PUB - Publikationen an der Universität Bielefeld

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711

e!DAL--a framework to store, share and publish research data.
Arend D, Lange M, Chen J, Colmsee C, Flemming S, Hecht D, Scholz U., BMC Bioinformatics 15(), 2014
PMID: 24958009

A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms.
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 PE, Muehlbauer GJ, Scholz U, Korol A, Mayer KF, Waugh R, Langridge P, Graner A, Stein N., Plant Physiol. 164(1), 2013
PMID: 24243933

Plantagora: modeling whole genome sequencing and assembly of plant genomes.
Barthelson R, McFarlin AJ, Rounsley SD, Young S., PLoS ONE 6(12), 2011
PMID: 22174807

A rapid alkaline extraction procedure for screening recombinant plasmid DNA.
Birnboim HC, Doly J., Nucleic Acids Res. 7(6), 1979
PMID: 388356

Scaffolding pre-assembled contigs using SSPACE.
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W., Bioinformatics 27(4), 2010
PMID: 21149342

A physical map of the short arm of wheat chromosome 1A.
Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Philippe R, Spielmeyer W, Simkova H, Safar J, Cattonaro F, Scalabrin S, Magni F, Vautrin S, Berges H; International Wheat Genome Sequencing Consortium, Paux E, Fahima T, Dolezel J, Korol A, Feuillet C, Keller B., PLoS ONE 8(11), 2013
PMID: 24278269

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J., Nat. Biotechnol. 31(12), 2013
PMID: 24185095

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.
Chapman JA, Mascher M, Buluc A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS., Genome Biol. 16(), 2015
PMID: 25637298

Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces.
Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier MC, Magdelenat G, Gonthier C, Couloux A, Budak H, Breen J, Pumphrey M, Liu S, Kong X, Jia J, Gut M, Brunel D, Anderson JA, Gill BS, Appels R, Keller B, Feuillet C., Plant Cell 22(6), 2010
PMID: 20581307

Structural and functional partitioning of bread wheat chromosome 3B.
Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C., Science 345(6194), 2014
PMID: 25035497

BARLEX - the Barley Draft Genome Explorer.
Colmsee C, Beier S, Himmelbach A, Schmutzer T, Stein N, Scholz U, Mascher M., Mol Plant 8(6), 2015
PMID: 25804976

Extensive error in the number of genes inferred from draft genome assemblies.
Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW., PLoS Comput. Biol. 10(12), 2014
PMID: 25474019

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.
Dohm JC, Lottaz C, Borodina T, Himmelbauer H., Nucleic Acids Res. 36(16), 2008
PMID: 18660515

Real-time DNA sequencing from single polymerase molecules.
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S., Science 323(5910), 2008
PMID: 19023044

Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology.
English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA., PLoS ONE 7(11), 2012
PMID: 23185243

Presidential address. Transposable elements, epigenetics, and genome evolution.
Fedoroff NV., Science 338(6108), 2012
PMID: 23145453

Integrating cereal genomics to support innovation in the Triticeae.
Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R., Funct. Integr. Genomics 12(4), 2012
PMID: 23161406

Transposons play an important role in the evolution and diversification of centromeres among closely related species.
Gao D, Jiang N, Wing RA, Jiang J, Jackson SA., Front Plant Sci 6(), 2015
PMID: 25904926

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.
Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz MC, McCombie WR., Genome Res. 25(11), 2015
PMID: 26447147

Against a whole-genome shotgun.
Green P., Genome Res. 7(5), 1997
PMID: 9149937

Analyses of pig genomes provide insight into porcine demography and evolution.
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshoj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB., Nature 491(7424), 2012
PMID: 23151582

QUAST: quality assessment tool for genome assemblies.
Gurevich A, Saveliev V, Vyahhi N, Tesler G., Bioinformatics 29(8), 2013
PMID: 23422339

Plant sequence capture optimised for Illumina sequencing
AUTHOR UNKNOWN, 2014

The zebrafish reference genome sequence and its relationship to the human genome.
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assuncao JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliot D, Eliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Mortimer B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Urun Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberlander M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nusslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, Stemple DL., Nature 496(7446), 2013
PMID: 23594743

