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Items: 26

1.

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
2.

Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars.

Thind AK, Wicker T, Müller T, Ackermann PM, Steuernagel B, Wulff BBH, Spannagl M, Twardziok SO, Felder M, Lux T, Mayer KFX; International Wheat Genome Sequencing Consortium, Keller B, Krattinger SG.

Genome Biol. 2018 Aug 17;19(1):104. doi: 10.1186/s13059-018-1477-2.

3.

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.

4.

The repetitive landscape of the 5100 Mbp barley genome.

Wicker T, Schulman AH, Tanskanen J, Spannagl M, Twardziok S, Mascher M, Springer NM, Li Q, Waugh R, Li C, Zhang G, Stein N, Mayer KFX, Gundlach H.

Mob DNA. 2017 Dec 20;8:22. doi: 10.1186/s13100-017-0102-3. eCollection 2017.

5.

The pseudogenes of barley.

Prade VM, Gundlach H, Twardziok S, Chapman B, Tan C, Langridge P, Schulman AH, Stein N, Waugh R, Zhang G, Platzer M, Li C, Spannagl M, Mayer KFX.

Plant J. 2018 Feb;93(3):502-514. doi: 10.1111/tpj.13794. Epub 2018 Jan 7.

PMID:
29205595
6.

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J.

Nature. 2017 Nov 23;551(7681):498-502. doi: 10.1038/nature24486. Epub 2017 Nov 15.

PMID:
29143815
7.

Light and Plastid Signals Regulate Different Sets of Genes in the Albino Mutant Pap7-1.

Grübler B, Merendino L, Twardziok SO, Mininno M, Allorent G, Chevalier F, Liebers M, Blanvillain R, Mayer KFX, Lerbs-Mache S, Ravanel S, Pfannschmidt T.

Plant Physiol. 2017 Nov;175(3):1203-1219. doi: 10.1104/pp.17.00982. Epub 2017 Sep 21.

8.

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.

Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A.

Science. 2017 Jul 7;357(6346):93-97. doi: 10.1126/science.aan0032.

PMID:
28684525
9.

A chromosome conformation capture ordered sequence of the barley genome.

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, 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 JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N.

Nature. 2017 Apr 26;544(7651):427-433. doi: 10.1038/nature22043.

PMID:
28447635
10.

Towards a whole-genome sequence for rye (Secale cereale L.).

Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KF, Schmid K, Schön CC, Scholz U.

Plant J. 2017 Mar;89(5):853-869. doi: 10.1111/tpj.13436. Epub 2017 Feb 8.

11.

Probiotic Treatment Decreases the Number of CD14-Expressing Cells in Porcine Milk Which Correlates with Several Intestinal Immune Parameters in the Piglets.

Scharek-Tedin L, Kreuzer-Redmer S, Twardziok SO, Siepert B, Klopfleisch R, Tedin K, Zentek J, Pieper R.

Front Immunol. 2015 Mar 10;6:108. doi: 10.3389/fimmu.2015.00108. eCollection 2015.

12.

Elevated dietary zinc oxide levels do not have a substantial effect on porcine reproductive and respiratory syndrome virus (PPRSV) vaccination and infection.

Chai W, Wang Z, Janczyk P, Twardziok S, Blohm U, Osterrieder N, Burwinkel M.

Virol J. 2014 Aug 8;11:140. doi: 10.1186/1743-422X-11-140.

13.

Effects of age and zinc supplementation on transport properties in the jejunum of piglets.

Gefeller EM, Martens H, Aschenbach JR, Klingspor S, Twardziok S, Wrede P, Pieper R, Lodemann U.

J Anim Physiol Anim Nutr (Berl). 2015 Jun;99(3):542-52. doi: 10.1111/jpn.12232. Epub 2014 Jul 21.

PMID:
25039419
14.

High-dose dietary zinc oxide mitigates infection with transmissible gastroenteritis virus in piglets.

Chai W, Zakrzewski SS, Günzel D, Pieper R, Wang Z, Twardziok S, Janczyk P, Osterrieder N, Burwinkel M.

BMC Vet Res. 2014 Mar 28;10:75. doi: 10.1186/1746-6148-10-75.

15.

The general composition of the faecal virome of pigs depends on age, but not on feeding with a probiotic bacterium.

Sachsenröder J, Twardziok SO, Scheuch M, Johne R.

PLoS One. 2014 Feb 19;9(2):e88888. doi: 10.1371/journal.pone.0088888. eCollection 2014.

16.

Cross-talk Between Host, Microbiome and Probiotics: A Systems Biology Approach for Analyzing the Effects of Probiotic Enterococcus faecium NCIMB 10415 in Piglets.

