Publikationen

Autoren Titel
2021
Blätke M-A, Szymanski J J, Gladilin E, Scholz U, Beier S Editorial: Advances in applied bioinformatics in crops. Front. Plant Sci. 12 (2021) 640394. dx.doi.org/10.3389/fpls.2021.640394
Ma W, Liu Z J, Beier S, Houben A, Carpentier S Identification of rye B chromosome-associated peptides by mass spectrometry. New Phytol. 230 (2021) 2179-2185. dx.doi.org/10.1111/nph.17238
Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh C S, Ens J, Gundlach H, Boston L B, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer K F X, Spannagl M, Pozniak C J, Sharpe A G, Šimková H, Moscou M J, Grimwood J, Schmutz J, Stein N Long-read sequence assembly: a technical evaluation in barley. Plant Cell 33 (2021) 1888-1906. dx.doi.org/10.1093/plcell/koab077
Mayer G, Müller W, Schork K, Uszkoreit J, Weidemann A, Wittig U, Rey M, Quast C, Felden J, Glöckner F O, Lange M, Arend D, Beier S, Junker A, Scholz U, Schüler D, Kestler H A, Wibberg D, Pühler A, Twardziok S, Eils J, Eils R, Hoffmann S, Eisenacher M, Turewicz M Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. Brief. Bioinform. (2021) Epub ahead of print. dx.doi.org/10.1093/bib/bbab010
Pommier C, Gruden K, Junker A, Coppens F, Finkers R, Hassani-Pak K, Faria D, Hancock J M, Beier S, Costa B, Miguel C, Chaves I, Davey R, Contreras-Moreira B ELIXIR Plant sciences 2020-2023 Roadmap [version 1; not peer reviewed]. F1000Research 10 (2021) 145. doi.org/10.7490/f1000research.1118482.1
Rabanus-Wallace M T, Hackauf B, Mascher M, Lux T, Wicker T, Gundlach H, Baez M, Houben A, Mayer K F X, Guo L, Poland J, Pozniak C J, Walkowiak S, Melonek J, Praz C R, Schreiber M, Budak H, Heuberger M, Steuernagel B, Wulff B, Börner A, Byrns B, Čížková J, Fowler D B, Fritz A, Himmelbach A, Kaithakottil G, Keilwagen J, Keller B, Konkin D, Larsen J, Li Q, Myśków B, Padmarasu S, Rawat N, Sesiz U, Biyiklioglu-Kaya S, Sharpe A, Šimková H, Small I, Swarbreck D, Toegelová H, Tsvetkova N, Voylokov A V, Vrána J, Bauer E, Bolibok-Bragoszewska H, Doležel J, Hall A, Jia J, Korzun V, Laroche A, Ma X-F, Ordon F, Özkan H, Rakoczy-Trojanowska M, Scholz U, Schulman A H, Siekmann D, Stojałowski S, Tiwari V K, Spannagl M, Stein N Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential. Nat. Genet. 53 (2021) 564–573. dx.doi.org/10.1038/s41588-021-00807-0
Ralf E Analyse und Implementierung von Information-Retrieval-Funktionen im Umfeld von heterogenen Forschungsdaten. (Bachelor Thesis) Wernigerode, Hochschule Harz (FH), Fachbereich Automatisierung und Informatik (2021) 44 pp.
