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Notch Signaling between Cerebellar Granule Cell Progenitors.
Published in:
eNeuro, 2021, v. 8, n. 3, p. 1, doi. 10.1523/ENEURO.0468-20.2021
By:
- Toma Adachi;
- Satoshi Miyashita;
- Mariko Yamashita;
- Mana Shimoda;
- Konstantin Okonechnikov;
- Lukas Chavez;
- Marcel Kool;
- Stefan M. Pfister;
- Takafumi Inoue;
- Daisuke Kawauchi;
- Mikio Hoshino
Publication type:
Article
QSEA--modelling of genome-wide DNA methylation from sequencing enrichment experiments.
Published in:
Nucleic Acids Research, 2017, v. 45, n. 6, p. 1, doi. 10.1093/nar/gkw1193
By:
- Lienhard, Matthias;
- Grasse, Sabrina;
- Rolff, Jana;
- Frese, Steffen;
- Schirmer, Uwe;
- Becker, Michael;
- Börno, Stefan;
- Timmermann, Bernd;
- Chavez, Lukas;
- Sültmann, Holger;
- Leschber, Gunda;
- Fichtner, Iduna;
- Schweiger, Michal R.;
- Herwig, Ralf
Publication type:
Article
Large conserved domains of low DNA methylation maintained by Dnmt3a.
Published in:
Nature Genetics, 2014, v. 46, n. 1, p. 17, doi. 10.1038/ng.2836
By:
- Jeong, Mira;
- Sun, Deqiang;
- Luo, Min;
- Huang, Yun;
- Challen, Grant A;
- Rodriguez, Benjamin;
- Zhang, Xiaotian;
- Chavez, Lukas;
- Wang, Hui;
- Hannah, Rebecca;
- Kim, Sang-Bae;
- Yang, Liubin;
- Ko, Myunggon;
- Chen, Rui;
- Göttgens, Berthold;
- Lee, Ju-Seog;
- Gunaratne, Preethi;
- Godley, Lucy A;
- Darlington, Gretchen J;
- Rao, Anjana
Publication type:
Article
Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data.
Published in:
PLoS ONE, 2013, v. 8, n. 1, p. 1, doi. 10.1371/journal.pone.0054359
By:
- Gerasimova, Anna;
- Chavez, Lukas;
- Bin Li;
- Seumois, Gregory;
- Greenbaum, Jason;
- Rao, Anjana;
- Vijayanand, Pandurangan;
- Peters, Bjoern
Publication type:
Article
A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells.
Published in:
PLoS ONE, 2010, v. 5, n. 5, p. 1, doi. 10.1371/journal.pone.0010709
By:
- Jung, Marc;
- Peterson, Hedi;
- Chavez, Lukas;
- Kahlem, Pascal;
- Lehrach, Hans;
- Vilo, Jaak;
- Adjaye, James
Publication type:
Article
In silico identification of a core regulatory network of OCT4 inhuman embryonic stem cells using an integrated approach.
Published in:
BMC Genomics, 2009, v. 10, p. 314, doi. 10.1186/1471-2164-10-314
By:
- Chavez, Lukas;
- Bais, Abha S.;
- Vingron, Martin;
- Lehrach, Hans;
- Adjaye, James;
- Herwig, Ralf
Publication type:
Article
The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine.
Published in:
Nature Cell Biology, 2015, v. 17, n. 5, p. 545, doi. 10.1038/ncb3147
By:
- Etchegaray, Jean-Pierre;
- Chavez, Lukas;
- Huang, Yun;
- Ross, Kenneth N.;
- Choi, Jiho;
- Martinez-Pastor, Barbara;
- Walsh, Ryan M.;
- Sommer, Cesar A.;
- Lienhard, Matthias;
- Gladden, Adrianne;
- Kugel, Sita;
- Silberman, Dafne M.;
- Ramaswamy, Sridhar;
- Mostoslavsky, Gustavo;
- Hochedlinger, Konrad;
- Goren, Alon;
- Rao, Anjana;
- Mostoslavsky, Raul
Publication type:
Article
PTEN deficiency leads to proteasome addiction: a novel vulnerability in glioblastoma.
