PUB - Publikationen an der Universität Bielefeld

Application of second-generation sequencing to cancer genomics.
Robison K., Brief. Bioinformatics 11(5), 2010
PMID: 20427421

A comprehensive catalogue of somatic mutations from a human cancer genome.
Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordonez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, Mudie LJ, Ning Z, Royce T, Schulz-Trieglaff OB, Spiridou A, Stebbings LA, Szajkowski L, Teague J, Williamson D, Chin L, Ross MT, Campbell PJ, Bentley DR, Futreal PA, Stratton MR., Nature 463(7278), 2009
PMID: 20016485

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes.
Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, Davies H, Edkins S, Hardy C, Latimer C, Teague J, Andrews J, Barthorpe S, Beare D, Buck G, Campbell PJ, Forbes S, Jia M, Jones D, Knott H, Kok CY, Lau KW, Leroy C, Lin ML, McBride DJ, Maddison M, Maguire S, McLay K, Menzies A, Mironenko T, Mulderrig L, Mudie L, O'Meara S, Pleasance E, Rajasingham A, Shepherd R, Smith R, Stebbings L, Stephens P, Tang G, Tarpey PS, Turrell K, Dykema KJ, Khoo SK, Petillo D, Wondergem B, Anema J, Kahnoski RJ, Teh BT, Stratton MR, Futreal PA., Nature 463(7279), 2010
PMID: 20054297

Personal genome sequencing: current approaches and challenges.
Snyder M, Du J, Gerstein M., Genes Dev. 24(5), 2010
PMID: 20194435

Challenges of sequencing human genomes.
Koboldt DC, Ding L, Mardis ER, Wilson RK., Brief. Bioinformatics 11(5), 2010
PMID: 20519329

End-sequence profiling: sequence-based analysis of aberrant genomes.
Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, Tao Q, Kowbel D, Huang G, Lapuk A, Kuo WL, Magrane G, De Jong P, Gray JW, Collins C., Proc. Natl. Acad. Sci. U.S.A. 100(13), 2003
PMID: 12788976

Fine-scale structural variation of the human genome.
Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE., Nat. Genet. 37(7), 2005
PMID: 15895083

Computational methods for discovering structural variation with next-generation sequencing.
Medvedev P, Stanciu M, Brudno M., Nat. Methods 6(11 Suppl), 2009
PMID: 19844226

Genome variation discovery with high-throughput sequencing data.
Dalca AV, Brudno M., Brief. Bioinformatics 11(1), 2010
PMID: 20053733

Genome structural variation discovery and genotyping.
Alkan C, Coe BP, Eichler EE., Nat. Rev. Genet. 12(5), 2011
PMID: 21358748

De novo assembly of short sequence reads.
Paszkiewicz K, Studholme DJ., Brief. Bioinformatics 11(5), 2010
PMID: 20724458

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z., Bioinformatics 25(21), 2009
PMID: 19561018

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, Pohl C, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Miner T, Fulton L, Magrini V, Wylie T, Glasscock J, Conyers J, Sander N, Shi X, Osborne JR, Minx P, Gordon D, Chinwalla A, Zhao Y, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson M, Baty J, Ivanovich J, Heath S, Shannon WD, Nagarajan R, Walter MJ, Link DC, Graubert TA, DiPersio JF, Wilson RK., Nature 456(7218), 2008
PMID: 18987736

Recurring mutations found by sequencing an acute myeloid leukemia genome.
Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ., N. Engl. J. Med. 361(11), 2009
PMID: 19657110

Genome remodelling in a basal-like breast cancer metastasis and xenograft.
Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM Jr, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER., Nature 464(7291), 2010
PMID: 20393555

Advances in understanding cancer genomes through second-generation sequencing.
Meyerson M, Gabriel S, Getz G., Nat. Rev. Genet. 11(10), 2010
PMID: 20847746

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER., Nat. Methods 6(9), 2009
PMID: 19668202

A geometric approach for classification and comparison of structural variants.
Sindi S, Helman E, Bashir A, Raphael BJ., Bioinformatics 25(12), 2009
PMID: 19477992

Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes
AUTHOR UNKNOWN, 2011

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.
Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM, Buetow KH., Bioinformatics 27(6), 2011
PMID: 21278191

vipR: variant identification in pooled DNA using R.
Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Muller-Myhsok B., Bioinformatics 27(13), 2011
PMID: 21685105

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors.
Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes AP, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA., Genome Biol. 11(8), 2010
PMID: 20696054

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC., Bioinformatics 26(12), 2010
PMID: 20529927

Mapping short DNA sequencing reads and calling variants using mapping quality scores.
Li H, Ruan J, Durbin R., Genome Res. 18(11), 2008
PMID: 18714091

A unified approach for reconstructing ancient gene clusters.
Stoye J, Wittler R., IEEE/ACM Trans Comput Biol Bioinform 6(3), 2009
PMID: 19644167

Minimal conflicting sets for the consecutive ones property in ancestral genome reconstruction.
Chauve C, Hausd UU, Stephen T, You VP., J. Comput. Biol. 17(9), 2010
PMID: 20874402

AUTHOR UNKNOWN, 1978

Loss of constitutional heterozygosity in human cancer.
Lasko D, Cavenee W, Nordenskjold M., Annu. Rev. Genet. 25(), 1991
PMID: 1687498

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions.
Lee S, Hormozdiari F, Alkan C, Brudno M., Nat. Methods 6(7), 2009
PMID: 19483690

MoGUL: Detecting Common Insertions and Deletions in a Population
AUTHOR UNKNOWN, 2010

Statistical aspects of discerning indel-type structural variation via DNA sequence alignment.
Wendl MC, Wilson RK., BMC Genomics 10(), 2009
PMID: 19656394

Paired-end mapping reveals extensive structural variation in the human genome.
Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M., Science 318(5849), 2007
PMID: 17901297

The European Genome-Phenome Archive
AUTHOR UNKNOWN, 0