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Items: 38

1.

Human-specific tandem repeat expansion and differential gene expression during primate evolution.

Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA; Human Genome Structural Variation Consortium, Warren WC, Pollen AA, Chaisson MJP, Eichler EE.

Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23243-23253. doi: 10.1073/pnas.1912175116. Epub 2019 Oct 28.

PMID:
31659027
2.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C.

Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z.

3.

Long-read sequence and assembly of segmental duplications.

Vollger MR, Dishuck PC, Sorensen M, Welch AE, Dang V, Dougherty ML, Graves-Lindsay TA, Wilson RK, Chaisson MJP, Eichler EE.

Nat Methods. 2019 Jan;16(1):88-94. doi: 10.1038/s41592-018-0236-3. Epub 2018 Dec 17.

4.

Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ.

Samstag CL, Hoekstra JG, Huang CH, Chaisson MJ, Youle RJ, Kennedy SR, Pallanck LJ.

PLoS Genet. 2018 Nov 19;14(11):e1007805. doi: 10.1371/journal.pgen.1007805. eCollection 2018 Nov.

5.

High-resolution comparative analysis of great ape genomes.

Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE.

Science. 2018 Jun 8;360(6393). pii: eaar6343. doi: 10.1126/science.aar6343.

6.

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data.

Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE.

Genome Res. 2018 Jan;28(1):144. doi: 10.1101/gr.233007.117. No abstract available.

7.

Resolving multicopy duplications de novo using polyploid phasing.

Chaisson MJ, Mukherjee S, Kannan S, Eichler EE.

Res Comput Mol Biol. 2017 May;10229:117-133. doi: 10.1007/978-3-319-56970-3_8. Epub 2017 Apr 12.

8.

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies.

Fan X, Chaisson M, Nakhleh L, Chen K.

Genome Res. 2017 May;27(5):793-800. doi: 10.1101/gr.214767.116. Epub 2017 Jan 19.

9.

Assembly of long error-prone reads using de Bruijn graphs.

Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):E8396-E8405. doi: 10.1073/pnas.1604560113. Epub 2016 Dec 12.

10.

Discovery and genotyping of structural variation from long-read haploid genome sequence data.

Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE.

Genome Res. 2017 May;27(5):677-685. doi: 10.1101/gr.214007.116. Epub 2016 Nov 28. Erratum in: Genome Res. 2018 Jan;28(1):144.

11.

Extensive sequencing of seven human genomes to characterize benchmark reference materials.

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M.

Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25.

12.

Long-read sequence assembly of the gorilla genome.

Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE.

Science. 2016 Apr 1;352(6281):aae0344. doi: 10.1126/science.aae0344.

13.

Genetic variation and the de novo assembly of human genomes.

Chaisson MJ, Wilson RK, Eichler EE.

Nat Rev Genet. 2015 Nov;16(11):627-40. doi: 10.1038/nrg3933. Epub 2015 Oct 7. Review.

14.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

15.

Resolving the complexity of the human genome using single-molecule sequencing.

Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE.

Nature. 2015 Jan 29;517(7536):608-11. doi: 10.1038/nature13907. Epub 2014 Nov 10.

16.

Reconstructing complex regions of genomes using long-read sequencing technology.

Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE.

Genome Res. 2014 Apr;24(4):688-96. doi: 10.1101/gr.168450.113. Epub 2014 Jan 13.

17.

STAR: ultrafast universal RNA-seq aligner.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR.

Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.

18.

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.

Chaisson MJ, Tesler G.

BMC Bioinformatics. 2012 Sep 19;13:238. doi: 10.1186/1471-2105-13-238.

19.

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers.

Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P.

J Comput Biol. 2011 Nov;18(11):1625-34. doi: 10.1089/cmb.2011.0151. Epub 2011 Oct 14.

20.

Uncommon osseous involvement in multisystemic sarcoidosis.

Rajebi MR, Shahrokni A, Chaisson M.

Ann Saudi Med. 2009 Nov-Dec;29(6):485-6. doi: 10.4103/0256-4947.57175. No abstract available.

21.

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Chaisson MJ, Brinza D, Pevzner PA.

Genome Res. 2009 Feb;19(2):336-46. doi: 10.1101/gr.079053.108. Epub 2008 Dec 3.

22.

Short read fragment assembly of bacterial genomes.

