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Items: 1 to 50 of 80

1.

Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression.

Tsankov AM, Wadsworth MH 2nd, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A.

Development. 2019 Sep 12;146(19). pii: dev174722. doi: 10.1242/dev.174722.

PMID:
31515224
2.

Increased methotrexate intolerance in juvenile idiopathic arthritis compared to acute lymphoblastic leukaemia in children.

Kyvsgaard N, Mikkelsen TS, Thastum M, Christensen AE, Wehner PS, Nysom K, Herlin T.

PLoS One. 2019 Jul 11;14(7):e0219539. doi: 10.1371/journal.pone.0219539. eCollection 2019.

3.

Plasma creatinine as predictor of delayed elimination of high-dose methotrexate in childhood acute lymphoblastic leukemia: A Danish population-based study.

Schmidt D, Kristensen K, Schroeder H, Wehner PS, Rosthøj S, Heldrup J, Damsgaard L, Schmiegelow K, Mikkelsen TS.

Pediatr Blood Cancer. 2019 Jun;66(6):e27637. doi: 10.1002/pbc.27637. Epub 2019 Mar 5.

PMID:
30835935
4.

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome.

Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C.

Cell Syst. 2018 Sep 26;7(3):258-268.e3. doi: 10.1016/j.cels.2018.07.006. Epub 2018 Sep 5.

5.

Identification of Functional Variants in the FAM13A Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Locus by Massively Parallel Reporter Assays.

Castaldi PJ, Guo F, Qiao D, Du F, Naing ZZC, Li Y, Pham B, Mikkelsen TS, Cho MH, Silverman EK, Zhou X.

Am J Respir Crit Care Med. 2019 Jan 1;199(1):52-61. doi: 10.1164/rccm.201802-0337OC.

PMID:
30079747
6.

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2018 Feb 22;172(5):1132-1134. doi: 10.1016/j.cell.2018.02.021. No abstract available.

7.

Parallel derivation of isogenic human primed and naive induced pluripotent stem cells.

Kilens S, Meistermann D, Moreno D, Chariau C, Gaignerie A, Reignier A, Lelièvre Y, Casanova M, Vallot C, Nedellec S, Flippe L, Firmin J, Song J, Charpentier E, Lammers J, Donnart A, Marec N, Deb W, Bihouée A, Le Caignec C, Pecqueur C, Redon R, Barrière P, Bourdon J, Pasque V, Soumillon M, Mikkelsen TS, Rougeulle C, Fréour T, David L; Milieu Intérieur Consortium.

Nat Commun. 2018 Jan 24;9(1):360. doi: 10.1038/s41467-017-02107-w.

8.

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells.

Semrau S, Goldmann JE, Soumillon M, Mikkelsen TS, Jaenisch R, van Oudenaarden A.

Nat Commun. 2017 Oct 23;8(1):1096. doi: 10.1038/s41467-017-01076-4.

9.

Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues.

Kadoki M, Patil A, Thaiss CC, Brooks DJ, Pandey S, Deep D, Alvarez D, von Andrian UH, Wagers AJ, Nakai K, Mikkelsen TS, Soumillon M, Chevrier N.

Cell. 2017 Oct 5;171(2):398-413.e21. doi: 10.1016/j.cell.2017.08.024. Epub 2017 Sep 21.

10.

Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity.

Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS, Cheng ZF, Kaddis JS, Han A, Roelf K, Calderon RI, Cynn E, Hu X, Mandleywala K, Wilhelmy J, Grimes SM, Corney DC, Boutet SC, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Wang F, von Furstenberg RJ, Smith NR, Chandrakesan P, May R, Chrissy MAS, Jain R, Cartwright CA, Niland JC, Hong YK, Carrington J, Breault DT, Epstein J, Houchen CW, Lynch JP, Martin MG, Plevritis SK, Curtis C, Ji HP, Li L, Henning SJ, Wong MH, Kuo CJ.

Cell Stem Cell. 2017 Jul 6;21(1):78-90.e6. doi: 10.1016/j.stem.2017.06.014.

11.

Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem-cell self-renewal.

