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Items: 1 to 50 of 275

1.

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data.

Porubsky D, Sanders AD, Taudt A, Colomé-Tatché M, Lansdorp PM, Guryev V.

Bioinformatics. 2019 Aug 30. pii: btz681. doi: 10.1093/bioinformatics/btz681. [Epub ahead of print]

PMID:
31504176
2.

Ongoing chromosomal instability and karyotype evolution in human colorectal cancer organoids.

Bolhaqueiro ACF, Ponsioen B, Bakker B, Klaasen SJ, Kucukkose E, van Jaarsveld RH, Vivié J, Verlaan-Klink I, Hami N, Spierings DCJ, Sasaki N, Dutta D, Boj SF, Vries RGJ, Lansdorp PM, van de Wetering M, van Oudenaarden A, Clevers H, Kranenburg O, Foijer F, Snippert HJG, Kops GJPL.

Nat Genet. 2019 May;51(5):824-834. doi: 10.1038/s41588-019-0399-6. Epub 2019 Apr 29.

PMID:
31036964
3.

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.

4.

Quantification of Aneuploidy in Mammalian Systems.

van den Bos H, Bakker B, Taudt A, Guryev V, Colomé-Tatché M, Lansdorp PM, Foijer F, Spierings DCJ.

Methods Mol Biol. 2019;1896:159-190. doi: 10.1007/978-1-4939-8931-7_15.

PMID:
30474848
5.

BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes.

van Wietmarschen N, Merzouk S, Halsema N, Spierings DCJ, Guryev V, Lansdorp PM.

Nat Commun. 2018 Jan 18;9(1):271. doi: 10.1038/s41467-017-02760-1.

6.

Maintenance of telomere length in AML.

Lansdorp PM.

Blood Adv. 2017 Nov 28;1(25):2467-2472. doi: 10.1182/bloodadvances.2017012112. eCollection 2017 Nov 28. Review.

7.

Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq.

Claussin C, Porubský D, Spierings DC, Halsema N, Rentas S, Guryev V, Lansdorp PM, Chang M.

Elife. 2017 Dec 12;6. pii: e30560. doi: 10.7554/eLife.30560.

8.

Dense and accurate whole-chromosome haplotyping of individual genomes.

Porubsky D, Garg S, Sanders AD, Korbel JO, Guryev V, Lansdorp PM, Marschall T.

Nat Commun. 2017 Nov 3;8(1):1293. doi: 10.1038/s41467-017-01389-4.

9.

Single-cell sequencing to quantify genomic integrity in cancer.

van den Bos H, Bakker B, Spierings DCJ, Lansdorp PM, Foijer F.

Int J Biochem Cell Biol. 2018 Jan;94:146-150. doi: 10.1016/j.biocel.2017.09.016. Epub 2017 Sep 23. Review.

PMID:
28951245
10.

p53 Prohibits Propagation of Chromosome Segregation Errors that Produce Structural Aneuploidies.

Soto M, Raaijmakers JA, Bakker B, Spierings DCJ, Lansdorp PM, Foijer F, Medema RH.

Cell Rep. 2017 Jun 20;19(12):2423-2431. doi: 10.1016/j.celrep.2017.05.055.

11.

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs.

Sanders AD, Falconer E, Hills M, Spierings DCJ, Lansdorp PM.

Nat Protoc. 2017 Jun;12(6):1151-1176. doi: 10.1038/nprot.2017.029. Epub 2017 May 11.

PMID:
28492527
12.

Assembling draft genomes using contiBAIT.

O'Neill K, Hills M, Gottlieb M, Borkowski M, Karsan A, Lansdorp PM.

Bioinformatics. 2017 Sep 1;33(17):2737-2739. doi: 10.1093/bioinformatics/btx281.

13.

Detection of G-quadruplex DNA in mammalian cells.

Henderson A, Wu Y, Huang YC, Chavez EA, Platt J, Johnson FB, Brosh RM Jr, Sen D, Lansdorp PM.

Nucleic Acids Res. 2017 Jun 2;45(10):6252. doi: 10.1093/nar/gkx300. No abstract available.

14.

Guanine quadruplex monoclonal antibody 1H6 cross-reacts with restrained thymidine-rich single stranded DNA.

Kazemier HG, Paeschke K, Lansdorp PM.

