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Wülpern M:

Vergleich von GBS-, WGS, und SNP-Chip-Datensätzen zur Eignung für die phylogenetische Bauminferenz mit der Neighbor-Joining-Methode am Beispiel von Gerste. (Bachelor Thesis) Emden, Hochschule Emden-Leer (FH), Fachbereich Technik - Naturwissenschaftliche Technik (2024) 41 pp.

Arend D, Scholz U, Lange M:

The Plant Genomic and Phenomics Research Data Repository: an on-premise approach for FAIR-compliant data acquisition. In: Garcia S, Nualart N (Eds.): Plant genomic and cytogenetic databases. (Series: Methods in molecular biology, Vol. 2703) New York: Humana (2023) ISBN 978-1-0716-3389-2, 3-22. https://dx.doi.org/10.1007/978-1-0716-3389-2_1

Arumuham Vivekanantha S:

Population genetics: genotype data-based hierarchical clustering phylogenetic tree inference. (Master Thesis) Berlin, Freie Universität zu Berlin, Fachbereich Mathematik und Informatik (2023) 70 pp.

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Diversifying resistance mechanisms in cereal crops using microphenomics. Plant Phenomics 5 (2023) 0023. https://dx.doi.org/10.34133/plantphenomics.0023

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High-throughput imaging of powdery mildew resistance of the winter wheat collection hosted at the German Federal ex situ Genebank for Agricultural and Horticultural Crops. GigaScience 12 (2023) giad007. https://dx.doi.org/10.1093/gigascience/giad007

Kloppe T, Whetten R B, Kim S-B, Powell O R, Lück S, Douchkov D, Whetten R W, Hulse-Kemp A M, Balint-Kurti P, Cowger C:

Two pathogen loci determine Blumeria graminis f. sp. tritici virulence to wheat resistance gene Pm1a. New Phytol. 238 (2023) 1546-1561. https://dx.doi.org/10.1111/nph.18809

König P, Beier S, Mascher M, Stein N, Lange M, Scholz U:

DivBrowse—interactive visualization and exploratory data analysis of variant call matrices. GigaScience 12 (2023) giad025. https://dx.doi.org/10.1093/gigascience/giad025

Specka X, Martini D, Weiland C, Arend D, Asseng S, Boehm F, Feike T, Fluck J, Gackstetter D, Gonzales-Mellado A, Hartmann T, Haunert J-H, Hoedt F, Hoffmann C, König P, Lange M, Lesch S, Lindstädt B, Lischeid G, Möller M, Rascher U, Reif J C, Schmalzl M, Senft M, Stahl U, Svoboda N, Usadel B, Webber H, Ewert F:

FAIRagro: Ein Konsortium in der Nationalen Forschungsdateninfrastruktur (NFDI) für Forschungsdaten in der Agrosystemforschung. Informatik Spektrum 46 (2023) 24-35. https://dx.doi.org/10.1007/s00287-022-01520-w

Verwaaijen B, Alcock T D, Spitzer C, Liu Z, Fiebig A, Bienert M D, Bräutigam A, Bienert G P:

The Brassica napus boron deficient inflorescence transcriptome resembles a wounding and infection response. Physiol. Plant. 175 (2023) e14088. https://dx.doi.org/10.1111/ppl.14088

Arend D, Beier S, König P, Lange M, Memon J A, Oppermann M, Scholz U, Weise S:

From genotypes to phenotypes – a plant perspective on current developments in data management and data publication. In: Chen M, Hofestädt R (Eds.): Integrative Bioinformatics – History and Future. Singapore: Springer Singapore (2022) ISBN 978-981-16-6795-4, 11-43. https://dx.doi.org/10.1007/978-981-16-6795-4_2

Arend D, Psaroudakis D, Memon J A, Rey-Mazón E, Schüler D, Szymanski J J, Scholz U, Junker A, Lange M:

From data to knowledge - big data needs stewardship, a plant phenomics perspective. Plant J. 111 (2022) 335-347. https://dx.doi.org/10.1111/tpj.15804

Beier S, Fiebig A, Pommier C, Liyanage I, Lange M, Kersey P J, Weise S, Finkers R, Koylass B, Cezard T, Courtot M, Contreras-Moreira B, Naamati G, Dyer S, Scholz U:

Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR [version 2; peer review: 2 approved]. F1000Research 11 (2022) 231. https://dx.doi.org/10.12688/f1000research.109080.2

Boudichevskaia A, Fiebig A, Kumke K, Himmelbach A, Houben A:

Rye B chromosomes differently influence the expression of A chromosome-encoded genes depending on the host species. Chromosome Res. 30 (2022) 335-349. https://dx.doi.org/10.1007/s10577-022-09704-6

Feser M, König P, Fiebig A, Arend D, Lange M, Scholz U:

On the way to plant data commons - a genotyping use case. J. Integr. Bioinform. 19 (2022) 20220033. https://dx.doi.org/10.1515/jib-2022-0033

Habekost P-K:

Data Engineering und Data Exploration im Bereich digitaler Sequenzinformationen und Forschungsdaten. (Master Thesis) Wernigerode, Hochschule Harz (FH), Fachbereich Automatisierung und Informatik (2022) 44 pp.

Hinterberger V, Douchkov D, Lück S, Kale S, Mascher M, Stein N, Reif J C, Schulthess A W:

Mining for new sources of resistance to powdery mildew in genetic resources of winter wheat. Front. Plant Sci. 13 (2022) 836723. https://dx.doi.org/10.3389/fpls.2022.836723

Lehnert H, Berner T, Lang D, Beier S, Stein N, Himmelbach A, Kilian B, Keilwagen J:

Insights into breeding history, hotspot regions of selection and untapped allelic diversity for bread wheat breeding. Plant J. 112 (2022) 897-918. https://dx.doi.org/10.1111/tpj.15952

Röckel F, Schreiber T, Schüler D, Braun U, Krukenberg I, Schwander F, Peil A, Brandt C, Willner E, Gransow D, Scholz U, Kecke S, Maul E, Lange M, Töpfer R:

PhenoApp: A mobile tool for plant phenotyping to record field and greenhouse observations [version 2; peer review: 2 approved]. F1000Research 11 (2022) 12. https://dx.doi.org/10.12688/f1000research.74239.2

Schulthess A W, Kale S M, Liu F, Zhao Y, Philipp N, Rembe M, Jiang Y, Beukert U, Serfling A, Himmelbach A, Fuchs J, Oppermann M, Weise S, Boeven P H G, Schacht J, Longin C F H, Kollers S, Pfeiffer N, Korzun V, Lange M, Scholz U, Stein N, Mascher M, Reif J C:

Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat. Genet. 54 (2022) 1544-1552. https://dx.doi.org/10.1038/s41588-022-01189-7

Schulthess A W, Kale S M, Zhao Y, Gogna A, Rembe M, Philipp N, Liu F, Beukert U, Serfling A, Himmelbach A, Oppermann M, Weise S, Boeven P H G, Schacht J, Longin C F H, Kollers S, Pfeiffer N, Korzun V, Fiebig A, Schüler D, Lange M, Scholz U, Stein N, Mascher M, Reif J C:

Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding. Sci. Data 9 (2022) 784. https://dx.doi.org/10.1038/s41597-022-01891-5

Beukert U, Pfeiffer N, Ebmeyer E, Hinterberger V, Lueck S, Serfling A, Ordon F, Schulthess A W, Reif J C:

Efficiency of a seedling phenotyping strategy to support European wheat breeding focusing on leaf rust resistance. Biology 10 (2021) 628. https://dx.doi.org/10.3390/biology10070628

Blätke M-A, Beier S, Scholz U, Gladilin E, Szymanski J J (Eds.):

Front. Plant Sci., Frontiers Research Topic “Advances in Applied Bioinformatics in Crops." Lausanne: Frontiers Media SA (2021) https://dx.doi.org/10.3389/978-2-88966-620-1

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. https://dx.doi.org/10.3389/fpls.2021.640394

Lange M, Alako B T F, Cochrane G, Ghaffar M, Mascher M, Habekost P-K, Hillebrand U, Scholz U, Schorch F, Freitag J, Scholz A H:

Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature. GigaScience 10 (2021) giab084. https://dx.doi.org/10.1093/gigascience/giab084

Li M, Hensel G, Melzer M, Junker A, Tschiersch H, Ruwe H, Arend D, Kumlehn J, Börner T, Stein N:

Mutation of the ALBOSTRIANS ohnologous gene HvCMF3 impairs chloroplast development and thylakoid architecture in barley. Front. Plant Sci. 12 (2021) 732608. https://dx.doi.org/10.3389/fpls.2021.732608

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Identification of rye B chromosome-associated peptides by mass spectrometry. New Phytol. 230 (2021) 2179-2185. https://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. https://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. 22 (2021) bbab010. https://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. https://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, Stojalowski 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. https://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.

