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Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization.
Published in:
Nucleic Acids Research, 2015, v. 43, n. 14, p. 1, doi. 10.1093/nar/gkv303
By:
- Locati, Mauro D.;
- Terpstra, Inez;
- de Leeuw, Wim C.;
- Kuzak, Mateusz;
- Rauwerda, Han;
- Ensink, Wim A.;
- van Leeuwen, Selina;
- Nehrdich, Ulrike;
- Spaink, Herman P.;
- Jonker, Martijs J.;
- Breit, Timo M.;
- Dekker, Rob J.
Publication type:
Article
Absence/presence calling in microarray-based CGH experiments with non-model organisms.
Published in:
Nucleic Acids Research, 2014, v. 42, n. 11, p. e94, doi. 10.1093/nar/gku343
By:
- Jonker, Martijs J.;
- de Leeuw, Wim C.;
- Marinković, Marino;
- Wittink, Floyd R. A.;
- Rauwerda, Han;
- Bruning, Oskar;
- Ensink, Wim A.;
- Fluit, Ad C.;
- Boel, C. H.;
- Jong, Mark de;
- Breit, Timo M.
Publication type:
Article
Operon structure of Staphylococcus aureus.
Published in:
Nucleic Acids Research, 2010, v. 38, n. 10, p. 3263, doi. 10.1093/nar/gkq058
By:
- ten Broeke-Smits, Nicole J. P.;
- Pronk, Tessa E.;
- Jongerius, Ilse;
- Bruning, Oskar;
- Wittink, Floyd R.;
- Breit, Timo M.;
- van Strijp, Jos A. G.;
- Fluit, Ad C.;
- Boel, C. H. Edwin
Publication type:
Article
The scid mouse environment causes immunophenotypic changes in human immature T-cell lines.
Published in:
International Journal of Cancer, 1994, v. 56, n. 4, p. 546, doi. 10.1002/ijc.2910560414
By:
- Uittenbogaart, Christel H.;
- Anisman, Deborah J.;
- Tary-Lehmann, Magdalena;
- Vollger, Leanne W.;
- Breit, Timo M.;
- van Dongen, Jacques J. M.;
- Saxon, Andrew
Publication type:
Article
WRKY40 and WRKY6 act downstream of the green leaf volatile E-2-hexenal in Arabidopsis.
Published in:
Plant Journal, 2015, v. 83, n. 6, p. 1082, doi. 10.1111/tpj.12953
By:
- Mirabella, Rossana;
- Rauwerda, Han;
- Allmann, Silke;
- Scala, Alessandra;
- Spyropoulou, Eleni A.;
- Vries, Michel;
- Boersma, Maaike R.;
- Breit, Timo M.;
- Haring, Michel A.;
- Schuurink, Robert C.
Publication type:
Article
A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of <i>In-Vitro</i> and <i>In-Vivo</i> Murine UV Exposure.
Published in:
PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0097089
By:
- Bruning, Oskar;
- Rodenburg, Wendy;
- van Oostrom, Conny T.;
- Jonker, Martijs J.;
- de Jong, Mark;
- Dekker, Rob J.;
- Rauwerda, Han;
- Ensink, Wim A.;
- de Vries, Annemieke;
- Breit, Timo M.
Publication type:
Article
Combining Next-Generation Sequencing and Microarray Technology into a Transcriptomics Approach for the Non-Model Organism Chironomus riparius.
Published in:
PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0048096
By:
- Marinković, Marino;
- de Leeuw, Wim C.;
- de Jong, Mark;
- Kraak, Michiel H. S.;
- Admiraal, Wim;
- Breit, Timo M.;
- Jonker, Martijs J.
Publication type:
Article
Gene Expression Profiling in a Mouse Model Identifies Fetal Liver- and Placenta-Derived Potential Biomarkers for Down Syndrome Screening.
