Sunday, January 31, 2010

Next Generation Sequencing: Deep and Fast!

The Next Generation Sequencing field is fast moving. A simple NGS search in PubMed already yields 51 articles for 2010. At his rate there will be over 600 papers this year that use NGS, review NGS progress, or introduce new NGS analysis methods.

The references retrieved from the search are listed below.

1: Marguerat S, Bahler J. RNA-seq: from technology to biology. Cell Mol Life Sci. 2010 Feb;67(4):569-79. Epub 2009 Oct 27. Review. PubMed PMID: 19859660.

2: Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generationsequencing. Nat Methods. 2010 Feb;7(2):111-8. PubMed PMID: 20111037.

3: Jex AR, Hall RS, Littlewood DT, Gasser RB. An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Res. 2010 Feb;38(2):522-33. Epub 2009 Nov 5. PubMed PMID: 19892826; PubMed Central PMCID: PMC2811008.

4: Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Jan 28. [Epub ahead of print] PubMed PMID: 20110278.

5: Gottlieb B, Beitel LK, Alvarado C, Trifiro MA. Selection and mutation in the "new" genetics: an emerging hypothesis. Hum Genet. 2010 Jan 23. [Epub ahead of print] PubMed PMID: 20099069.

6: Monger WA, Alicai T, Ndunguru J, Kinyua ZM, Potts M, Reeder RH, Miano DW, Adams IP, Boonham N, Glover RH, Smith J. The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence. Arch Virol. 2010 Jan 22. [Epub ahead of print] PubMed PMID: 20094895.

7: Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010 Jan 22. [Epub ahead of print] PubMed PMID: 20098412.

8: Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J. The sequence and de novo assembly of the giant panda genome. Nature. 2010 Jan 21;463(7279):311-7. Epub 2009 Dec 13. PubMed PMID: 20010809.

9: Falgueras J, Lara AJ, Fernandez-Pozo N, Canton FR, Perez-Trabado G, Claros MG. SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads. BMC Bioinformatics. 2010 Jan 20;11(1):38. [Epub ahead of print] PubMed PMID: 20089148.

10: Beck AH, Weng Z, Witten DM, Zhu S, Foley JW, Lacroute P, Smith CL, Tibshirani R, van de Rijn M, Sidow A, West RB. 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One. 2010 Jan 19;5(1):e8768. PubMed PMID: 20098735; PubMed Central PMCID: PMC2808244. 11: Webb KM, Rosenthal BM. Deep resequencing of Trichinella spiralis reveals previously un-described single nucleotide polymorphisms and intra-isolate variation within the mitochondrial genome. Infect Genet Evol. 2010 Jan 18. [Epub ahead of print] PubMed PMID: 20083232.

12: Galvez S, Diaz D, Hernandez P, Esteban FJ, Caballero JA, Dorado G. Next-Generation Bioinformatics: Using Many-Core Processor Architecture to Develop a Web Service for Sequence Alignment. Bioinformatics. 2010 Jan 16. [Epub ahead of print] PubMed PMID: 20081221.

13: Gilchrist E, Haughn G. Reverse genetics techniques: engineering loss and gain of gene function in plants. Brief Funct Genomic Proteomic. 2010 Jan 16. [Epub ahead of print] PubMed PMID: 20081218.

14: Lavoie PM, Dube MP. Genetics of bronchopulmonary dysplasia in the age of genomics. Curr Opin Pediatr. 2010 Jan 16. [Epub ahead of print] PubMed PMID: 20087186.

15: Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics. 2010 Jan 15;11(1):38. [Epub ahead of print] PubMed PMID: 20078886.

16: Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik-Zainal S, Davies HR, Ordonez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen L, Jia M, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, Costa GL, Lee CC, Minna JD, Gazdar A, Birney E, Rhodes MD, McKernan KJ, Stratton MR, Futreal PA, Campbell PJ. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature. 2010 Jan 14;463(7278):184-90. Epub 2009 Dec 16. PubMed PMID: 20016488.

