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• Article

  Transcriptional Dynamics at Brain Enhancers: from Functional Specialization to Neurodegeneration

  Vermunt, M. W. & Creyghton, M. P., 2016, In: Current Neurology and Neuroscience Reports. 16, 10, p. 94

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

• Transcriptional profiling of CD11c-positive microglia accumulating around amyloid plaques in a mouse model for Alzheimer's disease

  Kamphuis, W., Kooijman, L., Schetters, S., Orre, M. & Hol, E. M., 2016, In: Biochimica et Biophysica Acta- Molecular Basis of Disease. 1862, p. 1847-1860

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcriptional profiling of cells sorted by RNA abundance

  Klemm, S., Semrau, S., Wiebrands, K., Mooijman, D., Faddah, D. A., Jaenisch, R. & van Oudenaarden, A., May 2014, In: Nature Methods. 11, 5, p. 549-51 3 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds

  Scheublin, T. R., Deusch, S., Moreno-Forero, S. K., Müller, J. A., van der Meer, J. R. & Leveau, J. H. J., 2014, In: Environmental Microbiology. 16, 7, p. 2212-2225

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcriptional profiling of human microglia reveals grey-white matter heterogeneity and multiple sclerosis-associated changes.

  van der Poel, M., Ulas, T., Mizee, M. R., Hsiao, C. C., Miedema, S. S. M., Adelia, Schuurman, K., Helder, B., Tas, S. W., Schultze, J. L., Hamann, J. & Huitinga, I., 13 Mar 2019, In: Nature Communications. 10, 1139.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcriptional regulation of CD4 gene expression by T cell factor-1/beta-catenin pathway.

  Huang, Z., Xie, H., Ioannidis, V., Held, W., Clevers, J. C., Sadim, M. S. & Sun, Z., 2006, In: Journal of Immunology. 176, p. 4880-4887

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp Strain Karsten under Soil-Mimicking Conditions

  Ul Haq, I., Dini-Andreote, F. & van Elsas, J. D., Jan 2017, In: Microbial Ecology. 73, 1, p. 236-252

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcription factor achaete-scute homologue 2 initiates follicular T-helper-cell development

  Liu, X., Chen, X., Zhong, B., Wang, A., Wang, X., Chu, F., Nurieva, R. I., Yan, X., Chen, P., van der Flier, L. G., Nakatsukasa, H., Neelapu, S. S., Chen, W., Clevers, H., Tian, Q., Qi, H., Wei, L. & Dong, C., 27 Mar 2014, In: Nature. 507, 7493, p. 513-8 6 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcription factor achaete scute-like 2 controls intestinal stem cell fate.

  van der Flier, L. G., van Gijn, M. E., Hatzis, P., Kujala, P., Haegebarth, A., Stange, D. E., Begthel, H. L., van den Born, M. M. W., Guryev, V., Oving, I. M., van Es, J. H., Barker, N., Peters, P. J., van de Wetering, M. L. & Clevers, H., 2009, In: Cell. 136, 5, p. 903-912

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcription factor Ascl2 promotes germinal center B cell responses by directly regulating AID transcription

  Sun, L., Zhao, X., Liu, X., Zhong, B., Tang, H., Jin, W., Clevers, H., Wang, H., Wang, X. & Dong, C., 01 Jun 2021, In: Cell Reports. 35, 9, p. 109188

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

• Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm

  Yang, X. H., Nadadur, R. D., Hilvering, C. R., Bianchi, V., Werner, M., Mazurek, S. R., Gadek, M., Shen, K. M., Goldman, J. A., Tyan, L., Bekeny, J., Hall, J. M., Lee, N., Perez-Cervantes, C., Burnicka-Turek, O., Poss, K. D., Weber, C. R., de Laat, W., Ruthenburg, A. J. & Moskowitz, I. P., 27 Dec 2017, In: eLife. 6

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

• Transcription factors in early T cell development

  Clevers, J. C., Oosterwegel, M. A. & Georgopoulos, K., 1993, In: Immunology Today. 14, p. 591-596

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcription factor target practice.