Nucleic Acids Res. 2017 Jun 2;45(10):5913-5919. doi: 10.1093/nar/gkx245.

15.

Guanine quadruplex structures localize to heterochromatin.

Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AHG, Nishida K, Romashchenko AV, Postberg J, Lipps H, Berezikov E, Sibon OCM, Giepmans BNG, Lansdorp PM.

Nucleic Acids Res. 2017 Jun 2;45(10):6253. doi: 10.1093/nar/gkx301. No abstract available.

16.

Copy number alterations assessed at the single-cell level revealed mono- and polyclonal seeding patterns of distant metastasis in a small-cell lung cancer patient.

Ferronika P, van den Bos H, Taudt A, Spierings DCJ, Saber A, Hiltermann TJN, Kok K, Porubsky D, van der Wekken AJ, Timens W, Foijer F, Colomé-Tatché M, Groen HJM, Lansdorp PM, van den Berg A.

Ann Oncol. 2017 Jul 1;28(7):1668-1670. doi: 10.1093/annonc/mdx182. No abstract available.

PMID:
28419234
17.

Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma.

Foijer F, Albacker LA, Bakker B, Spierings DC, Yue Y, Xie SZ, Davis S, Lutum-Jehle A, Takemoto D, Hare B, Furey B, Bronson RT, Lansdorp PM, Bradley A, Sorger PK.

Elife. 2017 Mar 20;6. pii: e20873. doi: 10.7554/eLife.20873.

18.

Centrosome Amplification Is Sufficient to Promote Spontaneous Tumorigenesis in Mammals.

Levine MS, Bakker B, Boeckx B, Moyett J, Lu J, Vitre B, Spierings DC, Lansdorp PM, Cleveland DW, Lambrechts D, Foijer F, Holland AJ.

Dev Cell. 2017 Feb 6;40(3):313-322.e5. doi: 10.1016/j.devcel.2016.12.022. Epub 2017 Jan 26.

19.

Defects in lymphocyte telomere homeostasis contribute to cellular immune phenotype in patients with cartilage-hair hypoplasia.

Aubert G, Strauss KA, Lansdorp PM, Rider NL.

J Allergy Clin Immunol. 2017 Oct;140(4):1120-1129.e1. doi: 10.1016/j.jaci.2016.11.051. Epub 2017 Jan 23.

PMID:
28126377
20.

Direct chromosome-length haplotyping by single-cell sequencing.

Porubský D, Sanders AD, van Wietmarschen N, Falconer E, Hills M, Spierings DC, Bevova MR, Guryev V, Lansdorp PM.

Genome Res. 2016 Nov;26(11):1565-1574. Epub 2016 Sep 19.

21.

Characterizing polymorphic inversions in human genomes by single-cell sequencing.

Sanders AD, Hills M, Porubský D, Guryev V, Falconer E, Lansdorp PM.

Genome Res. 2016 Nov;26(11):1575-1587. Epub 2016 Jul 29.

22.

Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons.

van den Bos H, Spierings DC, Taudt AS, Bakker B, Porubský D, Falconer E, Novoa C, Halsema N, Kazemier HG, Hoekstra-Wakker K, Guryev V, den Dunnen WF, Foijer F, Tatché MC, Boddeke HW, Lansdorp PM.

Genome Biol. 2016 May 31;17(1):116. doi: 10.1186/s13059-016-0976-2. Erratum in: Genome Biol. 2016 Jun 30;17(1):143.

23.

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies.

Bakker B, Taudt A, Belderbos ME, Porubsky D, Spierings DC, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ES, van den Berg A, Guryev V, Lansdorp PM, Colomé-Tatché M, Foijer F.

Genome Biol. 2016 May 31;17(1):115. doi: 10.1186/s13059-016-0971-7.

24.

Telomeres on Steroids--Turning Back the Mitotic Clock?

Lansdorp PM.

N Engl J Med. 2016 May 19;374(20):1978-80. doi: 10.1056/NEJMe1602822. No abstract available.

PMID:
27192677
25.

Bromodeoxyuridine does not contribute to sister chromatid exchange events in normal or Bloom syndrome cells.

van Wietmarschen N, Lansdorp PM.

Nucleic Acids Res. 2016 Aug 19;44(14):6787-93. doi: 10.1093/nar/gkw422. Epub 2016 May 16.

26.

Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells.