Scholz A H, Lange M, Habekost P, Oldham P, Cancio I, Cochrane G, Freitag J:

Myth-busting the provider-user relationship for digital sequence information. GigaScience 10 (2021) giab085. https://dx.doi.org/10.1093/gigascience/giab085

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. https://dx.doi.org/10.1126/sciadv.abf9106

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. https://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. https://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. https://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. https://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. https://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) https://dx.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. https://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. https://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. https://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. https://dx.doi.org/10.1111/pbi.13303

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BluVision Macro – a software for automated powdery mildew and rust disease quantification on detached leaves. JOSS 5 (2020) 2259. https://doi.org/10.21105/joss.02259

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Mobilizing crop biodiversity. Mol. Plant 13 (2020) 1341-1344. https://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. https://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. https://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. https://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. https://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, NDiaye 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. https://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. https://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.

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. https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://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.

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) ISBN 978-3-319-92528-8, 377-394. https://dx.doi.org/10.1007/978-3-319-92528-8_21

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. https://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) giy001. https://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. https://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) ISBN: 9781450365017, 64-71. https://dx.doi.org/10.1145/3231622.3231639

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. https://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. https://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. https://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.

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. https://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. https://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. https://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. https://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. https://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) ISSN 1613-0073, 11-12. https://ceur-ws.org/Vol-1858/paper3.pdf

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. https://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. https://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. https://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. https://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. https://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. https://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. https://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. Lausanne: Frontiers Media (2017) 209-220. https://dx.doi.org/10.3389/978-2-88945-115-9

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. https://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. Sci. Data 3 (2016) 160055. https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://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.

Aliyeva-Schnorr L, Beier S, Karafiátová M, Schmutzer T, Scholz U, Doležel J, Stein N, Houben A:

Cytogenetic mapping with centromeric BAC contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. Plant J. 84 (2015) 385–394. https://dx.doi.org/10.1111/tpj.13006

Cao H X, Schmutzer T, Scholz U, Pecinka A, Schubert I, Vu G T H:

Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. Front. Microbiol. 6 (2015) 526. https://dx.doi.org/10.3389/fmicb.2015.00526

Chapman J A, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Seghal S, Oliker L, Schmutz J, Yelick K A, Scholz U, Waugh R, Poland J A, Muehlbauer G J, Stein N, Rokhsar D S:

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol. 16 (2015) 26. https://dx.doi.org/10.1186/s13059-015-0582-8

Colmsee C, Beier S, Himmelbach A, Schmutzer T, Stein N, Scholz U, Mascher M:

BARLEX – the barley draft genome explorer. Mol. Plant 8 (2015) 964-966. https://dx.doi.org/10.1016/j.molp.2015.03.009

Esch M, Chen J, Colmsee C, Klapperstück M, Grafahrend-Belau E, Scholz U, Lange M:

LAILAPS – the plant science search engine. Plant Cell Physiol. 56 (2015) e8. https://dx.doi.org/10.1093/pcp/pcu185

Gerlach N, Schmitz J, Polatajko A, Schlüter U, Fahnenstich H, Witt S, Fernie A R, Uroic K, Scholz U, Sonnewald U, Bucher M:

An integrated functional approach to dissect systemic responses in maize to arbuscular mycorrhizal symbiosis. Plant Cell Environ. 38 (2015) 1591-1612. https://dx.doi.org/10.1111/pce.12508

Krajewski P, Chen D, Ćwiek H, van Dijk A D J, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap J P, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S:

Towards recommendations for metadata and data handling in plant phenotyping. J. Exp. Bot. 66 (2015) 5417-5427. https://dx.doi.org/10.1093/jxb/erv271

Muraya M M, Schmutzer T, Ulpinnis C, Scholz U, Altmann T:

Targeted sequencing reveals large-scale sequence polymorphism in maize candidate genes for biomass production and composition. PLoS One 10 (2015) e0132120. https://dx.doi.org/10.1371/journal.pone.0132120

Schilling F:

Analyse von Genstrukturen in der Kulturpflanze Gerste. (Bachelor Thesis) Köthen, Hochschule Anhalt (FH) (2015) 91 pp.

Schmutzer T, Samans B, Dyrszka E, Ulpinnis C, Weise S, Stengel D, Colmsee C, Lespinasse D, Micic Z, Abel S, Duchscherer P, Breuer F, Abbadi A, Leckband G, Snowdon R, Scholz U:

Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus. Sci. Data 2 (2015) 150072. https://dx.doi.org/10.1038/sdata.2015.72

Snowdon R J, Abbadi A, Kox T, Schmutzer T, Leckband G:

Heterotic Haplotype Capture: precision breeding for hybrid performance. Trends Plant Sci. 20 (2015) 410-413. https://dx.doi.org/10.1016/j.tplants.2015.04.013

Spannagl M, Alaux M, Lange M, Bolser D M, Bader K C, Letellier T, Kimmel E, Flores R, Pommier C, Kerhornou A, Walts B, Nussbaumer T, Grabmuller C, Chen J, Colmsee C, Beier S, Mascher M, Schmutzer T, Arend D, Thanki A, Ramirez-Gonzalez R, Ayling M, Ayling S, Caccamo M, Mayer K F X, Scholz U, Steinbach D, Quesneville H, Kersey P J:

transPLANT resources for Triticeae genomic data. Plant Genome 9 (2015) 1-13. https://dx.doi.org/10.3835/plantgenome2015.06.0038

Sretenovic Rajicic T, Lübberstedt T, Bach Jensen L, Scholz U, Weber E, Graner A, Dehmer K J:

Single nucleotide polymorphism (SNP) markers for allele quantification in Lolium (Poaceae): development and first applications. In: Budak H, Spangenberg G (Eds.): The Proceedings of the 8th International Symposium on the Molecular Breeding of Forage and Turf. Cham: Springer (2015) 143-163.

Tavakol E, Okagaki R, Verderio G, Shariati V, Hussien A, Bilgic H, Scanlon M J, Todt N R, Close T J, Druka A, Waugh R, Steuernagel B, Ariyadasa R, Himmelbach A, Stein N, Muehlbauer G J, Rossini L:

The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning. Plant Physiol. 168 (2015) 164-174. https://dx.doi.org/10.1104/pp.114.252882

Vu G T H, Schmutzer T, Bull F, Cao H X, Fuchs J, Tran D T, Jovtchev G, Pistrick K, Stein N, Pecinka A, Neumann P, Novák P, Macas J, Dear P H, Blattner F R, Scholz U, Schubert I:

Comparative genome analysis reveals divergent genome size evolution in a carnivorous plant genus. Plant Genome 8 (2015) 1-14. https://dx.doi.org/10.3835/plantgenome2015.04.0021

Zang W, Eckstein P E, Colin M, Voth D, Himmelbach A, Beier S, Stein N, Scoles G J, Beattie A D:

Fine mapping and identification of a candidate gene for the barley Un8 true loose smut resistance gene. Theor. Appl. Genet. 128 (2015) 1343-1357. https://dx.doi.org/10.1007/s00122-015-2510-4

Ahkami A, Scholz U, Steuernagel B, Strickert M, Haensch K T, Druege U, Reinhardt D, Nouri E, von Wirén N, Franken P, Hajirezaei M-R:

Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida. PLoS One 9 (2014) e100997. https://dx.doi.org/10.1371/journal.pone.0100997

Arend D, Colmsee C, Knüpffer H, Oppermann M, Scholz U, Schüler D, Weise S, Lange M:

Data management experiences and best practices from the perspective of a plant research institute. In: Galhardas H, Rahm E (Eds.): Data integration in the life sciences: 10th international conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014; proceedings (Series: Lecture Notes in Computer Science, Vol. 8574) Berlin [u.a.]: Springer (2014) ISBN 978-3-319-08589-0, 41-49. https://dx.doi.org/10.1007/978-3-319-08590-6_4

Arend D, Lange M, Chen J, Colmsee C, Flemming S, Hecht D, Scholz U:

e!DAL - a framework to store, share and publish research data. BMC Bioinformatics 15 (2014) 214. https://dx.doi.org/10.1186/1471-2105-15-214

Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley P E, Muehlbauer G J, Scholz U, Korol A, Mayer K F X, Waugh R, Langridge P, Graner A, Stein N:

A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. Plant Physiol. 164 (2014) 412-423. https://dx.doi.org/10.1104/pp.113.228213

Bolger M E, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer K F:

Plant genome sequencing - applications for crop improvement. Curr. Opin. Biotechnol. 26 (2014) 31-37. https://dx.doi.org/10.1016/j.copbio.2013.08.019

Colmsee C:

Datenmanagement und Visualisierung von BAC-Netzwerken zur Unterstützung der Sequenzierung des Gerstengenoms. (Master Thesis) Wernigerode, Hochschule Harz, Fachbereich Automatisierung und Informatik (2014) 72 pp.

