Sambamba: fast processing of NGS alignment formats
Tarasov, Artem, Vilella, Albert J, Cuppen, Edwin, Nijman, Isaac J, Prins, Pjotr
Published in Bioinformatics (Oxford, England) (15.06.2015)
Published in Bioinformatics (Oxford, England) (15.06.2015)
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A systematic genome-wide analysis of zebrafish protein-coding gene function
Kettleborough, Ross N. W., Busch-Nentwich, Elisabeth M., Harvey, Steven A., Dooley, Christopher M., de Bruijn, Ewart, van Eeden, Freek, Sealy, Ian, White, Richard J., Herd, Colin, Nijman, Isaac J., Fényes, Fruzsina, Mehroke, Selina, Scahill, Catherine, Gibbons, Richard, Wali, Neha, Carruthers, Samantha, Hall, Amanda, Yen, Jennifer, Cuppen, Edwin, Stemple, Derek L.
Published in Nature (London) (25.04.2013)
Published in Nature (London) (25.04.2013)
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Loss-of-Function Mutations in the WNT Co-receptor LRP6 Cause Autosomal-Dominant Oligodontia
Massink, Maarten P.G., Créton, Marijn A., Spanevello, Francesca, Fennis, Willem M.M., Cune, Marco S., Savelberg, Sanne M.C., Nijman, Isaäc J., Maurice, Madelon M., van den Boogaard, Marie-José H., van Haaften, Gijs
Published in American journal of human genetics (01.10.2015)
Published in American journal of human genetics (01.10.2015)
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Effectiveness of whole-exome sequencing and costs of the traditional diagnostic trajectory in children with intellectual disability
Monroe, Glen R., Frederix, Gerardus W., Savelberg, Sanne M. C., de Vries, Tamar I., Duran, Karen J., van der Smagt, Jasper J., Terhal, Paulien A., van Hasselt, Peter M., Kroes, Hester Y., Verhoeven-Duif, Nanda M., Nijman, Isaäc J., Carbo, Ellen C., van Gassen, Koen L., Knoers, Nine V., Hövels, Anke M., van Haelst, Mieke M., Visser, Gepke, van Haaften, Gijs
Published in Genetics in medicine (01.09.2016)
Published in Genetics in medicine (01.09.2016)
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Loss of Syntaxin 3 Causes Variant Microvillus Inclusion Disease
Wiegerinck, Caroline L, Janecke, Andreas R, Schneeberger, Kerstin, Vogel, Georg F, van Haaften–Visser, Désirée Y, Escher, Johanna C, Adam, Rüdiger, Thöni, Cornelia E, Pfaller, Kristian, Jordan, Alexander J, Weis, Cleo–Aron, Nijman, Isaac J, Monroe, Glen R, van Hasselt, Peter M, Cutz, Ernest, Klumperman, Judith, Clevers, Hans, Nieuwenhuis, Edward E.S, Houwen, Roderick H.J, van Haaften, Gijs, Hess, Michael W, Huber, Lukas A, Stapelbroek, Janneke M, Müller, Thomas, Middendorp, Sabine
Published in Gastroenterology (New York, N.Y. 1943) (01.07.2014)
Published in Gastroenterology (New York, N.Y. 1943) (01.07.2014)
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Pseudobudding: ruptured glands do not represent true tumor buds
Haddad, Tariq Sami, Dobbelsteen, Luuk, Öztürk, Sonay K, Geene, Robin, Nijman, Isaäc J, Verrijp, Kiek, Jamieson, Nigel B, Wood, Colin, Vliet, Shannon, Reuvers, Luuk, Achouiti, Soumia, Rutgers, Natasja, Brouwer, Nelleke, Simmer, Femke, Zlobec, Inti, Lugli, Alessandro, Nagtegaal, Iris D
Published in The Journal of pathology (01.09.2023)
Published in The Journal of pathology (01.09.2023)
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Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples
Cuppen, Edwin, Nijman, Isaäc J, Mokry, Michal, van Boxtel, Ruben, Toonen, Pim, de Bruijn, Ewart
Published in Nature methods (01.11.2010)
Published in Nature methods (01.11.2010)
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Genome-Wide Pattern of TCF7L2/TCF4 Chromatin Occupancy in Colorectal Cancer Cells
Hatzis, Pantelis, van der Flier, Laurens G., van Driel, Marc A., Guryev, Victor, Nielsen, Fiona, Denissov, Sergei, Nijman, Isaäc J., Koster, Jan, Santo, Evan E., Welboren, Willem, Versteeg, Rogier, Cuppen, Edwin, van de Wetering, Marc, Clevers, Hans, Stunnenberg, Hendrik G.
