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Community Detection in Large-Scale Bipartite Biological Networks.
Published in:
Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.649440
By:
- Calderer, Genís;
- Kuijjer, Marieke L.
Publication type:
Article
Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma.
Published in:
Journal of Pathology, 2023, v. 259, n. 1, p. 56, doi. 10.1002/path.6019
By:
- Birkeälv, Sofia;
- Harland, Mark;
- Matsuyama, Larissa Satiko Alcantara Sekimoto;
- Rashid, Mamun;
- Mehta, Ishan;
- Laye, Jonathan P;
- Haase, Kerstin;
- Mell, Tracey;
- Iyer, Vivek;
- Robles‐Espinoza, Carla Daniela;
- McDermott, Ultan;
- van Loo, Peter;
- Kuijjer, Marieke L;
- Possik, Patricia A;
- Maria Engler, Silvya Stuchi;
- Bishop, D Timothy;
- Newton‐Bishop, Julia;
- Adams, David J
Publication type:
Article
Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation.
Published in:
Journal of Clinical Investigation, 2013, v. 123, n. 12, p. 5351, doi. 10.1172/JCI70559
By:
- Kansara, Maya;
- Huei San Leong;
- Dan Mei Lin;
- Popkiss, Sophie;
- Puiyi Pang;
- Garsed, Dale W.;
- Walkley, Carl R.;
- Cullinane, Carleen;
- Ellul, Jason;
- Haynes, Nicole M.;
- Hicks, Rod;
- Kuijjer, Marieke L.;
- Cleton-Jansen, Anne-Marie;
- Hinds, Philip W.;
- Smyth, Mark J.;
- Thomas, David M.
Publication type:
Article
gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit.
Published in:
NAR Genomics & Bioinformatics, 2022, v. 4, n. 1, p. 1, doi. 10.1093/nargab/lqac002
By:
- Guebila, Marouen Ben;
- Morgan, Daniel C;
- Glass, Kimberly;
- Kuijjer, Marieke L;
- DeMeo, Dawn L;
- Quackenbush, John
Publication type:
Article
Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome.
Published in:
Nature Genetics, 2011, v. 43, n. 12, p. 1256, doi. 10.1038/ng.1004
By:
- Pansuriya, Twinkal C;
- van Eijk, Ronald;
- d'Adamo, Pio;
- van Ruler, Maayke A J H;
- Kuijjer, Marieke L;
- Oosting, Jan;
- Cleton-Jansen, Anne-Marie;
- van Oosterwijk, Jolieke G;
- Verbeke, Sofie L J;
- Meijer, Daniëlle;
- van Wezel, Tom;
- Nord, Karolin H;
- Sangiorgi, Luca;
- Toker, Berkin;
- Liegl-Atzwanger, Bernadette;
- San-Julian, Mikel;
- Sciot, Raf;
- Limaye, Nisha;
- Kindblom, Lars-Gunnar;
- Daugaard, Soeren
Publication type:
Article
The Variable Genomic Landscape During Osteosarcoma Progression: Insights From a Longitudinal WGS Analysis.
Published in:
Genes, Chromosomes & Cancer, 2024, v. 63, n. 7, p. 1, doi. 10.1002/gcc.23253
By:
- Meijer, Debora M.;
- Ruano, Dina;
- Briaire‐de Bruijn, Inge H.;
- Wijers‐Koster, Pauline M.;
- van de Sande, Michiel A. J.;
- Gelderblom, Hans;
- Cleton‐Jansen, Anne‐Marie;
- de Miranda, Noel F. C. C.;
- Kuijjer, Marieke L.;
- Bovée, Judith V. M. G.
Publication type:
Article
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database.
Published in:
Bioinformatics, 2022, v. 38, n. 2, p. 580, doi. 10.1093/bioinformatics/btab549
By:
- Osorio, Daniel;
- Kuijjer, Marieke L;
- Cai, James J
Publication type:
Article
Modulation of the Osteosarcoma Expression Phenotype by MicroRNAs.
Published in:
PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0048086
By:
- Namløs, Heidi M.;
- Meza-Zepeda, Leonardo A.;
- Barøy, Tale;
- Østensen, Ingrid H. G.;
- Kresse, Stine H.;
- Kuijjer, Marieke L.;
- Serra, Massimo;
- Bürger, Horst;
- Cleton-Jansen, Anne-Marie;
- Myklebost, Ola
Publication type:
Article
Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-08081-1
By:
- Wong, Kim;
- van der Weyden, Louise;
- Schott, Courtney R.;
- Foote, Alastair;
- Constantino-Casas, Fernando;
- Smith, Sionagh;
- Dobson, Jane M.;
- Murchison, Elizabeth P.;
- Wu, Hong;
- Yeh, Iwei;
- Fullen, Douglas R.;
- Joseph, Nancy;
- Bastian, Boris C.;
- Patel, Rajiv M.;
- Martincorena, Inigo;
- Robles-Espinoza, Carla Daniela;
- Iyer, Vivek;
- Kuijjer, Marieke L.;
- Arends, Mark J.;
- Brenn, Thomas
Publication type:
Article
Macrophages inhibit human osteosarcoma cell growth after activation with the bacterial cell wall derivative liposomal muramyl tripeptide in combination with interferon-γ.