Esch M, Chen J, Weise S, Hassani-Pak K, Scholz U, Lange M:

A query suggestion workflow for life science IR-systems. J. Integr. Bioinform. 11 (2014) 237. https://dx.doi.org/doi:10.2390/biecoll-jib-2014-237

Gawroński P, Ariyadasa R, Himmelbach A, Poursarebani N, Kilian B, Stein N, Steuernagel B, Hensel G, Kumlehn J, Sehgal S K, Gill B S, Gould P, Hall A, Schnurbusch T:

A distorted circadian clock causes early flowering and temperature-dependent variation in spike development in the Eps-3Am mutant of einkorn wheat. Genetics 196 (2014) 1253-1261. https://dx.doi.org/10.1534/genetics.113.158444

Kuhlmann M, Finke A, Mascher M, Mette M F:

DNA methylation maintenance consolidates RNA-directed DNA methylation and transcriptional gene silencing over generations in Arabidopsis thaliana. Plant J. 80 (2014) 269-281. https://dx.doi.org/10.1111/tpj.12630

Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz J A, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski P P, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard G-F, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman D J, Stein N, Straub M-L, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet J-L, Wincker P, Scholz U, Neuvéglise C:

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. Biotechnol. Biofuels 7 (2014) 66. https://dx.doi.org/10.1186/1754-6834-7-66

Lange M, Henkel R, Müller W, Waltemath D, Weise S:

Information retrieval in life sciences: a programmatic survey. In: Chen M, Hofestädt R (Eds.): Approaches in integrative bioinformatics: towards the virtual cell. Berlin [u.a.]: Springer (2014) ISBN 978-3-642-41280-6, 73-109. https://dx.doi.org/10.1007/978-3-642-41281-3_3

Lüpken T, Stein N, Perovic D, Habekuß A, Serfling A, Krämer I, Hähnel U, Steuernagel B, Scholz U, Ariyadasa R, Martis M M, Mayer K F X, Niks R E, Collins N C, Friedt W, Ordon F:

High resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV. Mol. Breed. 33 (2014) 477-488. https://dx.doi.org/10.1007/s11032-013-9966-1

Mascher M:

POPSEQ Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing. (PhD Thesis) Bielefeld, Universität Bielefeld, Technische Fakultät (2014) 133 pp.

Mascher M, Gerlach N, Gahrtz M, Bucher M, Scholz U, Dresselhaus T:

Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype. PLoS One 9 (2014) e96782. https://dx.doi.org/10.1371/journal.pone.0096782

Mascher M, Jost M, Kuon J E, Himmelbach A, Assfalg A, Beier S, Scholz U, Graner A, Stein N:

Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol. 15 (2014) R78. https://dx.doi.org/10.1186/gb-2014-15-6-r78

Mascher M, Stein N:

Genetic anchoring of whole-genome shotgun assemblies. Front. Genet. 5 (2014) 208. https://dx.doi.org/10.3389/fgene.2014.00208

Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, Gandolfi F, Tenedini E, Bernardis I, Tagliafico E, Pecchioni N, Francia E:

The barley Frost resistance-H2 locus. Funct. Integr. Genomics 14 (2014) 85-100. https://dx.doi.org/10.1007/s10142-014-0360-9

Poursarebani N, Ma L, Schmutzer T, Houben A, Stein N:

FISH mapping for physical map improvement in the large genome of barley: a case study on chromosome 2H. Cytogenet. Genome Res. 143 (2014) 275-279. https://dx.doi.org/10.1159/000366028

Schmutzer T, Ma L, Pousarebani N, Bull F, Stein N, Houben A, Scholz U:

Kmasker – a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare. Cytogenet. Genome Res. 142 (2014) 66-78. https://dx.doi.org/10.1159/000356460

Schwender J, König C, Klapperstück M, Heinzel N, Munz E, Hebbelmann I, Hay J O, Denolf P, de Bodt S, Redestig H, Caestecker E, Jakob P M, Borisjuk L, Rolletschek H:

Transcript abundance on its own cannot be used to infer fluxes in central metabolism. Front. Plant Sci. 5 (2014) 668. https://dx.doi.org/10.3389/fpls.2014.00668

Stein N, Steuernagel B:

Advances in sequencing the barley genome. In: Tuberosa R, Graner A, Frison E (Eds.): Genomics of plant genetic resources. Vol. 1. Managing, sequencing and mining genetic resources. Dordrecht [u.a.]: Springer (2014) ISBN 978-94-007-7571-8, 391-403. https://dx.doi.org/10.1007/978-94-007-7572-5_16

The International Wheat Genome Sequencing Consortium (IWGSC; IPK Authors: Mascher M, Scholz, U. & Stein, N.):

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345 (2014) 1251788. https://dx.doi.org/10.1126/science.1251788

Wendler N, Mascher M, Nöh C, Himmelbach A, Scholz U, Ruge-Wehling B, Stein N:

Unlocking the secondary gene-pool of barley with next-generation sequencing. Plant Biotechnol. J. 12 (2014) 1122-1131. https://dx.doi.org/10.1111/pbi.12219

Yang P, Lüpken T, Habekuss A, Hensel G, Steuernagel B, Kilian B, Ariyadasa R, Himmelbach A, Kumlehn J, Scholz U, Ordon F, Stein N:

PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses. Proc. Natl. Acad. Sci. U.S.A. 111 (2014) 2104-2109. https://dx.doi.org/10.1073/pnas.1320362111

Zanke C, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, 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. Front. Plant Sci. 5 (2014) 217. https://dx.doi.org/10.3389/fpls.2014.00217

Arend D, Lange M, Chen J, Colmsee C, Flemming S, Scholz U:

The e!DAL JAVA-API: Store, share and cite primary data in life sciences. In: Schreiber F, Hofestädt R, Lange M, Scholz U, Czauderna T, Schnee R, Weise S (Eds.): Proceedings of the 9th International Symposium on Integrative Bioinformatics 2013, March 18 - 20, 2013, Gatersleben, Germany. Gatersleben: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) (2013) 143-154.

Behrens A-K:

Modellierung und Simulation des Purin-Abbaus in der Hefe Arxula adeninivorans. (Bachelor Thesis) Köthen, Hochschule Anhalt (FH), Fachbereich Angewandte Biowissenschaften und Prozesstechnik (2013) 69 pp.

Biselli C, Urso S, Tacconi G, Steuernagel B, Schulte D, Gianinetti A, Bagnaresi P, Stein N, Cattivelli L, Valè G:

Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus. Theor. Appl. Genet. 126 (2013) 1575-1586. https://dx.doi.org/10.1007/s00122-013-2075-z

Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Lange M, Mascher M, Weise S, Scholz U, Schreiber F:

OPTIMAS-DW, MetaCrop and VANTED: a case study for data integration, curation and visualisation in life sciences. In: Horbach M (Ed.): GI-Jahrestagung. (Series: LNI, Vol. 220) (2013) ISBN 978-3-88579-614-5, 1834-1840.

Colmsee C, Keller E R J, Oppermann M, Senula A, Zanke C, Funke T, Weise S, Scholz U:

The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2013).