17: Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D. Rapid genomic characterization of the genus vitis. PLoS One. 2010 Jan 13;5(1):e8219. PubMed PMID: 20084295; PubMed Central PMCID: PMC2805708.

18: Santuari L, Pradervand S, Amiguet-Vercher AM, Thomas J, Dorcey E, Harshman K, Xenarios I, Juenger TE, Hardtke CS. Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biol. 2010 Jan 12;11(1):R4. [Epub ahead of print] PubMed PMID: 20067627.

19: Pool J, Hellmann I, Jensen J, Nielsen R. Population genetics of genome-scale sequence variation. Genome Res. 2010 Jan 12. [Epub ahead of print] PubMed PMID: 20067940.

20: Duncan EL, Brown MA. Mapping genes for osteoporosis-Old dogs and new tricks. Bone. 2010 Jan 11. [Epub ahead of print] PubMed PMID: 20060943.

21: Byrne SL, Durandeau K, Nagy I, Barth S. Identification of ABC transporters from Lolium perenne L. that are regulated by toxic levels of selenium. Planta. 2010 Jan 9. [Epub ahead of print] PubMed PMID: 20063009.

22: Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ. Deep sequencing identifies novel and conserved microRNAs in peanut (Arachis hypogaea L.). BMC Plant Biol. 2010 Jan 5;10(1):3. [Epub ahead of print] PubMed PMID: 20047695.

23: Medina M, Sachs JL. Symbiont genomics, our new tangled bank. Genomics. 2010 Jan 4. [Epub ahead of print] PubMed PMID: 20053372.

24: Hittinger CT, Johnston M, Tossberg JT, Rokas A. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc Natl Acad Sci U S A. 2010 Jan 4. [Epub ahead of print] PubMed PMID: 20080632.

25: Volpi L, Roversi G, Colombo EA, Leijsten N, Concolino D, Calabria A, Mencarelli MA, Fimiani M, Macciardi F, Pfundt R, Schoenmakers EF, Larizza L. Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene. Am J Hum Genet. 2010 Jan;86(1):72-6. Epub 2009 Dec 10. PubMed PMID: 20004881.

26: Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med. 2010;61:437-55. PubMed PMID: 20059347.

27: Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns
BR, Johnson WE. The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics. 2010 Jan 1;26(1):38-45. Epub 2009 Oct 27. PubMed PMID: 19861355.

28: Arner E, Hayashizaki Y, Daub CO. NGSView: an extensible open source editor for next-generation sequencing data. Bioinformatics. 2010 Jan 1;26(1):125-6. Epub 2009 Oct 24. PubMed PMID: 19855106; PubMed Central PMCID: PMC2796816.

29: Jex AR, Littlewood DT, Gasser RB. Toward next-generation sequencing of mitochondrial genomes--focus on parasitic worms of animals and biotechnological implications. Biotechnol Adv. 2010 Jan-Feb;28(1):151-9. Epub . Review. PubMed PMID: 19913084.

30: Jex AR, Gasser RB. Genetic richness and diversity in Cryptosporidium hominis
and C. parvum reveals major knowledge gaps and a need for the application of "next generation" technologies--research review. Biotechnol Adv. 2010 Jan-Feb;28(1):17-26. Epub . Review. PubMed PMID: 19699288.

31: Chou LS, Liu CS, Boese B, Zhang X, Mao R. DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: neurofibromatosis type 1 gene as a model. Clin Chem. 2010 Jan;56(1):62-72. Epub 2009 Nov 12. PubMed PMID: 19910506.

32: Nagalakshmi U, Waern K, Snyder M. RNA-Seq: a method for comprehensive transcriptome analysis. Curr Protoc Mol Biol. 2010 Jan;Chapter 4:Unit 4.11.1-13. PubMed PMID: 20069539.