A physical, genetic and functional sequence assembly of the barley genome.
International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, Wise RP, Stein N, Mayer KF, Waugh R, Langridge P, Close TJ, Wise RP, Graner A, Matsumoto T, Sato K, Schulman A, Muehlbauer GJ, Stein N, Ariyadasa R, Schulte D, Poursarebani N, Zhou R, Steuernagel B, Mascher M, Scholz U, Shi B, Langridge P, Madishetty K, Svensson JT, Bhat P, Moscou M, Resnik J, Close TJ, Muehlbauer GJ, Hedley P, Liu H, Morris J, Waugh R, Frenkel Z, Korol A, Berges H, Graner A, Stein N, Steuernagel B, Scholz U, Taudien S, Felder M, Groth M, Platzer M, Stein N, Steuernagel B, Scholz U, Himmelbach A, Taudien S, Felder M, Platzer M, Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Ciardo G, Ma Y, Wanamaker S, Close TJ, Stein N, Cattonaro F, Vendramin V, Scalabrin S, Radovic S, Wing R, Schulte D, Steuernagel B, Morgante M, Stein N, Waugh R, Nussbaumer T, Gundlach H, Martis M, Ariyadasa R, Poursarebani N, Steuernagel B, Scholz U, Wise RP, Poland J, Stein N, Mayer KF, Spannagl M, Pfeifer M, Gundlach H, Mayer KF, Gundlach H, Moisy C, Tanskanen J, Scalabrin S, Zuccolo A, Vendramin V, Morgante M, Schulman A, Pfeifer M, Spannagl M, Hedley P, Morris J, Russell J, Druka A, Marshall D, Bayer M, Swarbreck D, Sampath D, Ayling S, Febrer M, Caccamo M, Matsumoto T, Tanaka T, Sato K, Wise RP, Close TJ, Wannamaker S, Muehlbauer GJ, Stein N, Waugh R, Steuernagel B, Schmutzer T, Mascher M, Scholz U, Taudien S, Platzer M, Sato K, Marshall D, Bayer M, Waugh R, Stein N., Nature 491(7426), 2012
PMID: 23075845

A physical, genetic and functional sequence assembly of the barley genome.
International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, Wise RP, Stein N, Mayer KF, Waugh R, Langridge P, Close TJ, Wise RP, Graner A, Matsumoto T, Sato K, Schulman A, Muehlbauer GJ, Stein N, Ariyadasa R, Schulte D, Poursarebani N, Zhou R, Steuernagel B, Mascher M, Scholz U, Shi B, Langridge P, Madishetty K, Svensson JT, Bhat P, Moscou M, Resnik J, Close TJ, Muehlbauer GJ, Hedley P, Liu H, Morris J, Waugh R, Frenkel Z, Korol A, Berges H, Graner A, Stein N, Steuernagel B, Scholz U, Taudien S, Felder M, Groth M, Platzer M, Stein N, Steuernagel B, Scholz U, Himmelbach A, Taudien S, Felder M, Platzer M, Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Ciardo G, Ma Y, Wanamaker S, Close TJ, Stein N, Cattonaro F, Vendramin V, Scalabrin S, Radovic S, Wing R, Schulte D, Steuernagel B, Morgante M, Stein N, Waugh R, Nussbaumer T, Gundlach H, Martis M, Ariyadasa R, Poursarebani N, Steuernagel B, Scholz U, Wise RP, Poland J, Stein N, Mayer KF, Spannagl M, Pfeifer M, Gundlach H, Mayer KF, Gundlach H, Moisy C, Tanskanen J, Scalabrin S, Zuccolo A, Vendramin V, Morgante M, Schulman A, Pfeifer M, Spannagl M, Hedley P, Morris J, Russell J, Druka A, Marshall D, Bayer M, Swarbreck D, Sampath D, Ayling S, Febrer M, Caccamo M, Matsumoto T, Tanaka T, Sato K, Wise RP, Close TJ, Wannamaker S, Muehlbauer GJ, Stein N, Waugh R, Steuernagel B, Schmutzer T, Mascher M, Scholz U, Taudien S, Platzer M, Sato K, Marshall D, Bayer M, Waugh R, Stein N., Nature 491(7426), 2012
PMID: 23075845

Finishing the euchromatic sequence of the human genome.
International Human Genome Sequencing Consortium., Nature 431(7011), 2004
PMID: 15496913

The map-based sequence of the rice genome.
International Rice Genome Sequencing Project., Nature 436(7052), 2005
PMID: 16100779

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.
International Wheat Genome Sequencing Consortium (IWGSC), Mayer KF, Rogers J, Dolezel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubalakova M, Cihalikova J, Dubska Z, Vrana J, Sperkova R, Simkova H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu J, Ogihara Y, Handa H, Maclachlan PR, Sharpe A, Klassen D, Edwards D, Batley J, Olsen OA, Sandve SR, Lien S, Steuernagel B, Wulff B, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Pfeifer M, Spannagl M, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S., Science 345(6194), 2014
PMID: 25035500

High-throughput genome scaffolding from in vivo DNA interaction frequency.
Kaplan N, Dekker J., Nat. Biotechnol. 31(12), 2013
PMID: 24270850

Assembly of the working draft of the human genome with GigAssembler.
Kent WJ, Haussler D., Genome Res. 11(9), 2001
PMID: 11544197

Long-read, whole-genome shotgun sequence data for five model organisms.
Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM., Sci Data 1(), 2014
PMID: 25977796

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform.
Kircher M, Sawyer S, Meyer M., Nucleic Acids Res. 40(1), 2011
PMID: 22021376