Esch M:

Effizienzsteigerung des Life-Science-IR-Systems LAILAPS mittels Suchanfragenerweiterung. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 94 pp.

Gellner M:

Evaluating the impact of genome quality on RNA-seq analysis. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 48 pp.

Hecht D:

Konzeption und Implementierung eines Freigabeservices zur Registrierung von DOI-Nummern für IPK-Primärdaten. (Bachelor Thesis) Wernigerode, Hochschule Harz (FH), Fachbereich Automatisierung und Informatik (2013) 49 pp.

Hofestädt R, Kormeier B, Lange M, Schreiber F, Sommer B, Weise S:

Editorial. J. Integr. Bioinform. 10 (2013) e226. https://dx.doi.org/10.2390/biecoll-jib-2013-226

Keller E R J, Zanke C, Scholz U:

EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound. euralliveg.ipk-gatersleben.de (2013).

Lüpken T, Stein N, Perovic D, Habekuss A, Kramer I, Hähnel U, Steuernagel B, Scholz U, Zhou R, Ariyadasa R, Taudien S, Platzer M, Martis M, Mayer K, Friedt W, Ordon F:

Genomics-based high-resolution mapping of the BaMMV/BaYMV resistance gene rym11 in barley (Hordeum vulgare L.). Theor. Appl. Genet. 126 (2013) 1201-1212. https://dx.doi.org/10.1007/s00122-013-2047-3

Martis M M, Zhou R, Haseneyer G, Schmutzer T, Vrána J, Kubaláková M, König S, Kugler K G, Scholz U, Hackauf B, Korzun V, Schön C-C, Doležel J, Bauer E, Mayer K F X, Stein N:

Reticulate evolution of the rye genome. Plant Cell 25 (2013) 3685-3698. https://dx.doi.org/10.1105/tpc.113.114553

Mascher M, Muehlbauer G J, Rokhsar D S, Chapman J, Schmutz J, Barry K, Munoz-Amatriain M, Close T J, Wise R P, Schulman A H, Himmelbach A, Mayer K F, Scholz U, Poland J A, Stein N, Waugh R:

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 76 (2013) 718-727. https://dx.doi.org/10.1111/tpj.12319

Mascher M, Richmond T A, Gerhardt D J, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, DAscenzo M, Akhunov E D, Hedley P E, Gonzales A M, Morrell P L, Kilian B, Blattner F R, Scholz U, Mayer K F, Flavell A J, Muehlbauer G J, Waugh R, Jeddeloh J A, Stein N:

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 76 (2013) 494-505. https://dx.doi.org/10.1111/tpj.12294

Mascher M, Schubert I, Scholz U, Friedel S:

Patterns of nucleotide asymmetries in plant and animal genomes. Biosystems 111 (2013) 181-189. https://dx.doi.org/10.1016/j.biosystems.2013.02.001

Mascher M, Wu S, Amand P S, Stein N, Poland J:

Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 8 (2013) e76925. https://dx.doi.org/10.1371/journal.pone.0076925

Matthies I E, Weise S, Förster J, Korzun V, Stein N, Röder M S:

Nitrogen-metabolism related genes in barley - haplotype diversity, linkage mapping and associations with malting and kernel quality parameters. BMC Genet 14 (2013) e77. https://dx.doi.org/10.1186/1471-2156-14-77

Mehlhorn H, Lange M, Scholz U, Schreiber F:

Extraction and prediction of biomedical database identifier using neural networks towards data network construction. In: Ordóñez de Pablos P, Lytras M D, Tennyson R, Labra Gayo J E (Eds.): Cases on open-linked data and semantic web applications. Hershey: Information Science Reference (2013) ISBN 978-1-4666-2827-4, 58-83.

Muñoz-Amatriaín M, Eichten S R, Wicker T, Richmond T A, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer K F X, Taudien S, Platzer M, Jeddeloh J A, Springer N M, Muehlbauer G J, Stein N:

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 14 (2013) R58. https://dx.doi.org/10.1186/gb-2013-14-6-r58

Pellino M, Hojsgaard D, Schmutzer T, Scholz U, Hörandl E, Vogel H, Sharbel T F:

Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation. Mol. Ecol. 22 (2013) 5908-5921. https://dx.doi.org/10.1111/mec.12533

Peukert M, Weise S, Röder M S, Matthies I E:

Development of SNP markers for genes of the phenylpropanoid pathway and their association to kernel and malting traits in barley. BMC Genet. 14 (2013) e97. https://dx.doi.org/10.1186/1471-2156-14-97

Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, Martis M M, Graner A, Schweizer P, Scholz U, Mayer K, Stein N:

Conserved synteny-based anchoring of the barley genome physical map. Funct. Integr. Genomics 13 (2013) 339-350. https://dx.doi.org/10.1007/s10142-013-0327-2

Pratzka V:

In silico analysis of genes involved in the initiation of barley pollen embryogenesis. (Bachelor Thesis) Mittweida, Hochschule Mittweida (FH) (2013) 54 pp.

Schlüter U, Colmsee C, Scholz U, Bräutigam A, Weber A P M, Zellerhoff N, Bucher M, Fahnenstich H, Sonnewald U:

Adaptation of maize source leaf metabolism to stress related disturbances in carbon, nitrogen and phosphorus balance. BMC Genomics 14 (2013) e442. https://dx.doi.org/10.1186/1471-2164-14-442

Schreiber F, Hofestädt R, Lange M, Scholz U, Czauderna T, Schnee R, Weise S (Eds.):

Proceedings of the 9th International Symposium on Integrative Bioinformatics 2013: 18 - 20 March 2013, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben. Gatersleben (2013) 214 pp.

Ulpinnis C:

Evaluation von Fehlerkorrektur-Algorithmen für Sequenzdaten in komplexen Pflanzengenomen. (Bachelor Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 119 pp.

Arend D:

Konzeption und Implementierung einer Datenhaltungsinfrastruktur zur digitalen Langzeitarchivierung und dauerhaften Zitierbarkeit biologischer Primärdaten am Beispiel von ”Next-Generation-Sequencing“-Daten. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2012) 121 pp.

Arend D:

The e!DAL JAVA-API – store, share and cite primary data in life sciences. In: Hofestädt R, Kolchanov N (Eds.): German/Russian Network of Computational Systems Biology: Report 2012. (Series: Berichte aus der Medizinischen Informatik und Bioinformatik) Aachen: Shaker (2012) ISBN 978-3-8440-1573-7, 46-47.

Arend D, Lange M, Colmsee C, Flemming S, Chen J, Scholz U:

The e!DAL JAVA-API: Store, share and cite primary data in life sciences. In: Gao J, Alhaij R, Dubitzky W, Ungar L, Wu C, Christianson A, Liebman M, Hu X (Eds.): IEEE International Conference on Bioinformatics and Biomedicine workshops (BIBMW 2012), 4–7 October 2012, Philadelphia, U.S.A., proceedings. Piscataway, NJ: IEEE (2012) ISBN 978-1-4673-2746-6, 511-515. https://dx.doi.org/10.1109/BIBM.2012.6392737

Cockram J, Thiel T, Steuernagel B, Stein N, Taudien S, Bailey P C, OSullivan D M:

Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae. PLoS One 7 (2012) e45307. https://dx.doi.org/10.1371/journal.pone.0045307

Colmsee C, Keller E R J, Zanke C, Senula A, Funke T, Oppermann M, Weise S, Scholz U:

The Garlic and Shallot Core Collection image database of IPK presenting two vegetatively maintained crops in the Federal ex situ genebank for agricultural and horticultural crops at Gatersleben, Germany. Genet. Resour. Crop Evol. 59 (2012) 1407-1415. https://dx.doi.org/10.1007/s10722-011-9768-4

Colmsee C, Mascher M, Czauderna T, Hartmann A, Schlüter U, Zellerhoff N, Schmitz J, Bräutigam A, Pick T R, Alter P, Gahrtz M, Witt S, Fernie A R, Börnke F, Fahnenstich H, Bucher M, Dresselhaus T, Weber A P, Schreiber F, Scholz U, Sonnewald U:

OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC Plant Biol. 12 (2012) 245. https://dx.doi.org/10.1186/1471-2229-12-245

Colmsee C, Zanke C, Funke T, Weise S, Keller E R J, Scholz U:

The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2012).