Yan KS, Janda CY, Chang J, Zheng GXY, Larkin KA, Luca VC, Chia LA, Mah AT, Han A, Terry JM, Ootani A, Roelf K, Lee M, Yuan J, Li X, Bolen CR, Wilhelmy J, Davies PS, Ueno H, von Furstenberg RJ, Belgrader P, Ziraldo SB, Ordonez H, Henning SJ, Wong MH, Snyder MP, Weissman IL, Hsueh AJ, Mikkelsen TS, Garcia KC, Kuo CJ.

Nature. 2017 May 11;545(7653):238-242. doi: 10.1038/nature22313. Epub 2017 May 3.

12.

Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci.

Pashos EE, Park Y, Wang X, Raghavan A, Yang W, Abbey D, Peters DT, Arbelaez J, Hernandez M, Kuperwasser N, Li W, Lian Z, Liu Y, Lv W, Lytle-Gabbin SL, Marchadier DH, Rogov P, Shi J, Slovik KJ, Stylianou IM, Wang L, Yan R, Zhang X, Kathiresan S, Duncan SA, Mikkelsen TS, Morrisey EE, Rader DJ, Brown CD, Musunuru K.

Cell Stem Cell. 2017 Apr 6;20(4):558-570.e10. doi: 10.1016/j.stem.2017.03.017.

13.

Systematic dissection of genomic features determining transcription factor binding and enhancer function.

Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1291-E1300. doi: 10.1073/pnas.1621150114. Epub 2017 Jan 30.

14.

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.

Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA.

Nucleic Acids Res. 2017 Feb 17;45(3):1567-1568. doi: 10.1093/nar/gkx032. No abstract available.

15.

Massively parallel digital transcriptional profiling of single cells.

Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BJ, Bielas JH.

Nat Commun. 2017 Jan 16;8:14049. doi: 10.1038/ncomms14049.

16.

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.

Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA.

Nucleic Acids Res. 2017 Feb 17;45(3):1553-1565. doi: 10.1093/nar/gkw1226. Erratum in: Nucleic Acids Res. 2017 Feb 17;45(3):1567-1568.

17.

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.

Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M.

Nat Biotechnol. 2016 Nov;34(11):1180-1190. doi: 10.1038/nbt.3678. Epub 2016 Oct 3.

18.

Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants.

Brenan L, Andreev A, Cohen O, Pantel S, Kamburov A, Cacchiarelli D, Persky NS, Zhu C, Bagul M, Goetz EM, Burgin AB, Garraway LA, Getz G, Mikkelsen TS, Piccioni F, Root DE, Johannessen CM.

Cell Rep. 2016 Oct 18;17(4):1171-1183. doi: 10.1016/j.celrep.2016.09.061.

19.

Prophylactic Trimethoprim-Sulfamethoxazole Does Not Affect Pharmacokinetics or Pharmacodynamics of Methotrexate.

Watts CS, Sciasci JN, Pauley JL, Panetta JC, Pei D, Cheng C, Christensen CM, Mikkelsen TS, Pui CH, Jeha S, Relling MV.

J Pediatr Hematol Oncol. 2016 Aug;38(6):449-52. doi: 10.1097/MPH.0000000000000606.

20.

Consensus definitions of 14 severe acute toxic effects for childhood lymphoblastic leukaemia treatment: a Delphi consensus.

Schmiegelow K, Attarbaschi A, Barzilai S, Escherich G, Frandsen TL, Halsey C, Hough R, Jeha S, Kato M, Liang DC, Mikkelsen TS, Möricke A, Niinimäki R, Piette C, Putti MC, Raetz E, Silverman LB, Skinner R, Tuckuviene R, van der Sluis I, Zapotocka E; Ponte di Legno toxicity working group.

Lancet Oncol. 2016 Jun;17(6):e231-e239. doi: 10.1016/S1470-2045(16)30035-3. Review.

21.

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits.

Ulirsch JC, Nandakumar SK, Wang L, Giani FC, Zhang X, Rogov P, Melnikov A, McDonel P, Do R, Mikkelsen TS, Sankaran VG.

Cell. 2016 Jun 2;165(6):1530-1545. doi: 10.1016/j.cell.2016.04.048.

22.

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2016 Jun 2;165(6):1519-1529. doi: 10.1016/j.cell.2016.04.027. Erratum in: Cell. 2018 Feb 22;172(5):1132-1134.

23.

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.

