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Items: 1 to 50 of 195

1.

Damaging de novo mutations diminish motor skills in children on the autism spectrum.

Buja A, Volfovsky N, Krieger AM, Lord C, Lash AE, Wigler M, Iossifov I.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1859-E1866. doi: 10.1073/pnas.1715427115. Epub 2018 Feb 6.

2.

Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer.

Alexander J, Kendall J, McIndoo J, Rodgers L, Aboukhalil R, Levy D, Stepansky A, Sun G, Chobardjiev L, Riggs M, Cox H, Hakker I, Nowak DG, Laze J, Llukani E, Srivastava A, Gruschow S, Yadav SS, Robinson B, Atwal G, Trotman LC, Lepor H, Hicks J, Wigler M, Krasnitz A.

Cancer Res. 2018 Jan 15;78(2):348-358. doi: 10.1158/0008-5472.CAN-17-1138. Epub 2017 Nov 27.

PMID:
29180472
3.

Partial bisulfite conversion for unique template sequencing.

Kumar V, Rosenbaum J, Wang Z, Forcier T, Ronemus M, Wigler M, Levy D.

Nucleic Acids Res. 2018 Jan 25;46(2):e10. doi: 10.1093/nar/gkx1054.

4.

Measuring shared variants in cohorts of discordant siblings with applications to autism.

Ye K, Iossifov I, Levy D, Yamrom B, Buja A, Krieger AM, Wigler M.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7073-7076. doi: 10.1073/pnas.1700439114. Epub 2017 Jun 19.

5.

Early Detection of Cancer in Blood Using Single-Cell Analysis: A Proposal.

Krasnitz A, Kendall J, Alexander J, Levy D, Wigler M.

Trends Mol Med. 2017 Jul;23(7):594-603. doi: 10.1016/j.molmed.2017.05.005. Epub 2017 Jun 3. Review.

6.

Indel variant analysis of short-read sequencing data with Scalpel.

Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O'Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, Lyon GJ, Wigler M, Schatz MC, Narzisi G.

Nat Protoc. 2016 Dec;11(12):2529-2548. doi: 10.1038/nprot.2016.150. Epub 2016 Nov 17.

7.

SMASH, a fragmentation and sequencing method for genomic copy number analysis.

Wang Z, Andrews P, Kendall J, Ma B, Hakker I, Rodgers L, Ronemus M, Wigler M, Levy D.

Genome Res. 2016 Jun;26(6):844-51. doi: 10.1101/gr.201491.115. Epub 2016 Apr 14.

8.

Corrigendum: Genome-wide copy number analysis of single cells.

Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, Troge J, Ravi K, Esposito D, Lakshmi B, Wigler M, Navin N, Hicks J.

Nat Protoc. 2016 Mar;11(3):616. doi: 10.1038/nprot0316.616b. Epub 2016 Feb 25. No abstract available.

PMID:
26914320
9.

Low load for disruptive mutations in autism genes and their biased transmission.

Iossifov I, Levy D, Allen J, Ye K, Ronemus M, Lee YH, Yamrom B, Wigler M.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):E5600-7. doi: 10.1073/pnas.1516376112. Epub 2015 Sep 23.

10.

Interactive analysis and assessment of single-cell copy-number variations.

Garvin T, Aboukhalil R, Kendall J, Baslan T, Atwal GS, Hicks J, Wigler M, Schatz MC.

Nat Methods. 2015 Nov;12(11):1058-60. doi: 10.1038/nmeth.3578. Epub 2015 Sep 7.

11.

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling.

Baslan T, Kendall J, Ward B, Cox H, Leotta A, Rodgers L, Riggs M, D'Italia S, Sun G, Yong M, Miskimen K, Gilmore H, Saborowski M, Dimitrova N, Krasnitz A, Harris L, Wigler M, Hicks J.

Genome Res. 2015 May;25(5):714-24. doi: 10.1101/gr.188060.114. Epub 2015 Apr 9.

12.

Stable heteroplasmy at the single-cell level is facilitated by intercellular exchange of mtDNA.

Jayaprakash AD, Benson EK, Gone S, Liang R, Shim J, Lambertini L, Toloue MM, Wigler M, Aaronson SA, Sachidanandam R.

Nucleic Acids Res. 2015 Feb 27;43(4):2177-87. doi: 10.1093/nar/gkv052. Epub 2015 Feb 4.

13.

Quantitative multigene FISH on breast carcinomas identifies der(1;16)(q10;p10) as an early event in luminal A tumors.