Keller E R J, Zanke C, Scholz U:

EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound. euralliveg.ipk-gatersleben.de (2012).

Kohl S, Hollmann J, Blattner F R, Radchuk V, Andersch F, Steuernagel B, Schmutzer T, Scholz U, Krupinska K, Weber H, Weschke W:

A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq. BMC Plant Biol. 12 (2012) 154. https://dx.doi.org/10.1186/1471-2229-12-154

Lange M:

Management of scientific data at the IPK Gatersleben. In: Hofestädt R, Kolchanov N (Eds.): German/Russian Network of Computational Systems Biology: Report 2012. (Series: Berichte aus der Medizinischen Informatik und Bioinformatik) Aachen: Shaker (2012) ISBN 978-3-8440-1573-7, 32-33.

Lange M, Chen J, Scholz U:

LAILAPS– The Life Science Search Engine. lailaps.ipk-gatersleben.de (2012).

Lange M, Chen J, Scholz U:

The LAILAPS Search Engine. In: U. Goltz, M. Magnor, H.-J. Appelrath, H. K. Matthies, W.-T. Balke, Wolf L (Eds.): Informatik 2012: Was bewegt uns in der/die Zukunft?: 42. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 16. bis 21.9.2012, TU Braunschweig. (Series: GI-Edition, Lecture notes in informatics, Vol. 208) Bonn: Ges. für Informatik (2012) ISBN 978-3-88579-602-2, 1552-1558.

Lange M, Chen J, Scholz U:

The LAILAPS search engine: new features. Proceedings of the 8th International Symposium on Integrative Bioinformatics (IB2012), Zhejiang University, Hangzhou, China, April 2 - 4, 2012 (2012) 155-157.

Mameaux S, Cockram J, Thiel T, Steuernagel B, Stein N, Taudien S, Jack P, Werner P, Gray J C, Greenland A J, Powell W:

Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae. Plant Biotechnol. J. 10 (2012) 67-82. https://dx.doi.org/10.1111/j.1467-7652.2011.00645.x

Martis M M, Klemme S, Banaei Moghaddam A M, Blattner F R, Macas J, Schmutzer T, Scholz U, Gundlach H, Wicker T, Šimková H, Novák P, Neumann P, Kubaláková M, Bauer E, Haseneyer G, Fuchs J, Doležel J, Stein N, Mayer K F X, Houben A:

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc. Natl. Acad. Sci. U.S.A. 109 (2012) 13343-13346. https://dx.doi.org/10.1073/pnas.1204237109

Matthies I E, Sharma S, Weise S, Röder M S:

Sequence variation in the barley genes encoding sucrose synthase I and sucrose phosphate synthase II, and its association with variation in grain traits and malting quality. Euphytica 184 (2012) 73-83. https://dx.doi.org/10.1007/s10681-011-0563-2

Matthies I E, van Hintum T, Weise S, Röder M S:

Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars. Mol. Breed. 30 (2012) 951-966. https://dx.doi.org/10.1007/s11032-011-9678-3

Matthies I E, Weise S, Förster K, Röder M S:

Association mapping and marker development of the candidate genes (1->3),(1->4)-β-D-Glucan-4-glucanohydrolase and (1->4)-β-Xylan-endohydrolase 1 for malting quality in barley. pgrc.ipk-gatersleben.de/glb, pgrc.ipk-gatersleben.de/X-1 & pgrc.ipk-gatersleben.de/Phendat (2012).

Matthies I E, Weise S, Röder M S:

Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley. pgrc.ipk-gatersleben.de/alpha-amylase (2012).

Mayer K F X, Waugh R, Langridge P, Close T J, Wise R P, Graner A, Matsumoto T, Sato K, Schulman A, Ariyadasa R, Schulte D, Poursarebani N, Zhou R, Steuernagel B, Mascher M, Scholz U, Shi B, Madishetty K, Svensson J T, Bhat P, Moscou M, Resnik J, Muehlbauer G J, Hedley P, Liu H, Morris J, Frenkel Z, Korol A, Bergès H, Taudien S, Felder M, Groth M, Platzer M, Himmelbach A, Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Ciardo G, Ma Y, Wanamaker S, Cattonaro F, Vendramin V, Scalabrin S, Radovic S, Wing R, Morgante M, Nussbaumer T, Gundlach H, Martis M, Poland J, Pfeifer M, Moisy C, Tanskanen J, Zuccolo A, Spannagl M, Russell J, Druka A, Marshall D, Bayer M, Swarbreck D, Sampath D, Ayling S, Febrer M, Caccamo M, Tanaka T, Wannamaker S, Schmutzer T, Brown J W S, Fincher G B, Stein N:

A physical, genetic and functional sequence assembly of the barley genome. Nature 491 (2012) 711-716. https://dx.doi.org/10.1038/nature11543

Mehlhorn H, Lange M, Scholz U, Schreiber F:

IDPredictor: predict database links in biomedical database. J. Integr. Bioinform. 9 (2012) e190. https://dx.doi.org/10.2390/biecoll-jib-2012-190

Röhl B:

Entwurf und Implementierung einer Software zur Registrierung von DOI-Nummern für IPK-Primärdaten. (Bachelor Thesis) Magdeburg, Otto-von-Guericke-Universität Magdeburg, Fakultät für Informatik (2012) 54 pp.

Schlüter U, Mascher M, Colmsee C, Scholz U, Bräutigam A, Fahnenstich H, Sonnewald U:

Maize source leaf adaptation to nitrogen deficiency effects not only nitrogen and carbon metabolism but also control of phosphate homeostasis. Plant Physiol. 160 (2012) 1384-1406. https://dx.doi.org/10.1104/pp.112.204420

Scholz U, Künne C, Lange M, Miehe H, Funke T:

CR-EST: a resource for crop ESTs. pgrc.ipk-gatersleben.de/cr-est (2012).

Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Klapperstück M, Scholz U, Weise S:

MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res. 40 (2012) D1173-D1177. https://dx.doi.org/10.1093/nar/gkr1004

Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Koschützki D, Scholz U, Weise S:

MetaCrop 2.0. metacrop.ipk-gatersleben.de (2012).

Silvar C, Perovic D, Scholz U, Casas A M, Igartua E, Ordon F:

Fine mapping and comparative genomics integration of two quantitative trait loci controlling resistance to powdery mildew in a Spanish barley landrace. Theor. Appl. Genet. 124 (2012) 49-62. https://dx.doi.org/10.1007/s00122-011-1686-5

Steuernagel B:

Next generation sequence analysis of the highly repetitive barley genome. (PhD Thesis) Jena, Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät (2012) 115 pp.

Thiel J, Hollmann J, Rutten T, Weber H, Scholz U, Weschke W:

454 transcriptome sequencing suggests a role for two-component signalling in cellularization and differentiation of barley endosperm transfer cells. PLoS One 7 (2012) e41867. https://dx.doi.org/10.1371/journal.pone.0041867

Weise S, Harrer S, Grosse I, Knüpffer H, Willner E:

The European Poa Database (EPDB). poa.ipk-gatersleben.de (2012).

Weise S, Scholz U, Röder M S, Matthies I E:

MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2012).

Wolff D:

Sequenzanalyse und Visualisierung von Triticum aestivum BACs. (Bachelor Thesis) Köthen, Hochschule Anhalt (FH), Fachbereich Angewandte Biowissenschaften und Prozesstechnik (2012) 68 pp.

Zakhrabekova S, Gough S P, Braumann I, Müller A H, Lundqvist J, Ahmann K, Dockter C, Matyszczak I, Kurowska M, Druka A, Waugh R, Graner A, Stein N, Steuernagel B, Lundqvist U, Hansson M:

Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley. Proc. Natl. Acad. Sci. U.S.A. 109 (2012) 4326-4331. https://dx.doi.org/10.1073/pnas.1113009109

Bachmann A:

Anfrageranking in Suchmaschinen der Lebenswissenschaften unter Berücksichtigung der Bewertung von Querverweisen. (Bachelor Thesis) Magdeburg, Otto-von-Guericke Universität Magdeburg, Fakultät für Informatik (2011) 71 pp.