Benchetrit H, Herman S, van Wietmarschen N, Wu T, Makedonski K, Maoz N, Yom Tov N, Stave D, Lasry R, Zayat V, Xiao A, Lansdorp PM, Sebban S, Buganim Y.

Cell Stem Cell. 2015 Nov 5;17(5):543-56. doi: 10.1016/j.stem.2015.08.006. Epub 2015 Sep 24.

27.

Guanine quadruplex structures localize to heterochromatin.

Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AH, Nishida K, Romashchenko AV, Postberg J, Lipps H, Berezikov E, Sibon OC, Giepmans BN, Lansdorp PM.

Nucleic Acids Res. 2016 Jan 8;44(1):152-63. doi: 10.1093/nar/gkv900. Epub 2015 Sep 17. Erratum in: Nucleic Acids Res. 2017 Jun 2;45(10):6253.

28.

How to count chromosomes in a cell: An overview of current and novel technologies.

Bakker B, van den Bos H, Lansdorp PM, Foijer F.

Bioessays. 2015 May;37(5):570-7. doi: 10.1002/bies.201400218. Epub 2015 Mar 4. Review.

PMID:
25739518
29.

The developmental potential of iPSCs is greatly influenced by reprogramming factor selection.

Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R.

Cell Stem Cell. 2014 Sep 4;15(3):295-309. doi: 10.1016/j.stem.2014.07.003.

30.

Resolution of telomere associations by TRF1 cleavage in mouse embryonic stem cells.

Lisaingo K, Uringa EJ, Lansdorp PM.

Mol Biol Cell. 2014 Jul 1;25(13):1958-68. doi: 10.1091/mbc.E13-10-0564. Epub 2014 May 14.

31.

Detection of G-quadruplex DNA in mammalian cells.

Henderson A, Wu Y, Huang YC, Chavez EA, Platt J, Johnson FB, Brosh RM Jr, Sen D, Lansdorp PM.

Nucleic Acids Res. 2014 Jan;42(2):860-9. doi: 10.1093/nar/gkt957. Epub 2013 Oct 24.

32.

BAIT: Organizing genomes and mapping rearrangements in single cells.

Hills M, O'Neill K, Falconer E, Brinkman R, Lansdorp PM.

Genome Med. 2013 Sep 13;5(9):82. doi: 10.1186/gm486. eCollection 2013.

33.

Strand-seq: a unifying tool for studies of chromosome segregation.

Falconer E, Lansdorp PM.

Semin Cell Dev Biol. 2013 Aug-Sep;24(8-9):643-52. doi: 10.1016/j.semcdb.2013.04.005. Epub 2013 May 8. Review.

34.

The mammalian proteins MMS19, MIP18, and ANT2 are involved in cytoplasmic iron-sulfur cluster protein assembly.

van Wietmarschen N, Moradian A, Morin GB, Lansdorp PM, Uringa EJ.

J Biol Chem. 2012 Dec 21;287(52):43351-8. doi: 10.1074/jbc.M112.431270. Epub 2012 Nov 13.

35.

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.

Falconer E, Hills M, Naumann U, Poon SS, Chavez EA, Sanders AD, Zhao Y, Hirst M, Lansdorp PM.

Nat Methods. 2012 Nov;9(11):1107-12. doi: 10.1038/nmeth.2206. Epub 2012 Oct 7.

36.

Cord blood T cells retain early differentiation phenotype suitable for immunotherapy after TCR gene transfer to confer EBV specificity.

Frumento G, Zheng Y, Aubert G, Raeiszadeh M, Lansdorp PM, Moss P, Lee SP, Chen FE.

Am J Transplant. 2013 Jan;13(1):45-55. doi: 10.1111/j.1600-6143.2012.04286.x. Epub 2012 Sep 27.

37.

Epigenetic differences between sister chromatids?

Lansdorp PM, Falconer E, Tao J, Brind'Amour J, Naumann U.

Ann N Y Acad Sci. 2012 Aug;1266:1-6. doi: 10.1111/j.1749-6632.2012.06505.x. Review.

38.

Collapse of telomere homeostasis in hematopoietic cells caused by heterozygous mutations in telomerase genes.

Aubert G, Baerlocher GM, Vulto I, Poon SS, Lansdorp PM.

