K, Usadel B |
From plant genomes to phenotypes. J. Biotechnol. 261 (2017) 46-52. dx.doi.org/10.1016/j.jbiotec.2017.06.003 |
| Bustamante F O, Aliyeva-Schnorr L, Fuchs J, Beier S, Houben A |
Correlating the genetic and physical map of barley chromosome 3H revealed limitations of the FISH-based mapping of nearby single-copy probes caused by the dynamic structure of metaphase chromosomes. Cytogenet. Genome Res. 152 (2017) 90-96. dx.doi.org/10.1159/000478631 |
| Lange M |
Application of database to manage, preserve and analyse plant genomics and phenomics data (extended abstract of invited talk). In: Schneider K, Specht G (Eds.): CEUR Workshop Proceedings, Vol. 1858 (Proceedings of the 29th GI-Workshop Grundlagen von Datenbanken, Blankenburg/Harz, Germany, May 30 - June 02, 2017). (2017) 11-12. ceur-ws.org/Vol-1858/paper3.pdf ISSN 1613-0073 |
| Ma W, Gabriel T S, Martis M M, Gursinsky T, Schubert V, Vrana J, Dolezel J, Grundlach H, Altschmied L, Scholz U, Himmelbach A, Behrens S E, Banaei-Moghaddam A M, Houben A |
Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog. New Phytol. 213 (2017) 916-928. dx.doi.org/10.1111/nph.14110 |
| Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok S O, Wicker T, Radchuk V, Dockter C, Hedley P E, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang X-Q, Zhang Q, Barrero R A, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke J K, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland J A, Bellgard M I, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer G J, Clark M D, Caccamo M, Schulman A H, Mayer K F X, Platzer M, Close T J, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N |
A chromosome conformation capture ordered sequence of the barley genome. Nature 544 (2017) 427-433. dx.doi.org/10.1038/nature22043 |
| Meier A, Worch S, Böer E, Hartmann A, Mascher M, Marzec M, Scholz U, Riechen J, Baronian K, Schauer F, Bode R, Kunze G |
Agdc1p – a gallic acid decarboxylase involved in the degradation of 1 tannic acid in the yeast Blastobotrys (Arxula) adeninivorans. Front. Microbiol. 8 (2017) 1777. dx.doi.org/10.3389/fmicb.2017.01777 |
| Oeser B, Kind S, Schurack S, Schmutzer T, Tudzynski P, Hinsch J |
Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale. BMC Genomics 18 (2017) 273. dx.doi.org/10.1186/s12864-017-3619-4 |
| Romano P, Hofestädt R, Lange M, D’Elia D |
The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes. BMC Bioinformatics 18 (2017) 101. dx.doi.org/10.1186/s12859-017-1532-0 |
| Ruban A, Schmutzer T, Scholz U, Houben A |
How next-generation sequencing has aided our understanding of the sequence composition and origin of B chromosomes. Genes 8 (2017) 294. dx.doi.org/10.3390/genes8110294 |
| Schmutzer T, Bolger M E, Rudd S, Chen J, Gundlach H, Arend D, Oppermann M, Weise S, Lange M, Spannagl M, Usadel B, Mayer K F X, Scholz U |
Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives. J. Biotechnol. 261 (2017) 37-45. dx.doi.org/10.1016/j.jbiotec.2017.07.006 |
| Ulpinnis C |
Entwicklung einer Pipeline für eine verbesserte Genvorhersage durch die Verknüpfung von Assemblierungsdaten mittels RNA-seq Daten. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2017) 124 pp. |
| Zanke C, Ling J, Plieske J, Kollers S, Ebmeyer E, Argillier O, Stiewe G, Hinze M, Beier S, Ganal M W, Röder M S |
Genetic architecture of main effect QTL for heading date in European winter wheat. In: Jung C, Pillen K, Staiger D, Coupland G, von Korff M (Eds.): Recent advances in flowering time control. (ebook: doi: 10.3389/978-2-88945-115-9). Lausanne: Frontiers Media (2017) 209-220. |
| 2016 |
| Arend D, Junker A, Scholz U, Schüler D, Wylie J, Lange M |
PGP repository: a plant phenomics and genomics data publication infrastructure. Database 2016 (2016) 1-10. dx.doi.org/10.1093/database/baw033 |
| Arend D, Lange M, Pape J-M, Weigelt-Fischer K, Arana-Ceballos F, Mücke I, Klukas C, Altmann T, Scholz U, Junker A |
Quantitative monitoring of Arabidopsis thaliana growth and development using high-throughput plant phenotyping. Scientific Data 3 (2016) 160055. dx.doi.org/10.1038/sdata.2016.55 |
| Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer K F X, Platzer M, Stein N, Scholz U, Mascher M |
Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. Plant Biotechnol. J. 14 (2016) 1511-1522. dx.doi.org/10.1111/pbi.12511 |
| Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D, Cornut G, Fiorani F, Frohmberg W, Junker A, Klukas C, Lange M, Mazurek C, Nafissi A, Neveu P, van Oeveren J, Pommier C, Poorter H, Rocca-Serra P, Sansone S-A, Scholz U, van Schriek M, Seren Ü, Usadel B, Weise S, Kersey P, Krajewski P |
Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods 12 (2016) 44. dx.doi.org/10.1186/s13007-016-0144-4 |
| Fíla J, Radau S, Matros A, Hartmann A, Scholz U, Feciková J, Mock H-P, Ĉapková V, Zahedi R P, Honys D |
Phosphoproteomics profiling of tobacco mature pollen and pollen activated in vitro. Mol. Cell. Proteomics 15 (2016) 1338-1350. dx.doi.org/10.1074/mcp.M115.051672 |
| Jöst M, Hensel G, Kappel C, Druka A, Sicard A, Hohmann U, Beier S, Himmelbach A, Waugh R, Kumlehn J, Stein N, Lenhard M |
The INDETERMINATE DOMAIN protein BROAD LEAF1 limits barley leaf width by restricting lateral proliferation. Curr. Biol. 26 (2016) 903-909. dx.doi.org/10.1016/j.cub.2016.01.047 |
| Jost M, Taketa S, Mascher M, Himmelbach A, Yuo T, Shahinnia F, Rutten T, Druka A, Schmutzer T, Steuernagel B, Beier S, Taudien S, Scholz U, Morgante M, Waugh R, Stein N |
A homolog of Blade-On-Petiole 1 and 2 (BOP1/2) controls internode length and homeotic changes of the barley inflorescence. Plant Physiol. 171 (2016) 1113-1127. dx.doi.org/10.1104/pp.16.00124 |
| Ma W, Schubert V, Martis M M, Hause G, Liu Z, Shen Y, Conrad U, Shi W, Scholz U, Taudien S, Cheng Z, Houben A |
The distribution of alpha-kleisin during meiosis in the holocentromeric plant Luzula elegans. Chromosome Res. 24 (2016) 393-405. dx.doi.org/10.1007/s10577-016-9529-5 |
| Rauter M, Kasprzak J, Becker K, Riechen J, Worch S, Hartmann A, Mascher M, Scholz U, Baronian K, Bode R, Schauer F, Matthias Vorbrodt H, Kunze G |
Aadh2p: an Arxula adeninivorans alcohol dehydrogenase involved in the first step of the 1-butanol degradation pathway. Microb. Cell Fact. 15 (2016) 175. dx.doi.org/10.1186/s12934-016-0573-9 |
| Schmutzer T |
Strategies to detect genetic diversity in plants. (PhD Thesis) Jena, Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät (2016) 150 pp. |
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