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Templated insertions at VD and DJ junctions create unique B‐cell receptors in the healthy B‐cell repertoire.
Published in:
European Journal of Immunology, 2020, v. 50, n. 12, p. 2099, doi. 10.1002/eji.202048828
By:
- Koning, Marvyn T.;
- Vletter, Esther M.;
- Rademaker, Rik;
- Vergroesen, Rochelle D.;
- Trollmann, Ignis J.M.;
- Parren, Paul;
- Bergen, Cornelis A.M.;
- Scherer, Hans U.;
- Kiełbasa, Szymon M.;
- Toes, René E.M.;
- Veelken, Hendrik
Publication type:
Article
The Cortisol Response of Male and Female Choroidal Endothelial Cells: Implications for Central Serous Chorioretinopathy.
Published in:
Journal of Clinical Endocrinology & Metabolism, 2022, v. 107, n. 2, p. 512, doi. 10.1210/clinem/dgab670
By:
- Brinks, Joost;
- van Dijk, Elon H. C.;
- Kiełbasa, Szymon M.;
- Mei, Hailiang;
- van der Veen, Isa;
- Peters, Hendrika A. B.;
- Sips, Hetty C. M.;
- Notenboom, Robbert G. E.;
- Quax, Paul H. A.;
- Boon, Camiel J. F.;
- Meijer, Onno C.
Publication type:
Article
RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting.
Published in:
BMC Biology, 2019, v. 17, n. 1, p. 1, doi. 10.1186/s12915-019-0674-0
By:
- Jadhav, Bharati;
- Monajemi, Ramin;
- Gagalova, Kristina K.;
- Ho, Daniel;
- Draisma, Harmen H. M.;
- van de Wiel, Mark A.;
- Franke, Lude;
- Heijmans, Bastiaan T.;
- van Meurs, Joyce;
- Jansen, Rick;
- 't Hoen, Peter A. C.;
- Sharp, Andrew J.;
- Kiełbasa, Szymon M.
Publication type:
Article
Targetfinder.org: a resource for systematic discovery of transcription factor target genes.
Published in:
Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W233, doi. 10.1093/nar/gkq374
By:
- Kiełbasa, Szymon M.;
- Blüthgen, Nils;
- Fähling, Michael;
- Mrowka, Ralf
Publication type:
Article
TransFind—predicting transcriptional regulators for gene sets.
Published in:
Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W275, doi. 10.1093/nar/gkq438
By:
- Kiełbasa, Szymon M.;
- Klein, Holger;
- Roider, Helge G.;
- Vingron, Martin;
- Blüthgen, Nils
Publication type:
Article
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells.
Published in:
Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00842-w
By:
- Shafighi, Shadi Darvish;
- Kiełbasa, Szymon M.;
- Sepúlveda-Yáñez, Julieta;
- Monajemi, Ramin;
- Cats, Davy;
- Mei, Hailiang;
- Menafra, Roberta;
- Kloet, Susan;
- Veelken, Hendrik;
- van Bergen, Cornelis A.M.;
- Szczurek, Ewa
Publication type:
Article
ARTISAN PCR: rapid identification of full-length immunoglobulin rearrangements without primer binding bias.
Published in:
British Journal of Haematology, 2017, v. 178, n. 6, p. 983, doi. 10.1111/bjh.14180
By:
- Koning, Marvyn T.;
- Kiełbasa, Szymon M.;
- Boersma, Vesna;
- Buermans, Henk P. J.;
- Zeeuw, Sander A. J.;
- Bergen, Cornelis A. M.;
- Cleven, Arjen H. G.;
- Kluin, Philip M.;
- Griffioen, Marieke;
- Navarrete, Marcelo A.;
- Veelken, Hendrik
Publication type:
Article
Selection patterns of B-cell receptors and the natural history of follicular lymphoma.
Published in:
British Journal of Haematology, 2016, v. 175, n. 5, p. 972, doi. 10.1111/bjh.13901
By:
- Scherer, Florian;
- Burgt, Marlon;
- Kiełbasa, Szymon M.;
- Bertinetti ‐ Lapatki, Cristina;
- Dühren von Minden, Marcus;
- Mikesch, Kristina;
- Zirlik, Katja;
- Wreede, Liesbeth;
- Veelken, Hendrik;
- Navarrete, Marcelo A.
