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Items: 1 to 20 of 67

1.

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB.

Neurol Genet. 2017 Jul 11;3(4):e164. doi: 10.1212/NXG.0000000000000164. eCollection 2017 Aug.

2.

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases.

Greer SU, Nadauld LD, Lau BT, Chen J, Wood-Bouwens C, Ford JM, Kuo CJ, Ji HP.

Genome Med. 2017 Jun 19;9(1):57. doi: 10.1186/s13073-017-0447-8.

3.

PGBD5 promotes site-specific oncogenic mutations in human tumors.

Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A.

Nat Genet. 2017 Jul;49(7):1005-1014. doi: 10.1038/ng.3866. Epub 2017 May 15.

PMID:
28504702
4.

NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.

Lee S, Lee S, Ouellette S, Park WY, Lee EA, Park PJ.

Nucleic Acids Res. 2017 Mar 23. doi: 10.1093/nar/gkx193. [Epub ahead of print]

5.

Pysim-sv: a package for simulating structural variation data with GC-biases.

Xia Y, Liu Y, Deng M, Xi R.

BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):53. doi: 10.1186/s12859-017-1464-8.

6.

The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers.

Alver BH, Kim KH, Lu P, Wang X, Manchester HE, Wang W, Haswell JR, Park PJ, Roberts CW.

Nat Commun. 2017 Mar 6;8:14648. doi: 10.1038/ncomms14648.

7.

Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors.

Schütte M, Risch T, Abdavi-Azar N, Boehnke K, Schumacher D, Keil M, Yildiriman R, Jandrasits C, Borodina T, Amstislavskiy V, Worth CL, Schweiger C, Liebs S, Lange M, Warnatz HJ, Butcher LM, Barrett JE, Sultan M, Wierling C, Golob-Schwarzl N, Lax S, Uranitsch S, Becker M, Welte Y, Regan JL, Silvestrov M, Kehler I, Fusi A, Kessler T, Herwig R, Landegren U, Wienke D, Nilsson M, Velasco JA, Garin-Chesa P, Reinhard C, Beck S, Schäfer R, Regenbrecht CR, Henderson D, Lange B, Haybaeck J, Keilholz U, Hoffmann J, Lehrach H, Yaspo ML.

Nat Commun. 2017 Feb 10;8:14262. doi: 10.1038/ncomms14262.

8.

MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples.

Huang AY, Zhang Z, Ye AY, Dou Y, Yan L, Yang X, Zhang Y, Wei L.

Nucleic Acids Res. 2017 Jun 2;45(10):e76. doi: 10.1093/nar/gkx024.

9.

Identifying the clonal origin of synchronous multifocal tumors in the hepatobiliary and pancreatic system using multi-omic platforms.

Jiang W, Ding Y, Shen Y, Fan L, Zhou L, Li Z, Zheng Y, Zhao P, Liu L, Tong Z, Fang W, Wang W.

Oncotarget. 2017 Jan 17;8(3):5016-5025. doi: 10.18632/oncotarget.14018.

10.

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response.

Biswas R, Gao S, Cultraro CM, Maity TK, Venugopalan A, Abdullaev Z, Shaytan AK, Carter CA, Thomas A, Rajan A, Song Y, Pitts S, Chen K, Bass S, Boland J, Hanada KI, Chen J, Meltzer PS, Panchenko AR, Yang JC, Pack S, Giaccone G, Schrump DS, Khan J, Guha U.

Cold Spring Harb Mol Case Stud. 2016 Nov;2(6):a001263.

11.

Low-, high-coverage, and two-stage DNA sequencing in the design of the genetic association study.

Xu C, Wu K, Zhang JG, Shen H, Deng HW.

Genet Epidemiol. 2017 Apr;41(3):187-197. doi: 10.1002/gepi.22015. Epub 2016 Nov 4.

PMID:
27813156
12.

PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.

Malekpour SA, Pezeshk H, Sadeghi M.

BMC Bioinformatics. 2016 Nov 3;18(1):30. doi: 10.1186/s12859-016-1296-y.

13.

Genomic and Epigenomic Alterations in Cancer.

Chakravarthi BV, Nepal S, Varambally S.

Am J Pathol. 2016 Jul;186(7):1724-35. doi: 10.1016/j.ajpath.2016.02.023. Review.

14.

The oncocytic subtype is genetically distinct from other pancreatic intraductal papillary mucinous neoplasm subtypes.

Basturk O, Tan M, Bhanot U, Allen P, Adsay V, Scott SN, Shah R, Berger MF, Askan G, Dikoglu E, Jobanputra V, Wrzeszczynski KO, Sigel C, Iacobuzio-Donahue C, Klimstra DS.

Mod Pathol. 2016 Sep;29(9):1058-69. doi: 10.1038/modpathol.2016.98. Epub 2016 Jun 10.

15.

Copy number variants in the sheep genome detected using multiple approaches.

Jenkins GM, Goddard ME, Black MA, Brauning R, Auvray B, Dodds KG, Kijas JW, Cockett N, McEwan JC.

BMC Genomics. 2016 Jun 8;17:441. doi: 10.1186/s12864-016-2754-7.

16.

Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum.

Kasuga T, Bui M, Bernhardt E, Swiecki T, Aram K, Cano LM, Webber J, Brasier C, Press C, Grünwald NJ, Rizzo DM, Garbelotto M.

BMC Genomics. 2016 May 20;17:385. doi: 10.1186/s12864-016-2717-z.

17.

Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine.

Kotelnikova EA, Pyatnitskiy M, Paleeva A, Kremenetskaya O, Vinogradov D.

Oncotarget. 2016 Aug 9;7(32):52493-52516. doi: 10.18632/oncotarget.9370. Review.

18.

Globally prevalent PfMDR1 mutations modulate Plasmodium falciparum susceptibility to artemisinin-based combination therapies.

Veiga MI, Dhingra SK, Henrich PP, Straimer J, Gnädig N, Uhlemann AC, Martin RE, Lehane AM, Fidock DA.

Nat Commun. 2016 May 18;7:11553. doi: 10.1038/ncomms11553.

19.

Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data.

Jang H, Hur Y, Lee H.

Sci Rep. 2016 May 9;6:25582. doi: 10.1038/srep25582.

20.

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.

Talevich E, Shain AH, Botton T, Bastian BC.

PLoS Comput Biol. 2016 Apr 21;12(4):e1004873. doi: 10.1371/journal.pcbi.1004873. eCollection 2016 Apr.

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