Published in:
Neuro-Oncology, 2021, v. 23, n. 7, p. 1072, doi. 10.1093/neuonc/noab001
By:
- Benitez, Jorge A;
- Finlay, Darren;
- Castanza, Anthony;
- Parisian, Alison D;
- Ma, Jianhui;
- Longobardi, Ciro;
- Campos, Alex;
- Vadla, Raghavendra;
- Izurieta, Alejandro;
- Scerra, Gianluca;
- Koga, Tomoyuki;
- Long, Tao;
- Chavez, Lukas;
- Mesirov, Jill P;
- Vuori, Kristiina;
- Furnari, Frank
Publication type:
Article
Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma.
Published in:
Neuro-Oncology, 2021, v. 23, n. 2, p. 226, doi. 10.1093/neuonc/noaa191
By:
- Ecker, Jonas;
- Thatikonda, Venu;
- Sigismondo, Gianluca;
- Selt, Florian;
- Valinciute, Gintvile;
- Oehme, Ina;
- Müller, Carina;
- Buhl, Juliane L;
- Ridinger, Johannes;
- Usta, Diren;
- Qin, Nan;
- Tilburg, Cornelis M van;
- Herold-Mende, Christel;
- Remke, Marc;
- Sahm, Felix;
- Westermann, Frank;
- Kool, Marcel;
- Wechsler-Reya, Robert J;
- Chavez, Lukas;
- Krijgsveld, Jeroen
Publication type:
Article
GENE-02. CHROMOSOME CONFORMATION ANALYSIS OF EPENDYMOMA IDENTIFIES PUTATIVE TUMOR DEPENDENCY GENES ACTIVATED BY DISTAL ONCOGENIC ENHANCERS.
Published in:
Neuro-Oncology, 2019, v. 21, p. ii80, doi. 10.1093/neuonc/noz036.073
By:
- Okonechnikov, Konstantin;
- Hübner, Jens-Martin;
- Kraft, Katerina;
- Hidalgo, Rocio Acuna;
- Bump, Rosalind;
- Chandran, Sahaana;
- Mundlos, Stefan;
- Mesirov, Jill;
- Pajtler, Kristian;
- Dixon, Jesse;
- Pfister, Stefan;
- Kool, Marcel;
- Chavez, Lukas
Publication type:
Article
Telomerase activation in posterior fossa group A ependymomas is associated with dismal prognosis and chromosome 1q gain.
Published in:
Neuro-Oncology, 2017, v. 19, n. 9, p. 1183, doi. 10.1093/neuonc/nox027
By:
- Gojo, Johannes;
- Lötsch, Daniela;
- Spiegl-Kreinecker, Sabine;
- Pajtler, Kristian W.;
- Neumayer, Katharina;
- Korbel, Pia;
- Araki, Asuka;
- Brandstetter, Anita;
- Mohr, Thomas;
- Hovestadt, Volker;
- Chavez, Lukas;
- Kirchhofer, Dominik;
- Ricken, Gerda;
- Stefanits, Harald;
- Korshunov, Andrey;
- Pfister, Stefan M.;
- Dieckmann, Karin;
- Azizi, Amedeo A.;
- Czech, Thomas;
- Filipits, Martin
Publication type:
Article
Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development.
Published in:
PLoS Computational Biology, 2011, v. 7, n. 12, p. 1, doi. 10.1371/journal.pcbi.1002304
By:
- Göke, Jonathan;
- Jung, Marc;
- Behrens, Sarah;
- Chavez, Lukas;
- O'Keeffe, Sean;
- Timmermann, Bernd;
- Lehrach, Hans;
- Adjaye, James;
- Vingron, Martin
Publication type:
Article
Epigenomic analysis of primary human T cells reveals enhancers associated with T<sub>H</sub>2 memory cell differentiation and asthma susceptibility.