Twardziok SO, Pieper R, Aschenbach JR, Bednorz C, Brockmann GA, Fromm M, Klingspor S, Kreuzer S, Lodemann U, Martens H, Martin L, Richter JF, Scharek-Tedin L, Siepert BF, Starke IC, Tedin K, Vahjen W, Wieler LH, Zakrzewski SS, Zentek J, Wrede P.

Mol Inform. 2014 Mar;33(3):171-82. doi: 10.1002/minf.201300147. Epub 2014 Feb 12.

PMID:
27485687
17.

Dietary Enterococcus faecium NCIMB 10415 and zinc oxide stimulate immune reactions to trivalent influenza vaccination in pigs but do not affect virological response upon challenge infection.

Wang Z, Burwinkel M, Chai W, Lange E, Blohm U, Breithaupt A, Hoffmann B, Twardziok S, Rieger J, Janczyk P, Pieper R, Osterrieder N.

PLoS One. 2014 Jan 28;9(1):e87007. doi: 10.1371/journal.pone.0087007. eCollection 2014.

18.

Enterococcus faecium NCIMB 10415 supplementation affects intestinal immune-associated gene expression in post-weaning piglets.

Siepert B, Reinhardt N, Kreuzer S, Bondzio A, Twardziok S, Brockmann G, Nöckler K, Szabó I, Janczyk P, Pieper R, Tedin K.

Vet Immunol Immunopathol. 2014 Jan 15;157(1-2):65-77. doi: 10.1016/j.vetimm.2013.10.013. Epub 2013 Oct 28.

PMID:
24246154
19.

Porcine intestinal mast cells. Evaluation of different fixatives for histochemical staining techniques considering tissue shrinkage.

Rieger J, Twardziok S, Huenigen H, Hirschberg RM, Plendl J.

Eur J Histochem. 2013 Jul 30;57(3):e21. doi: 10.4081/ejh.2013.e21.

20.

Characterization of the effects of Enterococcus faecium on intestinal epithelial transport properties in piglets.

Klingspor S, Martens H, Caushi D, Twardziok S, Aschenbach JR, Lodemann U.

J Anim Sci. 2013 Apr;91(4):1707-18. doi: 10.2527/jas.2012-5648. Epub 2013 Jan 23.

PMID:
23345556
21.

Inhibitory influence of Enterococcus faecium on the propagation of swine influenza A virus in vitro.

Wang Z, Chai W, Burwinkel M, Twardziok S, Wrede P, Palissa C, Esch B, Schmidt MF.

PLoS One. 2013;8(1):e53043. doi: 10.1371/journal.pone.0053043. Epub 2013 Jan 7.

22.

Antiviral effects of a probiotic Enterococcus faecium strain against transmissible gastroenteritis coronavirus.

Chai W, Burwinkel M, Wang Z, Palissa C, Esch B, Twardziok S, Rieger J, Wrede P, Schmidt MF.

Arch Virol. 2013 Apr;158(4):799-807. doi: 10.1007/s00705-012-1543-0. Epub 2012 Nov 28.

PMID:
23188495
23.

Identification of an avian group A rotavirus containing a novel VP4 gene with a close relationship to those of mammalian rotaviruses.

Trojnar E, Sachsenröder J, Twardziok S, Reetz J, Otto PH, Johne R.

J Gen Virol. 2013 Jan;94(Pt 1):136-42. doi: 10.1099/vir.0.047381-0. Epub 2012 Oct 10.

PMID:
23052396
24.

Allelic variations in coding regions of the vitamin D receptor gene in dairy cows and potential susceptibility to periparturient hypocalcaemia.

Deiner C, Reiche M, Lassner D, Grienitz D, Twardziok S, Moesch A, Wenning P, Martens H.

J Dairy Res. 2012 Nov;79(4):423-8. doi: 10.1017/S0022029912000465. Epub 2012 Sep 11.

PMID:
22963675
25.

Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing.

Sachsenröder J, Twardziok S, Hammerl JA, Janczyk P, Wrede P, Hertwig S, Johne R.

PLoS One. 2012;7(4):e34631. doi: 10.1371/journal.pone.0034631. Epub 2012 Apr 13.

26.

Evidence for regulated interleukin-4 expression in chondrocyte-scaffolds under in vitro inflammatory conditions.

Rai MF, Graeve T, Twardziok S, Schmidt MF.

PLoS One. 2011;6(10):e25749. doi: 10.1371/journal.pone.0025749. Epub 2011 Oct 3.

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