{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T01:53:13Z","timestamp":1761961993944,"version":"build-2065373602"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,11,23]],"date-time":"2010-11-23T00:00:00Z","timestamp":1290470400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1471-2105-11-572","type":"journal-article","created":{"date-parts":[[2010,11,23]],"date-time":"2010-11-23T19:15:19Z","timestamp":1290539719000},"source":"Crossref","is-referenced-by-count":50,"title":["Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing"],"prefix":"10.1186","volume":"11","author":[{"given":"Cristian","family":"Coarfa","sequence":"first","affiliation":[]},{"given":"Fuli","family":"Yu","sequence":"additional","affiliation":[]},{"given":"Christopher A","family":"Miller","sequence":"additional","affiliation":[]},{"given":"Zuozhou","family":"Chen","sequence":"additional","affiliation":[]},{"given":"R Alan","family":"Harris","sequence":"additional","affiliation":[]},{"given":"Aleksandar","family":"Milosavljevic","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,11,23]]},"reference":[{"key":"4155_CR1","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1038\/nbt1010-1053","volume":"28","author":"A Milosavljevic","year":"2010","unstructured":"Milosavljevic A: Putting epigenome comparison into practice. Nat Biotechnol 2010, 28: 1053\u20131056. 10.1038\/nbt1010-1053","journal-title":"Nat Biotechnol"},{"key":"4155_CR2","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1038\/nature06008","volume":"448","author":"TS Mikkelsen","year":"2007","unstructured":"Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim T, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448: 553\u2013560. 10.1038\/nature06008","journal-title":"Nature"},{"key":"4155_CR3","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.1038\/nbt.1682","volume":"28","author":"RA Harris","year":"2010","unstructured":"Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung W, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, et al.: Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010, 28: 1097\u20131105. 10.1038\/nbt.1682","journal-title":"Nat Biotechnol"},{"key":"4155_CR4","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.ajhg.2010.01.021","volume":"86","author":"B Tycko","year":"2010","unstructured":"Tycko B: Mapping allele-specific DNA methylation: a new tool for maximizing information from GWAS. Am J Hum Genet 2010, 86: 109\u2013112. 10.1016\/j.ajhg.2010.01.021","journal-title":"Am J Hum Genet"},{"key":"4155_CR5","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1016\/j.ajhg.2010.01.014","volume":"86","author":"LC Schalkwyk","year":"2010","unstructured":"Schalkwyk LC, Meaburn EL, Smith R, Dempster EL, Jeffries AR, Davies MN, Plomin R, Mill J: Allelic skewing of DNA methylation is widespread across the genome. Am J Hum Genet 2010, 86: 196\u2013212. 10.1016\/j.ajhg.2010.01.014","journal-title":"Am J Hum Genet"},{"key":"4155_CR6","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1038\/nbt.1681","volume":"28","author":"C Bock","year":"2010","unstructured":"Bock C, Tomazou EM, Brinkman AB, M\u00fcller F, Simmer F, Gu H, J\u00e4ger N, Gnirke A, Stunnenberg HG, Meissner A: Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010, 28: 1106\u20131114. 10.1038\/nbt.1681","journal-title":"Nat Biotechnol"},{"key":"4155_CR7","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/nature08514","volume":"462","author":"R Lister","year":"2009","unstructured":"Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo Q, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462: 315\u2013322. 10.1038\/nature08514","journal-title":"Nature"},{"key":"4155_CR8","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981, 147: 195\u2013197. 10.1016\/0022-2836(81)90087-5","journal-title":"J Mol Biol"},{"key":"4155_CR9","first-page":"307","volume":"24","author":"WR Pearson","year":"1994","unstructured":"Pearson WR: Using the FASTA program to search protein and DNA sequence databases. Methods Mol Biol 1994, 24: 307\u2013331.","journal-title":"Methods Mol Biol"},{"key":"4155_CR10","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Sch\u00e4ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"key":"4155_CR11","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ: BLAT--the BLAST-like alignment tool. Genome Res 2002, 12: 656\u2013664.","journal-title":"Genome Res"},{"key":"4155_CR12","doi-asserted-by":"publisher","first-page":"1725","DOI":"10.1101\/gr.194201","volume":"11","author":"Z Ning","year":"2001","unstructured":"Ning Z, Cox AJ, Mullikin JC: SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11: 1725\u20131729. 10.1101\/gr.194201","journal-title":"Genome Res"},{"key":"4155_CR13","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1093\/bib\/6.1.6","volume":"6","author":"S Batzoglou","year":"2005","unstructured":"Batzoglou S: The many faces of sequence alignment. Brief Bioinform 2005, 6: 6\u201322. 10.1093\/bib\/6.1.6","journal-title":"Brief Bioinform"},{"key":"4155_CR14","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H Li","year":"2008","unstructured":"Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18: 1851\u20131858. 10.1101\/gr.078212.108","journal-title":"Genome Res"},{"key":"4155_CR15","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10: R25. 10.1186\/gb-2009-10-3-r25","journal-title":"Genome Biol"},{"key":"4155_CR16","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25: 1754\u20131760. 10.1093\/bioinformatics\/btp324","journal-title":"Bioinformatics"},{"key":"4155_CR17","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1093\/bib\/bbq015","volume":"11","author":"H Li","year":"2010","unstructured":"Li H, Homer N: A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 2010, 11: 473\u201383. 10.1093\/bib\/bbq015","journal-title":"Brief Bioinform"},{"key":"4155_CR18","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1016\/j.gde.2006.10.009","volume":"16","author":"DR Bentley","year":"2006","unstructured":"Bentley DR: Whole-genome re-sequencing. Curr Opin Genet Dev 2006, 16: 545\u2013552. 