  Hostege, F. C. P. & Clevers, J. C., 2006, In: Cell. 124, p. 21-23

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

  Austenaa, L. M. I., Barozzi, I., Simonatto, M., Masella, S., Della Chiara, G., Ghisletti, S., Curina, A., de Wit, E., Bouwman, B. A. M., de Pretis, S., Piccolo, V., Termanini, A., Prosperini, E., Pelizzola, M., de Laat, W. & Natoli, G., 05 Nov 2015, In: Molecular Cell. 60, 3, p. 460-74 15 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast

  van Werven, F. J., Neuert, G., Hendrick, N., Lardenois, A., Buratowski, S., van Oudenaarden, A., Primig, M. & Amon, A., 2012, In: Cell. 150, 6, p. 1170-1181

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse

  de Souza, W. R., de Gouvea, P. F., Savoldi, M., Malavazi, I., de Souza Bernardes, L. A., Goldman, M. H. S., de Vries, R. P., de Castro Oliveira, J. V. & Goldman, G. H., 2011, In: Biotechnology for Biofuels. 4

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network

  Khosravi, C., Kowalczyk, J. E., Chroumpi, T., Battaglia, E., Aguilar Pontes, M-V., Peng, M., Wiebenga, A., Ng, V., Lipzen, A., He, G., Bauer, D., Grigoriev, I. V. & de Vries, R. P., 14 Nov 2019, In: BMC Genomics. 20, 1, p. 853

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

• Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis

  Melief, J., Orre, M., Bossers, K., van Eden, C. G., Schuurman, K. G., Mason, M. R. J., Verhaagen, J., Hamann, J. & Huitinga, I., 25 Apr 2019, In: Acta neuropathologica communications. 7, 1, 60.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcriptome and proteome analyses of proteases in biotroph fungal pathogen Cladosporium fulvum

  Karimi Jashni, M., van der Burgt, A., Battaglia, E., Mehrabi, R., Collemare, J. & de Wit, P. J. G. M., 01 May 2020, In: Journal of Plant Pathology. 102, 2, p. 377-386 10 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

• Transcriptome and proteome profiling of neural stem cells from the human subventricular zone in Parkinson's disease

  Donega, V., Burm, S. M., van Strien, M. E., van Bodegraven, E. J., Paliukhovich, I., Geut, H., van de Berg, W. D. J., Li, K. W., Smit, A. B., Basak, O. & Hol, E. M., Apr 2019, In: Acta neuropathologica communications. 7, 1, p. 4

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcriptome profiling of Ricinus communis L. provides new insights underlying the mechanisms towards thermotolerance during seed imbibition and germination

  Ribeiro, P. R., Willems, L. A. J., Silva, A. T., Fernandez, L. G., de Castro, R. D., Bucher, J., Snoek, B. L., Hilhorst, H. W. M. & Ligterink, W., 15 Dec 2018, In: Industrial Crops and Products. 126, p. 380-393 14 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans

  Jovic, K., Grilli, J., Sterken, M. G., Snoek, B. L., Riksen, J. A. G., Allesina, S. & Kammenga, J. E., 10 Dec 2019, In: BMC Biology. 17, 1, p. 102

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcriptomic and Epigenomic Profiling of Histone Deacetylase Inhibitor Treatment Reveals Distinct Gene Regulation Profiles Leading to Impaired Neutrophil Development

  Govers, A. M. A. P., Wiggers, C. R. M., van Boxtel, R., Mokry, M., Nieuwenhuis, E. E. S., Creyghton, M. P., Bartels, M. & Coffer, P. J., Aug 2019, In: HemaSphere. 3, 4, p. e270

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

• Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806

  Makower, A. K., Schuurmans, J. M., Groth, D., Zilliges, Y., Matthijs, H. C. P. & Dittmann, E., 2015, In: Applied and Environmental Microbiology. 81, 2, p. 544-554

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcript profiling indicates that the absence of PsbO affects the coordination of C and N metabolism in Synechocystis sp. PCC 6803