Published in Molecular and Cellular Biology (01.04.2008)
Published in Molecular and Cellular Biology (01.04.2008)
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Myeloid lineage–restricted somatic mosaicism of NLRP3 mutations in patients with variant Schnitzler syndrome
de Koning, Heleen D., MD, van Gijn, Mariëlle E., MD, PhD, Stoffels, Monique, PhD, Jongekrijg, Johanna, BSc, Zeeuwen, Patrick L.J.M., PhD, Elferink, Martin G., PhD, Nijman, Isaac J., PhD, Jansen, Patrick A.M., PhD, Neveling, Kornelia, PhD, van der Meer, Jos W.M., MD, PhD, Schalkwijk, Joost, PhD, Simon, Anna, MD, PhD
Published in Journal of allergy and clinical immunology (01.02.2015)
Published in Journal of allergy and clinical immunology (01.02.2015)
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Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island
van Schaik, Willem, Top, Janetta, Riley, David R, Boekhorst, Jos, Vrijenhoek, Joyce E P, Schapendonk, Claudia M E, Hendrickx, Antoni P A, Nijman, Isaäc J, Bonten, Marc J M, Tettelin, Hervé, Willems, Rob J L
Published in BMC genomics (14.04.2010)
Published in BMC genomics (14.04.2010)
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Targeted next-generation sequencing: A novel diagnostic tool for primary immunodeficiencies
Nijman, Isaac J., PhD, van Montfrans, Joris M., MD, PhD, Hoogstraat, Marlous, BAS, Boes, Marianne L., PhD, van de Corput, Lisette, PhD, Renner, Ellen D., MD, PhD, van Zon, Patrick, BSc, van Lieshout, Stef, BSc, Elferink, Martin G., PhD, van der Burg, Mirjam, PhD, Vermont, Clementien L., MD, PhD, van der Zwaag, Bert, PhD, Janson, Esther, BSc, Cuppen, Edwin, PhD, Ploos van Amstel, Johannes K., PhD, van Gijn, Marielle E., PhD
Published in Journal of allergy and clinical immunology (01.02.2014)
Published in Journal of allergy and clinical immunology (01.02.2014)
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Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
Kloosterman, Wigard P, Hoogstraat, Marlous, Paling, Oscar, Tavakoli-Yaraki, Masoumeh, Renkens, Ivo, Vermaat, Joost S, van Roosmalen, Markus J, van Lieshout, Stef, Nijman, Isaac J, Roessingh, Wijnand, van’t Slot, Ruben, van de Belt, José, Guryev, Victor, Koudijs, Marco, Voest, Emile, Cuppen, Edwin
Published in Genome Biology (19.10.2011)
Published in Genome Biology (19.10.2011)
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Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity
Josifova, Dragana J, Monroe, Glen R, Tessadori, Federico, de Graaff, Esther, van der Zwaag, Bert, Mehta, Sarju G, Harakalova, Magdalena, Duran, Karen J, Savelberg, Sanne M C, Nijman, Isaäc J, Jungbluth, Heinz, Hoogenraad, Casper C, Bakkers, Jeroen, Knoers, Nine V, Firth, Helen V, Beales, Philip L, van Haaften, Gijs, van Haelst, Mieke M
Published in Human molecular genetics (01.06.2016)
Published in Human molecular genetics (01.06.2016)
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Genomic and transcriptomic plasticity in treatment-naive ovarian cancer
