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Items: 29

1.

Accurate prediction of cell type-specific transcription factor binding.

Keilwagen J, Posch S, Grau J.

Genome Biol. 2019 Jan 10;20(1):9. doi: 10.1186/s13059-018-1614-y.

2.

Towards map-based cloning of FB_Mfu10: identification of a receptor-like kinase candidate gene underlying the Malus fusca fire blight resistance locus on linkage group 10.

Emeriewen OF, Richter K, Piazza S, Micheletti D, Broggini GAL, Berner T, Keilwagen J, Hanke MV, Malnoy M, Peil A.

Mol Breed. 2018;38(8):106. doi: 10.1007/s11032-018-0863-5. Epub 2018 Aug 6.

3.

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

International Wheat Genome Sequencing Consortium (IWGSC); IWGSC RefSeq principal investigators:, Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N; IWGSC whole-genome assembly principal investigators:, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG; Whole-genome sequencing and assembly:, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin AA; Hi-C data-based scaffolding:, Stein N, Mascher M, Himmelbach A; Whole-genome assembly quality control and analyses:, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin AA, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V; Pseudomolecule assembly:, Choulet F, Keeble-Gagnère G, Mascher M, Josselin AA, Rogers J; RefSeq genome structure and gene analyses:, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T; Automated annotation:, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L; Manual gene curation:, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G; Subgenome comparative analyses:, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T; Transposable elements:, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M; Phylogenomic analyses:, Lang D, Spannagl M, Appels R, Fischer I; Transcriptome analyses and RNA-seq data:, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH; Whole-genome methylome:, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A; Histone mark analyses:, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D; BAC chromosome MTP IWGSC–Bayer Whole-Genome Profiling (WGP) tags:, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S; Chromosome LTC mapping and physical mapping quality control:, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J; RH mapping:, Tiwari V, Gill B, Paux E, Poland J; Optical mapping:, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J; Recombination analyses:, Sourdille P, Darrier B; Gene family analyses:, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V; CBF gene family:, Barabaschi D, Cattivelli L; Dehydrin gene family:, Hernandez P, Galvez S, Budak H; NLR gene family:, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G; PPR gene family:, Small I, Melonek J, Zhou R; Prolamin gene family:, Juhász A, Belova T, Appels R, Olsen OA; WAK gene family:, Kanyuka K, King R; Stem solidness (SSt1) QTL team:, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D; Flowering locus C (FLC) gene team:, Rohde A, Golds T; Genome size analysis:, Doležel J, Čížková J, Tibbits J; MicroRNA and tRNA annotation:, Budak H, Akpinar BA, Biyiklioglu S; Genetic maps and mapping:, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A; BAC libraries and chromosome sorting:, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J; BAC pooling, BAC library repository, and access:, Berges H, Bellec A, Vautrin S; IWGSC sequence and data repository and access:, Alaux M, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H; Physical maps and BAC-based sequences:; 1A BAC sequencing and assembly:, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T; 1B BAC sequencing and assembly:, Choulet F, Paux E, Alberti A, Aury JM, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P; 1D, 4D, and 6D physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 2AL physical mapping:, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B; 2AS physical mapping:, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS; 2B, 2D, 4B, 5BL, and 5DL IWGSC–Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S; 3AL physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 3DS physical mapping and BAC sequencing and assembly:, Bartoš J, Holušová K, Plíhal O; 3DL BAC sequencing and assembly:, Clark MD, Heavens D, Kettleborough G, Wright J; 4A physical mapping, BAC sequencing, assembly, and annotation:, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M; 5BS BAC sequencing and assembly:, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E; 6B BAC sequencing and assembly:, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J; 7A physical mapping and BAC sequencing:, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J; 7B physical mapping, BAC sequencing, and assembly:, Olsen OA, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B; 7DS BAC sequencing and assembly:, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P; 7DL physical mapping and BAC sequencing:, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L; Figures:, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L; Manuscript writing team:, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C.