Published in:
Nature Immunology, 2014, v. 15, n. 8, p. 777, doi. 10.1038/ni.2937
By:
- Seumois, Grégory;
- Chavez, Lukas;
- Gerasimova, Anna;
- Lienhard, Matthias;
- Omran, Nada;
- Kalinke, Lukas;
- Vedanayagam, Maria;
- Ganesan, Asha Purnima V;
- Chawla, Ashu;
- Djukanović, Ratko;
- Ansel, K Mark;
- Peters, Bjoern;
- Rao, Anjana;
- Vijayanand, Pandurangan
Publication type:
Article
17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells.
Published in:
Nature Communications, 2016, v. 7, n. 11, p. 13426, doi. 10.1038/ncomms13426
By:
- Schmiedel, Benjamin Joachim;
- Seumois, Grégory;
- Samaniego-Castruita, Daniela;
- Cayford, Justin;
- Schulten, Veronique;
- Chavez, Lukas;
- Ay, Ferhat;
- Sette, Alessandro;
- Peters, Bjoern;
- Vijayanand, Pandurangan
Publication type:
Article
Acute loss of TET function results in aggressive myeloid cancer in mice.
Published in:
Nature Communications, 2015, v. 6, n. 11, p. 10071, doi. 10.1038/ncomms10071
By:
- An, Jungeun;
- González-Avalos, Edahí;
- Chawla, Ashu;
- Jeong, Mira;
- López-Moyado, Isaac F.;
- Li, Wei;
- Goodell, Margaret A.;
- Chavez, Lukas;
- Ko, Myunggon;
- Rao, Anjana
Publication type:
Article
A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.
Published in:
Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0911-6
By:
- Äijö, Tarmo;
- Yun Huang;
- Mannerström, Henrik;
- Chavez, Lukas;
- Tsagaratou, Ageliki;
- Rao, Anjana;
- Lähdesmäki, Harri
Publication type:
Article
Epithelioid glioblastomas stratify into established diagnostic subsets upon integrated molecular analysis.
Published in:
Brain Pathology, 2018, v. 28, n. 5, p. 656, doi. 10.1111/bpa.12566
By:
- Korshunov, Andrey;
- Chavez, Lukas;
- Sharma, Tanvi;
- Ryzhova, Marina;
- Schrimpf, Daniel;
- Stichel, Damian;
- Capper, David;
- Sturm, Dominik;
- Kool, Marcel;
- Habel, Antje;
- Kleinschmidt‐DeMasters, Bette K.;
- Rosenblum, Marc;
- Absalyamova, Oksana;
- Golanov, Andrey;
- Lichter, Peter;
- Pfister, Stefan M.;
- Jones, David T.W.;
- Perry, Arie;
- von Deimling, Andreas
Publication type:
Article
Second-generation molecular subgrouping of medulloblastoma: an international meta-analysis of Group 3 and Group 4 subtypes.
Published in:
Acta Neuropathologica, 2019, v. 138, n. 2, p. 309, doi. 10.1007/s00401-019-02020-0
By:
- Sharma, Tanvi;
- Schwalbe, Edward C.;
- Williamson, Daniel;
- Sill, Martin;
- Hovestadt, Volker;
- Mynarek, Martin;
- Rutkowski, Stefan;
- Robinson, Giles W.;
- Gajjar, Amar;
- Cavalli, Florence;
- Ramaswamy, Vijay;
- Taylor, Michael D.;
- Lindsey, Janet C.;
- Hill, Rebecca M.;
- Jäger, Natalie;
- Korshunov, Andrey;
- Hicks, Debbie;
- Bailey, Simon;
- Kool, Marcel;
- Chavez, Lukas
Publication type:
Article
Molecular heterogeneity and CXorf67 alterations in posterior fossa group A (PFA) ependymomas.