Rye IH, Lundin P, Månér S, Fjelldal R, Naume B, Wigler M, Hicks J, Børresen-Dale AL, Zetterberg A, Russnes HG.

Genes Chromosomes Cancer. 2015 Apr;54(4):235-48. doi: 10.1002/gcc.22237. Epub 2014 Dec 26.

14.

The contribution of de novo coding mutations to autism spectrum disorder.

Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M.

Nature. 2014 Nov 13;515(7526):216-21. doi: 10.1038/nature13908. Epub 2014 Oct 29.

15.

Facilitated sequence counting and assembly by template mutagenesis.

Levy D, Wigler M.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):E4632-7. doi: 10.1073/pnas.1416204111. Epub 2014 Oct 13.

16.

Accurate de novo and transmitted indel detection in exome-capture data using microassembly.

Narzisi G, O'Rawe JA, Iossifov I, Fang H, Lee YH, Wang Z, Wu Y, Lyon GJ, Wigler M, Schatz MC.

Nat Methods. 2014 Oct;11(10):1033-6. doi: 10.1038/nmeth.3069. Epub 2014 Aug 17.

17.

Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells.

Dago AE, Stepansky A, Carlsson A, Luttgen M, Kendall J, Baslan T, Kolatkar A, Wigler M, Bethel K, Gross ME, Hicks J, Kuhn P.

PLoS One. 2014 Aug 1;9(8):e101777. doi: 10.1371/journal.pone.0101777. eCollection 2014.

18.

The role of de novo mutations in the genetics of autism spectrum disorders.

Ronemus M, Iossifov I, Levy D, Wigler M.

Nat Rev Genet. 2014 Feb;15(2):133-41. doi: 10.1038/nrg3585. Epub 2014 Jan 16. Review.

PMID:
24430941
19.

Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation.

Shi J, Whyte WA, Zepeda-Mendoza CJ, Milazzo JP, Shen C, Roe JS, Minder JL, Mercan F, Wang E, Eckersley-Maslin MA, Campbell AE, Kawaoka S, Shareef S, Zhu Z, Kendall J, Muhar M, Haslinger C, Yu M, Roeder RG, Wigler MH, Blobel GA, Zuber J, Spector DL, Young RA, Vakoc CR.

Genes Dev. 2013 Dec 15;27(24):2648-62. doi: 10.1101/gad.232710.113. Epub 2013 Nov 27.

20.

The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease.

Warburton D, Ronemus M, Kline J, Jobanputra V, Williams I, Anyane-Yeboa K, Chung W, Yu L, Wong N, Awad D, Yu CY, Leotta A, Kendall J, Yamrom B, Lee YH, Wigler M, Levy D.

Hum Genet. 2014 Jan;133(1):11-27. doi: 10.1007/s00439-013-1353-9. Epub 2013 Aug 25.

21.

Target inference from collections of genomic intervals.

Krasnitz A, Sun G, Andrews P, Wigler M.

Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):E2271-8. doi: 10.1073/pnas.1306909110. Epub 2013 Jun 6.

22.

Broad applications of single-cell nucleic acid analysis in biomedical research.

Wigler M.

Genome Med. 2012 Oct 30;4(10):79. doi: 10.1186/gm380. eCollection 2012. No abstract available.

23.

The cancer stem cell: cell type or cell state?

Donnenberg AD, Hicks JB, Wigler M, Donnenberg VS.

Cytometry A. 2013 Jan;83(1):5-7. doi: 10.1002/cyto.a.22208. Epub 2012 Oct 18. No abstract available.

24.

Rare de novo germline copy-number variation in testicular cancer.

Stadler ZK, Esposito D, Shah S, Vijai J, Yamrom B, Levy D, Lee YH, Kendall J, Leotta A, Ronemus M, Hansen N, Sarrel K, Rau-Murthy R, Schrader K, Kauff N, Klein RJ, Lipkin SM, Murali R, Robson M, Sheinfeld J, Feldman D, Bosl G, Norton L, Wigler M, Offit K.

Am J Hum Genet. 2012 Aug 10;91(2):379-83. doi: 10.1016/j.ajhg.2012.06.019. Epub 2012 Aug 2.

25.

A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions.

Xue W, Kitzing T, Roessler S, Zuber J, Krasnitz A, Schultz N, Revill K, Weissmueller S, Rappaport AR, Simon J, Zhang J, Luo W, Hicks J, Zender L, Wang XW, Powers S, Wigler M, Lowe SW.