Chaisson MJ, Pevzner PA.

Genome Res. 2008 Feb;18(2):324-30. Epub 2007 Dec 14.

23.

Microinversions in mammalian evolution.

Chaisson MJ, Raphael BJ, Pevzner PA.

Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19824-9. Epub 2006 Dec 22.

24.

The RANK/RANKL/OPG triad in cancer-induced bone diseases.

Dougall WC, Chaisson M.

Cancer Metastasis Rev. 2006 Dec;25(4):541-9. Review.

PMID:
17180711
25.

Reciprocal and coordinate regulation of serum amyloid A versus apolipoprotein A-I and paraoxonase-1 by inflammation in murine hepatocytes.

Han CY, Chiba T, Campbell JS, Fausto N, Chaisson M, Orasanu G, Plutzky J, Chait A.

Arterioscler Thromb Vasc Biol. 2006 Aug;26(8):1806-13. Epub 2006 May 18.

PMID:
16709944
26.

[Monoclonal antibody targeting RANKL as a therapy for cancer-induced bone diseases].

Dougall W, Chaisson M.

Clin Calcium. 2006 Apr;16(4):627- 35. Review. Japanese.

PMID:
16582514
27.

Osteoclast differentiation is impaired in the absence of inhibitor of kappa B kinase alpha.

Chaisson ML, Branstetter DG, Derry JM, Armstrong AP, Tometsko ME, Takeda K, Akira S, Dougall WC.

J Biol Chem. 2004 Dec 24;279(52):54841-8. Epub 2004 Oct 14.

28.

Fragment assembly with short reads.

Chaisson M, Pevzner P, Tang H.

Bioinformatics. 2004 Sep 1;20(13):2067-74. Epub 2004 Apr 1.

PMID:
15059830
29.

Hepatocyte-specific inhibition of NF-kappaB leads to apoptosis after TNF treatment, but not after partial hepatectomy.

Chaisson ML, Brooling JT, Ladiges W, Tsai S, Fausto N.

J Clin Invest. 2002 Jul;110(2):193-202.

30.

Bcl-2 expression delays hepatocyte cell cycle progression during liver regeneration.

Vail ME, Chaisson ML, Thompson J, Fausto N.

Oncogene. 2002 Feb 28;21(10):1548-55.

31.

Disruption of redox homeostasis in tumor necrosis factor-induced apoptosis in a murine hepatocyte cell line.

Pierce RH, Campbell JS, Stephenson AB, Franklin CC, Chaisson M, Poot M, Kavanagh TJ, Rabinovitch PS, Fausto N.

Am J Pathol. 2000 Jul;157(1):221-36.

32.

Tumor necrosis factor induces DNA replication in hepatic cells through nuclear factor kappaB activation.

Kirillova I, Chaisson M, Fausto N.

Cell Growth Differ. 1999 Dec;10(12):819-28.

33.

NF-kappaB mediates alphavbeta3 integrin-induced endothelial cell survival.

Scatena M, Almeida M, Chaisson ML, Fausto N, Nicosia RF, Giachelli CM.

J Cell Biol. 1998 May 18;141(4):1083-93.

34.

Ethanol administration alters the proteolytic activity of hepatic lysosomes.

Donohue TM Jr, McVicker DL, Kharbanda KK, Chaisson ML, Zetterman RK.

Alcohol Clin Exp Res. 1994 Jun;18(3):536-41.

PMID:
7943651
35.

Plasma protein catabolism in ethanol- and colchicine-treated liver slices.

Donohue TM Jr, Chaisson ML, Zetterman RK.

Alcohol Clin Exp Res. 1991 Feb;15(1):7-12.

PMID:
2024734
36.

Treating the depressed elderly.

Chaisson M, Beutler L, Yost E, Allender J.

J Psychosoc Nurs Ment Health Serv. 1984 May;22(5):25-30. No abstract available.

PMID:
6563085
37.

Psych nurse helps others see how Jews view death.

Chaisson M.

Am Nurse. 1983 Jan;15(1):13. No abstract available.

PMID:
6549729
38.

Life cycle: a social-simulation game to improve attitudes and responses to the elderly.

Chaisson M.

J Gerontol Nurs. 1980 Oct;6(10):587-92. No abstract available.

PMID:
7002996

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