  Schriek, S., Aguirre-von-Wobeser, E., Nodop, A., Becker, A., Ibelings, B. W., Bok, J. M., Staiger, D., Matthijs, H. C. P., Pistorius, E. K. & Michel, K-P., 2008, In: Physiologia Plantarum. 133, 3, p. 525-543

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review
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• Transcript profiling of different types of multiple sclerosis lesions yields FGF1 as a promoter of remyelination

  Mohan, H., Friese, A., Albrecht, S., Krumbholz, M., Elliott, C. L., Arthur, A., Menon, R., Farina, C., Junker, A., Stadelmann, C., Barnett, S. C., Huitinga, I., Wekerle, H., Hohlfeld, R., Lassmann, H., Kuhlmann, T., Linington, C. & Meinl, E., 11 Dec 2014, In: Acta neuropathologica communications. 2, 1, p. 178

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transcutaneous electrical nerve stimulation (TENS) improves circadian rhythm disturbances in Alzheimer's disease

  Someren, E. J. W. V., Scherder, E. J. A. & Swaab, D. F., 1998, In: Alzheimer Disease and Associated Disorders. 12, p. 114-118

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transcutaneous electrical nerve stimulation (TENS) improves the rest-activity rhythm in midstage Alzheimer's disease

  Scherder, E. J. A., Someren, E. J. W. V. & Swaab, D. F., 2000, In: Behavioural Brain Research. 101, p. 105-107

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transdiagnostic comparison of visual working memory capacity in bipolar disorder and schizophrenia

  Barnes-Scheufler, C. V., Passow, C., Rösler, L., Mayer, J. S., Oertel, V., Kittel-Schneider, S., Matura, S., Reif, A. & Bittner, R. A., 2021, In: International journal of bipolar disorders. 9, 1, p. 12

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transfer and Integration of Latin and Vernacular Drama in the Early Modern Period. The case of Everyman, Elckerlijc, Homulus, and Hecastus.

  Bloemendal, J., 2010, In: Arcadia. p. 274-288

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transfer learning of deep neural network representations for fMRI decoding

  Svanera, M., Savardi, M., Benini, S., Signoroni, A., Raz, G., Hendler, T., Muckli, L., Goebel, R. & Valente, G., 01 Aug 2019, In: Journal of Neuroscience Methods. 328, p. 108319

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transfer of maternal antibodies against avian influenza virus in mallards (Anas platyrhynchos)

  Van Dijk, J. G. B., Mateman, A. C. & Klaassen, M. R. J., 2014, In: PLoS One. 9, 11, e112595.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2

  Simmini, S., Bialecka, M., Huch, M., Kester, L., van de Wetering, M., Sato, T., Beck, F., van Oudenaarden, A., Clevers, H. & Deschamps, J., 2014, In: Nature Communications. 5, p. 5728

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transformative innovation policy: Addressing variety in an emerging policy paradigm

  Diercks, G., Larsen, H. & Steward, F., 13 Nov 2018, In: Research Policy.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transgene expression in rat fetal brain grafts is maintained for 7 months after ex vivo adenoviral vector-mediated gene transfer

  van Esseveldt, K. E., Hermens, W. T. J. M. C., Verhaagen, J. & Boer, G. J., 09 Jan 1998, In: Neuroscience Letters. 240, 2, p. 116-20 5 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transgenerational Effects and Epigenetic Memory in the Clonal Plant Trifolium repens

  Rendina González, A. P., Preite, V., Verhoeven, K. J. F. & Latzel, V., 2018, In: Frontiers in Plant Science. 9, p. 1677 1 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transgenerational effects of stress exposure on offspring phenotypes in apomictic dandelion

  Verhoeven, K. J. F. & Van Gurp, T. P., 2012, In: PLoS One. 7, 6, e38605.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Trans generational effects of the neurotoxin BMAA on the aquatic grazer Daphnia magna

  Faassen, E. J., García-Altares, M., Mendes e Mello, M. & Lürling, M., Nov 2015, In: Aquatic Toxicology. 168, p. 98-107 10 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review
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• Transgenic expression of B-50/GAP-43 in mature olfactory neurons triggers downregulation of native B-50/GAP-43 expression in immature olfactory neurons

  Holtmaat, A. J. D. G., Huizinga, C. T., Margolis, F. L., Gispen, W. H. & Verhaagen, J., 10 Dec 1999, In: Molecular Brain Research. 74, 1-2, p. 197-207 11 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transgenic organisms: should we use them or not?