Publication type:
Article
RNA‐seq analysis of Lgr6<sup>+</sup> stem cells and identification of an Lgr6 isoform.
Published in:
Experimental Dermatology, 2018, v. 27, n. 10, p. 1172, doi. 10.1111/exd.13453
By:
- Glind, Gerline C.;
- Bastidas Torres, Armando N.;
- Zoutman, Willem H.;
- Zeeuw, Sander A. J.;
- Kiełbasa, Szymon M.;
- Gruijl, Frank R.;
- Tensen, Cornelis P.
Publication type:
Article
Human Bone Marrow-Resident Natural Killer Cells Have a Unique Transcriptional Profile and Resemble Resident Memory CD8<sup>+</sup> T Cells.
Published in:
Frontiers in Immunology, 2018, p. N.PAG, doi. 10.3389/fimmu.2018.01829
By:
- Melsen, Janine E.;
- Lugthart, Gertjan;
- Vervat, Carly;
- van Ostaijen-ten Dam, Monique M.;
- Lankester, Arjan C.;
- Schilham, Marco W.;
- Kielbasa, Szymon M.;
- van der Zeeuw, Sander A. J.;
- Buermans, Henk P. J.
Publication type:
Article
Regulation of Clock-Controlled Genes in Mammals.
Published in:
PLoS ONE, 2009, v. 4, n. 3, p. 1, doi. 10.1371/journal.pone.0004882
By:
- Bozek, Katarzyna;
- Relógio, Angela;
- Kielbasa, Szymon M.;
- Heine, Markus;
- Dame, Christof;
- Kramer, Achim;
- Herzel, Hanspeter
Publication type:
Article
Transcriptional Autoregulatory Loops Are Highly Conserved in Vertebrate Evolution.
Published in:
PLoS ONE, 2008, v. 3, n. 9, p. 1, doi. 10.1371/journal.pone.0003210
By:
- Kiełbasa, Szymon M.;
- Vingron, Martin
Publication type:
Article
Statistical method for modeling sequencing data from different technologies in longitudinal studies with application to Huntington disease.
Published in:
Biometrical Journal, 2021, v. 63, n. 4, p. 745, doi. 10.1002/bimj.201900235
By:
- Fuady, Angga M.;
- van Roon‐Mom, Willeke M. C.;
- Kiełbasa, Szymon M.;
- Uh, Hae‐Won;
- Houwing‐Duistermaat, Jeanine J.
Publication type:
Article
Optimized Whole Genome Association Scanning for Discovery of HLA Class I-Restricted Minor Histocompatibility Antigens.
Published in:
Frontiers in Immunology, 2020, v. 11, p. 1, doi. 10.3389/fimmu.2020.00659
By:
- Fuchs, Kyra J.;
- Honders, M. Willy;
- van der Meijden, Edith D.;
- Adriaans, Alwin E.;
- van der Lee, Dyantha I.;
- Pont, Margot J.;
- Monajemi, Ramin;
- Kielbasa, Szymon M.;
- 't Hoen, Peter A. C.;
- van Bergen, Cornelis A. M.;
- Falkenburg, J. H. Frederik;
- Griffioen, Marieke
Publication type:
Article
Peripheral IgE Repertoires of Healthy Donors Carry Moderate Mutation Loads and Do Not Overlap With Other Isotypes.
Published in:
Frontiers in Immunology, 2019, p. 1, doi. 10.3389/fimmu.2019.01543
By:
- Koning, Marvyn T.;
- Trollmann, Ignis J. M.;
- van Bergen, Cornelis A. M.;
- Alvarez Saravia, Diego;
- Navarrete, Marcelo A.;
- Kiełbasa, Szymon M.;
- Veelken, Hendrik
Publication type:
Article
MDMX Regulates Transcriptional Activity of p53 and FOXO Proteins to Stimulate Proliferation of Melanoma Cells.
Published in:
Cancers, 2022, v. 14, n. 18, p. N.PAG, doi. 10.3390/cancers14184482
By:
- Heijkants, Renier C.;
- Teunisse, Amina F. A. S.;
- de Jong, Danielle;
- Glinkina, Kseniya;
- Mei, Hailiang;
- Kielbasa, Szymon M.;
- Szuhai, Karoly;
- Jochemsen, Aart G.