Published in:
Acta Neuropathologica, 2018, v. 136, n. 2, p. 211, doi. 10.1007/s00401-018-1877-0
By:
- Pajtler, Kristian W.;
- Wen, Ji;
- Sill, Martin;
- Lin, Tong;
- Orisme, Wilda;
- Tang, Bo;
- Hübner, Jens-Martin;
- Ramaswamy, Vijay;
- Jia, Sujuan;
- Dalton, James D.;
- Haupfear, Kelly;
- Rogers, Hazel A.;
- Punchihewa, Chandanamali;
- Lee, Ryan;
- Easton, John;
- Wu, Gang;
- Ritzmann, Timothy A.;
- Chapman, Rebecca;
- Chavez, Lukas;
- Boop, Fredrick A.
Publication type:
Article
Deep sequencing of WNT-activated medulloblastomas reveals secondary SHH pathway activation.
Published in:
Acta Neuropathologica, 2018, v. 135, n. 4, p. 635, doi. 10.1007/s00401-018-1819-x
By:
- Iorgulescu, J. Bryan;
- Van Ziffle, Jessica;
- Stevers, Meredith;
- Grenert, James P.;
- Bastian, Boris C.;
- Chavez, Lukas;
- Stichel, Damian;
- Buchhalter, Ivo;
- Samuel, David;
- Nicolaides, Theodore;
- Banerjee, Anuradha;
- Mueller, Sabine;
- Gupta, Nalin;
- Tihan, Tarik;
- Bollen, Andrew W.;
- Northcott, Paul A.;
- Kool, Marcel;
- Pfister, Stefan;
- Korshunov, Andrey;
- Perry, Arie
Publication type:
Article
DNA-methylation profiling discloses significant advantages over NanoString method for molecular classification of medulloblastoma.
Published in:
2017
By:
- Korshunov, Andrey;
- Chavez, Lukas;
- Northcott, Paul;
- Sharma, Tanvi;
- Ryzhova, Marina;
- Jones, David;
- Deimling, Andreas;
- Pfister, Stefan;
- Kool, Marcel
Publication type:
Letter
Immunohistochemical analysis of H3K27me3 demonstrates global reduction in group-A childhood posterior fossa ependymoma and is a powerful predictor of outcome.
Published in:
Acta Neuropathologica, 2017, v. 134, n. 5, p. 705, doi. 10.1007/s00401-017-1752-4
By:
- Panwalkar, Pooja;
- Clark, Jonathan;
- Ramaswamy, Vijay;
- Hawes, Debra;
- Yang, Fusheng;
- Dunham, Christopher;
- Yip, Stephen;
- Hukin, Juliette;
- Sun, Yilun;
- Schipper, Matthew;
- Chavez, Lukas;
- Margol, Ashley;
- Pekmezci, Melike;
- Chung, Chan;
- Banda, Adam;
- Bayliss, Jill;
- Curry, Sarah;
- Santi, Mariarita;
- Rodriguez, Fausto;
- Snuderl, Matija
Publication type:
Article
H3-/IDH-wild type pediatric glioblastoma is comprised of molecularly and prognostically distinct subtypes with associated oncogenic drivers.
Published in:
Acta Neuropathologica, 2017, v. 134, n. 3, p. 507, doi. 10.1007/s00401-017-1710-1
By:
- Korshunov, Andrey;
- Schrimpf, Daniel;
- Ryzhova, Marina;
- Sturm, Dominik;
- Chavez, Lukas;
- Hovestadt, Volker;
- Sharma, Tanvi;
- Habel, Antje;
- Burford, Anna;
- Jones, Chris;
- Zheludkova, Olga;
- Kumirova, Ella;
- Kramm, Christof;
- Golanov, Andrey;
- Capper, David;
- Deimling, Andreas;
- Pfister, Stefan;
- Jones, David
Publication type:
Article
Polymorphous low-grade neuroepithelial tumor of the young (PLNTY): an epileptogenic neoplasm with oligodendroglioma-like components, aberrant CD34 expression, and genetic alterations involving the MAP kinase pathway.