  Van Damme, J. M. M., 1999, In: Journal of Evolutionary Biology. 12, p. 188

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transgenic plants as vital components of integrated pest management

  Kos, M., van Loon, J. J. A., Dicke, M. & Vet, L. E. M., 2009, In: Trends in Biotechnology. 27, 11, p. 621-627

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development

  Andreote, F. D., Mendes, R., Dini-Andreote, F., Rossetto, P. B., Labate, C. A., Pizzirani-Kleiner, A. A., van Elsas, J. D., Azevedo, J. L. & Araujo, W. L., May 2008, In: Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology. 93, 4, p. 415-424

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transhepatic bile acid kinetics in pigs and humans

  Eggink, H. M., van Nierop, F. S., Schooneman, M. G., Boelen, A., Kalsbeek, A., Koehorst, M., Ten Have, G. A. M., de Brauw, L. M., Groen, A. K., Romijn, J. A., Deutz, N. E. P. & Soeters, M. R., 2018, In: Clinical Nutrition. 37, p. 1406-1414

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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• Transient, tidal-scale, nitrogen transformations in an estuarine turbidity maximum-fluid mud system (The Gironde, S.W. France)

  Abril, G., Riou, S. A., Etcheber, H., Frankignoulle, M., De Wit, R. & Middelburg, J. J., 2000, In: Estuarine Coastal and Shelf Science. 50, 5, p. 703-715

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review
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• Transient but not genetic loss of miR-451 is protective in the development of pulmonary arterial hypertension

  Grant, J. S., Morecroft, I., Dempsie, Y., van Rooij, E., MacLean, M. R. & Baker, A. H., Dec 2013, In: Pulmonary Circulation. 3, 4, p. 840-50 11 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transient downregulation of Sema3A mRNA in a rat model for temporal lobe epilepsy. A novel molecular event potentially contributing to mossy fiber sprouting

  Holtmaat, A. J. D. G., Gorter, J. A., de Wit, J., Tolner, E. A., Spijker, S., Giger, R. J., Lopes da Silva, F. H. & Verhaagen, J., Jul 2003, In: Experimental Neurology. 182, 1, p. 142-50 9 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transient gene transfer to neurons and glia: analysis of adenoviral vector performance in the CNS and PNS

  Hermens, W. T. J. M. C., Giger, R. J., Holtmaat, A. J. D. G., Dijkhuizen, P. A., Houweling, D. A. & Verhaagen, J., Jan 1997, In: Journal of Neuroscience Methods. 71, 1, p. 85-98 14 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

• Transient negative biochar effects on plant growth are strongest after microbial species loss

  Hol, W. H. G., Vestergård, M., Ten Hooven, F. C., Duyts, H., Van de Voorde, T. F. J. & Bezemer, T. M., 2017, In: Soil Biology & Biochemistry. 115, December, p. 442-451

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review
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• Transition of a lake to turbid state six years after biomanipulation: Mechanisms and pathways

  Van Donk, E. & Gulati, R. D., 1995, In: Water Science and Technology. 32, 4, p. 197-206

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review
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• Transitions in diatom assemblages and pigments through dry and wet season conditions in the red river, hanoi (vietnam)

  Duong, T. T., Nguyen, H. Y., Nguyen, T. K., Dang, D. K., Vu, T. N., Le, T. P. Q., Le, N. D., Panizzo, V. & McGowan, S., 2019, In: Plant Ecology and Evolution. 152, 2, p. 163-177 15 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access