Published in:
PLoS ONE, 2011, v. 6, n. 4, p. 1, doi. 10.1371/journal.pone.0018866
By:
- Pennings, Jeroen L. A.;
- Rodenburg, Wendy;
- Imholz, Sandra;
- Koster, Maria P. H.;
- van Oostrom, Conny T. M.;
- Breit, Timo M.;
- Schielen, Peter C. J. I.;
- de Vries, Annemieke
Publication type:
Article
Primary Nasal Epithelium Exposed to House Dust Mite Extract Shows Activated Expression in Allergic Individuals.
Published in:
American Journal of Respiratory Cell & Molecular Biology, 2008, v. 38, n. 3, p. 293, doi. 10.1165/rcmb.2007-0278OC
By:
- Vroling, Aram B.;
- Jonker, Martijs J.;
- Luiten, Silvia;
- Breit, Timo M.;
- Fokkens, Wytske J.;
- van Drunen, Cornelis M.
Publication type:
Article
Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity.
Published in:
Nature Cell Biology, 2009, v. 11, n. 5, p. 604, doi. 10.1038/ncb1866
By:
- Garinis, George A.;
- Uittenboogaard, Lieneke M.;
- Stachelscheid, Heike;
- Fousteri, Maria;
- van Ijcken, Wilfred;
- Breit, Timo M.;
- van Steeg, Harry;
- Mullenders, Leon H. F.;
- van der Horst, Gijsbertus T. J.;
- Brüning, Jens C.;
- Niessen, Carien M.;
- Hoeijmakers, Jan H. J.;
- Schumacher, Björn
Publication type:
Article
Integrating heterogeneous sequence informationfor transcriptome-wide microarray design; aZebrafish example.
Published in:
BMC Research Notes, 2010, v. 3, p. 192, doi. 10.1186/1756-0500-3-192
By:
- Rauwerda, Han;
- de Jong, Mark;
- de Leeuw, Wim C.;
- Spaink, Herman P.;
- Breit, Timo M.
Publication type:
Article
RNA isolation method for single embryotranscriptome analysis in zebrafish.
Published in:
BMC Research Notes, 2010, v. 3, p. 73, doi. 10.1186/1756-0500-3-73
By:
- de Jong, Mark;
- Rauwerda, Han;
- Bruning, Oskar;
- Verkooijen, Jurgo;
- Spaink, Herman P.;
- Breit, Timo M.
Publication type:
Article
miRNA repertoire and host immune factor regulation upon avian coronavirus infection in eggs.
Published in:
Archives of Virology, 2020, v. 165, n. 4, p. 835, doi. 10.1007/s00705-020-04527-4
By:
- Kemp, Vera;
- Laconi, Andrea;
- Cocciolo, Giulio;
- Berends, Alinda J.;
- Breit, Timo M.;
- Verheije, M. Hélène
Publication type:
Article
Finding transcriptomics biomarkers for in vivo identification of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models.
Published in:
Carcinogenesis, 2009, v. 30, n. 10, p. 1805, doi. 10.1093/carcin/bgp190
By:
- Jonker, Martijs J.;
- Bruning, Oskar;
- Van Iterson, Maarten;
- Schaap, Mirjam M.;
- Van der Hoeven, Tessa V.;
- Vrieling, Harry;
- Beems, Rudolf B.;
- De Vries, Annemieke;
- Van Steeg, Harry;
- Breit, Timo M.;
- Luijten, Mirjam
Publication type:
Article
Delayed expression of apoptotic and cell-cycle control genes in carcinogen-exposed bladders of mice lacking p53.S389 phosphorylation.
Published in:
Carcinogenesis, 2007, v. 28, n. 8, p. 1814, doi. 10.1093/carcin/bgm041
By:
- Bruins, Wendy;
- Jonker, Martijs J.;
- Bruning, Oskar;
- Pennings, Jeroen L. A.;
- Schaap, Mirjam M.;
- Hoogervorst, Esther M.;
- Steeg, Harry van;
- Breit, Timo M.;
- De Vries, Annemieke
Publication type:
Article
Single cell transcriptomics of neighboring hyphae of Aspergillus niger.
Published in:
Genome Biology, 2011, v. 12, n. 8, p. 1, doi. 10.1186/gb-2011-12-8-r71
By:
- de Bekker, Charissa;
- Bruning, Oskar;
- Jonker, Martijs J.;
- Breit, Timo M.;
- Wösten, Han A.B.
