Teer JK, Mullikin JC: Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet. 2010, 19 (R2): R145-151. 10.1093/hmg/ddq333.
Article
PubMed Central
CAS
PubMed
Google Scholar
Biesecker LG, Shianna KV, Mullikin JC: Exome sequencing: the expert view. Genome Biol. 2011, 12 (9): 128-10.1186/gb-2011-12-9-128.
Article
PubMed Central
PubMed
Google Scholar
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447 (7146): 799-816. 10.1038/nature05874.
Article
CAS
PubMed
Google Scholar
Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R: An integrated encyclopedia of DNA elements in the human genome. Nature. 2012, 489 (7414): 57-74. 10.1038/nature11247.
Article
CAS
Google Scholar
Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ: Direct selection of human genomic loci by microarray hybridization. Nat Methods. 2007, 4 (11): 903-905. 10.1038/nmeth1111.
Article
CAS
PubMed
Google Scholar
Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME: Microarray-based genomic selection for high-throughput resequencing. Nat Methods. 2007, 4 (11): 907-909. 10.1038/nmeth1109.
Article
CAS
PubMed
Google Scholar
Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C: Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009, 27 (2): 182-189. 10.1038/nbt.1523.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu YQ, Newsham I, Richmond TA: Whole exome capture in solution with 3Gbp of data. Genome Biol. 2010, 11 (6): R62-10.1186/gb-2010-11-6-r62.
Article
PubMed Central
PubMed
Google Scholar
Ibrahim SF, van den Engh G: High-speed chromosome sorting. Chromosome Res. 2004, 12 (1): 5-14.
Article
CAS
PubMed
Google Scholar
Dolezel J, Vrana J, Safar J, Bartos J, Kubalakova M, Simkova H: Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics. 2012, 12 (3): 397-416. 10.1007/s10142-012-0293-0.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD: Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biol. 2009, 10 (10): R112-10.1186/gb-2009-10-10-r112.
Article
PubMed Central
PubMed
Google Scholar
Mayer KF, Taudien S, Martis M, Simkova H, Suchankova P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B: Gene content and virtual gene order of barley chromosome 1H. Plant Physiol. 2009, 151 (2): 496-505. 10.1104/pp.109.142612.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mayer KF, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H: Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell. 2011, 23 (4): 1249-1263. 10.1105/tpc.110.082537.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wicker T, Mayer KF, Gundlach H, Martis M, Steuernagel B, Scholz U, Simkova H, Kubalakova M, Choulet F, Taudien S: Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell. 2011, 23 (5): 1706-1718. 10.1105/tpc.111.086629.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vitulo N, Albiero A, Forcato C, Campagna D, Dal Pero F, Bagnaresi P, Colaiacovo M, Faccioli P, Lamontanara A, Simkova H: First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One. 2011, 6 (10): e26421-10.1371/journal.pone.0026421.
Article
PubMed Central
CAS
PubMed
Google Scholar
Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EY, Stiller J, Smits L, Imelfort M, Manoli S: Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J. 2011, 9 (7): 768-775. 10.1111/j.1467-7652.2010.00587.x.
Article
CAS
PubMed
Google Scholar
Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubalakova M, Simkova H: Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet. 2012, 124 (3): 423-432. 10.1007/s00122-011-1717-2.
Article
CAS
PubMed
Google Scholar
Hernandez P, Martis M, Dorado G, Pfeifer M, Galvez S, Schaaf S, Jouve N, Simkova H, Valarik M, Dolezel J: Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J. 2012, 69 (3): 377-386. 10.1111/j.1365-313X.2011.04808.x.
Article
CAS
PubMed
Google Scholar
Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, Schulz MH, Erdogan F, Li N, Kijas Z, Arkesteijn G: Mapping translocation breakpoints by next-generation sequencing. Genome Res. 2008, 18 (7): 1143-1149. 10.1101/gr.076166.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yang H, Chen X, Wong WH: Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci USA. 2011, 108 (1): 12-17. 10.1073/pnas.1016725108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ: The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009, 19 (7): 1316-1323. 10.1101/gr.080531.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ, Margulies EH, Green ED: Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res. 2010, 20 (10): 1420-1431. 10.1101/gr.106716.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP: BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009, 6 (9): 677-681. 10.1038/nmeth.1363.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009, 25 (21): 2865-2871. 10.1093/bioinformatics/btp394.
Article
PubMed Central
CAS
PubMed
Google Scholar
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C: Detection of large-scale variation in the human genome. Nat Genet. 2004, 36 (9): 949-951. 10.1038/ng1416.
Article
CAS
PubMed
Google Scholar
Ng BL, Carter NP: Laser excitation power and the flow cytometric resolution of complex karyotypes. Cytometry A. 2010, 77 (6): 585-588.
Article
PubMed Central
PubMed
Google Scholar
Stanyon R, Stone G: Phylogenomic analysis by chromosome sorting and painting. Methods Mol Biol. 2008, 422: 13-29. 10.1007/978-1-59745-581-7_2.
Article
CAS
PubMed
Google Scholar
Telenius H, Pelmear AH, Tunnacliffe A, Carter NP, Behmel A, Ferguson-Smith MA, Nordenskjold M, Pfragner R, Ponder BA: Cytogenetic analysis by chromosome painting using DOP-PCR amplified flow-sorted chromosomes. Genes Chromosom Cancer. 1992, 4 (3): 257-263. 10.1002/gcc.2870040311.
Article
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.
Article
PubMed Central
PubMed
Google Scholar
Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26 (6): 841-842. 10.1093/bioinformatics/btq033.
Article
PubMed Central
CAS
PubMed
Google Scholar