PLoS Genet. 2012;8(5):e1002696. doi: 10.1371/journal.pgen.1002696. Epub 2012 May 17.

39.

RTEL1 contributes to DNA replication and repair and telomere maintenance.

Uringa EJ, Lisaingo K, Pickett HA, Brind'Amour J, Rohde JH, Zelensky A, Essers J, Lansdorp PM.

Mol Biol Cell. 2012 Jul;23(14):2782-92. doi: 10.1091/mbc.E12-03-0179. Epub 2012 May 16.

40.

Telomere length is associated with disease severity and declines with age in dyskeratosis congenita.

Alter BP, Rosenberg PS, Giri N, Baerlocher GM, Lansdorp PM, Savage SA.

Haematologica. 2012 Mar;97(3):353-9. doi: 10.3324/haematol.2011.055269. Epub 2011 Nov 4.

41.

Prolonged self-renewal activity unmasks telomerase control of telomere homeostasis and function of mouse hematopoietic stem cells.

Sekulovic S, Gylfadottir V, Vulto I, Gasparetto M, Even Y, Brookes C, Smith C, Eaves CJ, Lansdorp PM, Rossi FM, Humphries RK.

Blood. 2011 Aug 18;118(7):1766-73. doi: 10.1182/blood-2010-11-319632. Epub 2011 Jul 5.

42.

Telomere length measurement-caveats and a critical assessment of the available technologies and tools.

Aubert G, Hills M, Lansdorp PM.

Mutat Res. 2012 Feb 1;730(1-2):59-67. doi: 10.1016/j.mrfmmm.2011.04.003. Epub 2011 Jun 12. Review.

43.

Analysis of repetitive DNA in chromosomes by flow cytometry.

Brind'Amour J, Lansdorp PM.

Nat Methods. 2011 Jun;8(6):484-6. doi: 10.1038/nmeth.1601. Epub 2011 May 1.

44.

Ancestral mutation in telomerase causes defects in repeat addition processivity and manifests as familial pulmonary fibrosis.

Alder JK, Cogan JD, Brown AF, Anderson CJ, Lawson WE, Lansdorp PM, Phillips JA 3rd, Loyd JE, Chen JJ, Armanios M.

PLoS Genet. 2011 Mar;7(3):e1001352. doi: 10.1371/journal.pgen.1001352. Epub 2011 Mar 31.

45.

Telomere elongation followed by telomere length reduction, in leukocytes from divers exposed to intense oxidative stress--implications for tissue and organismal aging.

Shlush LI, Skorecki KL, Itzkovitz S, Yehezkel S, Segev Y, Shachar H, Berkovitz R, Adir Y, Vulto I, Lansdorp PM, Selig S.

Mech Ageing Dev. 2011 Mar;132(3):123-30. doi: 10.1016/j.mad.2011.01.005. Epub 2011 Feb 12.

PMID:
21320523
46.

RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination.

Uringa EJ, Youds JL, Lisaingo K, Lansdorp PM, Boulton SJ.

Nucleic Acids Res. 2011 Mar;39(5):1647-55. doi: 10.1093/nar/gkq1045. Epub 2010 Nov 18. Review.

47.

Synchrony of telomere length among hematopoietic cells.

Kimura M, Gazitt Y, Cao X, Zhao X, Lansdorp PM, Aviv A.

Exp Hematol. 2010 Oct;38(10):854-9. doi: 10.1016/j.exphem.2010.06.010. Epub 2010 Jun 25.

48.

Chromosome orientation fluorescence in situ hybridization to study sister chromatid segregation in vivo.

Falconer E, Chavez E, Henderson A, Lansdorp PM.

Nat Protoc. 2010 Jul;5(7):1362-77. doi: 10.1038/nprot.2010.102. Epub 2010 Jul 1.

49.

Telomere length is inherited with resetting of the telomere set-point.

Chiang YJ, Calado RT, Hathcock KS, Lansdorp PM, Young NS, Hodes RJ.

Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10148-53. doi: 10.1073/pnas.0913125107. Epub 2010 May 17.

50.

Identification of sister chromatids by DNA template strand sequences.

Falconer E, Chavez EA, Henderson A, Poon SS, McKinney S, Brown L, Huntsman DG, Lansdorp PM.

Nature. 2010 Jan 7;463(7277):93-7. doi: 10.1038/nature08644. Epub 2009 Dec 16.

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