PUB - Publikationen an der Universität Bielefeld

Equivalent indels--ambiguous functional classes and redundancy in databases.
Assmus J, Kleffe J, Schmitt AO, Brockmann GA., PLoS ONE 8(5), 2013
PMID: 23658777

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

The variant call format and VCFtools.
, Bioinformatics 27(15), 2011
PMID: 21653522

Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B., Genome Res. 21(12), 2011
PMID: 21926179

An algebraic dynamic programming approach to the analysis of recombinant DNA sequences
Giegerich, 1999

AUTHOR UNKNOWN, 0

The Ensembl genome database project.
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M., Nucleic Acids Res. 30(1), 2002
PMID: 11752248

Microindel detection in short-read sequence data.
Krawitz P, Rodelsperger C, Jager M, Jostins L, Bauer S, Robinson PN., Bioinformatics 26(6), 2010
PMID: 20144947

Detecting and annotating genetic variations using the HugeSeq pipeline.
Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M., Nat. Biotechnol. 30(3), 2012
PMID: 22398614

AUTHOR UNKNOWN, 0

The diploid genome sequence of an individual human.
Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC., PLoS Biol. 5(10), 2007
PMID: 17803354

Uncertainty in homology inferences: assessing and improving genomic sequence alignment.
Lunter G, Rocco A, Mimouni N, Heger A, Caldeira A, Hein J., Genome Res. 18(2), 2007
PMID: 18073381

Haploid to diploid alignment for variation calling assessment.
Makinen V, Rahkola J., BMC Bioinformatics 14 Suppl 15(), 2013
PMID: 24564537

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.
Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM., Genome Res. 23(5), 2013
PMID: 23410887

CLEVER: clique-enumerating variant finder.
Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schonhuth A., Bioinformatics 28(22), 2012
PMID: 23060616

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.
Marschall T, Hajirasouliha I, Schonhuth A., Bioinformatics 29(24), 2013
PMID: 24072733

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

Chapter 6: Structural variation and medical genomics.
Raphael BJ., PLoS Comput. Biol. 8(12), 2012
PMID: 23300412

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SRF; WGS500 Consortium, Wilkie AOM, McVean G, Lunter G., Nat. Genet. 46(8), 2014
PMID: 25017105

dbSNP: the NCBI database of genetic variation.
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K., Nucleic Acids Res. 29(1), 2001
PMID: 11125122

Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting.
Teer JK, Johnston JJ, Anzick SL, Pineda M, Stone G; NISC Comparative Sequencing Program, Meltzer PS, Mullikin JC, Biesecker LG., BMC Genomics 14(), 2013
PMID: 23586822

A map of human genome variation from population-scale sequencing.
Y, Nature 467(7319), 2010
PMID: 20981092

Whole-genome sequence variation, population structure and demographic history of the Dutch population.
Genome of the Netherlands Consortium, Francioli LC, Menelaou A, Pulit SL, van Dijk F, Palamara PF, Elbers CC, Neerincx PB, Ye K, Guryev V, Kloosterman WP, Deelen P, Abdellaoui A, van Leeuwen EM, van Oven M, Vermaat M, Li M, Laros JF, Karssen LC, Kanterakis A, Amin N, Hottenga JJ, Lameijer EW, Kattenberg M, Dijkstra M, Byelas H, van Setten J, van Schaik BD, Bot J, Nijman IJ, Renkens I, Marschall T, Schonhuth A, Hehir-Kwa JY, Handsaker RE, Polak P, Sohail M, Vuzman D, Hormozdiari F, van Enckevort D, Mei H, Koval V, Moed MH, van der Velde KJ, Rivadeneira F, Estrada K, Medina-Gomez C, Isaacs A, McCarroll SA, Beekman M, de Craen AJ, Suchiman HE, Hofman A, Oostra B, Uitterlinden AG, Willemsen G, Study LC, Platteel M, Veldink JH, van den Berg LH, Pitts SJ, Potluri S, Sundar P, Cox DR, Sunyaev SR, den Dunnen JT, Stoneking M, de Knijff P, Kayser M, Li Q, Li Y, Du Y, Chen R, Cao H, Li N, Cao S, Wang J, Bovenberg JA, Pe'er I, Slagboom PE, van Duijn CM, Boomsma DI, van Ommen GJ, de Bakker PI, Swertz MA, Wijmenga C., Nat. Genet. 46(8), 2014
PMID: 24974849

Repetitive DNA and next-generation sequencing: computational challenges and solutions
Treangen, Nat. Rev. Genet. 13(), 2012

Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes.
Trubetskoy V, Rodriguez A, Dave U, Campbell N, Crawford EL, Cook EH, Sutcliffe JS, Foster I, Madduri R, Cox NJ, Davis LK., Bioinformatics 31(2), 2014
PMID: 25270638

Detecting structural variations in the human genome using next generation sequencing.
Xi R, Kim TM, Park PJ., Brief Funct Genomics 9(5-6), 2010
PMID: 21216738

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

Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome.
Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW., Cytogenet. Genome Res. 115(3-4), 2006
PMID: 17124402