Deliverables
This report will provide targeted profiles of selected biopsies and will be used improve clone inference in WP1, prognostic-biomarker inference in WP3, tumour classification WP4, sample and assay selection in WP6. Results will influence the construction of amplicon deliverables in D2.3.
Targeted ultra-deep sequencing of cancer-gene lociThis report will provide targeted profiles of selected biopsies and will be used to improve clone inference in WP1, prognostic-biomarker inference in WP3, and tumour classification in WP4. Results will influence the construction of amplicon deliverables in D2.2 and D2.3.
Generate amplicon sequencing profiles from sample punches prepared in D.6.2This deliverable converts the validation cohort tissue samples into quantitative genomic amplicon profiles.
Robust cross-cohort clinical patient classifierWe will provide molecular signatures and/or biomarkers of clinical groups based on the integration of all analyzed data types.
Generic modelIn this deliverable, we will construct a generic logical model that will include altered signalling pathways identified by WP3 and WP4, complemented by pathways that are known to be frequently altered in cancer.
Data Management PlanThe purpose of the DMP is to provide an analysis of the main elements of the data management policy that will be used by the applications with regard to all the datasets that will be generated by the project. The DMP is not a fixed document, but evolves during the lifespan of the project.
Project quality planThe project quality plan (the project handbook) constitutes a set of project templates, explanations on the project management process, review process, quality checks, meeting organisation, which is communicated to all partners.
Generate cell line drug sensitivity/resistance validation assaysThis deliverable will validate the drug predictions for prostatic cell lines inferred in WP5.
Proteomic data sets in cancer cell linesIn this deliverable the data required to train the logical models will be provided.
Clonal classification of tumoursClassification of tumours according to dominant clonal content.
Final clone inferenceRefined clonality models and associated biomarkers.
Generate SWATH proteome profiles from sample punches prepared in D.6.2This deliverable converts the validation cohort tissue samples into quantitative protein profiles.
1st Interim Progress ReportThe interim project progress report will address the main achievements and concrete key outcomes of the first project year (project summary, work performed and main results, risk assessment, list of scientific publications and dissemination activities). All work packages will summarize their work, challenges and outcomes in order to contribute to this report.
Targeted profiling of prospective cohortThis report will provide profiles of selected biopsies and will be used to inform sample and assay selection in WP6.
Final regulatory network inferenceRefined reversed engineered regulatory networks in PC tumours based on updated methodology for network integration and analyses of small datasets.
A complete catalogue of targeted profilesThis report will provide normalized molecular profiles, including DNA and protein-expression profiles, of all biopsies studied in WP2.
2nd Interim Progress ReportThe interim project progress report will address the main achievements and concrete key outcomes of the second project year (project summary, work performed and main results, risk assessment, list of scientific publications and dissemination activities). All work packages will summarize their work, challenges and outcomes in order to contribute to this report.
Catalogue of molecular alterations and dysregulated pathwaysWe will provide lists of molecular alterations and targeted pathways. The list will be segregated according to pathological stage (Gleason score), clonal structure and patient.
We will finalize dashboard implementation and interface with data access and depository, refactored methods, ACSN, and Watson. Integration of data and methods will be followed by extensive application testing.
First data-driven reconstruction of context-specific networkProteome networks based on MS and phospho-MS data from prostatic cells lines and from samples of the proCOC and MetaProC biopsies.
Computational pipeline to extract prior network information at the proteomic levelProvides a computational tool to extract and to mathematically aggregate prior information for later use in data-driven network reconstruction.
Network reconstruction algorithms for MS dataProvides novel algorithms for protein network reconstruction tailored to the MS data format of partner ETH and evaluated on the already existing prostatic cell line data of ETH.
Re-implement methodsAnalyses methods will be refactored and re-implemented within the framework.
Data input and input interfaceWe will input data and implement a framework for depositing future data into SmartBiobank.
Design and integrate pathway visualizationWe will provide visual profiles of data from patients, clones and cell lines using ACSN and networks created in WP3 and WP5.
Identification of systematic alterations of networks for different prognosis and for different clonal compositionFound alterations enable the comparison with the genomic analysis of WP1 and provide predictions to be validated in WP6.
Interactome of molecular interactions in prostate cancerThis deliverable provides comprehensive information of all known and inferred interactions in prostate cancer.
The external IT communication infrastructure constitutes a guideline for communication of the PrECISE project to external target groups including conferences, marketing measures and communication channels. Furthermore this deliverable constitutes the launch of the internal PrECISE communication infrastructure including the establishment of mailing lists or a subversion server, and the PrECISE website.