Zhao Y, Thorwarth P, Jiang Y, Philipp N, Schulthess A W, Gils M, Boeven P H G, Longin C F H, Schacht J, Ebmeyer E, Korzun V, Mirdita V, Dörnte J, Avenhaus U, Horbach R, Cöster H, Holzapfel J, Ramgraber L, Kühnle S, Varenne P, Starke A, Schürmann F, Beier S, Scholz U, Liu F, Schmidt R H, Reif J C Unlocking big data doubled the accuracy in predicting the grain yield in hybrid wheat. Sci. Adv. 7 (2021) eabf9106. dx.doi.org/10.1126/sciadv.abf9106
2020
Arend D, König P, Junker A, Scholz U, Lange M The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition. Gigascience 9 (2020) giaa107. doi.org/10.1093/gigascience/giaa107
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. 102 (2020) 631-642. dx.doi.org/10.1111/tpj.14645
Boeven P H G, Zhao Y, Thorwarth P, Liu F, Maurer H P, Gils M, Schachschneider R, Schacht J, Ebmeyer E, Kazman E, Mirdita V, Dörnte J, Kontowski S, Horbach R, Cöster H, Holzapfel J, Jacobi A, Ramgraber L, Reinbrecht C, Starck N, Varenne P, Starke A, Schürmann F, Ganal M, Polley A, Hartung J, Beier S, Scholz U, Longin C F H, Reif J C, Jiang Y, Würschum T Negative dominance and dominance-by-dominance epistatic effects reduce grain-yield heterosis in wide crosses in wheat. Sci. Adv. 6 (2020) eaay4897. dx.doi.org/10.1126/sciadv.aay4897
Boudichevskaia A, Ruban A, Thiel J, Fiebig A, Houben A Tissue-specific transcriptome analysis reveals candidate genes associated with the process of programmed chromosome limination in Aegilops speltoides. Int. J. Mol. Sci. 21 (2020) 7596. doi.org/10.3390/ijms21207596
Chu J, Zhao Y, Beier S, Schulthess A W, Stein N, Philipp N, Röder M S, Reif J C Suitability of single-nucleotide polymorphism arrays versus genotyping-by-sequencing for genebank genomics in wheat. Front. Plant Sci. 11 (2020) 42. dx.doi.org/10.3389/fpls.2020.00042
Glöckner F O, Diepenbroek M, Felden J, Güntsch A, Stoye J, Overmann J, Wimmers K, Kostadinov I, Yahyapour R, Müller W, Scholz U, Triebel D, Frenzel M, Gemeinholzer B, Goesmann A, König-Ries B, Bonn A, Seeger B NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI). Zenodo July 14 (2020) doi.org/10.5281/zenodo.3943645.
Hoang P T N, Fiebig A, Novák P, Macas J, Cao H X, Stepanenko A, Chen G, Borisjuk N, Scholz U, Schubert I Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. Sci. Rep. 10 (2020) 19230. dx.doi.org/10.1038/s41598-020-75728-9
Jayakodi M, Padmarasu S, Haberer G, Bonthala V S, Gundlach H, Monat C, Lux T, Kamal N, Lang D, Himmelbach A, Ens J, Zhang X Q, Angessa T T, Zhou G, Tan C, Hill C, Wang P, Schreiber M, Boston L B, Plott C, Jenkins J, Guo Y, Fiebig A, Budak H, Xu D, Zhang J, Wang C, Grimwood J, Schmutz J, Guo G, Zhang G, Mochida K, Hirayama T, Sato K, Chalmers K J, Langridge P, Waugh R, Pozniak C J, Scholz U, Mayer K F X, Spannagl M, Li C, Mascher M, Stein N The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 588 (2020) 284-289. dx.doi.org/10.1038/s41586-020-2947-8
König P, Beier S, Basterrechea M, Schüler D, Arend D, Mascher M, Stein N, Scholz U, Lange M BRIDGE – a visual analytics web tool for barley genebank genomics. Front. Plant Sci. 11 (2020) 701. dx.doi.org/10.3389/fpls.2020.00701
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. 18 (2020) 1396-1408. dx.doi.org/10.1111/pbi.13303
Lueck S, Beukert U, Douchkov D BluVision Macro – a software for automated powdery mildew and rust disease quantification on detached leaves. JOSS 5 (2020) 2259. doi.org/10.21105/joss.02259
