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Items: 32


A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection.

Cheng AP, Burnham P, Lee JR, Cheng MP, Suthanthiran M, Dadhania D, De Vlaminck I.

Proc Natl Acad Sci U S A. 2019 Sep 10;116(37):18738-18744. doi: 10.1073/pnas.1906320116. Epub 2019 Aug 26.


Donor-derived cell-free DNA predicts allograft failure and mortality after lung transplantation.

Agbor-Enoh S, Wang Y, Tunc I, Jang MK, Davis A, De Vlaminck I, Luikart H, Shah PD, Timofte I, Brown AW, Marishta A, Bhatti K, Gorham S, Fideli U, Wylie J, Grimm D, Goodwin N, Yang Y, Patel K, Zhu J, Iacono A, Orens JB, Nathan SD, Marboe C, Berry GJ, Quake SR, Khush K, Valantine HA.

EBioMedicine. 2019 Feb;40:541-553. doi: 10.1016/j.ebiom.2018.12.029. Epub 2019 Jan 26.


Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells.

Saikia M, Burnham P, Keshavjee SH, Wang MFZ, Heyang M, Moral-Lopez P, Hinchman MM, Danko CG, Parker JSL, De Vlaminck I.

Nat Methods. 2019 Jan;16(1):59-62. doi: 10.1038/s41592-018-0259-9. Epub 2018 Dec 17.


Biopsy-free screening for glioma.

Cheng AP, Burnham P, De Vlaminck I.

EMBO Mol Med. 2018 Dec;10(12). pii: e9484. doi: 10.15252/emmm.201809484. No abstract available.


Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract.

Burnham P, Dadhania D, Heyang M, Chen F, Westblade LF, Suthanthiran M, Lee JR, De Vlaminck I.

Nat Commun. 2018 Jun 20;9(1):2412. doi: 10.1038/s41467-018-04745-0.


Myriad Applications of Circulating Cell-Free DNA in Precision Organ Transplant Monitoring.

Burnham P, Khush K, De Vlaminck I.

Ann Am Thorac Soc. 2017 Sep;14(Supplement_3):S237-S241. doi: 10.1513/AnnalsATS.201608-634MG. Review.


Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA.

Kowarsky M, Camunas-Soler J, Kertesz M, De Vlaminck I, Koh W, Pan W, Martin L, Neff NF, Okamoto J, Wong RJ, Kharbanda S, El-Sayed Y, Blumenfeld Y, Stevenson DK, Shaw GM, Wolfe ND, Quake SR.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9623-9628. doi: 10.1073/pnas.1707009114. Epub 2017 Aug 22.


Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype.

Sharon E, Shi H, Kharbanda S, Koh W, Martin LR, Khush KK, Valantine H, Pritchard JK, De Vlaminck I.

PLoS Comput Biol. 2017 Aug 3;13(8):e1005629. doi: 10.1371/journal.pcbi.1005629. eCollection 2017 Aug.


Precision monitoring of immunotherapies in solid organ and hematopoietic stem cell transplantation.

DiLoreto R, Khush K, De Vlaminck I.

Adv Drug Deliv Rev. 2017 May 15;114:272-284. doi: 10.1016/j.addr.2017.06.009. Epub 2017 Jun 15. Review.


Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation.

Agbor-Enoh S, Tunc I, De Vlaminck I, Fideli U, Davis A, Cuttin K, Bhatti K, Marishta A, Solomon MA, Jackson A, Graninger G, Harper B, Luikart H, Wylie J, Wang X, Berry G, Marboe C, Khush K, Zhu J, Valantine H.

J Heart Lung Transplant. 2017 Sep;36(9):1004-1012. doi: 10.1016/j.healun.2017.05.026. Epub 2017 May 20.


Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.

Burnham DR, Nijholt B, De Vlaminck I, Quan J, Yusufzai T, Dekker C.

Nucleic Acids Res. 2017 May 5;45(8):4687-4695. doi: 10.1093/nar/gkx147.


Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma.

Burnham P, Kim MS, Agbor-Enoh S, Luikart H, Valantine HA, Khush KK, De Vlaminck I.

Sci Rep. 2016 Jun 14;6:27859. doi: 10.1038/srep27859.


Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes.

Becraft ED, Dodsworth JA, Murugapiran SK, Ohlsson JI, Briggs BR, Kanbar J, De Vlaminck I, Quake SR, Dong H, Hedlund BP, Swingley WD.

Appl Environ Microbiol. 2015 Dec 4;82(4):992-1003. doi: 10.1128/AEM.03140-15. Print 2016 Feb 15.


Monitoring pharmacologically induced immunosuppression by immune repertoire sequencing to detect acute allograft rejection in heart transplant patients: a proof-of-concept diagnostic accuracy study.

Vollmers C, De Vlaminck I, Valantine HA, Penland L, Luikart H, Strehl C, Cohen G, Khush KK, Quake SR.

PLoS Med. 2015 Oct 14;12(10):e1001890. doi: 10.1371/journal.pmed.1001890. eCollection 2015 Oct.


Noninvasive monitoring of infection and rejection after lung transplantation.

De Vlaminck I, Martin L, Kertesz M, Patel K, Kowarsky M, Strehl C, Cohen G, Luikart H, Neff NF, Okamoto J, Nicolls MR, Cornfield D, Weill D, Valantine H, Khush KK, Quake SR.