Publication type:
Article
Gene Expression Analysis of Tuberous Sclerosis Complex Cortical Tubers Reveals Increased Expression of Adhesion and Inflammatory Factors.
Published in:
Brain Pathology, 2010, v. 20, n. 4, p. 704, doi. 10.1111/j.1750-3639.2009.00341.x
By:
- Boer, Karin;
- Crino, Peter B.;
- Gorter, Jan A.;
- Nellist, Mark;
- Jansen, Floor E.;
- Spliet, Wim G.M.;
- van Rijen, Peter C.;
- Wittink, Floyd R.A.;
- Breit, Timo M.;
- Troost, Dirk;
- Wadman, Wytse J.;
- Aronica, Eleonora
Publication type:
Article
Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos.
Published in:
BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3672-z
By:
- Rauwerda, Han;
- Pagano, Johanna F. B.;
- de Leeuw, Wim C.;
- Ensink, Wim;
- Nehrdich, Ulrike;
- de Jong, Mark;
- Jonker, Martijs;
- Spaink, Herman P.;
- Breit, Timo M.
Publication type:
Article
Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs.
Published in:
PLoS ONE, 2016, v. 11, n. 1, p. 1, doi. 10.1371/journal.pone.0147151
By:
- Rauwerda, Han;
- Wackers, Paul;
- Pagano, Johanna F. B.;
- de Jong, Mark;
- Ensink, Wim;
- Dekker, Rob;
- Nehrdich, Ulrike;
- Spaink, Herman P.;
- Jonker, Martijs;
- Breit, Timo M.
Publication type:
Article
Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment.
Published in:
PLoS ONE, 2016, v. 11, n. 1, p. 1, doi. 10.1371/journal.pone.0145252
By:
- Bruning, Oskar;
- Rodenburg, Wendy;
- Wackers, Paul F. K.;
- van Oostrom, Conny;
- Jonker, Martijs J.;
- Dekker, Rob J.;
- Rauwerda, Han;
- Ensink, Wim A.;
- de Vries, Annemieke;
- Breit, Timo M.
Publication type:
Article
Identifying small RNAs derived from maternal- and somatic-type rRNAs in zebrafish development.
Published in:
Genome, 2018, v. 61, n. 5, p. 371, doi. 10.1139/gen-2017-0202
By:
- Locati, Mauro D.;
- Pagano, Johanna F.B.;
- Abdullah, Farah;
- Ensink, Wim A.;
- van Olst, Marina;
- van Leeuwen, Selina;
- Nehrdich, Ulrike;
- Spaink, Herman P.;
- Rauwerda, Han;
- Jonker, Martijs J.;
- Dekker, Rob J.;
- Breit, Timo M.;
- Crease, T.
Publication type:
Article
A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data.
Published in:
Bioinformatics, 2007, v. 23, n. 22, p. 3080, doi. 10.1093/bioinformatics/btm461
By:
- Lennart J. G. Post;
- Marco Roos;
- M. Scott Marshall;
- Roel van Driel;
- Timo M. Breit
Publication type:
Article
OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity.
Published in:
BMC Proceedings, 2009, v. 3, p. 1, doi. 10.1186/1753-6561-3-S4-S4
By:
- Neerincx, Pieter B. T.;
- Rauwerda, Han;
- Haisheng Nie;
- Groenen, Martien A. M.;
- Breit, Timo M.;
- Leunissen, Jack A. M.
Publication type:
Article
Collaborative e-Science Experiments and Scientific Workflows.
Published in:
IEEE Internet Computing, 2011, v. 15, n. 4, p. 39, doi. 10.1109/MIC.2011.87
By:
- Belloum, Adam;
- Inda, Marcia A.;
- Vasunin, Dmitry;
- Korkhov, Vladimir;
- Zhao, Zhiming;
- Rauwerda, Han;
- Breit, Timo M.;
- Bubak, Marian;
- Hertzberger, Luis O.
Publication type:
Article
Delayed and Accelerated Aging Share Common Longevity Assurance Mechanisms.