Hoogstraat, Marlous, de Pagter, Mirjam S, Cirkel, Geert A, van Roosmalen, Markus J, Harkins, Timothy T, Duran, Karen, Kreeftmeijer, Jennifer, Renkens, Ivo, Witteveen, Petronella O, Lee, Clarence C, Nijman, Isaac J, Guy, Tanisha, van 't Slot, Ruben, Jonges, Trudy N, Lolkema, Martijn P, Koudijs, Marco J, Zweemer, Ronald P, Voest, Emile E, Cuppen, Edwin, Kloosterman, Wigard P
Published in Genome research (01.02.2014)
Published in Genome research (01.02.2014)
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Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing
Harakalova, Magdalena, Mokry, Michal, Hrdlickova, Barbara, Renkens, Ivo, Duran, Karen, van Roekel, Henk, Lansu, Nico, van Roosmalen, Mark, de Bruijn, Ewart, Nijman, Isaac J, Kloosterman, Wigard P, Cuppen, Edwin
Published in Nature protocols (01.12.2011)
Published in Nature protocols (01.12.2011)
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Multiplex spatial omics reveals changes in immune-epithelial crosstalk during inflammation and dysplasia development in chronic IBD patients
Baars, Matthijs J.D., Floor, Evelien, Sinha, Neeraj, ter Linde, José J.M., van Dam, Stephanie, Amini, Mojtaba, Nijman, Isaäc J., ten Hove, Joren R., Drylewicz, Julia, Offerhaus, G.Johan A., Laclé, Miangela M., Oldenburg, Bas, Vercoulen, Yvonne
Published in iScience (16.08.2024)
Published in iScience (16.08.2024)
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Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries
Mokry, Michal, Feitsma, Harma, Nijman, Isaac J, de Bruijn, Ewart, van der Zaag, Pieter J, Guryev, Victor, Cuppen, Edwin
Published in Nucleic acids research (01.06.2010)
Published in Nucleic acids research (01.06.2010)
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Investigation of Genetic Modifiers of Copper Toxicosis in Labrador Retrievers
Wu, Xiaoyan, den Boer, Elise R., Vos-Loohuis, Manon, Steenbeek, Frank G. van, Monroe, Glen R., Nijman, Isaäc J., Leegwater, Peter. A. J., Fieten, Hille
Published in Life (Basel, Switzerland) (31.10.2020)
Published in Life (Basel, Switzerland) (31.10.2020)
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Somatic alterations compromised molecular diagnosis of DOCK8 hyper-IgE syndrome caused by a novel intronic splice site mutation
Hagl, Beate, Spielberger, Benedikt D., Thoene, Silvia, Bonnal, Sophie, Mertes, Christian, Winter, Christof, Nijman, Isaac J., Verduin, Shira, Eberherr, Andreas C., Puel, Anne, Schindler, Detlev, Ruland, Jürgen, Meitinger, Thomas, Gagneur, Julien, Orange, Jordan S., van Gijn, Marielle E., Renner, Ellen D.
Published in Scientific reports (13.11.2018)
Published in Scientific reports (13.11.2018)
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Genetic etiology of renal agenesis: fine mapping of Renag1 and identification of Kit as the candidate functional gene
Samanas, Nyssa Becker, Commers, Tessa W, Dennison, Kirsten L, Harenda, Quincy Eckert, Kurz, Scott G, Lachel, Cynthia M, Wavrin, Kristen Leland, Bowler, Michael, Nijman, Isaac J, Guryev, Victor, Cuppen, Edwin, Hubner, Norbert, Sullivan, Ruth, Vezina, Chad M, Shull, James D
Published in PloS one (18.02.2015)
Published in PloS one (18.02.2015)
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