Proc Natl Acad Sci U S A. 2012 May 22;109(21):8212-7. doi: 10.1073/pnas.1206062109. Epub 2012 May 7.

26.

Genome-wide copy number analysis of single cells.

Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, Troge J, Ravi K, Esposito D, Lakshmi B, Wigler M, Navin N, Hicks J.

Nat Protoc. 2012 May 3;7(6):1024-41. doi: 10.1038/nprot.2012.039. Erratum in: Nat Protoc. 2016 Mar;11(3):616.

27.

De novo gene disruptions in children on the autistic spectrum.

Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee YH, Narzisi G, Leotta A, Kendall J, Grabowska E, Ma B, Marks S, Rodgers L, Stepansky A, Troge J, Andrews P, Bekritsky M, Pradhan K, Ghiban E, Kramer M, Parla J, Demeter R, Fulton LL, Fulton RS, Magrini VJ, Ye K, Darnell JC, Darnell RB, Mardis ER, Wilson RK, Schatz MC, McCombie WR, Wigler M.

Neuron. 2012 Apr 26;74(2):285-99. doi: 10.1016/j.neuron.2012.04.009.

28.

Reducing system noise in copy number data using principal components of self-self hybridizations.

Lee YH, Ronemus M, Kendall J, Lakshmi B, Leotta A, Levy D, Esposito D, Grubor V, Ye K, Wigler M, Yamrom B.

Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):E103-10. doi: 10.1073/pnas.1106233109. Epub 2011 Dec 29.

29.

Dosage-dependent phenotypes in models of 16p11.2 lesions found in autism.

Horev G, Ellegood J, Lerch JP, Son YE, Muthuswamy L, Vogel H, Krieger AM, Buja A, Henkelman RM, Wigler M, Mills AA.

Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):17076-81. doi: 10.1073/pnas.1114042108. Epub 2011 Oct 3.

30.

Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses.

Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D.

Neuron. 2011 Jun 9;70(5):898-907. doi: 10.1016/j.neuron.2011.05.021.

31.

Rare de novo and transmitted copy-number variation in autistic spectrum disorders.

Levy D, Ronemus M, Yamrom B, Lee YH, Leotta A, Kendall J, Marks S, Lakshmi B, Pai D, Ye K, Buja A, Krieger A, Yoon S, Troge J, Rodgers L, Iossifov I, Wigler M.

Neuron. 2011 Jun 9;70(5):886-97. doi: 10.1016/j.neuron.2011.05.015.

32.

Tumour evolution inferred by single-cell sequencing.

Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M.

Nature. 2011 Apr 7;472(7341):90-4. doi: 10.1038/nature09807. Epub 2011 Mar 13.

33.

DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables.

Kamalakaran S, Varadan V, Giercksky Russnes HE, Levy D, Kendall J, Janevski A, Riggs M, Banerjee N, Synnestvedt M, Schlichting E, Kåresen R, Shama Prasada K, Rotti H, Rao R, Rao L, Eric Tang MH, Satyamoorthy K, Lucito R, Wigler M, Dimitrova N, Naume B, Borresen-Dale AL, Hicks JB.

Mol Oncol. 2011 Feb;5(1):77-92. doi: 10.1016/j.molonc.2010.11.002. Epub 2010 Dec 2.

34.

Genomic architecture characterizes tumor progression paths and fate in breast cancer patients.

Russnes HG, Vollan HKM, Lingjærde OC, Krasnitz A, Lundin P, Naume B, Sørlie T, Borgen E, Rye IH, Langerød A, Chin SF, Teschendorff AE, Stephens PJ, Månér S, Schlichting E, Baumbusch LO, Kåresen R, Stratton MP, Wigler M, Caldas C, Zetterberg A, Hicks J, Børresen-Dale AL.

Sci Transl Med. 2010 Jun 30;2(38):38ra47. doi: 10.1126/scitranslmed.3000611.

35.

Inferring tumor progression from genomic heterogeneity.

Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M.

Genome Res. 2010 Jan;20(1):68-80. doi: 10.1101/gr.099622.109. Epub 2009 Nov 10.

36.

Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model.

Bric A, Miething C, Bialucha CU, Scuoppo C, Zender L, Krasnitz A, Xuan Z, Zuber J, Wigler M, Hicks J, McCombie RW, Hemann MT, Hannon GJ, Powers S, Lowe SW.

Cancer Cell. 2009 Oct 6;16(4):324-35. doi: 10.1016/j.ccr.2009.08.015.