McCouch S, Navabi K, Abberton M, Anglin N L, Barbieri R L, Baum M, Bett K, Booker H, Brown G L, Bryan G J, Cattivelli L, Charest D, Eversole K, Freitas M, Ghamkhar K, Grattapaglia D, Henry R, Valadares Inglis M C, Islam T, Kehel Z, Kersey P J, Kresovich S, Marden E, Mayes S, Ndjiondjop M N, Nguyen H T, Paiva S, Papa R, Phillips P W B, Rasheed A, Richards C, Rouard M, Amstalden Sampaio M J, Scholz U, Shaw P D, Sherman B, Staton S E, Stein N, Svensson J, Tester M, Montenegro Valls J F, Varshney R, Visscher S, von Wettberg E, Waugh R, Wenzl P W B, Rieseberg L H Mobilizing crop biodiversity. Mol. Plant 13 (2020) 1341-1344. dx.doi.org/10.1016/j.molp.2020.08.011
Papoutsoglou E A, Faria D, Arend D, Arnaud E, Athanasiadis I N, Chaves I, Coppens F, Cornut G, Costa B V, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King G J, Krajewski P, Lange M, Laporte M-A, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı́rez-Gonzalez R, Ramšak Ž, Reif J C, Rocca-Serra P, Sansone S-A, Scholz U, Tardieu F, Uauy C, Usadel B, Visser R G F, Weise S, Kersey P J, Miguel C M, Adam-Blondon A-F, Pommier C Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol. 227 (2020) 260-273. dx.doi.org/10.1111/nph.16544
Psaroudakis D, Liu F, König P, Scholz U, Junker A, Lange M, Arend D isa4j: a scalable Java library for creating ISA-Tab metadata [version 1; peer review: 2 approved]. F1000Research 9(ELIXIR) (2020) 1388. doi.org/10.12688/f1000research.27188.1
Ruban A, Schmutzer T, Wu D D, Fuchs J, Boudichevskaia A, Rubtsova M, Pistrick K, Melzer M, Himmelbach A, Schubert V, Scholz U, Houben A Supernumerary B chromosomes of Aegilops speltoides undergo precise elimination in roots early in embryo development. Nat. Commun. 11 (2020) 2764. dx.doi.org/10.1038/s41467-020-16594-x
Soleimani B, Lehnert H, Keilwagen J, Plieske J, Ordon F, Naseri Rad S, Ganal M, Beier S, Perovic D Comparison between core set selection methods using different Illumina marker platforms: a case study of assessment of diversity in wheat. Front. Plant Sci. 11 (2020) 1040. dx.doi.org/10.3389/fpls.2020.01040
Walkowiak S, Gao L, Monat C, Haberer G, Kassa M T, Brinton J, Ramirez-Gonzalez R H, Kolodziej M C, Delorean E, Thambugala D, Klymiuk V, Byrns B, Gundlach H, Bandi V, Siri J N, Nilsen K, Aquino C, Himmelbach A, Copetti D, Ban T, Venturini L, Bevan M, Clavijo B, Koo D H, Ens J, Wiebe K, N'Diaye A, Fritz A K, Gutwin C, Fiebig A, Fosker C, Fu B X, Accinelli G G, Gardner K A, Fradgley N, Gutierrez-Gonzalez J, Halstead-Nussloch G, Hatakeyama M, Koh C S, Deek J, Costamagna A C, Fobert P, Heavens D, Kanamori H, Kawaura K, Kobayashi F, Krasileva K, Kuo T, McKenzie N, Murata K, Nabeka Y, Paape T, Padmarasu S, Percival-Alwyn L, Kagale S, Scholz U, Sese J, Juliana P, Singh R, Shimizu-Inatsugi R, Swarbreck D, Cockram J, Budak H, Tameshige T, Tanaka T, Tsuji H, Wright J, Wu J, Steuernagel B, Small I, Cloutier S, Keeble-Gagnere G, Muehlbauer G, Tibbets J, Nasuda S, Melonek J, Hucl P J, Sharpe A G, Clark M, Legg E, Bharti A, Langridge P, Hall A, Uauy C, Mascher M, Krattinger S G, Handa H, Shimizu K K, Distelfeld A, Chalmers K, Keller B, Mayer K F X, Poland J, Stein N, McCartney C A, Spannagl M, Wicker T, Pozniak C J Multiple wheat genomes reveal global variation in modern breeding. Nature 588 (2020) 277-283. dx.doi.org/10.1038/s41586-020-2961-x
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 2; peer review: 2 approved]. F1000Research 8(ELIXIR) (2020) 1877. dx.doi.org/10.12688/f1000research.20244.2
Zimmer T C Integration von Daten und Methoden zum Zugriff und zur Analyse von Genotypisierungsdaten im edge computing Umfeld mittels Datencontainer. (Bachelor Thesis) Mittweida, Hochschule Mittweida, Fakultät Angewandte Computer- und Biowissenschaften (2020) 58 pp.
2019
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.
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.
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
González 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.