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13336-41. doi: 10.1073/pnas.1517494112. Epub 2015 Oct 12.


Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

Huang Q, Briggs BR, Dong H, Jiang H, Wu G, Edwardson C, De Vlaminck I, Quake S.

PLoS One. 2014 Nov 3;9(11):e111681. doi: 10.1371/journal.pone.0111681. eCollection 2014. Erratum in: PLoS One. 2014;9(12):e116444.


Skewed brownian fluctuations in single-molecule magnetic tweezers.

Burnham DR, De Vlaminck I, Henighan T, Dekker C.

PLoS One. 2014 Sep 29;9(9):e108271. doi: 10.1371/journal.pone.0108271. eCollection 2014.


A quantitative comparison of single-cell whole genome amplification methods.

de Bourcy CF, De Vlaminck I, Kanbar JN, Wang J, Gawad C, Quake SR.

PLoS One. 2014 Aug 19;9(8):e105585. doi: 10.1371/journal.pone.0105585. eCollection 2014.


Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection.

De Vlaminck I, Valantine HA, Snyder TM, Strehl C, Cohen G, Luikart H, Neff NF, Okamoto J, Bernstein D, Weisshaar D, Quake SR, Khush KK.

Sci Transl Med. 2014 Jun 18;6(241):241ra77. doi: 10.1126/scitranslmed.3007803.


Temporal response of the human virome to immunosuppression and antiviral therapy.

De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, Okamoto J, Snyder TM, Cornfield DN, Nicolls MR, Weill D, Bernstein D, Valantine HA, Quake SR.

Cell. 2013 Nov 21;155(5):1178-87. doi: 10.1016/j.cell.2013.10.034.


Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers.

van Loenhout MT, De Vlaminck I, Flebus B, den Blanken JF, Zweifel LP, Hooning KM, Kerssemakers JW, Dekker C.

PLoS One. 2013 Jun 3;8(6):e65329. doi: 10.1371/journal.pone.0065329. Print 2013.


Magnetic forces and DNA mechanics in multiplexed magnetic tweezers.

De Vlaminck I, Henighan T, van Loenhout MT, Burnham DR, Dekker C.

PLoS One. 2012;7(8):e41432. doi: 10.1371/journal.pone.0041432. Epub 2012 Aug 3.


Non-bias-limited tracking of spherical particles, enabling nanometer resolution at low magnification.

van Loenhout MT, Kerssemakers JW, De Vlaminck I, Dekker C.

Biophys J. 2012 May 16;102(10):2362-71. doi: 10.1016/j.bpj.2012.03.073. Epub 2012 May 15.


Mechanism of homology recognition in DNA recombination from dual-molecule experiments.

De Vlaminck I, van Loenhout MT, Zweifel L, den Blanken J, Hooning K, Hage S, Kerssemakers J, Dekker C.

Mol Cell. 2012 Jun 8;46(5):616-24. doi: 10.1016/j.molcel.2012.03.029. Epub 2012 May 3.


Recent advances in magnetic tweezers.

De Vlaminck I, Dekker C.

Annu Rev Biophys. 2012;41:453-72. doi: 10.1146/annurev-biophys-122311-100544. Epub 2012 Mar 14. Review.


Highly parallel magnetic tweezers by targeted DNA tethering.

De Vlaminck I, Henighan T, van Loenhout MT, Pfeiffer I, Huijts J, Kerssemakers JW, Katan AJ, van Langen-Suurling A, van der Drift E, Wyman C, Dekker C.

Nano Lett. 2011 Dec 14;11(12):5489-93. doi: 10.1021/nl203299e. Epub 2011 Oct 27.


Torsional regulation of hRPA-induced unwinding of double-stranded DNA.

De Vlaminck I, Vidic I, van Loenhout MT, Kanaar R, Lebbink JH, Dekker C.

Nucleic Acids Res. 2010 Jul;38(12):4133-42. doi: 10.1093/nar/gkq067. Epub 2010 Mar 2.


Focusing plasmons in nanoslits for surface-enhanced Raman scattering.

Chen C, Hutchison JA, Van Dorpe P, Kox R, De Vlaminck I, Uji-I H, Hofkens J, Lagae L, Maes G, Borghs G.

Small. 2009 Dec;5(24):2876-82. doi: 10.1002/smll.200901312.


Tunable optical forces between nanophotonic waveguides.

Roels J, De Vlaminck I, Lagae L, Maes B, Van Thourhout D, Baets R.

Nat Nanotechnol. 2009 Aug;4(8):510-3. doi: 10.1038/nnano.2009.186. Epub 2009 Jul 13.


Localized surface plasmon resonance biosensor integrated with microfluidic chip.

Huang C, Bonroy K, Reekmans G, Laureyn W, Verhaegen K, De Vlaminck I, Lagae L, Borghs G.

Biomed Microdevices. 2009 Aug;11(4):893-901. doi: 10.1007/s10544-009-9306-8.


Multifunctional nanomechanical systems via tunably coupled piezoelectric actuation.

Masmanidis SC, Karabalin RB, De Vlaminck I, Borghs G, Freeman MR, Roukes ML.

Science. 2007 Aug 10;317(5839):780-3.


Local electrical detection of single nanoparticle plasmon resonance.

De Vlaminck I, Van Dorpe P, Lagae L, Borghs G.

Nano Lett. 2007 Mar;7(3):703-6. Epub 2007 Feb 22.


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