Publication type:
Article
HuSiDa—the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells.
Published in:
Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d108
By:
- Truss, Matthias;
- Swat, Maciej;
- Kielbasa, Szymon M.;
- Schäfer, Reinhold;
- Herzel, Hanspeter;
- Hagemeier, Christian
Publication type:
Article
Inferring combinatorial regulation of transcription in silico.
Published in:
Nucleic Acids Research, 2005, v. 33, n. 1, p. 272
By:
- Bluthgen, Nils;
- Kiełbasa, Szymon M.;
- Herzel, Hanspeter
Publication type:
Article
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.
Published in:
Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w235
By:
- Hu, Zhenjun;
- Fu, Yutao;
- Halees, Anason S.;
- Kielbasa, Szymon M.;
- Weng, Zhiping
Publication type:
Article
NKG2A is a late immune checkpoint on CD8 T cells and marks repeated stimulation and cell division.
Published in:
International Journal of Cancer, 2022, v. 150, n. 4, p. 688, doi. 10.1002/ijc.33859
By:
- Borst, Linda;
- Sluijter, Marjolein;
- Sturm, Gregor;
- Charoentong, Pornpimol;
- Santegoets, Saskia J.;
- van Gulijk, Mandy;
- van Elsas, Marit J.;
- Groeneveldt, Christianne;
- van Montfoort, Nadine;
- Finotello, Francesca;
- Trajanoski, Zlatko;
- Kiełbasa, Szymon M.;
- van der Burg, Sjoerd H.;
- van Hall, Thorbald
Publication type:
Article
Brain Transcriptomic Analysis of Hereditary Cerebral Hemorrhage With Amyloidosis-Dutch Type.
Published in:
Frontiers in Aging Neuroscience, 2018, p. 1, doi. 10.3389/fnagi.2018.00102
By:
- Grand Moursel, Laure;
- van Roon-Mom, Willeke M. C.;
- Kiełbasa, Szymon M.;
- Mei, Hailiang;
- Buermans, Henk P. J.;
- van der Graaf, Linda M.;
- Hettne, Kristina M.;
- de Meijer, Emile J.;
- van Duinen, Sjoerd G.;
- Laros, Jeroen F. J.;
- van Buchem, Mark A.;
- ‘t Hoen, Peter A. C.;
- van der Maarel, Silvère M.;
- van der Weerd, Louise
Publication type:
Article
The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs.
Published in:
FASEB Journal, 2018, v. 32, n. 3, p. 1579, doi. 10.1096/fj.201700861R
By:
- Raz, Vered;
- Riaz, Muhammad;
- Tatum, Zuotian;
- Kielbasa, Szymon M.;
- Hoen, Peter A. C. 't
Publication type:
Article
New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration.
Published in:
FASEB Journal, 2017, v. 31, n. 1, p. 238, doi. 10.1096/fj.201600675r
By:
- Pasteuning‐Vuhman, Svitlana;
- Boertje‐van der Meulen, Johanna W.;
- Putten, Maaike Van;
- Overzier, Maurice;
- Dijke, Peter;
- Kielbasa, Szymon M.;
- Arindrarto, Wibowo;
- Wolterbeek, Ron;
- Lezhnina, Ksenia V.;
- Ozerov, Ivan V.;
- Aliper, Aleksandr M.;
- Hoogaars, Willem M.;
- Aartsma‐Rus, Annemieke;
- Loomans, Cindy J. M.
Publication type:
Article
New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration.
Published in:
FASEB Journal, 2017, v. 31, n. 1, p. 238, doi. 10.1096/fj.201600675R
By:
- Pasteuning-Vuhman, Svitlana;
- Boertje-van der Meulen, Johanna W.;
- van Putten, Maaike;
- Overzier, Maurice;
- ten Dijke, Peter;
- Kiełbasa, Szymon M.;
- Arindrarto, Wibowo;
- Wolterbeek, Ron;
- Lezhnina, Ksenia V.;
- Ozerov, Ivan V.;
- Aliper, Aleksandr M.;
- Hoogaars, Willem M.;
- Aartsma-Rus, Annemieke;
- Loomans, Cindy J. M.