Published in:
Journal of Experimental & Clinical Cancer Research (17569966), 2014, v. 33, n. 1, p. 1, doi. 10.1186/1756-9966-33-27
By:
- Pahl, Jens H. W.;
- Kwappenberg, Kitty M. C.;
- Varypataki, Eleni M.;
- Santos, Susy J.;
- Kuijjer, Marieke L.;
- Mohamed, Susan;
- Wijnen, Juul T.;
- van Tol, Maarten J. D.;
- Cleton-Jansen, Anne-Marie;
- Egeler, R. Maarten;
- Jiskoot, Wim;
- Lankester, Arjan C.;
- Schilham, Marco W.
Publication type:
Article
Kinome and mRNA expression profiling of high-grade osteosarcoma cell lines implies Akt signaling as possible target for therapy.
Published in:
BMC Medical Genomics, 2014, v. 7, n. 1, p. 1, doi. 10.1186/1755-8794-7-4
By:
- Kuijjer, Marieke L.;
- van den Akker, Brendy E. W. M.;
- Hilhorst, Riet;
- Mommersteeg, Monique;
- Buddingh, Emilie P.;
- Serra, Massimo;
- Bürger, Horst;
- Hogendoorn, Pancras C. W.;
- Cleton-Jansen, Anne-Marie
Publication type:
Article
Regulatory network changes between cell lines and their tissues of origin.
Published in:
BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4111-x
By:
- Lopes-Ramos, Camila M.;
- Paulson, Joseph N.;
- Cho-Yi Chen;
- Kuijjer, Marieke L.;
- Fagny, Maud;
- Platig, John;
- Sonawane, Abhijeet R.;
- DeMeo, Dawn L.;
- Quackenbush, John;
- Glass, Kimberly
Publication type:
Article
lionessR: single sample network inference in R.
Published in:
2019
By:
- Kuijjer, Marieke L;
- Hsieh, Ping-Han;
- Quackenbush, John;
- Glass, Kimberly
Publication type:
journal article
Heterogeneity in the gene regulatory landscape of leiomyosarcoma.
Published in:
NAR Cancer, 2023, v. 5, n. 3, p. 1, doi. 10.1093/narcan/zcad037
By:
- Belova, Tatiana;
- Biondi, Nicola;
- Ping-Han Hsieh;
- Lutsik, Pavlo;
- Chudasama, Priya;
- Kuijjer, Marieke L.
Publication type:
Article
Genome-wide analyses on high-grade osteosarcoma: Making sense of a genomically most unstable tumor.
Published in:
International Journal of Cancer, 2013, v. 133, n. 11, p. 2512, doi. 10.1002/ijc.28124
By:
- Kuijjer, Marieke L.;
- Hogendoorn, Pancras C.W.;
- Cleton‐Jansen, Anne‐Marie
Publication type:
Article
Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data.
Published in:
Genes, Chromosomes & Cancer, 2012, v. 51, n. 7, p. 696, doi. 10.1002/gcc.21956
By:
- Kuijjer, Marieke L.;
- Rydbeck, Halfdan;
- Kresse, Stine H.;
- Buddingh, Emilie P.;
- Lid, Ana B.;
- Roelofs, Helene;
- Bürger, Horst;
- Myklebost, Ola;
- Hogendoorn, Pancras C. W.;
- Meza-Zepeda, Leonardo A.;
- Cleton-Jansen, Anne-Marie
Publication type:
Article
Linking Immunity with Genomics in Sarcomas: Is Genomic Complexity an Immunogenic Trigger?
Published in:
Biomedicines, 2021, v. 9, n. 8, p. 1048, doi. 10.3390/biomedicines9081048
By:
- van Oost, Siddh;
- Meijer, Debora M.;
- Kuijjer, Marieke L.;
- Bovée, Judith V. M. G.;
- de Miranda, Noel F. C. C.
Publication type:
Article
Editorial: Applications and Methods in Genomic Networks.
Published in:
2022
By:
- Fagny, Maud;
- Glass, Kimberly;
- Kuijjer, Marieke L.