Published in:
Acta Neuropathologica, 2017, v. 133, n. 3, p. 417, doi. 10.1007/s00401-016-1639-9
By:
- Huse, Jason;
- Snuderl, Matija;
- Jones, David;
- Brathwaite, Carole;
- Altman, Nolan;
- Lavi, Ehud;
- Saffery, Richard;
- Sexton-Oates, Alexandra;
- Blumcke, Ingmar;
- Capper, David;
- Karajannis, Matthias;
- Benayed, Ryma;
- Chavez, Lukas;
- Thomas, Cheddhi;
- Serrano, Jonathan;
- Borsu, Laetitia;
- Ladanyi, Marc;
- Rosenblum, Marc
Publication type:
Article
Genetic confirmation that ependymoma can arise as part of multiple endocrine neoplasia type 1 (MEN1) syndrome.
Published in:
2017
By:
- Cuevas-Ocampo, Areli;
- Bollen, Andrew;
- Goode, Benjamin;
- Pajtler, Kristian;
- Chavez, Lukas;
- Sharma, Tanvi;
- Dai, Sun-Chuan;
- McDermott, Michael;
- Perry, Arie;
- Korshunov, Andrey;
- Solomon, David
Publication type:
Letter
Evidence of H3 K27M mutations in posterior fossa ependymomas.
Published in:
2016
By:
- Gessi, Marco;
- Capper, David;
- Sahm, Felix;
- Huang, Kristin;
- Deimling, Andreas;
- Tippelt, Stephan;
- Fleischhack, Gudrun;
- Scherbaum, Daniel;
- Alfer, Joachim;
- Juhnke, Björn-Ole;
- Hoff, Katja;
- Rutkowski, Stefan;
- Warmuth-Metz, Monika;
- Chavez, Lukas;
- Pfister, Stefan;
- Pietsch, Torsten;
- Jones, David;
- Sturm, Dominik
Publication type:
Letter
Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX.
Published in:
Nature, 2013, v. 497, n. 7447, p. 122, doi. 10.1038/nature12052
By:
- Ko, Myunggon;
- An, Jungeun;
- Bandukwala, Hozefa S.;
- Chavez, Lukas;
- Äijö, Tarmo;
- Pastor, William A.;
- Segal, Matthew F.;
- Li, Huiming;
- Koh, Kian Peng;
- Lähdesmäki, Harri;
- Hogan, Patrick G.;
- Aravind, L.;
- Rao, Anjana
Publication type:
Article
InTAD: chromosome conformation guided analysis of enhancer target genes.
Published in:
BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2655-2
By:
- Okonechnikov, Konstantin;
- Erkek, Serap;
- Korbel, Jan O.;
- Pfister, Stefan M.;
- Chavez, Lukas
Publication type:
Article
DNA--Methylome Analysis of Mouse Intestinal Adenoma Identifies a Tumour-Specific Signature That Is Partly Conserved in Human Colon Cancer.
Published in:
PLoS Genetics, 2013, v. 9, n. 2, p. 1, doi. 10.1371/journal.pgen.1003250
By:
- Grimm, Christina;
- Chavez, Lukas;
- Vilardell, Mireia;
- Farrall, Alexandra L.;
- Tierling, Sascha;
- Böhm, Julia W.;
- Grote, Phillip;
- Lienhard, Matthias;
- Dietrich, Jörn;
- Timmermann, Bernd;
- Walter, Jörn;
- Schweiger, Michal R.;
- Lehrach, Hans;
- Herwig, Ralf;
- Herrmann, Bernhard G.;
- Morkel, Markus
Publication type:
Article
MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments.
Published in:
Bioinformatics, 2014, v. 30, n. 2, p. 284, doi. 10.1093/bioinformatics/btt650
By:
- Lienhard, Matthias;
- Grimm, Christina;
- Morkel, Markus;
- Herwig, Ralf;
- Chavez, Lukas
Publication type:
Article

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