Publication type:
Article
Two Plasmodium 6-Cys family-related proteins have distinct and critical roles in liver-stage development.
Published in:
FASEB Journal, 2014, v. 28, n. 5, p. 2158, doi. 10.1096/fj.13-241570
By:
- Annoura, Takeshi;
- van Schaijk, Ben C. L.;
- Ploemen, Ivo H. J.;
- Sajid, Mohammed;
- Jing-wen Lin;
- Vos, Martijn W.;
- Dinmohamed, Avinash G.;
- Inaoka, Daniel K.;
- Rijpma, Sanna R.;
- van Gemert, Geert-Jan;
- Chevalley-Maurel, Severine;
- Kielbasa, Szymon M.;
- Scheltinga, Fay;
- Franke-Fayard, Blandine;
- Klop, Onny;
- Hermsen, Cornelus C.;
- Kita, Kiyoshi;
- Gego, Audrey;
- Franetmh, Jean-Francois;
- Mazier, Dominique
Publication type:
Article
A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts.
Published in:
FEBS Journal, 2009, v. 276, n. 4, p. 1024, doi. 10.1111/j.1742-4658.2008.06846.x
By:
- Blüthgen, Nils;
- Legewie, Stefan;
- Kielbasa, Szymon M.;
- Schramme, Anja;
- Tchernitsa, Oleg;
- Keil, Jana;
- Solf, Andrea;
- Vingron, Martin;
- Schäfer, Reinhold;
- Herzel, Hanspeter;
- Sers, Christine
Publication type:
Article
Single-cell immune profiling reveals thymus-seeding populations, T cell commitment, and multilineage development in the human thymus.
Published in:
Science Immunology, 2022, v. 7, n. 77, p. 1, doi. 10.1126/sciimmunol.ade0182
By:
- Cordes, Martijn;
- Canté-Barrett, Kirsten;
- van den Akker, Erik B.;
- Moretti, Federico A.;
- Kiełbasa, Szymon M.;
- Vloemans, Sandra A.;
- Garcia-Perez, Laura;
- Teodosio, Cristina;
- van Dongen, Jacques J. M.;
- Pike-Overzet, Karin;
- Reinders, Marcel J. T.;
- Staal, Frank J. T.
Publication type:
Article
Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression.
Published in:
Nature Communications, 2016, v. 7, n. 3, p. 10846, doi. 10.1038/ncomms10846
By:
- de Bruin, Ruben G.;
- Shiue, Lily;
- Prins, Jurriën;
- de Boer, Hetty C.;
- Singh, Anjana;
- Fagg, W. Samuel;
- van Gils, Janine M.;
- Duijs, Jacques M. G. J.;
- Katzman, Sol;
- Kraaijeveld, Adriaan O.;
- Böhringer, Stefan;
- Leung, Wai Y.;
- Kielbasa, Szymon M.;
- Donahue, John P.;
- van der Zande, Patrick H.J.;
- Sijbom, Rick;
- van Alem, Carla M. A.;
- Bot, Ilze;
- van Kooten, Cees;
- Jukema, J. Wouter
Publication type:
Article
CpG Deamination Creates Transcription Factor–Binding Sites with High Efficiency.
Published in:
Genome Biology & Evolution, 2011, v. 3, p. 1304, doi. 10.1093/gbe/evr107
By:
- Żemojtel, Tomasz;
- kiełbasa, Szymon M.;
- Arndt, Peter F.;
- Behrens, Sarah;
- Bourque, Guillaume;
- Vingron, Martin
Publication type:
Article
Hippocampal glucocorticoid target genes associated with enhancement of memory consolidation.
Published in:
European Journal of Neuroscience, 2022, v. 55, n. 9/10, p. 2666, doi. 10.1111/ejn.15226
By:
- Buurstede, Jacobus C.;
- van Weert, Lisa T.C.M.;
- Colucci, Paola;
- Gentenaar, Max;
- Viho, Eva M.G.;
- Koorneef, Lisa L.;
- Schoonderwoerd, Robin A.;
- Lanooij, Suzanne D.;
- Moustakas, Ioannis;
- Balog, Judit;
- Mei, Hailiang;
- Kielbasa, Szymon M.;
- Campolongo, Patrizia;
- Roozendaal, Benno;
- Meijer, Onno C.