Publications
Author(s):
Matteo Manica, Philippe Chouvarine, Roland Mathis, Ulrich Wagner, Kathrin Oehl, Karim Saba, Laura De Vargas Roditi, Arati N Pati, Maria Rodriguez-Martinez, Peter J Wild, Pavel Sumazin
Published in:
ISMB 2017, 2017
Publisher:
ISMB conference
DOI:
10.5281/zenodo.841110
Author(s):
Mathis, Roland; Manica, Matteo; Rodriguez Martinez, Maria
Published in:
ISMB 2017, 2017
Publisher:
ISMB conference
DOI:
10.5281/zenodo.841164
Author(s):
Linzner, Dominik
Koeppl, Heinz
Published in:
ISMB 2017, 2017
Publisher:
ISMB Conference
DOI:
10.5281/zenodo.841160
Author(s):
Al- Sayed, Sara
Department of Electrical Engineering Technische Universität Darmstadt, Germany
; Koeppl, Heinz
Published in:
IEEE MLSP 2018, 2018
Publisher:
IEEE MLSP conference
DOI:
10.5281/zenodo.1488636
Author(s):
Oskooei, Ali; Born, Jannis; Manica, Matteo; Subramanian, Vigneshwari; Saez-Rodriguez, Julio; Rodriguez- Martinez, Maria
Published in:
32nd Conference on Neural Information Processing Systems (NIPS 2018), 2018
Publisher:
NeurIPs 2018
DOI:
10.5281/zenodo.1967105
Author(s):
Yang, Sikun
Koeppl, Heinz
Published in:
IEEE International conference on data mining (ICDM 2018), 2018
Publisher:
IEEE ICDM
DOI:
10.5281/zenodo.1966177
Author(s):
Linzner, Dominik
Koeppl, Heinz
Published in:
32nd Conference on Neural Information Processing Systems (NeurIPs 2018), 2018
Publisher:
NeurIPs 2018
DOI:
10.5281/zenodo.1966609
Author(s):
Yang, Sikun; Koeppl, Heinz
Published in:
AAAI 2018 - Association for the Advancement of Artificial Intelligence 2018, Issue 3, 2018
Publisher:
Zenodo
DOI:
10.5281/zenodo.1242987
Author(s):
Yang, Sikun; Koeppl, Heinz
Published in:
Issue 10, 2018
Publisher:
Zenodo
DOI:
10.5281/zenodo.1314290
Author(s):
Traynard, Pauline; Tobalina, Luis; Eduati, Federica; Calzone, Laurence; Saez-Rodriguez, Julio
Published in:
Issue 1, 2018
Publisher:
Zenodo
DOI:
10.5281/zenodo.841126
Author(s):
Oskooei, Ali; Born, Jannis; Manica, Matteo; Subramanian, Vigneshwari; Saez-Rodriguez, Julio; Rodriguez- Martinez, Maria
Published in:
Issue 7, 2018
Publisher:
Zenodo
DOI:
10.5281/zenodo.1967104
Author(s):
LInzner, Dominik; Koeppl, Heinz
Published in:
Issue 10, 2018
Publisher:
Arxiv
DOI:
10.5281/zenodo.1966608
Author(s):
Yang, Sikun; Koeppl, Heinz
Published in:
Issue 3, 2018
Publisher:
Zenodo
DOI:
10.5281/zenodo.1966176
Author(s):
Linzner, Dominik; Koepply, Heinz
Published in:
ISMB 2017 / CMSB 2017, 2017
Publisher:
Zenodo
DOI:
10.5281/zenodo.841159
Author(s):
Cuklina, Jelena; Lee, Chloe; Williams, Evan G.; Sajic, Tatjana; Collins, Ben; Rodriguez-Martinez, Maria; Pedrioli, Patrick; Aebersold, Ruedi
Published in:
Issue 10, 2018
Publisher:
Zenodo
DOI:
10.5281/zenodo.1446001
Author(s):
Traynard, Pauline; Beal, Jonas; Tobalina, Luis; Barillot, Emmanuel; Saez-Rodriguez, Julio; Calzone, Laurence
Published in:
ISMB 2017, Issue 9, 2017
Publisher:
ISMB conference
DOI:
10.5281/zenodo.841116
Author(s):
Al- Sayed, Sara; Koeppl, Heinz
Published in:
(MLSP 2018) 2018 IEEE International Workshop on Machine Learning for Signal Processing, Issue 2, 2018
Publisher:
IEEE
DOI:
10.5281/zenodo.1488635
Author(s):
Mathis, Roland; Manica, Matteo; Rodriguez Martinez, Maria
Published in:
Issue 2, 2017
Publisher:
Zenodo
DOI:
10.5281/zenodo.841163
Author(s):
Al-Sayed, Sara; Koeppl, Heinz
Published in:
ISMB 2017, Issue 5, 2017
Publisher:
ISMB Conference
DOI:
10.5281/zenodo.841132
Author(s):
Cuklina, Jelena; Wu, Yibo; Williams, Evan G.; Rodriguez Martinez, Maria; Aebersold, Ruedi
Published in:
ISMB 2017, Issue 6, 2017
Publisher:
ISMB Conference
DOI:
10.5281/zenodo.841208
Author(s):
Subramanian, Vigneshwari; Szalai, Bence; Tobalina, Luis; Saez-Rodriguez, Julio
Published in:
NETTAB 2017, Issue 4, 2017
Publisher:
NETTAB conference
DOI:
10.5281/zenodo.1066906
Author(s):
Mathis, Roland; Manica, Matteo; Martinez Rodriguez, Maria
Published in:
Issue 9, 2016
Publisher:
ROCKY 2016
DOI:
10.5281/zenodo.840078
Author(s):
Türei, Denes; Tobalina, Luis; Henriques, David; Traynard, Pauline; Calzone, Laurence; Korcsmáros, Tamás; Saez-Rodriguez, Julio
Published in:
Issue 4, 2016
Publisher:
ICSB 2016
DOI:
10.5281/zenodo.840094
Author(s):
Traynard, Pauline; Tobalina, Luis; Henriques, David; Barillot, Emmanuel; Saez-Rodriguez, Julio; Calzone, Laurence
Published in:
Issue 11, 2016
Publisher:
ICSB 2016
DOI:
10.5281/zenodo.840084
Author(s):
Manica, Matteo; Mathis, Roland; Martinez Rodriguez, Maria
Published in:
Issue 6, 2016
Publisher:
All SystemsX.ch Day 2016
DOI:
10.5281/zenodo.839692
Author(s):
Tobalina, Luis; Henriques, David; Saez-Rodriguez, Julio
Published in:
2016
Publisher:
byteMAL
DOI:
10.5281/zenodo.835692
Author(s):
Guo, Tiannan; Li, Li; Zhong, Qing; Rupp, Niels J.; Charmpi, Konstantina; Wong, Christine E.; Wagner, Ulrich; Rueschoff, Jan H.; Jochum, Wolfram; Fankhauser, Christian; Saba, Karim; Poyet, Cedric; Wild, Peter; Aebersold, Ruedi; Beyer, Andreas
Published in:
Issue 1, 2016
Publisher:
All SystemsX.ch Day 2016
DOI:
10.5281/zenodo.841216
Author(s):
Čuklina, Jelena; Wu, Yibo; Williams, Evan. G.; Rodríguez-Martínez, María; Aebersold, Ruedi
Published in:
Issue 8, 2016
Publisher:
LATSIS Symposium on Personalized Medicine
DOI:
10.5281/zenodo.846702
Author(s):
Traynard, Pauline; Tobalina, Luis; Eduati, Federica; Calzone, Laurence; Saez-Rodriguez, Julio
Published in:
ISMB 2017, 2017
Publisher:
ISMB conference
DOI:
10.5281/zenodo.841127
Author(s):
Cuklina, Jelena; Lee, Chloe; Williams, Evan G.; Sajic, Tatjana; Collins, Ben; Rodriguez-Martinez, Maria; Pedrioli, Patrick; Aebersold, Ruedi
Published in:
HUPO 2018, 2018
Publisher:
HUPO conference
DOI:
10.5281/zenodo.1446001
Author(s):
Tobalina, Luis
Published in:
Logic and System Biology Workshop, 2018
Publisher:
Logic and System Biology Workshop
DOI:
10.5281/zenodo.1474213
Author(s):
Menden, Michael P; Wang, Dennis; Guan, Yuanfang; Mason, Michael; Szalai, Bence; Bulusu, Krishna C; Yu, Thomas; Kang, Jaewoo; Jeon, Minji; Wolfinger, Russ; Nguyen, Tin; Zaskavskiy, Mikhail; DREAM consortium; Jang, In Sock; Ghazoui, Zara; Ahsen, Mehmet Eren; Vogel, Robert; Neto, Elias Chaibub; Norman, Thea; Tang, Eric KY; Garnett, Matthew J; Di Veroli, Giovanni; Fawell, Steve; Stolovitzky, Gustavo;
Published in:
DREAM Challenges 2017, 2017
Publisher:
DREAM Challenges
DOI:
10.1101/200451
Author(s):
Arnau Montagud, Jonas Béal, Pauline Traynard, Luis Tobalina, Julio Sáez-Rodríguez, Emmanuel Barillot and Laurence Calzone
Published in:
2018
Publisher:
ECCB 2018
DOI:
10.5281/zenodo.2416618
Author(s):
Jonas Béal, Arnau Montagud, Pauline Traynard, Emmanuel Barillot and Laurence Calzone
Published in:
2017
Publisher:
ECCB 2018
DOI:
10.5281/zenodo.2417118
Author(s):
Angeliki Kalamara, Luis Tobalina, Julio Saez-Rodriguez
Published in:
Current Opinion in Systems Biology, Issue 10, 2018, Page(s) 53-62, ISSN 2452-3100
Publisher:
ELSEVIER
DOI:
10.1016/j.coisb.2018.07.001
Author(s):
Dmytro Ustianenko, Hua-Sheng Chiu, Thomas Treiber, Sebastien M. Weyn-Vanhentenryck, Nora Treiber, Gunter Meister, Pavel Sumazin, Chaolin Zhang
Published in:
Molecular Cell, Issue 71/2, 2018, Page(s) 271-283.e5, ISSN 1097-2765
Publisher:
Cell Press
DOI:
10.1016/j.molcel.2018.06.029
Author(s):
Jonas Béal, Arnau Montagud, Pauline Traynard, Emmanuel Barillot, Laurence Calzone
Published in:
Frontiers in Physiology, Issue 9, 2019, ISSN 1664-042X
Publisher:
Frontiers Research Foundation
DOI:
10.3389/fphys.2018.01965
Author(s):
Gaelle Letort, Arnau Montagud, Gautier Stoll, Randy Heiland, Emmanuel Barillot, Paul Macklin, Andrei Zinovyev, Laurence Calzone
Published in:
Bioinformatics, 2018, ISSN 1367-4803
Publisher:
Oxford University Press
DOI:
10.1093/bioinformatics/bty766
Author(s):
Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei
Published in:
Current Opinion in Chemical Engineering 21 22-31, Issue 1, 2018, ISSN 2211-3398
Publisher:
Elsevier BV
DOI:
10.5281/zenodo.1243004
Author(s):
Pauline Traynard, Luis Tobalina, Federica Eduati, Laurence Calzone, Julio Saez-Rodriguez
Published in:
CPT: Pharmacometrics & Systems Pharmacology, Issue 6/8, 2017, Page(s) 499-511, ISSN 2163-8306
Publisher:
Nature Publishing Group
DOI:
10.1002/psp4.12225
Author(s):
Hua-Sheng Chiu, Sonal Somvanshi, Ektaben Patel, Ting-Wen Chen, Vivek P. Singh, Barry Zorman, Sagar L. Patil, Yinghong Pan, Sujash S. Chatterjee, Anil K. Sood, Preethi H. Gunaratne, Pavel Sumazin, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia
Published in:
Cell Reports, Issue 23/1, 2018, Page(s) 297-312.e12, ISSN 2211-1247
Publisher:
Cell Press
DOI:
10.1016/j.celrep.2018.03.064
Author(s):
Stoll, Gautier; Caron, Barthelemy; Viara, Eric; Dugourd, Aurelien; Zinovyev, Andrei; Naldi, Aurelien; Kroemer, Guido
Published in:
Bioinformatics, Issue 5, 2017, Page(s) 2226–2228, ISSN 1367-4803
Publisher:
Oxford University Press
DOI:
10.5281/zenodo.841168
Author(s):
Traynard, Pauline; Tobalina, Luis; Eduati, Federica; Calzone, Laurence; Saez-Rodriguez, Julio
Published in:
CPT: Pharmacometrics and Systems Pharmacology, Issue 5, 2017, ISSN 2163-8306
Publisher:
Nature Publishing Group
DOI:
10.5281/zenodo.841206
Author(s):
H. Alexander Ebhardt, Alex Root, Yansheng Liu, Nicholas Paul Gauthier, Chris Sander, Ruedi Aebersold
Published in:
npj Systems Biology and Applications, Issue 4/1, 2018, ISSN 2056-7189
Publisher:
Zenodo
DOI:
10.1038/s41540-018-0064-1
Author(s):
Tiannan Guo, Li Li, Qing Zhong, Niels J Rupp, Konstantina Charmpi, Christine E Wong, Ulrich Wagner, Jan H Rueschoff, Wolfram Jochum, Christian Daniel Fankhauser, Karim Saba, Cedric Poyet, Peter J Wild, Ruedi Aebersold, Andreas Beyer
Published in:
Life Science Alliance, Issue 1/2, 2018, Page(s) e201800042, ISSN 2575-1077
Publisher:
Life Science Alliance
DOI:
10.26508/lsa.201800042
Author(s):
Matteo Manica, Joris Cadow, Roland Mathis, María Rodríguez Martínez
Published in:
npj Systems Biology and Applications, Issue 5/1, 2019, ISSN 2056-7189
Publisher:
Cornell University
DOI:
10.1038/s41540-019-0086-3
Intellectual Property Rights
Application/Publication number:
US
94520169
Date:
2017-12-01
Applicant(s):
IBM RESEARCH GMBH
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