Bachmann A, Schult R, Lange M, Spiliopoulou M:

Extracting cross references from life science databases for search result ranking. In: Berendt B, de Vries A, Fan W, Macdonald C, Ounis I, Ruthven I (Eds.): Proceedings of the 20th ACM International Conference on Information and Knowledge Management, 24 - 28 October 2011, Glasgow, Scotland/UK. New York, NY, USA: ACM (2011) ISBN 978-1-4503-0717-8, 1253-1258. https://dx.doi.org/10.1145/2063576.2063758

Colmsee C, Flemming S, Klapperstück M, Lange M, Scholz U:

A case study for efficient management of high throughput primary lab data. BMC Res. Notes 4 (2011) 413. https://dx.doi.org/10.1186/1756-0500-4-413

Colmsee C, Zanke C, Funke T, Weise S, Keller E R J, Scholz U:

The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2011).

Friedrich C:

Entwurf und Implementierung einer JAVA-API zum Zugriff und zur DBMS-unabhängigen Persistierung von Bild- und Metadaten aus einer Pflanzenphänotypisierungsanlage. (Diploma Thesis) Wernigerode, Hochschule Harz, Fachbereich Automatisierung und Informatik (2011) 147 pp.

Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schon C C, Taudien S, Scholz U, Stein N, Mayer K F, Bauer E:

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.). BMC Plant Biol. 11 (2011) 131. https://dx.doi.org/10.1186/1471-2229-11-131

Keller E R J, Zanke C, Scholz U:

EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound euralliveg.ipk-gatersleben.de (2011).

Lange M, Chen J, Scholz U:

LAILAPS– The Life Science Search Engine. lailaps.ipk-gatersleben.de (2011).

Matthies I E, Weise S, Förster K, Röder M S:

Association mapping and marker development of the candidate genes (1->3),(1->4)-β-D-Glucan-4-glucanohydrolase and (1->4)-β-Xylan-endohydrolase 1 for malting quality in barley. pgrc.ipk-gatersleben.de/glb, pgrc.ipk-gatersleben.de/X-1 & pgrc.ipk-gatersleben.de/Phendat (2011).

Matthies I E, Weise S, Röder M S:

Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley. pgrc.ipk-gatersleben.de/alpha-amylase (2011).

Mayer K F X, Martis M, Hedley P E, Šimková H, Liu H, Morris J A, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N:

Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23 (2011) 1249-1263. https://dx.doi.org/10.1105/tpc.110.082537

Pick T R, Bräutigam A, Schluter U, Denton A K, Colmsee C, Scholz U, Fahnenstich H, Pieruschka R, Rascher U, Sonnewald U, Weber A P:

Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. Plant Cell 23 (2011) 4208-4220. https://dx.doi.org/10.1105/tpc.111.090324

Scholz U, Künne C, Lange M, Miehe H, Funke T:

CR-EST: a resource for crop ESTs. pgrc.ipk-gatersleben.de/cr-est (2011).

Schönherr I S:

Assemblierung und Analyse des Vitis vinifera Genoms der Rebsorte Riesling. (Bachelor Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik (2011) 40 pp.

Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Koschützki D, Scholz U, Weise S:

MetaCrop 2.0. metacrop.ipk-gatersleben.de (2011).

Seiler C, Harshavardhan V T, Kalladan R, Reddy P S, Strickert M, Rolletschek H, Scholz U, Wobus U, Sreenivasulu N:

ABA biosynthesis and degradation contributing to ABA homeostasis during barley seed development under control and terminal drought-stress conditions. J. Exp. Bot. 62 (2011) 2615-2632. https://dx.doi.org/10.1093/jxb/erq446

Steuernagel B, Scholz U:

POCI annotation tool. pgrc.ipkgatersleben.de/poci (2011).

Taudien S, Steuernagel B, Ariyadasa R, Schulte D, Schmutzer T, Groth M, Felder M, Petzold A, Scholz U, Mayer K F, Stein N, Platzer M:

Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC Res Notes 4 (2011) 411. https://dx.doi.org/10.1186/1756-0500-4-411

Weise S, Chen J, Junker B H, Klapperstück M, Lange M, Schreiber F, Scholz U:

Das Informationssystem MetaCrop zur Unterstützung systembiologischer Forschung an Kulturpflanzen. it - Information Technology 53 (2011) 234-240. https://dx.doi.org/10.1524/itit.2011.0648

Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H:

Meta-All: A system for managing metabolic pathway information. meta-all.ipk-gatersleben.de (2011).

Weise S, Harrer S, Grosse I, Knüpffer H, Willner E:

The European Poa Database (EPDB). poa.ipk-gatersleben.de (2011).

Weise S, Scholz U, Röder M S, Matthies I E:

MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2011).

Wicker T, Mayer K F X, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Doležel J, Keller B, Stein N:

Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23 (2011) 1706-1718. https://dx.doi.org/10.1105/tpc.111.086629

Breuillin F, Schramm J, Hajirezaei M-R, Ahkami A, Favre P, Druege U, Hause B, Bucher M, Kretzschmar T, Bossolini E, Kuhlemeier C, Martinoia E, Franken P, Scholz U, Reinhardt D:

Phosphate systemically inhibits development of arbuscular mycorrhiza in Petunia hybrida and represses genes involved in mycorrhizal functioning. Plant J. 64 (2010) 1002-1017. https://dx.doi.org/10.1111/j.1365-313X.2010.04385.x

Cockram J, White J, Zuluaga D L, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey M J, Werner P, Harrap D, Tapsell C, Liu H, Hedley P E, Stein N, Schulte D, Steuernagel B, Marshall D F, Thomas W T, Ramsay L, Mackay I, Balding D J, Consortium T A, Waugh R, OSullivan D M:

Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc. Natl. Acad. Sci. U. S. A. 107 (2010) 21611-21616. https://dx.doi.org/10.1073/pnas.1010179107

Colmsee C, Zanke C, Funke T, Weise S, Keller E R J, Scholz U:

The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2010).

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2010).

Hippe K, Colmsee C, Czauderna T, Grafahrend-Belau E, Junker B H, Klukas C, Scholz U, Schreiber F, Weise S:

Novel developments of the MetaCrop information system for facilitating systems biological approaches. J. Integr. Bioinform. 7 (2010) e125. https://dx.doi.org/10.2390/biecoll-jib-2010-125

Keller E R J, Zanke C, Scholz U:

EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound euralliveg.ipk-gatersleben.de (2010).

Lange M, Bargsten J, Weißbach M, Spies K, Scholz U:

LAILAPS– The Life Science Search Engine. lailaps.ipk-gatersleben.de (2010).

Lange M, Rutkowski T, Stephanik A, Steuernagel B, Scholz U:

FLAREX – The IPK array experiment database. pgrc.ipk-gatersleben.de/flarex (2010).

Lange M, Spies K, Bargsten J, Haberhauer G, Klapperstück M, Leps M, Weinel C, Wunschiers R, Weissbach M, Stein J, Scholz U:

The LAILAPS search engine: relevance ranking in life science databases. J. Integr. Bioinform. 7 (2010) 110. https://dx.doi.org/10.2390/biecoll-jib-2010-110

Lange M, Spies K, Colmsee C, Flemming S, Klapperstück M, Scholz U:

The LAILAPS search engine: a feature model for relevance ranking in life science databases. J. Integr. Bioinform. 7 (2010) 118. https://dx.doi.org/10.2390/biecoll-jib-2010-118

Lange M, Weise S, Scholz U, Verrier P, Rawlings C (Eds.):

Proceedings of the 6th International Symposium on Integrative Bioinformatics 2010, 22 - 24 March 2010, Cambridge, United Kingdom. (2010) 406 pp.

Matthies I E, Weise S, Förster K, Röder M S:

Association mapping and marker development of the candidate genes (1->3),(1->4)-β-D-Glucan-4-glucanohydrolase and (1->4)-β-Xylan-endohydrolase 1 for malting quality in barley. pgrc.ipk-gatersleben.de/glb, pgrc.ipk-gatersleben.de/X-1 & pgrc.ipk-gatersleben.de/Phendat (2010).

Matthies I E, Weise S, Röder M S:

Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley. pgrc.ipk-gatersleben.de/alpha-amylase (2010).

Matthies I E, Weise S, Röder M S:

Assoziationskartierung in Gerste – Ein genomweiter und Kandidatengenansatz. In: Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs (Ed.): Züchtung und Genressourcen gegen abiotische Stressfaktoren, markergestützte Selektion in der Praxis: 60. Tagung, 24. - 26. November 2009. (Series: Tagung / Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs, Vol. 60) Irdning: Lehr- und Forschungsanstalt für Landwirtschaft Raumberg-Gumpenstein (2010) ISBN 978-3-902559-37-1, 91-96.