10.1016\/j.gde.2006.10.009","journal-title":"Curr Opin Genet Dev"},{"key":"4155_CR19","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","volume":"437","author":"M Margulies","year":"2005","unstructured":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437: 376\u2013380.","journal-title":"Nature"},{"key":"4155_CR20","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1038\/nmeth0810-576","volume":"7","author":"F Hach","year":"2010","unstructured":"Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC: mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat Methods 2010, 7: 576\u2013577. 10.1038\/nmeth0810-576","journal-title":"Nat Methods"},{"key":"4155_CR21","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/1471-2105-10-232","volume":"10","author":"Y Xi","year":"2009","unstructured":"Xi Y, Li W: BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 2009, 10: 232. 10.1186\/1471-2105-10-232","journal-title":"BMC Bioinformatics"},{"key":"4155_CR22","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/1471-2105-9-128","volume":"9","author":"AD Smith","year":"2008","unstructured":"Smith AD, Xuan Z, Zhang MQ: Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 2008, 9: 128. 10.1186\/1471-2105-9-128","journal-title":"BMC Bioinformatics"},{"key":"4155_CR23","doi-asserted-by":"publisher","first-page":"2841","DOI":"10.1093\/bioinformatics\/btp533","volume":"25","author":"AD Smith","year":"2009","unstructured":"Smith AD, Chung W, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ: Updates to the RMAP short-read mapping software. Bioinformatics 2009, 25: 2841\u20132842. 10.1093\/bioinformatics\/btp533","journal-title":"Bioinformatics"},{"key":"4155_CR24","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1093\/hmg\/ddp054","volume":"18","author":"M Zeschnigk","year":"2009","unstructured":"Zeschnigk M, Martin M, Betzl G, Kalbe A, Sirsch C, Buiting K, Gross S, Fritzilas E, Frey B, Rahmann S, Horsthemke B: Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete. Hum Mol Genet 2009, 18: 1439\u20131448. 10.1093\/hmg\/ddp054","journal-title":"Hum Mol Genet"},{"key":"4155_CR25","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1093\/bioinformatics\/btp706","volume":"26","author":"EY Harris","year":"2010","unstructured":"Harris EY, Ponts N, Levchuk A, Roch KL, Lonardi S: BRAT: bisulfite-treated reads analysis tool. Bioinformatics 2010, 26: 572\u2013573. 10.1093\/bioinformatics\/btp706","journal-title":"Bioinformatics"},{"key":"4155_CR26","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1101\/gr.1963804","volume":"14","author":"KJ Kalafus","year":"2004","unstructured":"Kalafus KJ, Jackson AR, Milosavljevic A: Pash: efficient genome-scale sequence anchoring by Positional Hashing. Genome Res 2004, 14: 672\u2013678. 10.1101\/gr.1963804","journal-title":"Genome Res"},{"key":"4155_CR27","first-page":"102","volume-title":"Pac Symp Biocomput","author":"C Coarfa","year":"2008","unstructured":"Coarfa C, Milosavljevic A: Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pac Symp Biocomput 2008, 102\u2013113."},{"key":"4155_CR28","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1093\/bioinformatics\/bth037","volume":"20","author":"KP Choi","year":"2004","unstructured":"Choi KP, Zeng F, Zhang L: Good spaced seeds for homology search. Bioinformatics 2004, 20: 1053\u20131059. 10.1093\/bioinformatics\/bth037","journal-title":"Bioinformatics"},{"key":"4155_CR29","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26: 589\u2013595. 10.1093\/bioinformatics\/btp698","journal-title":"Bioinformatics"},{"key":"4155_CR30","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1101\/gr.8.3.175","volume":"8","author":"B Ewing","year":"1998","unstructured":"Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8: 175\u2013185.","journal-title":"Genome Res"},{"key":"4155_CR31","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"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: 2078\u20132079. 10.1093\/bioinformatics\/btp352","journal-title":"Bioinformatics"},{"key":"4155_CR32","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1093\/nar\/29.1.308","volume":"29","author":"ST Sherry","year":"2001","unstructured":"Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29: 308\u2013311. 10.1093\/nar\/29.1.308","journal-title":"Nucleic Acids Res"},{"key":"4155_CR33","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","volume":"5","author":"AB Olshen","year":"2004","unstructured":"Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5: 557\u2013572. 10.1093\/biostatistics\/kxh008","journal-title":"Biostatistics"},{"key":"4155_CR34","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1038\/nature08516","volume":"464","author":"DF Conrad","year":"2010","unstructured":"Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AWC, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME: Origins and functional impact of copy number variation in the human genome. Nature 2010, 464: 704\u2013712. 10.1038\/nature08516","journal-title":"Nature"},{"key":"4155_CR35","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1038\/ng1416","volume":"36","author":"AJ Iafrate","year":"2004","unstructured":"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: 949\u2013951. 10.1038\/ng1416","journal-title":"Nat Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-572.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-572\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-572.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T13:56:32Z","timestamp":1548165392000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-572"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,11,23]]},"references-count":35,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["4155"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-572","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2010,11,23]]},"article-number":"572"}}