Published in:
PLoS Genetics, 2008, v. 4, n. 8, p. 1, doi. 10.1371/journal.pgen.1000161
By:
- Schumacher, Björn;
- van der Pluijm, Ingrid;
- Moorhouse, Michael J.;
- Kosteas, Theodore;
- Robinson, Andria Rasile;
- Yousin Suh;
- Breit, Timo M.;
- van Steeg, Harry;
- Niedernhofer, Laura J.;
- van IJcken, Wilfred;
- Bartke, Andrzej;
- Spindler, Stephen R.;
- Hoeijmakers, Jan H. J.;
- van der Horst, Gijsbertus T. J.;
- Garinis, George A.
Publication type:
Article
Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium.
Published in:
BMC Genomics, 2014, v. 15, n. 1, p. 915, doi. 10.1186/1471-2164-15-915
By:
- Tulinski, Pawel;
- Duim, Birgitta;
- Wittink, Floyd R.;
- Jonker, Martijs J.;
- Breit, Timo M.;
- van Putten, Jos P.;
- Wagenaar, Jaap A.;
- Fluit, Ad C.
Publication type:
Article
Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension.
Published in:
BMC Genomics, 2012, v. 13, n. 1, p. 167, doi. 10.1186/1471-2164-13-167
By:
- Doroszuk, Agnieszka;
- Jonker, Martijs J.;
- Pul, Nicolien;
- Breit, Timo M;
- Zwaan, Bas J.
Publication type:
Article
Finding maximal transcriptome differences between reprotoxic and non-reprotoxic phthalate responses in rat testis.
Published in:
Journal of Applied Toxicology, 2011, v. 31, n. 5, p. 421, doi. 10.1002/jat.1601
By:
- Yuan, Xiaolian;
- Jonker, Martijs J.;
- de Wilde, Jillian;
- Verhoef, Aart;
- Wittink, Floyd R.A.;
- van Benthem, Jan;
- Bessems, Jos G.;
- Hakkert, Betty C.;
- Kuiper, Raoul V.;
- van Steeg, Harry;
- Breit, Timo M.;
- Luijten, Mirjam
Publication type:
Article
Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs.
Published in:
Aging Cell, 2013, v. 12, n. 5, p. 901, doi. 10.1111/acel.12118
By:
- Jonker, Martijs J.;
- Melis, Joost P. M.;
- Kuiper, Raoul V.;
- Hoeven, Tessa V.;
- Wackers, Paul F. K.;
- Robinson, Joke;
- Horst, Gijsbertus T. J.;
- Dollé, Martijn E. T.;
- Vijg, Jan;
- Breit, Timo M.;
- Hoeijmakers, Jan H. J.;
- Steeg, Harry
Publication type:
Article
VLAM-G: Interactive data driven workflow engine for Grid-enabled resources.
Published in:
Scientific Programming, 2007, v. 15, n. 3, p. 173, doi. 10.1155/2007/812036
By:
- Korkhov, Vladimir;
- Vasyunin, Dmitry;
- Wibisono, Adianto;
- Belloum, Adam S. Z.;
- Inda, Márcia A.;
- Roos, Marco;
- Breit, Timo M.;
- Hertzberger, L. O.
Publication type:
Article
The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis.
Published in:
BMC Microbiology, 2010, v. 10, p. 252, doi. 10.1186/1471-2180-10-252
By:
- Brunner, Jorg;
- Wittink, Floyd R. A.;
- Jonker, Martijs J.;
- de Jong, Mark;
- Breit, Timo M.;
- Laine, Marja L.;
- de Soet, Johannes J.;
- Crielaard, Wim
Publication type:
Article
Comparative gene expression profiling in two congenic mouse strains following Bordetella pertussis infection.
Published in:
2007
By:
- Banus, Sander;
- Vandebriel, Rob J.;
- Pennings, Jeroen L. A.;
- Gremmer, Eric R.;
- Wester, Piet W.;
- van Kranen, Henk J.;
- Breit, Timo M.;
- Demant, Peter;
- Mooi, Frits R.;
- Hoebee, Barbara;
- Kimman, Tjeerd G.
Publication type:
Book Chapter

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