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.
Koren S, Phillippy AM., Curr. Opin. Microbiol. 23(), 2014
PMID: 25461581

Versatile and open software for comparing large genomes.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL., Genome Biol. 5(2), 2004
PMID: 14759262

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries.
Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M., Bioinformatics 30(4), 2013
PMID: 24297520

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.
Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, Brockman W, Daza R, Erlich RL, Giannoukos G, Green L, Hollinger A, Hoover CA, Jaffe DB, Juhn F, McCarthy D, Perrin D, Ponchner K, Powers TL, Rizzolo K, Robbins D, Ryan E, Russ C, Sparrow T, Stalker J, Steelman S, Weiand M, Zimmer A, Henn MR, Nusbaum C, Nicol R., Genome Biol. 11(2), 2010
PMID: 20137071

Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 25(14), 2009
PMID: 19451168

The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.
Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G, Percy RG, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, Liu X, Zhang X, Liu W, Wei H, Wei S, Huang G, Zhang X, Zhu S, Zhang H, Sun F, Wang X, Liang J, Wang J, He Q, Huang L, Wang J, Cui J, Song G, Wang K, Xu X, Yu JZ, Zhu Y, Yu S., Nat. Biotechnol. 33(5), 2015
PMID: 25893780

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A.
Lucas SJ, Akpınar BA, Kantar M, Weinstein Z, Aydınoglu F, Safar J, Simkova H, Frenkel Z, Korol A, Magni F, Cattonaro F, Vautrin S, Bellec A, Berges H, Dolezel J, Budak H., PLoS ONE 8(4), 2013
PMID: 23613713

High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis.
Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J., Genomics 82(3), 2003
PMID: 12906862

Transposable elements contribute to activation of maize genes in response to abiotic stress.
Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM., PLoS Genet. 11(1), 2015
PMID: 25569788

Reticulate evolution of the rye genome.
Martis MM, Zhou R, Haseneyer G, Schmutzer T, Vrana J, Kubalakova M, Konig S, Kugler KG, Scholz U, Hackauf B, Korzun V, Schon CC, Dolezel J, Bauer E, Mayer KF, Stein N., Plant Cell 25(10), 2013
PMID: 24104565

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).
Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Munoz-Amatriain M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KF, Scholz U, Poland JA, Stein N, Waugh R., Plant J. 76(4), 2013
PMID: 23998490

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.
Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N., Plant J. 76(3), 2013
PMID: 23889683

Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries.
Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, Fujii N, Hori K, Itoh T, Sato K., Plant Physiol. 156(1), 2011
PMID: 21415278

Unlocking the barley genome by chromosomal and comparative genomics.
Mayer KF, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubalakova M, Suchankova 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, Dolezel J, Waugh R, Stein N., Plant Cell 23(4), 2011
PMID: 21467582

Illumina sequencing library preparation for highly multiplexed target capture and sequencing.
Meyer M, Kircher M., Cold Spring Harb Protoc 2010(6), 2010
PMID: 20516186

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems.
Minoche AE, Dohm JC, Himmelbauer H., Genome Biol. 12(11), 2011
PMID: 22067484

Sequence-based physical mapping of complex genomes by whole genome profiling.
van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, Janssen A, Volpin H, Stormo KE, Bogden R, van Eijk MJ, Prins M., Genome Res. 21(4), 2011
PMID: 21324881

A physical map of the 1-gigabase bread wheat chromosome 3B.
Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Berges H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C., Science 322(5898), 2008
PMID: 18832645

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat.
Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Simkova H, Safar J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KF, Korol A, Berges H, Dolezel J, Feuillet C., Genome Biol. 14(6), 2013
PMID: 23800011

Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.
Poursarebani N, Nussbaumer T, Simkova H, Safar J, Witsenboer H, van Oeveren J, Dolezel J, Mayer KF, Stein N, Schnurbusch T., Plant J. 79(2), 2014
PMID: 24813060

BEDTools: a flexible suite of utilities for comparing genomic features.
Quinlan AR, Hall IM., Bioinformatics 26(6), 2010
PMID: 20110278

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution.
Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Simkova H, Magni F, Cattonaro F, Vautrin S, Berges H, Wicker T, Keller B, Leroy P, Philippe R, Paux E, Dolezel J, Feuillet C, Korol A, Fahima T., Genome Biol. 14(12), 2013
PMID: 24359668

Unlocking short read sequencing for metagenomics.
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW., PLoS ONE 5(7), 2010
PMID: 20676378

De novo sequencing of hazelnut bacterial artificial chromosomes (BACs) using multiplex Illumina sequencing and targeted marker development for eastern filbert blight resistance
AUTHOR UNKNOWN, 2013

Kmasker--a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare.
Schmutzer T, Ma L, Pousarebani N, Bull F, Stein N, Houben A, Scholz U., Cytogenet. Genome Res. 142(1), 2013
PMID: 24335088

The B73 maize genome: complexity, diversity, and dynamics.
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