Resultado final
Evaluated and implemented SOPs. SOPs for TCR repertoire. Samples used for generating data to develop the tools and validate the software: melanoma, colorectal cancer, and ovarian cancer.
Evaluation of the analytical pipeline for cancer vaccinesEvaluated and implemented SOPs. Samples used for generating data to develop the tools and validate the software: melanoma, glioblastoma, and breast cancer.
CRCclassifierA decision support model using the clinical parameters and the image descriptors derived from the analyses in task 2.1. The model will be a validated prototype using the available data. Samples used for generating data to develop the tools and validate the software: colorectal cancer.
SOPs for TIL quantificationEvaluated and implemented SOPs. SOPs for routine application in pathology labs. Samples used for generating data to develop the tools and validate the software: colorectal cancer.
TCR2epitopeSoftware tool for predicting epitope characteristics from the primary sequence information of TCRs. The software will include a method for identifying specificity of TCR-pMHC interaction (UU) as well as a web-database for TCRs with known specificities (MU). The data will be provided by NKI. Samples used for generating data to develop the tools and validate the software: melanoma, colorectal cancer, and ovarian cancer
Immuno Oncoclogy SuiteDatabase for molecular data (whole-exome sequencing data, microsatellite status, FACS data), clinical data (information about cancer patients, TNM staging, and density values of TILs used for immune score estimation), and imaging data (scanned whole-slide H&E images and stained IHC images) generated from colorectal cancer samples in WP2.
Software for selecting epitopes from large number of candidates. Samples used for generating data to develop the tools and validate the software: melanoma, glioblastoma, and breast cancer.
RDF databaseRDF version of the database ImmunoOncologySuite and SPARQL graphical editor
digital TILsorterMethod and software for TIL reconstruction employing a) deconvolution method (CNIC) and develop the algorithm for enumeration of immune cells, stromal cells, and tumour cells (I-MED). Samples used for generating data to develop the tools and validate the software: colorectal cancer.
Institution of APERIM web page: A webpage is an absolute requirement for dissemination Furthermore it supports the communication within the consortium.
Publicaciones
Autores:
Benjamin Schubert, Oliver Kohlbacher
Publicado en:
Genome Medicine, Edición 8/1, 2016, Página(s) 1-10, ISSN 1756-994X
Editor:
BioMed Central
DOI:
10.1186/s13073-016-0263-6
Autores:
Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, András Szolek, Christopher Mohr, Oliver Kohlbacher
Publicado en:
Bioinformatics, 2016, Página(s) btw113, ISSN 1367-4803
Editor:
Oxford University Press
DOI:
10.1093/bioinformatics/btw113
Autores:
Christopher Mohr, Andreas Friedrich, David Wojnar, Erhan Kenar, Aydin Can Polatkan, Marius Cosmin Codrea, Stefan Czemmel, Oliver Kohlbacher, Sven Nahnsen
Publicado en:
PLOS ONE, Edición 13/1, 2018, Página(s) e0191603, ISSN 1932-6203
Editor:
Public Library of Science
DOI:
10.1371/journal.pone.0191603
Autores:
Mikhail Shugay, Dmitriy V Bagaev, Ivan V Zvyagin, Renske M Vroomans, Jeremy Chase Crawford, Garry Dolton, Ekaterina A Komech, Anastasiya L Sycheva, Anna E Koneva, Evgeniy S Egorov, Alexey V Eliseev, Ewald Van Dyk, Pradyot Dash, Meriem Attaf, Cristina Rius, Kristin Ladell, James E McLaren, Katherine K Matthews, E Bridie Clemens, Daniel C Douek, Fabio Luciani, Debbie van Baarle, Katherine Kedzier
Publicado en:
Nucleic Acids Research, Edición 46/D1, 2017, Página(s) D419-D427, ISSN 0305-1048
Editor:
Oxford University Press
DOI:
10.1093/nar/gkx760
Autores:
Mirjana Efremova, Francesca Finotello, Dietmar Rieder, Zlatko Trajanoski
Publicado en:
Frontiers in Immunology, Edición 8, 2017, ISSN 1664-3224
Editor:
Frontiers Media SA
DOI:
10.3389/fimmu.2017.01679
Autores:
Pornpimol Charoentong, Francesca Finotello, Mihaela Angelova, Clemens Mayer, Mirjana Efremova, Dietmar Rieder, Hubert Hackl, Zlatko Trajanoski
Publicado en:
Cell Reports, Edición 18/1, 2017, Página(s) 248-262, ISSN 2211-1247
Editor:
Cell Press
DOI:
10.1016/j.celrep.2016.12.019
Autores:
Bernhard Mlecnik, Marc Van den Eynde, Gabriela Bindea, Sarah E Church, Angela Vasaturo, Tessa Fredriksen, Lucie Lafontaine, Nacilla Haicheur, Florence Marliot, Daphné Debetancourt, Géraldine Pairet, Anne Jouret-Mourin, Jean-Francois Gigot, Catherine Hubert, Etienne Danse, Cristina Dragean, Javier Carrasco, Yves Humblet, Viia Valge-Archer, Anne Berger, Franck Pagès, Jean-Pascal Machiels, Jérôm
Publicado en:
JNCI: Journal of the National Cancer Institute, Edición 110/1, 2017, Página(s) 97-108, ISSN 0027-8874
Editor:
Oxford University Press
DOI:
10.1093/jnci/djx123
Autores:
Mirjana Efremova, Dietmar Rieder, Victoria Klepsch, Pornpimol Charoentong, Francesca Finotello, Hubert Hackl, Natascha Hermann-Kleiter, Martin Löwer, Gottfried Baier, Anne Krogsdam, Zlatko Trajanoski
Publicado en:
Nature Communications, Edición 9/1, 2018, ISSN 2041-1723
Editor:
Nature Publishing Group
DOI:
10.1038/s41467-017-02424-0
Autores:
Hubert Hackl, Pornpimol Charoentong, Francesca Finotello, Zlatko Trajanoski
Publicado en:
Nature Reviews Genetics, Edición 17/8, 2016, Página(s) 441-458, ISSN 1471-0056
Editor:
Nature Publishing Group
DOI:
10.1038/nrg.2016.67
Autores:
Bernhard Mlecnik, Gabriela Bindea, Helen K. Angell, Pauline Maby, Mihaela Angelova, David Tougeron, Sarah E. Church, Lucie Lafontaine, Maria Fischer, Tessa Fredriksen, Maristella Sasso, Amélie M. Bilocq, Amos Kirilovsky, Anna C. Obenauf, Mohamad Hamieh, Anne Berger, Patrick Bruneval, Jean-Jacques Tuech, Jean-Christophe Sabourin, Florence Le Pessot, Jacques Mauillon, Arash Rafii, Pierre Laure
Publicado en:
Immunity, Edición 44/3, 2016, Página(s) 698-711, ISSN 1074-7613
Editor:
Cell Press
DOI:
10.1016/j.immuni.2016.02.025
Autores:
E. Stronen, M. Toebes, S. Kelderman, M. M. van Buuren, W. Yang, N. van Rooij, M. Donia, M.-L. Boschen, F. Lund-Johansen, J. Olweus, T. N. Schumacher
Publicado en:
Science, Edición 352/6291, 2016, Página(s) 1337-1341, ISSN 0036-8075
Editor:
American Association for the Advancement of Science
DOI:
10.1126/science.aaf2288
Autores:
B. Mlecnik, G. Bindea, A. Kirilovsky, H. K. Angell, A. C. Obenauf, M. Tosolini, S. E. Church, P. Maby, A. Vasaturo, M. Angelova, T. Fredriksen, S. Mauger, M. Waldner, A. Berger, M. R. Speicher, F. Pages, V. Valge-Archer, J. Galon
Publicado en:
Science Translational Medicine, Edición 8/327, 2016, Página(s) 327ra26-327ra26, ISSN 1946-6234
Editor:
American Association for the Advancement of Science
DOI:
10.1126/scitranslmed.aad6352
Autores:
Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer, Oliver Kohlbacher
Publicado en:
BMC Bioinformatics, Edición 18/1, 2017, ISSN 1471-2105
Editor:
BioMed Central
DOI:
10.1186/s12859-017-1667-z
Autores:
Francesca Finotello, Zlatko Trajanoski
Publicado en:
Genome Medicine, Edición 9/1, 2017, ISSN 1756-994X
Editor:
BioMed Central
DOI:
10.1186/s13073-017-0402-8
Autores:
Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski
Publicado en:
Bioinformatics, 2017, ISSN 1367-4803
Editor:
Oxford University Press
DOI:
10.1093/bioinformatics/btx377
Autores:
Dmitriy A. Shagin, Maria A. Turchaninova, Irina A. Shagina, Mikhail Shugay, Andrew R. Zaretsky, Olga I. Zueva, Dmitriy A. Bolotin, Sergey Lukyanov, Dmitriy M. Chudakov
Publicado en:
BMC Genomics, Edición 18/1, 2017, ISSN 1471-2164
Editor:
BioMed Central
DOI:
10.1186/s12864-017-3815-2
Autores:
Mikhail Shugay, Andrew R. Zaretsky, Dmitriy A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrew A. Shelenkov, Mikhail Y. Lebedin, Dmitriy V. Bagaev, Sergey Lukyanov, Dmitriy M. Chudakov
Publicado en:
PLOS Computational Biology, Edición 13/5, 2017, Página(s) e1005480, ISSN 1553-7358
Editor:
Paul P Gardner
DOI:
10.1371/journal.pcbi.1005480
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