Publication type:
Article
Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells.
Published in:
PLoS Pathogens, 2011, v. 7, n. 2, p. 1, doi. 10.1371/journal.pgen.1001231
By:
- Jürchott, Karsten;
- Kuban, Ralf-Jürgen;
- Krech, Till;
- Blüthgen, Nils;
- Stein, Ulrike;
- Walther, Wolfgang;
- Friese, Christian;
- Kielbasa, Szymon M.;
- Ungethüm, Ute;
- Lund, Per;
- Knösel, Thomas;
- Kemmner, Wolfgang;
- Morkel, Markus;
- Fritzmann, Johannes;
- Schlag, Peter M.;
- Birchmeier, Walter;
- Krueger, Tammo;
- Sperling, Silke;
- Sers, Christine;
- Royer, Hans-Dieter
Publication type:
Article
HomGL--comparing genelists across species and with different accession numbers.
Published in:
Bioinformatics, 2004, v. 20, n. 1, p. 125, doi. 10.1093/bioinformatics/btg379
By:
- Nils Blüthgen;
- Szymon M. Kiełbasa;
- Branka Čajavec;
- Hanspeter Herzel
Publication type:
Article
Combining frequency and positional information to predict transcription factor binding sites.
Published in:
Bioinformatics, 2001, v. 17, n. 11, p. 1019, doi. 10.1093/bioinformatics/17.11.1019
By:
- Kiełbasa, Szymon M.;
- Beule, Dieter;
- Schuchhardt, Johannes;
- Herzel, Hanspeter
Publication type:
Article
Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model.
Published in:
Molecular Neurodegeneration, 2018, v. 13, n. 1, p. N.PAG, doi. 10.1186/s13024-018-0261-9
By:
- Toonen, Lodewijk J. A.;
- Overzier, Maurice;
- Evers, Melvin M.;
- Leon, Leticia G.;
- van der Zeeuw, Sander A. J.;
- Mei, Hailiang;
- Kielbasa, Szymon M.;
- Goeman, Jelle J.;
- Hettne, Kristina M.;
- Magnusson, Olafur Th.;
- Poirel, Marion;
- Seyer, Alexandre;
- 't Hoen, Peter A. C.;
- van Roon-Mom, Willeke M. C.
Publication type:
Article
Integrating omics datasets with the OmicsPLS package.
Published in:
BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2371-3
By:
- Bouhaddani, Said el;
- Uh, Hae-Won;
- Jongbloed, Geurt;
- Hayward, Caroline;
- Klarić, Lucija;
- Kiełbasa, Szymon M.;
- Houwing-Duistermaat, Jeanine
Publication type:
Article
Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells.
Published in:
PLoS Genetics, 2010, v. 6, n. 12, p. 1, doi. 10.1371/journal.pgen.1001231
By:
- Jürchott, Karsten;
- Kuban, Ralf-Jürgen;
- Krech, Till;
- Blüthgen, Nils;
- Stein, Ulrike;
- Walther, Wolfgang;
- Friese, Christian;
- Kielbasa, Szymon M.;
- Ungethüm, Ute;
- Lund, Per;
- Knösel, Thomas;
- Kemmner, Wolfgang;
- Morkel, Markus;
- Fritzmann, Johannes;
- Schlag, Peter M.;
- Birchmeier, Walter;
- Krueger, Tammo;
- Sperling, Silke;
- Sers, Christine;
- Royer, Hans-Dieter
Publication type:
Article
Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome.
Published in:
PLoS ONE, 2018, v. 13, n. 7, p. 1, doi. 10.1371/journal.pone.0200652
By:
- Rovito, Roberta;
- Warnatz, Hans-Jörg;
- Kiełbasa, Szymon M.;
- Mei, Hailiang;
- Amstislavskiy, Vyacheslav;
- Arens, Ramon;
- Yaspo, Marie-Laure;
- Lehrach, Hans;
- Kroes, Aloys C. M.;
- Goeman, Jelle J.;
- Vossen, Ann C. T. M.
Publication type:
Article

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