Navakode S, Weidner A, Varshney R K, Lohwasser U, Scholz U, Röder M S, Börner A:

A genetic analysis of aluminium tolerance in cereals. Agriculturae Conspectus Scientificus 75 (2010) 191-196.

Scholz U, Künne C, Lange M, Miehe H, Funke T:

CR-EST: a resource for crop ESTs. pgrc.ipk-gatersleben.de/cr-est (2010).

Steuernagel B, Scholz U:

POCI annotation tool. pgrc.ipkgatersleben.de/poci (2010).

Weise S, Biermann N, Flemming S, Vorwald J, van Hintum T, Knüpffer H, Grosse I:

Proposal for improvement of PGR data exchange through XML. In: Proc. EPGRIS Final Conference, 11-13 September 2003, Prague, Czech Republic. International Plant Genetic Resources Institute (IPGRI). www.ecpgr.cgiar.org/Networks/Info_doc/FinalMeetingPresentations/Papers/Bierman_IPK_v0.14.doc (2010).

Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H:

Meta-All: A system for managing metabolic pathway information. meta-all.ipk-gatersleben.de (2010).

Weise S, Harrer S, Grosse I, Knüpffer H, Willner E:

The European Poa Database (EPDB). poa.ipk-gatersleben.de (2010).

Weise S, Scholz U, Röder M S, Matthies I E:

MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2010).

Bargsten J:

Nutzerprofilgestütztes Schätzen von Rankingparametern für Suchmaschinen-Anfragen an integrierte biologische Datenbanken. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2009) 103 pp.

Colmsee C:

Reengineering des SBML-Exporters für das metabolische Netzwerkinformationssystem MetaCrop. (Diploma Thesis) Wernigerode, Hochschule Harz (FH), Fachbereich Automatisierung und Informatik (2009) 99 pp.

Colmsee C, Zanke C, Funke T, Weise S, Keller E R J, Scholz U:

The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2009).

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2009).

Günther M:

Konzeption und Implementierung einer Textindexierungsinfrastruktur zur Parallelisierung von Suchmaschinen in den Lebenswissenschaften. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2009) 95 pp.

Keller E R J, Zanke C, Scholz U:

EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound euralliveg.ipk-gatersleben.de (2009).

Lange M, Bargsten J, Günther M, Spies K, Scholz U:

Lailaps – The Life Science Search Engine. lailaps.ipk-gatersleben.de (2009).

Matthies I E, Weise S, Förster J, Röder M S:

Association mapping and marker development of the candidate genes (1→3),(1→4)-β-D-Glucan-4-glucanohydrolase and (1→4)-β-Xylan-endohydrolase 1 for malting quality in barley. Euphytica 170 (2009) 109-122. https://dx.doi.org/10.1007/s10681-009-9915-6

Matthies I E, Weise S, Röder M S:

Association of haplotype diversity in the alpha-amylase gene amy1 with malting quality parameters in barley. Mol. Breed. 23 (2009) 139-152. https://dx.doi.org/10.1007/s11032-008-9221-3

Mayer K F, Taudien S, Martis M, Simkova H, Suchankova P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Dolezel J, Stein N:

Gene content and virtual gene order of barley chromosome 1H. Plant Physiol. 151 (2009) 496-505. https://dx.doi.org/10.1104/pp.109.142612

Nagel M, Vogel H, Landjeva S, Buck-Sorlin G, Lohwasser U, Scholz U, Börner A:

Seed conservation in ex situ genebank - genetic studies on longevity in barley. Euphytica 170 (2009) 5-14. https://dx.doi.org/10.1007/s10681-009-9975-7

Navakode S, Weidner A, Varshney R K, Lohwasser U, Scholz U, Börner A:

A QTL analysis of aluminium tolerance in barley, using gene-based markers. Cereal Res. Commun. 37 (2009) 531-540. https://dx.doi.org/10.1556/CRC.37.2009.4.6

Schäfer P, Pfiffi S, Voll L M, Zajic D, Chandler P M, Waller F, Scholz U, Pons-Kuhnemann J, Sonnewald S, Sonnewald U, Kogel K H:

Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica. Plant J. 59 (2009) 461-474. https://dx.doi.org/10.1111/j.1365-313X.2009.03887.x

Schäfer P, Pfiffi S, Voll L M, Zajic D, Chandler P M, Waller F, Scholz U, Pons-Kühnemann J, Sonnewald S, Sonnewald U, Kogel K H:

Phytohormones in plant root-Piriformospora indica mutualism. Plant Signal. Behav. 4 (2009) 669-671. https://dx.doi.org/10.4161/psb.4.7.9038

Schoor W, Mecke R, Seiffert U, Bollenbeck F, Schulz U:

Remote rendering of large biological datasets. In: Ranchordas A K, Pereira J, Richard P (Eds.): GRAPP 2009 - proceedings of the 4th International Conference on Computer Graphics Theory and Applications, Lisboa, Portugal, February 5-8, 2009. [Setúbal]: INSTICC Press (2009) ISBN 978-989-8111-67-8, 223-227.

Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D, Petzold A, Felder M, Graner A, Scholz U, Mayer K F, Platzer M, Stein N:

De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics 10 (2009) 547. https://dx.doi.org/10.1186/1471-2164-10-547

Sturm J:

Visualisierungsstrategien für bioinformatische Anwendungen. (Diploma Thesis) Köthen, Hochschule Anhalt (FH), Fachbereich Informatik (2009) 76 pp.

Weise S:

Integrierte Analyse pflanzenbiologischer Daten unter besonderer Berücksichtigung der Datenqualität. (PhD Thesis) Bielefeld, Universität Bielefeld, Technische Fakultät (2009) 187 pp.

Weise S, Colmsee C, Grafahrend-Belau E, Junker B, Klukas C, Lange M, Scholz U, Schreiber F:

Datenaustausch und Datenintegration zur Modellierung und Analyse metabolischer Netzwerke am Beispiel von Kulturpflanzen. In: Fischer S, Maehle E, Reischuk R (Eds.): Informatik 2009: im Focus das Leben, Beiträge der 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 28.9. - 2.10.2009 in Lübeck. (Series: GI-Edition, Lecture notes in informatics, Vol. 154) Bonn: Ges. für Informatik (2009) ISBN 978-3-88579-248-2, 693-697.

Weise S, Colmsee C, Grafahrend-Belau E, Junker B, Klukas C, Lange M, Scholz U, Schreiber F:

An integration and analysis pipeline for systems biology in crop plant metabolism. In: Paton N W, Missier P, Hedeler C (Eds.): Data integration in the life sciences: 6th international workshop, DILS 2009, Manchester, UK, July 20-22, 2009, proceedings. (Series: Lecture Notes in Computer Science, Vol. 5647) Berlin [u.a.]: Springer (2009) ISBN 978-3-642-02878-6, 196-203. https://dx.doi.org/10.1007/978-3-642-02879-3_16

Weise S, Scholz U, Röder M S, Matthies I E:

MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2009).

Weise S, Scholz U, Röder M S, Matthies I E:

Metabrew: A comprehensive database of malting quality traits in brewing barley. Barley Genet. Newsl. 39 (2009) 1-4.

Wittwer C:

Herleitung und Extraktion von Schematagraphen aus integrierten Datenbanken der Lebenswissenschaften. (Bachelor Thesis) Magdeburg, Otto-von-Guericke-Universität, Fakultät für Informatik, Institut für Technische und Betriebliche Informationssysteme (2009) 73 pp.

Grafahrend-Belau E, Junker B H, Koschützki D, Klukas C, Weise S, Scholz U, Schreiber F:

Towards systems biology of developing barley grains: a framework for modeling metabolism. In: Ahdesmäki M, Strimmer K, Radde N, Rahnenführer J, Klemm K, Lähdesmäki H, Yli-Harja O (Eds.): 5th International Workshop on Computational Systems Biology, WCSB 2008, June 11–13, 2008, Leipzig, Germany, proceedings. (TICSP series, Vol. 41) Tampere: Tampere International Center for Signal Processing (2008) ISBN 978-952-15-1988-8 41-44.