Science. 2018 Aug 17;361(6403). pii: eaar7191. doi: 10.1126/science.aar7191. Epub 2018 Aug 16.

PMID:
30115783
4.

Baculovirus Kimura two-parameter species demarcation criterion is confirmed by the distances of 38 core gene nucleotide sequences.

Wennmann JT, Keilwagen J, Jehle JA.

J Gen Virol. 2018 Sep;99(9):1307-1320. doi: 10.1099/jgv.0.001100. Epub 2018 Jul 27.

PMID:
30045782
5.

Leveraging the Use of Historical Data Gathered During Seed Regeneration of an ex Situ Genebank Collection of Wheat.

Philipp N, Weise S, Oppermann M, Börner A, Graner A, Keilwagen J, Kilian B, Zhao Y, Reif JC, Schulthess AW.

Front Plant Sci. 2018 May 8;9:609. doi: 10.3389/fpls.2018.00609. eCollection 2018.

6.

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi.

Keilwagen J, Hartung F, Paulini M, Twardziok SO, Grau J.

BMC Bioinformatics. 2018 May 30;19(1):189. doi: 10.1186/s12859-018-2203-5.

7.

Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes.

Babben S, Schliephake E, Janitza P, Berner T, Keilwagen J, Koch M, Arana-Ceballos FA, Templer SE, Chesnokov Y, Pshenichnikova T, Schondelmaier J, Börner A, Pillen K, Ordon F, Perovic D.

BMC Genomics. 2018 May 29;19(1):409. doi: 10.1186/s12864-018-4795-6.

8.

The Terpene Synthase Gene Family of Carrot (Daucus carota L.): Identification of QTLs and Candidate Genes Associated with Terpenoid Volatile Compounds.

Keilwagen J, Lehnert H, Berner T, Budahn H, Nothnagel T, Ulrich D, Dunemann F.

Front Plant Sci. 2017 Nov 9;8:1930. doi: 10.3389/fpls.2017.01930. eCollection 2017.

9.

Genetic architecture and temporal patterns of biomass accumulation in spring barley revealed by image analysis.

Neumann K, Zhao Y, Chu J, Keilwagen J, Reif JC, Kilian B, Graner A.

BMC Plant Biol. 2017 Aug 10;17(1):137. doi: 10.1186/s12870-017-1085-4.

10.

Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils.

Antweiler K, Schreiter S, Keilwagen J, Baldrian P, Kropf S, Smalla K, Grosch R, Heuer H.

Microb Biotechnol. 2017 Mar;10(2):434-449. doi: 10.1111/1751-7915.12595. Epub 2017 Jan 23.

11.

Using intron position conservation for homology-based gene prediction.

Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F.

Nucleic Acids Res. 2016 May 19;44(9):e89. doi: 10.1093/nar/gkw092. Epub 2016 Feb 17.

12.

DiffLogo: a comparative visualization of sequence motifs.

Nettling M, Treutler H, Grau J, Keilwagen J, Posch S, Grosse I.

BMC Bioinformatics. 2015 Nov 17;16:387. doi: 10.1186/s12859-015-0767-x.

13.

Varying levels of complexity in transcription factor binding motifs.

Keilwagen J, Grau J.

Nucleic Acids Res. 2015 Oct 15;43(18):e119. doi: 10.1093/nar/gkv577. Epub 2015 Jun 26.

14.

Chromosomal passports provide new insights into diffusion of emmer wheat.

Badaeva ED, Keilwagen J, Knüpffer H, Waßermann L, Dedkova OS, Mitrofanova OP, Kovaleva ON, Liapunova OA, Pukhalskiy VA, Özkan H, Graner A, Willcox G, Kilian B.

PLoS One. 2015 May 29;10(5):e0128556. doi: 10.1371/journal.pone.0128556. eCollection 2015.

15.

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R.

Grau J, Grosse I, Keilwagen J.