33: Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. PubMed PMID: 20069536.

34: Roukos DH. Novel clinico-genome network modeling for revolutionizing genotype-phenotype-based personalized cancer care. Expert Rev Mol Diagn. 2010 Jan;10(1):33-48. PubMed PMID: 20014921.

35: Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, Barbazuk WB, Springer NM, Schnable PS. High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics. 2010 Jan;184(1):19-26. Epub 2009 Nov 2. PubMed PMID: 19884313.

36: Day IN. dbSNP in the detail and copy number complexities. Hum Mutat. 2010 Jan;31(1):2-4. PubMed PMID: 20024941.

37: Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010 Jan;4(1):17-27. Epub 2009 Aug 27. PubMed PMID: 19710709; PubMed Central PMCID: PMC2797552.

38: Aparicio SA, Huntsman DG. Does massively parallel DNA resequencing signify the end of histopathology as we know it? J Pathol. 2010 Jan;220(2):307-15. PubMed PMID: 19921711.

39: Bell DW. Our changing view of the genomic landscape of cancer. J Pathol. 2010 Jan;220(2):231-43. PubMed PMID: 19918804.

40: Nobuta K, McCormick K, Nakano M, Meyers BC. Bioinformatics analysis of small RNAs in plants using next generation sequencing technologies. Methods Mol Biol. 2010;592:89-106. PubMed PMID: 19802591.

41: Salmon A, Ainouche ML. Polyploidy and DNA methylation: new tools available. Mol Ecol. 2010 Jan;19(2):213-5. PubMed PMID: 20078770.

42: Gathering clouds and a sequencing storm: why cloud computing could broaden community access to next-generation sequencing. Nat Biotechnol. 2010 Jan;28(1):1. PubMed PMID: 20062015.

43: Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010 Jan;11(1):31-46. Epub 2009 Dec 8. Review. PubMed PMID: 19997069.

44: Northcott PA, Rutka JT, Taylor MD. Genomics of medulloblastoma: from Giemsa-banding to next-generation sequencing in 20 years. Neurosurg Focus. 2010 Jan;28(1):E6. PubMed PMID: 20043721.

45: Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010 Jan;38(Database issue):D123-30. Epub 2009 Dec 4. PubMed PMID: 19966272; PubMed Central PMCID: PMC2808990.

46: Shumway M, Cochrane G, Sugawara H. Archiving next generation sequencing data. Nucleic Acids Res. 2010 Jan;38(Database issue):D870-1. Epub 2009 Dec 3. PubMed PMID: 19965774; PubMed Central PMCID: PMC2808927.

47: Brooksbank C, Cameron G, Thornton J. The European Bioinformatics Institute's
data resources. Nucleic Acids Res. 2010 Jan;38(Database issue):D17-25. Epub 2009 Nov 24. PubMed PMID: 19934258; PubMed Central PMCID: PMC2808956.

48: Kim P, Yoon S, Kim N, Lee S, Ko M, Lee H, Kang H, Kim J, Lee S. ChimerDB 2.0--a knowledgebase for fusion genes updated. Nucleic Acids Res. 2010 Jan;38(Database issue):D81-5. Epub 2009 Nov 11. PubMed PMID: 19906715; PubMed Central PMCID: PMC2808913.

49: Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G. Improvements to services at the European Nucleotide Archive. Nucleic Acids Res. 2010 Jan;38(Database issue):D39-45. Epub 2009 Nov 11. PubMed PMID: 19906712; PubMed Central PMCID: PMC2808951.

50: Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T, Nakamura Y. DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res. 2010 Jan;38(Database issue):D33-8. Epub 2009 Oct 22. PubMed PMID: 19850725; PubMed Central PMCID:

51: Jing H. [Advances in approaches for the quantitative detection of microRNAs.]. Yi Chuan. 2010 Jan;32(1):31-40. Chinese. PubMed PMID: 20085883.

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