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res. 36 (2008) D954-D958. https://dx.doi.org/10.1093/nar/gkm835

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop: a detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2008).

Hofestädt R, Köhler J, Lange M, Scholz U, Schreiber F, Verrier P (Eds.):

Proceedings of the 5th International Symposium on Integrative Bioinformatics 2008: 20 - 22 August 2008 Leucorea, Lutherstadt Wittenberg, Germany. Wittenberg (2008) 345 pp.

Kloosterman B, De Koeyer D, Griffiths R, Flinn B, Steuernagel B, Scholz U, Sonnewald S, Sonnewald U, Bryan G J, Prat S, Bánfalvi Z, Hammond J P, Geigenberger P, Nielsen K L, Visser R G, Bachem C W:

Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array. Funct. Integr. Genomics 8 (2008) 329-340. https://dx.doi.org/10.1007/s10142-008-0083-x

Lange M, Klapperstück M, Spies K, Scholz U:

DALIGRES: A graph query tool to unravel the life science database maze. (Best Paper Award). In: Borovska P (Ed.): Proceedings of the IV International Bulgarian-Greek Scientific Conference on Computer Science 2008, Kavala, Greece, 18-19 September 2008. Heron Press (2008) ISBN 978-954-580-254-6, 603-613.

Lange M, Rutkowski T, Stephanik A, Steuernagel B, Scholz U:

FLAREX – The IPK array experiment database. pgrc.ipk-gatersleben.de/flarex/ (2008).

Scholz U, Künne C, Lange M, Miehe H, Funke T:

IPK crop EST database: CR-EST (Version 1.5). pgrc.ipk-gatersleben.de/cr-est/ (2008).

Spies K, Klapperstück M, Bargsten J, Lange M, Scholz U:

LAILAPS – Life science search engine. lailaps.ipk-gatersleben.de (2008).

Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close T J, Stitt M, Graner A, Wobus U:

Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by New MapMan/PageMan profiling tools. Plant Physiol. 146 (2008) 1738-1758. https://dx.doi.org/10.1104/pp.107.111781

Steuernagel B, Scholz U:

POCI annotation tool. pgrc.ipk-gatersleben.de/poci/ (2008).

Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H:

Meta-All: A system for managing metabolic pathway Information. meta-all.ipk-gatersleben.de (2008).

Weise S, Scholz U, Röder M S, Matthies I:

MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2008).

Biemelt S, Senning M, Sonnewald U, Scholz U, Steuernagel B, Theres K, Schmitz G, Prat S, Navarro C, Cubas P, Traas J, Nikovics K, Laufs P:

GABI-GENOSOME: Ertrag und Lagerfähigkeit von Kartoffeln und Tomaten verbessern. GenomXPress Sonderausgabe März (2007) 21.

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2007).

Heiß S:

Entwicklung eines Data-Warehouses für pflanzengenetische Diversitätsstudien. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität Magdeburg (2007)

Keller E R J, Zanke C, Scholz U:

EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound euralliveg.ipk-gatersleben.de (2007).

Klapperstück M:

Konzeption und Umsetzung einer Graphanfragesprache zur nicht-materialisierten Integration biologischer Datenbanken. (Diploma Thesis) Halle, Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik (2007) 98 pp.

Koopmann J H:

Integrierte plattformübergreifende Normalisierung von Expressionsdaten. (Diploma Thesis) Halle, Martin-Luther-Universität Halle-Wittenberg (2007)

Kuenne C, Grosse I, Matthies I, Scholz U, Sretenovic-Rajicic T, Stein N, Stephanik A, Steuernagel B, Weise S:

Using data warehouse technology in crop plant bioinformatics. J. Integr. Bioinform. 4 (2007) 88. https://dx.doi.org/10.2390/biecoll-jib-2007-88

Lange M, Himmelbach A, Schweizer P, Scholz U:

Data Linkage Graph: computation, querying and knowledge discovery of life science database networks. J. Integr. Bioinform. 4 (2007) 68. https://dx.doi.org/10.2390/biecoll-jib-2007-68

Lange M, Scholz U:

Datenverarbeitung in der Biologie. Erbe Information. iX 3 (2007) 106-109.

Scholz U, Künne C, Lange M, Miehe H, Funke T:

IPK Crop EST Database: CR-EST (Version 1.5). pgrc.ipk-gatersleben.de/cr-est/ (2007).

Senning M, Steuernagel B, Hartmann A, Sonnewald U, Scholz U:

Regulation der Keimruhe von Kartoffelknollen. GenomXPress 3 (2007) 7-10.

Spies K:

Integration von Bioinformatikdatenbanken und -anwendungen des IPK Gatersleben mittels Web-Services in die internationale Bioinformatik-Infrastruktur. (Diploma Thesis) Halle, Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik (2007) 110 pp.

Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney R K, Perovic D, Grosse I, Graner A:

A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor. Appl. Genet. 114 (2007) 823-839. https://dx.doi.org/10.1007/s00122-006-0480-2

Suray M:

Methoden und Werkzeuge zur automatischen Indexierung und Schemaextraktion über Deep-Web-Datenquellen. (Diploma Thesis) Bielefeld, Universität Bielefeld, Technische Fakultät (2007) 95 pp.

Totz J:

Workflow-supported Analysis of Gene Expression Data. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität (2007)

Weise S, Harrer S, Grosse I, Knüpffer H, Willner E:

The European Poa Database (EPDB). Plant Genet. Resour. Newsl. 150 (2007) 64-70.

Xia M:

Hierarchische Datenbankanfrage auf integrierte Datenbanken zur Funktionsklassifikation von molekularbiologischen Daten. (Diploma Thesis) Bielefeld, Universität Bielefeld, Technische Fakultät (2007) 77 pp.

Eichmann R, Biemelt S, Schäfer P, Scholz U, Jansen C, Felk A, Schafer W, Langen G, Sonnewald U, Kogel K H, Hückelhoven R:

Macroarray expression analysis of barley susceptibility and nonhost resistance to Blumeria graminis. J. Plant Physiol. 163 (2006) 657-670. https://dx.doi.org/10.1016/j.jplph.2005.06.019

Funke T, Weise S, Knüpffer H, Grosse I:

Ein neues Gesicht für die Europäische Gerstendatenbank (EBDB). Vortr. Pflanzenzücht. 70 (2006) 79-80.

Große I, Funke T, Kuenne C, Neumannn S, Stephanik A, Thiel T, Weise S:

Integrative Datenanalyse mit dem Plant Data Warehouse. Vortr. Pflanzenzücht. 70 (2006) 50-53.

Kaule U:

Analyse und Strukturierung von Workflows im Anwendungsfeld bioinformatischer Prozesse. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität - Fakultät für Informatik Institut für Technische und Betriebliche Informationssysteme (2006)

Lange M:

Methoden zum homogenen Zugriff und zur Integration heterogener, biologischer Datenquellen mittels beschränkter Zugriffsmuster. (PhD Thesis) Magdeburg, Otto-von-Guericke-Universität - Fakultät für Informatik Institut für Technische und Betriebliche Informationssysteme (2006) 218 pp.

Riedel A:

Konzept zur Daten- und Anwendungsintegration zur Analyse von Gen-Expressionsdaten. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität - Fakultät für Informatik Institut für Technische und Betriebliche Informationssysteme (2006)

Spieß K:

Integration von Bioinformatikdatenbanken und -anwendungen des IPK Gatersleben mittels Web-Services in die internationale Bioinformatik-Infrastruktur. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle/Wittenberg, Institut für Informatik (2006)

Stephanik A, Bachmann H, Funke T, Kuenne C, Langer E, Thiel T, Weise S, Große I:

Das Plant Bioinformatics Portal. Vortr. Pflanzenzücht. 70 (2006) 81-83.

Tischler T:

Entwurf und Implementierung einer Integrationslösung für Anwendungen in der Bioinformatik. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität - Fakultät für Informatik, Institut für Technische und Betriebliche Informationssysteme (2006)

Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H:

Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics 7 (2006) 465. https://dx.doi.org/10.1186/1471-2105-7-465

Weise S, Knüpffer H, Vorwald J, Scholz U, Grosse I:

Integration von phänotypischen Daten in das Plant Data Warehouse. Vortr. Pflanzenzücht. 70 (2006) 84-86.