Bioinformatics. 2015 Aug 1;31(15):2595-7. doi: 10.1093/bioinformatics/btv153. Epub 2015 Mar 24.

16.

Separating the wheat from the chaff - a strategy to utilize plant genetic resources from ex situ genebanks.

Keilwagen J, Kilian B, Özkan H, Babben S, Perovic D, Mayer KF, Walther A, Poskar CH, Ordon F, Eversole K, Börner A, Ganal M, Knüpffer H, Graner A, Friedel S.

Sci Rep. 2014 Jun 10;4:5231. doi: 10.1038/srep05231.

17.

Area under precision-recall curves for weighted and unweighted data.

Keilwagen J, Grosse I, Grau J.

PLoS One. 2014 Mar 20;9(3):e92209. doi: 10.1371/journal.pone.0092209. eCollection 2014.

18.

On the value of intra-motif dependencies of human insulator protein CTCF.

Eggeling R, Gohr A, Keilwagen J, Mohr M, Posch S, Smith AD, Grosse I.

PLoS One. 2014 Jan 22;9(1):e85629. doi: 10.1371/journal.pone.0085629. eCollection 2014.

19.

A general approach for discriminative de novo motif discovery from high-throughput data.

Grau J, Posch S, Grosse I, Keilwagen J.

Nucleic Acids Res. 2013 Nov;41(21):e197. doi: 10.1093/nar/gkt831. Epub 2013 Sep 20.

20.

Mineralocorticoid receptor interaction with SP1 generates a new response element for pathophysiologically relevant gene expression.

Meinel S, Ruhs S, Schumann K, Strätz N, Trenkmann K, Schreier B, Grosse I, Keilwagen J, Gekle M, Grossmann C.

Nucleic Acids Res. 2013 Sep;41(17):8045-60. doi: 10.1093/nar/gkt581. Epub 2013 Jul 1.

21.

Dispom: a discriminative de-novo motif discovery tool based on the jstacs library.

Grau J, Keilwagen J, Gohr A, Paponov IA, Posch S, Seifert M, Strickert M, Grosse I.

J Bioinform Comput Biol. 2013 Feb;11(1):1340006. doi: 10.1142/S0219720013400064. Epub 2013 Jan 21.

PMID:
23427988
22.

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.

23.

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.

24.

De-novo discovery of differentially abundant transcription factor binding sites including their positional preference.

Keilwagen J, Grau J, Paponov IA, Posch S, Strickert M, Grosse I.

PLoS Comput Biol. 2011 Feb 10;7(2):e1001070. doi: 10.1371/journal.pcbi.1001070. Erratum in: PLoS Comput Biol. 2011 Oct;7(10). doi: 10.1371/annotation/a0b541dc-472b-4076-a435-499ce9519335.

25.

Probabilistic approaches to transcription factor binding site prediction.

Posch S, Grau J, Gohr A, Keilwagen J, Grosse I.

Methods Mol Biol. 2010;674:97-119. doi: 10.1007/978-1-60761-854-6_7.

PMID:
20827588
26.

Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis.

Keilwagen J, Grau J, Posch S, Grosse I.

BMC Bioinformatics. 2010 Mar 22;11:149. doi: 10.1186/1471-2105-11-149.

27.

Unifying generative and discriminative learning principles.

Keilwagen J, Grau J, Posch S, Strickert M, Grosse I.

BMC Bioinformatics. 2010 Feb 22;11:98. doi: 10.1186/1471-2105-11-98.

28.

MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations.

Keilwagen J, Baumbach J, Kohl TA, Grosse I.

Genome Biol. 2009;10(5):R46. doi: 10.1186/gb-2009-10-5-r46. Epub 2009 May 1.

29.

Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data.

Seifert M, Keilwagen J, Strickert M, Grosse I.

Bioinformatics. 2009 Aug 15;25(16):2118-25. doi: 10.1093/bioinformatics/btp276. Epub 2009 Apr 28.

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