Publication type:
Editorial
GRAND: a database of gene regulatory network models across human conditions.
Published in:
Nucleic Acids Research, 2022, v. 50, n. D1, p. D610, doi. 10.1093/nar/gkab778
By:
- Ben Guebila, Marouen;
- Lopes-Ramos, Camila M;
- Weighill, Deborah;
- Sonawane, Abhijeet Rajendra;
- Burkholz, Rebekka;
- Shamsaei, Behrouz;
- Platig, John;
- Glass, Kimberly;
- Kuijjer, Marieke L;
- Quackenbush, John
Publication type:
Article
An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets.
Published in:
Journal of Hematology & Oncology, 2017, v. 10, p. 1, doi. 10.1186/s13045-017-0465-4
By:
- Hill, Katherine E.;
- Kelly, Andrew D.;
- Kuijjer, Marieke L.;
- Barry, William;
- Rattani, Ahmed;
- Garbutt, Cassandra C.;
- Kissick, Haydn;
- Janeway, Katherine;
- Perez-Atayde, Antonio;
- Goldsmith, Jeffrey;
- Gebhardt, Mark C.;
- Arredouani, Mohamed S.;
- Cote, Greg;
- Hornicek, Francis;
- Choy, Edwin;
- Duan, Zhenfeng;
- Quackenbush, John;
- Haibe-Kains, Benjamin;
- Spentzos, Dimitrios
Publication type:
Article
Single-sample network modeling on omics data.
Published in:
BMC Biology, 2023, v. 21, n. 1, p. 1, doi. 10.1186/s12915-023-01783-z
By:
- De Marzio, Margherita;
- Glass, Kimberly;
- Kuijjer, Marieke L.
Publication type:
Article
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.
Published in:
BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1847-x
By:
- Paulson, Joseph N.;
- Cho-Yi Chen;
- Lopes-Ramos, Camila M.;
- Kuijjer, Marieke L.;
- Platig, John;
- Sonawane, Abhijeet R.;
- Fagny, Maud;
- Glass, Kimberly;
- Quackenbush, John
Publication type:
Article
EndNote: Feature-based classification of networks.
Published in:
Network Science, 2019, v. 7, n. 3, p. 438, doi. 10.1017/nws.2019.21
By:
- Barnett, Ian;
- Malik, Nishant;
- Kuijjer, Marieke L.;
- Mucha, Peter J.;
- Onnela, Jukka-Pekka
Publication type:
Article
Expression of the immune regulation antigen CD70 in osteosarcoma.
Published in:
Cancer Cell International, 2015, v. 15, n. 1, p. 1, doi. 10.1186/s12935-015-0181-5
By:
- Pahl, Jens H. W.;
- Santos, Susy J.;
- Kuijjer, Marieke L.;
- Boerman, Gerharda H.;
- Sand, Laurens G. L.;
- Szuhai, Karoly;
- Cleton-Jansen, Annemarie;
- Maarten Egeler, R.;
- Boveé, Judith V. M. G.;
- Schilham, Marco W.;
- Lankester, Arjan C.
Publication type:
Article
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas.
Published in:
PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006826
By:
- van IJzendoorn, David G. P.;
- Szuhai, Karoly;
- Briaire-de Bruijn, Inge H.;
- Kostine, Marie;
- Kuijjer, Marieke L.;
- Bovée, Judith V. M. G.
Publication type:
Article
PUMA: PANDA Using MicroRNA Associations.
Published in:
Bioinformatics, 2020, v. 36, n. 18, p. 4765, doi. 10.1093/bioinformatics/btaa571
By:
- Kuijjer, Marieke L;
- Fagny, Maud;
- Marin, Alessandro;
- Quackenbush, John;
- Glass, Kimberly
Publication type:
Article
PyPanda: a Python package for gene regulatory network reconstruction.
Published in:
Bioinformatics, 2016, v. 32, n. 21, p. 3363, doi. 10.1093/bioinformatics/btw422
By:
- van IJzendoorn, David G. P.;
- Glass, Kimberly;
- Quackenbush, John;
- Kuijjer, Marieke L.
Publication type:
Article
IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma.
Published in:
2013
By:
- Kuijjer, Marieke L.;
- Peterse, Elisabeth F. P.;
- van den Akker, Brendy E. W. M.;
- Briaire-de Bruijn, Inge H.;
- Serra, Massimo;
- Meza-Zepeda, Leonardo A.;
- Myklebost, Ola;
- Hassan, A. Bassim;
- Hogendoorn, Pancras C. W.;
- Cleton-Jansen, Anne-Marie
Publication type:
journal article

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