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Items: 30

1.

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks.

Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K.

Mol Syst Biol. 2019 May 22;15(5):e8339. doi: 10.15252/msb.20188339.

2.

Outpatient minor oral surgery in patients with hemophilia: A case series of 23 patients.

Ramos EA, Diamante M, Caruso D, Muiño JM, Baques A, Antonelli LB, Gutierrez J, Minigutti MO, Guerrero G.

J Clin Exp Dent. 2019 Apr 1;11(4):e395-e399. doi: 10.4317/jced.55506. eCollection 2019 Apr.

3.

PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity.

de Bruijn S, Zhao T, Muiño JM, Schranz EM, Angenent GC, Kaufmann K.

BMC Plant Biol. 2018 Dec 22;18(1):368. doi: 10.1186/s12870-018-1574-0.

4.

PUMPKIN, the Sole Plastid UMP Kinase, Associates with Group II Introns and Alters Their Metabolism.

Schmid LM, Ohler L, Möhlmann T, Brachmann A, Muiño JM, Leister D, Meurer J, Manavski N.

Plant Physiol. 2019 Jan;179(1):248-264. doi: 10.1104/pp.18.00687. Epub 2018 Nov 8.

5.

Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation.

Qu Y, Legen J, Arndt J, Henkel S, Hoppe G, Thieme C, Ranzini G, Muino JM, Weihe A, Ohler U, Weber G, Ostersetzer O, Schmitz-Linneweber C.

Front Plant Sci. 2018 Oct 4;9:1453. doi: 10.3389/fpls.2018.01453. eCollection 2018.

6.

Transcriptomic basis for reinforcement of elm antiherbivore defence mediated by insect egg deposition.

Altmann S, Muino JM, Lortzing V, Brandt R, Himmelbach A, Altschmied L, Hilker M.

Mol Ecol. 2018 Dec;27(23):4901-4915. doi: 10.1111/mec.14900. Epub 2018 Nov 22.

PMID:
30329187
7.

Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin.

Ntini E, Louloupi A, Liz J, Muino JM, Marsico A, Ørom UAV.

Nat Commun. 2018 Apr 24;9(1):1636. doi: 10.1038/s41467-018-04100-3.

8.

Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis.

Pajoro A, Muiño JM, Angenent GC, Kaufmann K.

Methods Mol Biol. 2018;1675:167-181. doi: 10.1007/978-1-4939-7318-7_11.

PMID:
29052192
9.

The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis.

Horstman A, Li M, Heidmann I, Weemen M, Chen B, Muino JM, Angenent GC, Boutilier K.

Plant Physiol. 2017 Oct;175(2):848-857. doi: 10.1104/pp.17.00232. Epub 2017 Aug 22.

10.

Differences in DNA Binding Specificity of Floral Homeotic Protein Complexes Predict Organ-Specific Target Genes.

Smaczniak C, Muiño JM, Chen D, Angenent GC, Kaufmann K.

Plant Cell. 2017 Aug;29(8):1822-1835. doi: 10.1105/tpc.17.00145. Epub 2017 Jul 21.

11.

FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture.

Bemer M, van Mourik H, Muiño JM, Ferrándiz C, Kaufmann K, Angenent GC.

J Exp Bot. 2017 Jun 15;68(13):3391-3403. doi: 10.1093/jxb/erx184.

12.

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor.

Muiño JM, de Bruijn S, Pajoro A, Geuten K, Vingron M, Angenent GC, Kaufmann K.

Mol Biol Evol. 2016 Jan;33(1):185-200. doi: 10.1093/molbev/msv210. Epub 2015 Oct 1.

13.

Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq: experimental protocol and computational analysis.

van Mourik H, Muiño JM, Pajoro A, Angenent GC, Kaufmann K.

Methods Mol Biol. 2015;1284:93-121. doi: 10.1007/978-1-4939-2444-8_5.

PMID:
25757769
14.

AIL and HDG proteins act antagonistically to control cell proliferation.

Horstman A, Fukuoka H, Muino JM, Nitsch L, Guo C, Passarinho P, Sanchez-Perez G, Immink R, Angenent G, Boutilier K.

Development. 2015 Feb 1;142(3):454-64. doi: 10.1242/dev.117168. Epub 2015 Jan 6.

15.

Evidence of a cancer type-specific distribution for consecutive somatic mutation distances.

Muiño JM, Kuruoğlu EE, Arndt PF.

Comput Biol Chem. 2014 Dec;53 Pt A:79-83. doi: 10.1016/j.compbiolchem.2014.08.012. Epub 2014 Aug 23.

PMID:
25179009
16.

Helicobacter pylori and oral pathology: relationship with the gastric infection.

Adler I, Muiño A, Aguas S, Harada L, Diaz M, Lence A, Labbrozzi M, Muiño JM, Elsner B, Avagnina A, Denninghoff V.