O'Connell DJ, Kolde R, Sooknah M, Graham DB, Sundberg TB, Latorre I, Mikkelsen TS, Xavier RJ.

Cell Syst. 2016 May 25;2(5):323-334. doi: 10.1016/j.cels.2016.04.011. Epub 2016 May 19.

24.

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface.

Ferreira LM, Meissner TB, Mikkelsen TS, Mallard W, O'Donnell CW, Tilburgs T, Gomes HA, Camahort R, Sherwood RI, Gifford DK, Rinn JL, Cowan CA, Strominger JL.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):5364-9. doi: 10.1073/pnas.1602886113. Epub 2016 Apr 13.

25.

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.

Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS.

Cell. 2015 Jul 16;162(2):412-424. doi: 10.1016/j.cell.2015.06.016.

26.

Dissecting neural differentiation regulatory networks through epigenetic footprinting.

Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A.

Nature. 2015 Feb 19;518(7539):355-359. doi: 10.1038/nature13990. Epub 2014 Dec 24.

27.

Altered chromatin occupancy of master regulators underlies evolutionary divergence in the transcriptional landscape of erythroid differentiation.

Ulirsch JC, Lacy JN, An X, Mohandas N, Mikkelsen TS, Sankaran VG.

PLoS Genet. 2014 Dec 18;10(12):e1004890. doi: 10.1371/journal.pgen.1004890. eCollection 2014 Dec.

28.

Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis.

Kang S, Tsai LT, Zhou Y, Evertts A, Xu S, Griffin MJ, Issner R, Whitton HJ, Garcia BA, Epstein CB, Mikkelsen TS, Rosen ED.

Nat Cell Biol. 2015 Jan;17(1):44-56. doi: 10.1038/ncb3080. Epub 2014 Dec 15.

29.

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.

Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC.

Genome Biol. 2014;15(11):519.

30.

Massively parallel reporter assays in cultured mammalian cells.

Melnikov A, Zhang X, Rogov P, Wang L, Mikkelsen TS.

J Vis Exp. 2014 Aug 17;(90). doi: 10.3791/51719.

31.

Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A.

Cell Rep. 2014 Jul 10;8(1):284-96. doi: 10.1016/j.celrep.2014.05.048. Epub 2014 Jun 26.

32.

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes.

Melnikov A, Rogov P, Wang L, Gnirke A, Mikkelsen TS.

Nucleic Acids Res. 2014 Aug;42(14):e112. doi: 10.1093/nar/gku511. Epub 2014 Jun 9.

33.

The regulatory landscape of osteogenic differentiation.

Håkelien AM, Bryne JC, Harstad KG, Lorenz S, Paulsen J, Sun J, Mikkelsen TS, Myklebost O, Meza-Zepeda LA.

Stem Cells. 2014 Oct;32(10):2780-93. doi: 10.1002/stem.1759.

34.

Analysis of the effects of five factors relevant to in vitro chondrogenesis of human mesenchymal stem cells using factorial design and high throughput mRNA-profiling.

Jakobsen RB, Østrup E, Zhang X, Mikkelsen TS, Brinchmann JE.

PLoS One. 2014 May 9;9(5):e96615. doi: 10.1371/journal.pone.0096615. eCollection 2014.

35.

ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells.

Jiang L, Wallerman O, Younis S, Rubin CJ, Gilbert ER, Sundström E, Ghazal A, Zhang X, Wang L, Mikkelsen TS, Andersson G, Andersson L.

PLoS One. 2014 Apr 8;9(4):e94187. doi: 10.1371/journal.pone.0094187. eCollection 2014.

36.

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.

Nat Biotechnol. 2014 Apr;32(4):381-386. doi: 10.1038/nbt.2859. Epub 2014 Mar 23.

37.

Brief report: importance of SOX8 for in vitro chondrogenic differentiation of human mesenchymal stromal cells.

Herlofsen SR, Høiby T, Cacchiarelli D, Zhang X, Mikkelsen TS, Brinchmann JE.

Stem Cells. 2014 Jun;32(6):1629-35. doi: 10.1002/stem.1642.

38.

High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.

Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A.

Cell. 2013 Dec 5;155(6):1409-21. doi: 10.1016/j.cell.2013.10.047. Epub 2013 Nov 21.

39.

