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Items: 1 to 20 of 102

1.

Clinical Genomics: Challenges and Opportunities.

Vijay P, McIntyre AB, Mason CE, Greenfield JP, Li S.

Crit Rev Eukaryot Gene Expr. 2016;26(2):97-113. doi: 10.1615/CritRevEukaryotGeneExpr.2016015724.

PMID:
27480773
2.

Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia.

Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Löwenberg B, Döhner H, Döhner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJ, D'Andrea RJ, Carroll M, Park CY, Neuberg D, Levine R, Melnick AM, Mason CE.

Nat Med. 2016 Jul;22(7):792-9. doi: 10.1038/nm.4125. Epub 2016 Jun 20.

PMID:
27322744
3.

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.

4.

Erratum to: A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 May 23;17(1):107. No abstract available.

5.

Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disability.

Maduro V, Pusey BN, Cherukuri PF, Atkins P, du Souich C, Rupps R, Limbos M, Adams DR, Bhatt SS, Eydoux P, Links AE, Lehman A, Malicdan MC, Mason CE, Morimoto M, Mullikin JC, Sear A, Van Karnebeek C, Stankiewicz P, Gahl WA, Toro C, Boerkoel CF.

Orphanet J Rare Dis. 2016 May 14;11(1):62. doi: 10.1186/s13023-016-0439-6.

6.

Genetic and epigenetic heterogeneity in acute myeloid leukemia.

Li S, Mason CE, Melnick A.

Curr Opin Genet Dev. 2016 Feb;36:100-6. doi: 10.1016/j.gde.2016.03.011. Epub 2016 May 7. Review.

PMID:
27162099
7.

Laminin regulates PDGFRβ(+) cell stemness and muscle development.

Yao Y, Norris EH, Mason CE, Strickland S.

Nat Commun. 2016 May 3;7:11415. doi: 10.1038/ncomms11415.

8.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):97-97.e3. doi: 10.1016/j.cels.2015.07.006. Epub 2015 Jul 29. No abstract available.

PMID:
27135689
9.

Modern Methods for Delineating Metagenomic Complexity.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):6-7. doi: 10.1016/j.cels.2015.07.007. Epub 2015 Jul 29. No abstract available.

PMID:
27135684
10.

A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 Apr 23;17:74. doi: 10.1186/s13059-016-0940-1. Erratum in: Genome Biol. 2016;17(1):107.

11.

The Power of Engaging Citizen Scientists for Scientific Progress.

Garbarino J, Mason CE.

J Microbiol Biol Educ. 2016 Mar 1;17(1):7-12. doi: 10.1128/jmbe.v17i1.1052. eCollection 2016 Mar.

12.

Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius.

Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE.

Nat Commun. 2016 Feb 2;7:10164. doi: 10.1038/ncomms10164.

13.

Genome Sequence and Analysis of Escherichia coli MRE600, a Colicinogenic, Nonmotile Strain that Lacks RNase I and the Type I Methyltransferase, EcoKI.

Kurylo CM, Alexander N, Dass RA, Parks MM, Altman RA, Vincent CT, Mason CE, Blanchard SC.

Genome Biol Evol. 2016 Jan 22;8(3):742-52. doi: 10.1093/gbe/evw008.

14.

Dnmt3a regulates myeloproliferation and liver-specific expansion of hematopoietic stem and progenitor cells.

Guryanova OA, Lieu YK, Garrett-Bakelman FE, Spitzer B, Glass JL, Shank K, Martinez AB, Rivera SA, Durham BH, Rapaport F, Keller MD, Pandey S, Bastian L, Tovbin D, Weinstein AR, Teruya-Feldstein J, Abdel-Wahab O, Santini V, Mason CE, Melnick AM, Mukherjee S, Levine RL.

Leukemia. 2016 May;30(5):1133-42. doi: 10.1038/leu.2015.358. Epub 2015 Dec 29.

15.

Erratum to: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.

Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D.

Genome Biol. 2015 Nov 23;16:261. doi: 10.1186/s13059-015-0813-z. No abstract available.

16.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):72-87. Epub 2015 Mar 3.

17.

Effects of Brown Marmorated Stink Bug (Hemiptera: Pentatomidae) Feeding Injury on Sweet Corn Yield and Quality.

Cissel WJ, Mason CE, Whalen J, Hough-Goldstein J, Hooks CR.

J Econ Entomol. 2015 Jun;108(3):1065-71. doi: 10.1093/jee/tov059. Epub 2015 Apr 9.

PMID:
26470230
18.

Response to Zhou and Robinson.

Betel D, Socci ND, Khanin R, Mason CE, Rapaport F.

Genome Biol. 2015 Oct 8;16:223. doi: 10.1186/s13059-015-0782-2. No abstract available.

19.

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, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, 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.

20.

Genomic DNA transposition induced by human PGBD5.

Henssen AG, Henaff E, Jiang E, Eisenberg AR, Carson JR, Villasante CM, Ray M, Still E, Burns M, Gandara J, Feschotte C, Mason CE, Kentsis A.

Elife. 2015 Sep 25;4. pii: e10565. doi: 10.7554/eLife.10565.

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