World J Gastroenterol. 2014 Aug 7;20(29):9922-35. doi: 10.3748/wjg.v20.i29.9922.

17.

Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development.

Pajoro A, Madrigal P, Muiño JM, Matus JT, Jin J, Mecchia MA, Debernardi JM, Palatnik JF, Balazadeh S, Arif M, Ó'Maoiléidigh DS, Wellmer F, Krajewski P, Riechmann JL, Angenent GC, Kaufmann K.

Genome Biol. 2014 Mar 3;15(3):R41. doi: 10.1186/gb-2014-15-3-r41.

18.

Arabidopsis JAGGED links floral organ patterning to tissue growth by repressing Kip-related cell cycle inhibitors.

Schiessl K, Muiño JM, Sablowski R.

Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2830-5. doi: 10.1073/pnas.1320457111. Epub 2014 Feb 4.

19.

The histone deacetylase inhibitor trichostatin a promotes totipotency in the male gametophyte.

Li H, Soriano M, Cordewener J, Muiño JM, Riksen T, Fukuoka H, Angenent GC, Boutilier K.

Plant Cell. 2014 Jan;26(1):195-209. doi: 10.1105/tpc.113.116491. Epub 2014 Jan 24.

20.

Structural determinants of DNA recognition by plant MADS-domain transcription factors.

Muiño JM, Smaczniak C, Angenent GC, Kaufmann K, van Dijk AD.

Nucleic Acids Res. 2014 Feb;42(4):2138-46. doi: 10.1093/nar/gkt1172. Epub 2013 Nov 25.

21.

Balancing of histone H3K4 methylation states by the Kdm5c/SMCX histone demethylase modulates promoter and enhancer function.

Outchkourov NS, Muiño JM, Kaufmann K, van Ijcken WF, Groot Koerkamp MJ, van Leenen D, de Graaf P, Holstege FC, Grosveld FG, Timmers HT.

Cell Rep. 2013 Apr 25;3(4):1071-9. doi: 10.1016/j.celrep.2013.02.030. Epub 2013 Mar 28.

22.

Arabidopsis class I and class II TCP transcription factors regulate jasmonic acid metabolism and leaf development antagonistically.

Danisman S, van der Wal F, Dhondt S, Waites R, de Folter S, Bimbo A, van Dijk AD, Muino JM, Cutri L, Dornelas MC, Angenent GC, Immink RG.

Plant Physiol. 2012 Aug;159(4):1511-23. doi: 10.1104/pp.112.200303. Epub 2012 Jun 20.

23.

Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.

Smaczniak C, Immink RG, Muiño JM, Blanvillain R, Busscher M, Busscher-Lange J, Dinh QD, Liu S, Westphal AH, Boeren S, Parcy F, Xu L, Carles CC, Angenent GC, Kaufmann K.

Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1560-5. doi: 10.1073/pnas.1112871109. Epub 2012 Jan 11.

24.

Visualizing and characterizing in vivo DNA-binding events and direct target genes of plant transcription factors.

Muiño JM, Angenent GC, Kaufmann K.

Methods Mol Biol. 2011;754:293-305. doi: 10.1007/978-1-61779-154-3_17. Review.

PMID:
21720960
25.

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.

Muiño JM, Hoogstraat M, van Ham RC, van Dijk AD.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W524-7. doi: 10.1093/nar/gkr373. Epub 2011 May 24.

26.

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions.

Muiño JM, Kaufmann K, van Ham RC, Angenent GC, Krajewski P.

Plant Methods. 2011 May 9;7:11. doi: 10.1186/1746-4811-7-11.

27.

Orchestration of floral initiation by APETALA1.

Kaufmann K, Wellmer F, Muiño JM, Ferrier T, Wuest SE, Kumar V, Serrano-Mislata A, Madueño F, Krajewski P, Meyerowitz EM, Angenent GC, Riechmann JL.

Science. 2010 Apr 2;328(5974):85-9. doi: 10.1126/science.1185244.

28.

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP).

Kaufmann K, Muiño JM, Østerås M, Farinelli L, Krajewski P, Angenent GC.

Nat Protoc. 2010 Mar;5(3):457-72. doi: 10.1038/nprot.2009.244. Epub 2010 Feb 18.

PMID:
20203663
29.

Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower.

Kaufmann K, Muiño JM, Jauregui R, Airoldi CA, Smaczniak C, Krajewski P, Angenent GC.

PLoS Biol. 2009 Apr 21;7(4):e1000090. doi: 10.1371/journal.pbio.1000090.

30.

A more flexible parametric estimation of univariate reference intervals: a new method based on the GS-distribution.

Trujillano J, Muiño JM, March J, Sorribas A.

Clin Chim Acta. 2007 Apr;379(1-2):71-80. Epub 2006 Dec 22.

PMID:
17276425

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