All publications (ORCID link)
http://mokrylab.org/wp-content/uploads/2020/05/CV_mokry2020_short.pdf
Selected publications
Meddens CA, Van Der List ACJ, Nieuwenhuis EES, Mokry M. Non-coding DNA in IBD: From sequence variation in DNA regulatory elements to novel therapeutic potential. Gut 2019.
Peeters JGC, Picavet LW, Coenen SGJM, Mauthe M, Vervoort SJ, Mocholi E, de Heus C, Klumperman J, Vastert SJ, Reggiori F, Coffer PJ, Mokry M, van Loosdregt J. Transcriptional and epigenetic profiling of nutrient-deprived cells to identify novel regulators of autophagy. Autophagy 2019;15:98-112.
Vervoort SJ, de Jong OG, Guy Roukens M, Frederiks CL, Vermeulen JF, Lourenço AR, Bella L, Vidakovic AT, Sandoval JL, Moelans C, van Amersfoort M, Dallman MJ, Bruna A, Caldas C, Nieuwenhuis E, van der Wall E, Derksen P, van Diest P, Verhaar MC, Lam EWF, Mokry M, Coffer PJ. Global transcriptional analysis identifies a novel role for SOX4 in tumor-induced angiogenesis. eLife 2018;7.
Petrelli A, Mijnheer G, Hoytema Van Konijnenburg DP, Van Der Wal MM, Giovannone B, Mocholi E, Vazirpanah N, Broen JC, Hijnen D, Oldenburg B, Coffer PJ, Vastert SJ, Prakken BJ, Spierings E, Pandit A, Mokry M, Van Wijk F. PD-1+CD8+ T cells are clonally expanding effectors in human chronic inflammation. Journal of Clinical Investigation 2018;128:4669-4681.
Paauw ND, Lely AT, Joles JA, Franx A, Nikkels PG, Mokry M, van Rijn BB. H3K27 acetylation and gene expression analysis reveals differences in placental chromatin activity in fetal growth restriction. Clinical Epigenetics 2018;10.
Brandt MM, Meddens CA, Louzao-Martinez L, Van Den Dungen NAM, Lansu NR, Nieuwenhuis EES, Duncker DJ, Verhaar MC, Joles JA, *Mokry M, *Cheng C. Chromatin Conformation Links Distal Target Genes to CKD Loci. Journal of the American Society of Nephrology 2018;29:462-476.
Haitjema S, Meddens CA, Van Der Laan SW, Kofink D, Harakalova M, Tragante V, Foroughi Asl H, Van Setten J, Brandt MM, Bis JC, O’Donnell C, Cheng C, Hoefer IE, Waltenberger J, Biessen E, Jukema JW, Doevendans PAFM, Nieuwenhuis EES, Erdmann J, Björkegren JLM, Pasterkamp G, *Asselbergs FW, Den *Ruijter HM, *Mokry M. Additional Candidate Genes for Human Atherosclerotic Disease Identified Through Annotation Based on Chromatin Organization. Circulation: Cardiovascular Genetics 2017;10.
Van Den Broek T, Delemarre EM, Janssen WJM, Nievelstein RAJ, Broen JC, Tesselaar K, Borghans JAM, Nieuwenhuis EES, Prakken BJ, Mokry M, Jansen NJG, Van Wijk F. Neonatal thymectomy reveals differentiation and plasticity within human naive T cells. Journal of Clinical Investigation 2016;126:1126-1136.
Peeters JGC, Vervoort SJ, Mijnheer G, de Roock S, Vastert SJ, Nieuwenhuis EES, van Wijk F, Prakken BJ, Mokry M, van Loosdregt J. Autoimmune disease-associated gene expression is reduced by BET-inhibition. Genomics Data 2016;7:14-17.
Mokry M, Harakalova M, Asselbergs FW, De Bakker PIW, Nieuwenhuis EES. Extensive association of common disease variants with regulatory sequence. PLoS ONE 2016;11.
Meddens CA, Harakalova M, van den Dungen NAM, Foroughi Asl H, Hijma HJ, Cuppen EPJG, Björkegren JLM, Asselbergs FW, Nieuwenhuis EES, Mokry M. Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease. Genome Biology 2016;17.
Kaaij LJT, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond ASJ, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD, Ketting RF. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biology 2016;17.
Fleskens V, Mokry M, Van Der Leun AM, Huppelschoten S, Pals CEGM, Peeters J, Coenen S, Cardoso BA, Barata JT, Van Loosdregt J, Coffer PJ. FOXP3 can modulate TAL1 transcriptional activity through interaction with LMO2. Oncogene 2016;35:4141-4148.
Blokzijl F, De Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P, Nijman IJ, Martincorena I, Mokry M, Wiegerinck CL, Middendorp S, Sato T, Schwank G, Nieuwenhuis EES, Verstegen MMA, Van Der Laan LJW, De Jonge J, Ijzermans JNM, Vries RG, Van De Wetering M, Stratton MR, Clevers H, Cuppen E, Van Boxtel R. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 2016;538:260-264.