Early B-cell factor-1 (EBF1) is a key regulator of metabolic and inflammatory signaling pathways in mature adipocytes.

Griffin MJ, Zhou Y, Kang S, Zhang X, Mikkelsen TS, Rosen ED.

J Biol Chem. 2013 Dec 13;288(50):35925-39. doi: 10.1074/jbc.M113.491936. Epub 2013 Oct 30.

40.

microRNA-140 targets RALA and regulates chondrogenic differentiation of human mesenchymal stem cells by translational enhancement of SOX9 and ACAN.

Karlsen TA, Jakobsen RB, Mikkelsen TS, Brinchmann JE.

Stem Cells Dev. 2014 Feb 1;23(3):290-304. doi: 10.1089/scd.2013.0209. Epub 2013 Nov 7.

PMID:
24063364
41.

Extended duration of prehydration does not prevent nephrotoxicity or delayed drug elimination in high-dose methotrexate infusions: a prospectively randomized cross-over study.

Mikkelsen TS, Mamoudou AD, Tuckuviene R, Wehner PS, Schroeder H.

Pediatr Blood Cancer. 2014 Feb;61(2):297-301. doi: 10.1002/pbc.24623. Epub 2013 Sep 3.

PMID:
24039194
42.

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.

Soumillon M, Necsulea A, Weier M, Brawand D, Zhang X, Gu H, Barthès P, Kokkinaki M, Nef S, Gnirke A, Dym M, de Massy B, Mikkelsen TS, Kaessmann H.

Cell Rep. 2013 Jun 27;3(6):2179-90. doi: 10.1016/j.celrep.2013.05.031. Epub 2013 Jun 20.

43.

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.

Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M.

Genome Res. 2013 May;23(5):800-11. doi: 10.1101/gr.144899.112. Epub 2013 Mar 19.

44.

Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells.

Herlofsen SR, Bryne JC, Høiby T, Wang L, Issner R, Zhang X, Coyne MJ, Boyle P, Gu H, Meza-Zepeda LA, Collas P, Mikkelsen TS, Brinchmann JE.

BMC Genomics. 2013 Feb 15;14:105. doi: 10.1186/1471-2164-14-105.

45.

OATP1B1 polymorphism as a determinant of erythromycin disposition.

Lancaster CS, Bruun GH, Peer CJ, Mikkelsen TS, Corydon TJ, Gibson AA, Hu S, Orwick SJ, Mathijssen RH, Figg WD, Baker SD, Sparreboom A.

Clin Pharmacol Ther. 2012 Nov;92(5):642-50. doi: 10.1038/clpt.2012.106. Epub 2012 Sep 19.

46.

Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica.

Das R, Anderson N, Koran MI, Weidman JR, Mikkelsen TS, Kamal M, Murphy SK, Linblad-Toh K, Greally JM, Jirtle RL.

BMC Genomics. 2012 Aug 16;13:394. doi: 10.1186/1471-2164-13-394.

47.

Influence of polymorphic OATP1B-type carriers on the disposition of docetaxel.

de Graan AJ, Lancaster CS, Obaidat A, Hagenbuch B, Elens L, Friberg LE, de Bruijn P, Hu S, Gibson AA, Bruun GH, Corydon TJ, Mikkelsen TS, Walker AL, Du G, Loos WJ, van Schaik RH, Baker SD, Mathijssen RH, Sparreboom A.

Clin Cancer Res. 2012 Aug 15;18(16):4433-40. Epub 2012 Jun 18.

48.

Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO.

Raghav SK, Waszak SM, Krier I, Gubelmann C, Isakova A, Mikkelsen TS, Deplancke B.

Mol Cell. 2012 May 11;46(3):335-50. doi: 10.1016/j.molcel.2012.03.017. Epub 2012 Apr 19.

49.

Contribution of tumoral and host solute carriers to clinical drug response.

Sprowl JA, Mikkelsen TS, Giovinazzo H, Sparreboom A.

Drug Resist Updat. 2012 Feb-Apr;15(1-2):5-20. doi: 10.1016/j.drup.2012.01.009. Epub 2012 Mar 28. Review.

50.

A unique regulatory phase of DNA methylation in the early mammalian embryo.

Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A.

Nature. 2012 Mar 28;484(7394):339-44. doi: 10.1038/nature10960.

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