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A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping.

Holtgräwe D, Rosleff Soerensen T, Hausmann L, Pucker B, Viehöver P, Töpfer R, Weisshaar B.

Front Plant Sci. 2020 Mar 4;11:156. doi: 10.3389/fpls.2020.00156. eCollection 2020.


High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing.

Siadjeu C, Pucker B, Viehöver P, Albach DC, Weisshaar B.

Genes (Basel). 2020 Mar 4;11(3). pii: E274. doi: 10.3390/genes11030274.


Genome Sequencing of Musa acuminata Dwarf Cavendish Reveals a Duplication of a Large Segment of Chromosome 2.

Busche M, Pucker B, Viehöver P, Weisshaar B, Stracke R.

G3 (Bethesda). 2020 Jan 7;10(1):37-42. doi: 10.1534/g3.119.400847.


Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome.

Pucker B, Rückert C, Stracke R, Viehöver P, Kalinowski J, Weisshaar B.

Genes (Basel). 2019 Sep 2;10(9). pii: E671. doi: 10.3390/genes10090671.


Characterization of genes and alleles involved in the control of flowering time in grapevine.

Kamal N, Ochßner I, Schwandner A, Viehöver P, Hausmann L, Töpfer R, Weisshaar B, Holtgräwe D.

PLoS One. 2019 Jul 3;14(7):e0214703. doi: 10.1371/journal.pone.0214703. eCollection 2019.


A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set.

Pucker B, Holtgräwe D, Stadermann KB, Frey K, Huettel B, Reinhardt R, Weisshaar B.

PLoS One. 2019 May 21;14(5):e0216233. doi: 10.1371/journal.pone.0216233. eCollection 2019.


Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence.

Pucker B, Holtgräwe D, Weisshaar B.

BMC Res Notes. 2017 Dec 4;10(1):667. doi: 10.1186/s13104-017-2985-y.


Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.

Capistrano-Gossmann GG, Ries D, Holtgräwe D, Minoche A, Kraft T, Frerichmann SLM, Rosleff Soerensen T, Dohm JC, González I, Schilhabel M, Varrelmann M, Tschoep H, Uphoff H, Schütze K, Borchardt D, Toerjek O, Mechelke W, Lein JC, Schechert AW, Frese L, Himmelbauer H, Weisshaar B, Kopisch-Obuch FJ.

Nat Commun. 2017 Jun 6;8:15708. doi: 10.1038/ncomms15708.


The AtMYB12 activation domain maps to a short C-terminal region of the transcription factor.

Stracke R, Turgut-Kara N, Weisshaar B.

Z Naturforsch C J Biosci. 2017 Jul 14;72(7-8):251-257. doi: 10.1515/znc-2016-0221.


Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation.

Kleinboelting N, Huep G, Weisshaar B.

Plant Cell Physiol. 2017 Jan 1;58(1):e7. doi: 10.1093/pcp/pcw205.


ReadXplorer 2-detailed read mapping analysis and visualization from one single source.

Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A.

Bioinformatics. 2016 Dec 15;32(24):3702-3708. Epub 2016 Aug 18.


A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny.

Pucker B, Holtgräwe D, Rosleff Sörensen T, Stracke R, Viehöver P, Weisshaar B.

PLoS One. 2016 Oct 6;11(10):e0164321. doi: 10.1371/journal.pone.0164321. eCollection 2016.


Chloroplast Genome Sequence of Arabidopsis thaliana Accession Landsberg erecta, Assembled from Single-Molecule, Real-Time Sequencing Data.

Stadermann KB, Holtgräwe D, Weisshaar B.

Genome Announc. 2016 Sep 22;4(5). pii: e00975-16. doi: 10.1128/genomeA.00975-16.


Analyzing Synthetic Promoters Using Arabidopsis Protoplasts.

Stracke R, Thiedig K, Kuhlmann M, Weisshaar B.

Methods Mol Biol. 2016;1482:67-81. doi: 10.1007/978-1-4939-6396-6_5.


Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris).

Kowar T, Zakrzewski F, Macas J, Kobližková A, Viehoever P, Weisshaar B, Schmidt T.

BMC Plant Biol. 2016 May 26;16(1):120. doi: 10.1186/s12870-016-0805-5.


Evolution of tonoplast P-ATPase transporters involved in vacuolar acidification.

Li Y, Provenzano S, Bliek M, Spelt C, Appelhagen I, Machado de Faria L, Verweij W, Schubert A, Sagasser M, Seidel T, Weisshaar B, Koes R, Quattrocchio F.

New Phytol. 2016 Aug;211(3):1092-107. doi: 10.1111/nph.14008. Epub 2016 May 23.


Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels.

Ries D, Holtgräwe D, Viehöver P, Weisshaar B.

BMC Genomics. 2016 Mar 15;17:236. doi: 10.1186/s12864-016-2566-9.


Natural variation in flavonol accumulation in Arabidopsis is determined by the flavonol glucosyltransferase BGLU6.

Ishihara H, Tohge T, Viehöver P, Fernie AR, Weisshaar B, Stracke R.