Schuijers J, Junker JP, Mokry M, Hatzis P, Koo BK, Sasselli V, Van Der Flier LG, Cuppen E, Van Oudenaarden A, Clevers H. Ascl2 acts as an R-spondin/wnt-responsive switch to control stemness in intestinal crypts. Cell Stem Cell 2015;16:158-170.
Peeters JGC, Vervoort SJ, Tan SC, Mijnheer G, de Roock S, Vastert SJ, Nieuwenhuis EES, van Wijk F, Prakken BJ, Creyghton MP, Coffer PJ, Mokry M, Van Loosdregt J. Inhibition of Super-Enhancer Activity in Autoinflammatory Site-Derived T Cells Reduces Disease-Associated Gene Expression. Cell Reports 2015;12:1986-1996.
Lindemans CA, Calafiore M, Mertelsmann AM, O’Connor MH, Dudakov JA, Jenq RR, Velardi E, Young LF, Smith OM, Lawrence G, Ivanov JA, Fu YY, Takashima S, Hua G, Martin ML, O’Rourke KP, Lo YH, Mokry M, Romera-Hernandez M, Cupedo T, Dow LE, Nieuwenhuis EE, Shroyer NF, Liu C, Kolesnick R, Van Den Brink MRM, Hanash AM. Interleukin-22 promotes intestinal-stem-cell-mediated epithelial regeneration. Nature 2015;528:560-564.
Harakalova M, Kummeling G, Sammani A, Linschoten M, Baas AF, Van Der Smagt J, Doevendans PA, Van Tintelen JP, Dooijes D, Mokry M, Asselbergs FW. A systematic analysis of genetic dilated cardiomyopathy reveals numerous ubiquitously expressed and muscle-specific genes. European Journal of Heart Failure 2015;17:484-493.
Schuijers J, Mokry M, Hatzis P, Cuppen E, Clevers H. Wnt-induced transcriptional activation is exclusively mediated by TCF/LEF. EMBO Journal 2014;33:146-156.
Mokry M, Middendorp S, Wiegerinck CL, Witte M, Teunissen H, Meddens CA, Cuppen E, Clevers H, Nieuwenhuis EES. Many inflammatory bowel disease risk loci include regions that regulate gene expression in immune cells and the intestinal epithelium. Gastroenterology 2014;146:1040-1047.
van Heesch S, Mokry M, Boskova V, Junker W, Mehon R, Toonen P, de Bruijn E, Shull JD, Aitman TJ, Cuppen E, Guryev V. Systematic biases in DNA copy number originate from isolation procedures. Genome Biology 2013;14.
Van Boxtel R, *Gomez-Puerto C, *Mokry M, Eijkelenboom A, Van Der Vos KE, Nieuwenhuis EE, Burgering BM, Lam EWF, Coffer PJ. FOXP1 acts through a negative feedback loop to suppress FOXO-induced apoptosis. Cell Death and Differentiation 2013;20:1219-1229.
*Eijkelenboom A, *Mokry M, Smits LM, Nieuwenhuis EE, Burgering BMT. FOXO3 selectively amplifies enhancer activity to establish target gene regulation. Cell Reports 2013;5:1664-1678.
Eijkelenboom A, Mokry M, De Wit E, Smits LM, Polderman PE, Van Triest MH, Van Boxtel R, Schulze A, De Laat W, Cuppen E, Burgering BMT. Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II profiling. Molecular Systems Biology 2013;9.
Westendorp B, Mokry M, Groot Koerkamp MJA, Holstege FCP, Cuppen E, De Bruin A. E2F7 represses a network of oscillating cell cycle genes to control S-phase progression. Nucleic Acids Research 2012;40:3511-3523.
*Mokry M, *Hatzis P, *Schuijers J, Lansu N, Ruzius FP, Clevers H, Cuppen E. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes. Nucleic Acids Research 2012;40:148-158.
Boj SF, Van Es JH, Huch M, Li VSW, José A, Hatzis P, Mokry M, Haegebarth A, Van Den Born M, Chambon P, Voshol P, Dor Y, Cuppen E, Fillat C, Clevers H. Diabetes risk gene and wnt effector Tcf7l2/TCF4 controls hepatic response to perinatal and adult metabolic demand. Cell 2012;151:1595-1607.
*Mokry M, *Nijman IJ, van Dijken A, Benjamins R, Heidstra R, Scheres B, Cuppen E. Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach. BMC Genomics 2011;12.
*Harakalova M, *Mokry M, Hrdlickova B, Renkens I, Duran K, Van Roekel H, Lansu N, Van Roosmalen M, De Bruijn E, Nijman IJ, Kloosterman WP, Cuppen E. Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing. Nature Protocols 2011;6:1870-1886.
*Nijman IJ, *Mokry M, *Van Boxtel R, Toonen P, De Bruijn E, Cuppen E. Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples. Nature Methods 2010;7:913-915.
Mokry M, Feitsma H, Nijman IJ, de Bruijn E, van der Zaag PJ, Guryev V, Cuppen E. Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries. Nucleic Acids Research 2010;38:e116-e116.
Mokry M, Cuppen E. The Atp1a1 gene from inbred Dahl salt sensitive rats does not contain the A1079T missense transversion. Hypertension 2008;51:922-927.