37.

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.

Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB.

Genome Res. 2009 Sep;19(9):1593-605. doi: 10.1101/gr.095190.109. Epub 2009 Jul 6.

38.

An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

Zender L, Xue W, Zuber J, Semighini CP, Krasnitz A, Ma B, Zender P, Kubicka S, Luk JM, Schirmacher P, McCombie WR, Wigler M, Hicks J, Hannon GJ, Powers S, Lowe SW.

Cell. 2008 Nov 28;135(5):852-64. doi: 10.1016/j.cell.2008.09.061. Epub 2008 Nov 13.

39.

Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA).

Grubor V, Krasnitz A, Troge JE, Meth JL, Lakshmi B, Kendall JT, Yamrom B, Alex G, Pai D, Navin N, Hufnagel LA, Lee YH, Cook K, Allen SL, Rai KR, Damle RN, Calissano C, Chiorazzi N, Wigler M, Esposito D.

Blood. 2009 Feb 5;113(6):1294-303. doi: 10.1182/blood-2008-05-158865. Epub 2008 Oct 15.

40.

DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma.

Xue W, Krasnitz A, Lucito R, Sordella R, Vanaelst L, Cordon-Cardo C, Singer S, Kuehnel F, Wigler M, Powers S, Zender L, Lowe SW.

Genes Dev. 2008 Jun 1;22(11):1439-44. doi: 10.1101/gad.1672608.

41.

Linkage, association, and gene-expression analyses identify CNTNAP2 as an autism-susceptibility gene.

Alarcón M, Abrahams BS, Stone JL, Duvall JA, Perederiy JV, Bomar JM, Sebat J, Wigler M, Martin CL, Ledbetter DH, Nelson SF, Cantor RM, Geschwind DH.

Am J Hum Genet. 2008 Jan;82(1):150-9. doi: 10.1016/j.ajhg.2007.09.005.

42.

Recurrent DNA copy number variation in the laboratory mouse.

Egan CM, Sridhar S, Wigler M, Hall IM.

Nat Genet. 2007 Nov;39(11):1384-9. Epub 2007 Oct 28.

PMID:
17965714
43.

Copy-number variants in patients with a strong family history of pancreatic cancer.

Lucito R, Suresh S, Walter K, Pandey A, Lakshmi B, Krasnitz A, Sebat J, Wigler M, Klein AP, Brune K, Palmisano E, Maitra A, Goggins M, Hruban RH.

Cancer Biol Ther. 2007 Oct;6(10):1592-9. Epub 2007 Jul 12.

PMID:
17912030
44.

A unified genetic theory for sporadic and inherited autism.

Zhao X, Leotta A, Kustanovich V, Lajonchere C, Geschwind DH, Law K, Law P, Qiu S, Lord C, Sebat J, Ye K, Wigler M.

Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12831-6. Epub 2007 Jul 25.

45.

Strong association of de novo copy number mutations with autism.

Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimäki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M.

Science. 2007 Apr 20;316(5823):445-9. Epub 2007 Mar 15.

46.

Identification of alterations in DNA copy number in host stromal cells during tumor progression.

Pelham RJ, Rodgers L, Hall I, Lucito R, Nguyen KC, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D.

Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19848-53. Epub 2006 Dec 13.

47.

Novel patterns of genome rearrangement and their association with survival in breast cancer.

Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Børresen-Dale AL, Naume B, Schlicting E, Norton L, Hägerström T, Skoog L, Auer G, Månér S, Lundin P, Zetterberg A.

Genome Res. 2006 Dec;16(12):1465-79.

48.

High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors.

Hicks J, Muthuswamy L, Krasnitz A, Navin N, Riggs M, Grubor V, Esposito D, Alexander J, Troge J, Wigler M, Maner S, Lundin P, Zetterberg A.

Cold Spring Harb Symp Quant Biol. 2005;70:51-63.

PMID:
16869738
49.

Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens.

Lakshmi B, Hall IM, Egan C, Alexander J, Leotta A, Healy J, Zender L, Spector MS, Xue W, Lowe SW, Wigler M, Lucito R.

Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11234-9. Epub 2006 Jul 14.

50.

Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach.

Zender L, Spector MS, Xue W, Flemming P, Cordon-Cardo C, Silke J, Fan ST, Luk JM, Wigler M, Hannon GJ, Mu D, Lucito R, Powers S, Lowe SW.

Cell. 2006 Jun 30;125(7):1253-67.

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