J Exp Bot. 2016 Mar;67(5):1505-17. doi: 10.1093/jxb/erv546. Epub 2015 Dec 29.


Diversification, evolution and methylation of short interspersed nuclear element families in sugar beet and related Amaranthaceae species.

Schwichtenberg K, Wenke T, Zakrzewski F, Seibt KM, Minoche A, Dohm JC, Weisshaar B, Himmelbauer H, Schmidt T.

Plant J. 2016 Jan;85(2):229-44. doi: 10.1111/tpj.13103.


SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome.

Stadermann KB, Weisshaar B, Holtgräwe D.

BMC Bioinformatics. 2015 Sep 16;16:295. doi: 10.1186/s12859-015-0726-6.


The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism.

Kleinboelting N, Huep G, Appelhagen I, Viehoever P, Li Y, Weisshaar B.

Mol Plant. 2015 Nov 2;8(11):1651-64. doi: 10.1016/j.molp.2015.08.011. Epub 2015 Sep 5.


Exploiting single-molecule transcript sequencing for eukaryotic gene prediction.

Minoche AE, Dohm JC, Schneider J, Holtgräwe D, Viehöver P, Montfort M, Sörensen TR, Weisshaar B, Himmelbauer H.

Genome Biol. 2015 Sep 2;16:184. doi: 10.1186/s13059-015-0729-7.


TRANSPARENT TESTA 13 is a tonoplast P3A -ATPase required for vacuolar deposition of proanthocyanidins in Arabidopsis thaliana seeds.

Appelhagen I, Nordholt N, Seidel T, Spelt K, Koes R, Quattrochio F, Sagasser M, Weisshaar B.

Plant J. 2015 Jun;82(5):840-9. doi: 10.1111/tpj.12854.


Fast forward genetics to identify mutations causing a high light tolerant phenotype in Chlamydomonas reinhardtii by whole-genome-sequencing.

Schierenbeck L, Ries D, Rogge K, Grewe S, Weisshaar B, Kruse O.

BMC Genomics. 2015 Feb 6;16:57. doi: 10.1186/s12864-015-1232-y.


The genomics revolution and its impact on future biotechnology.

Noll T, Pühler A, Weisshaar B, Wendisch VF.

J Biotechnol. 2014 Nov 20;190:1. doi: 10.1016/j.jbiotec.2014.10.009. Epub 2014 Oct 17. No abstract available.


An easy-to-use primer design tool to address paralogous loci and T-DNA insertion sites in the genome of Arabidopsis thaliana.

Huep G, Kleinboelting N, Weisshaar B.

Plant Methods. 2014 Sep 13;10:28. doi: 10.1186/1746-4811-10-28. eCollection 2014.


Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris).

Holtgräwe D, Sörensen TR, Viehöver P, Schneider J, Schulz B, Borchardt D, Kraft T, Himmelbauer H, Weisshaar B.

PLoS One. 2014 Oct 10;9(10):e110113. doi: 10.1371/journal.pone.0110113. eCollection 2014.


Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris).

Stracke R, Holtgräwe D, Schneider J, Pucker B, Sörensen TR, Weisshaar B.

BMC Plant Biol. 2014 Sep 25;14:249. doi: 10.1186/s12870-014-0249-8.


QTL analysis of flowering time and ripening traits suggests an impact of a genomic region on linkage group 1 in Vitis.

Fechter I, Hausmann L, Zyprian E, Daum M, Holtgräwe D, Weisshaar B, Töpfer R.

Theor Appl Genet. 2014 Sep;127(9):1857-72. doi: 10.1007/s00122-014-2310-2. Epub 2014 Aug 12.


Update on transparent testa mutants from Arabidopsis thaliana: characterisation of new alleles from an isogenic collection.

Appelhagen I, Thiedig K, Nordholt N, Schmidt N, Huep G, Sagasser M, Weisshaar B.

Planta. 2014 Nov;240(5):955-70. doi: 10.1007/s00425-014-2088-0. Epub 2014 Jun 6.


Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades.

Heitkam T, Holtgräwe D, Dohm JC, Minoche AE, Himmelbauer H, Weisshaar B, Schmidt T.

Plant J. 2014 Aug;79(3):385-97. doi: 10.1111/tpj.12565. Epub 2014 Jul 2.


Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes.

Dubos C, Kelemen Z, Sebastian A, Bülow L, Huep G, Xu W, Grain D, Salsac F, Brousse C, Lepiniec L, Weisshaar B, Contreras-Moreira B, Hehl R.

BMC Genomics. 2014 Apr 28;15:317. doi: 10.1186/1471-2164-15-317.


Plant genome sequencing - applications for crop improvement.

Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KF.

Curr Opin Biotechnol. 2014 Apr;26:31-7. doi: 10.1016/j.copbio.2013.08.019. Epub 2013 Sep 21. Review.


The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation.

Zakrzewski F, Schubert V, Viehoever P, Minoche AE, Dohm JC, Himmelbauer H, Weisshaar B, Schmidt T.

Plant J. 2014 Jun;78(6):937-50. doi: 10.1111/tpj.12519. Epub 2014 May 21.


The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).

Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H.

Nature. 2014 Jan 23;505(7484):546-9. doi: 10.1038/nature12817. Epub 2013 Dec 18.


GABI-DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana.

Bolle C, Huep G, Kleinbölting N, Haberer G, Mayer K, Leister D, Weisshaar B.

Plant J. 2013 Jul;75(1):157-171. doi: 10.1111/tpj.12197. Epub 2013 May 7.


Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration.

Weber B, Heitkam T, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T.

Mob DNA. 2013 Mar 1;4(1):8. doi: 10.1186/1759-8753-4-8.


Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome.

Wollrab C, Heitkam T, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T.

Plant J. 2012 Nov;72(4):636-51. doi: 10.1111/j.1365-313X.2012.05107.x. Epub 2012 Sep 24.


Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon.

Mönke G, Seifert M, Keilwagen J, Mohr M, Grosse I, Hähnel U, Junker A, Weisshaar B, Conrad U, Bäumlein H, Altschmied L.

Nucleic Acids Res. 2012 Sep 1;40(17):8240-54. Epub 2012 Jun 22.


The role of a pseudo-response regulator gene in life cycle adaptation and domestication of beet.

Pin PA, Zhang W, Vogt SH, Dally N, Büttner B, Schulze-Buxloh G, Jelly NS, Chia TY, Mutasa-Göttgens ES, Dohm JC, Himmelbauer H, Weisshaar B, Kraus J, Gielen JJ, Lommel M, Weyens G, Wahl B, Schechert A, Nilsson O, Jung C, Kraft T, Müller AE.

Curr Biol. 2012 Jun 19;22(12):1095-101. doi: 10.1016/j.cub.2012.04.007. Epub 2012 May 17.


Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana.

Junker A, Mönke G, Rutten T, Keilwagen J, Seifert M, Thi TM, Renou JP, Balzergue S, Viehöver P, Hähnel U, Ludwig-Müller J, Altschmied L, Conrad U, Weisshaar B, Bäumlein H.

Plant J. 2012 Aug;71(3):427-42. doi: 10.1111/j.1365-313X.2012.04999.x. Epub 2012 May 30.


Candidate genes within a 143 kb region of the flower sex locus in Vitis.

Fechter I, Hausmann L, Daum M, Sörensen TR, Viehöver P, Weisshaar B, Töpfer R.

Mol Genet Genomics. 2012 Mar;287(3):247-59. doi: 10.1007/s00438-012-0674-z. Epub 2012 Jan 19.


Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives.

Menzel G, Krebs C, Diez M, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T.

Plant Mol Biol. 2012 Mar;78(4-5):393-405. doi: 10.1007/s11103-011-9872-z. Epub 2012 Jan 13.


Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).

Dohm JC, Lange C, Holtgräwe D, Sörensen TR, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H.

Plant J. 2012 May;70(3):528-40. doi: 10.1111/j.1365-313X.2011.04898.x. Epub 2012 Feb 14. Erratum in: Plant J. 2012 Jul;71(1):182.


GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database.

Kleinboelting N, Huep G, Kloetgen A, Viehoever P, Weisshaar B.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1211-5. doi: 10.1093/nar/gkr1047. Epub 2011 Nov 12.


Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes.

Wenke T, Döbel T, Sörensen TR, Junghans H, Weisshaar B, Schmidt T.

Plant Cell. 2011 Sep;23(9):3117-28. doi: 10.1105/tpc.111.088682. Epub 2011 Sep 9.


The genome of the mesopolyploid crop species Brassica rapa.

Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z; Brassica rapa Genome Sequencing Project Consortium.

Nat Genet. 2011 Aug 28;43(10):1035-9. doi: 10.1038/ng.919.


Leucoanthocyanidin Dioxygenase in Arabidopsis thaliana: characterization of mutant alleles and regulation by MYB-BHLH-TTG1 transcription factor complexes.

Appelhagen I, Jahns O, Bartelniewoehner L, Sagasser M, Weisshaar B, Stracke R.

Gene. 2011 Sep 15;484(1-2):61-8. doi: 10.1016/j.gene.2011.05.031. Epub 2011 Jun 12.


Pasireotide (SOM230), a novel multireceptor-targeted somatostatin analogue, is well tolerated when administered as a continuous 7-day subcutaneous infusion in healthy male volunteers.

Petersenn S, Unger N, Hu K, Weisshaar B, Zhang Y, Bouillaud E, Reséndiz KH, Wang Y, Mann K.

J Clin Pharmacol. 2012 Jul;52(7):1017-27. doi: 10.1177/0091270011408727. Epub 2011 Jun 14.


Epigenetic profiling of heterochromatic satellite DNA.

Zakrzewski F, Weisshaar B, Fuchs J, Bannack E, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T.

Chromosoma. 2011 Aug;120(4):409-22. doi: 10.1007/s00412-011-0325-x. Epub 2011 May 19.


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