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PrECISE

PERSONALIZED ENGINE FOR CANCER INTEGRATIVE STUDY AND EVALUATION

Total Cost €

EC-Contrib. €

Partnership

Views

Outcomes and
results

PrECISE project word cloud

Explore the words cloud of the PrECISE project. It provides you a very rough idea of what is the project "PrECISE" about.

serve industrial individual share software predictive biomarker strategies cognitive implicated cell promise patients combines lines multiple translational lies prone metastatic generation computer death amongst data models proteomic tumour accessible coexist tools screenings statements infer last tumours heterogeneity prostate biomedical therapies deposit framework prognosis drug recommend treatment driving intervention disease difficult alterations transcriptomic mathematical optimized integration visualize actionable panel single recommendations clinical therapeutic proof primary subclones graphical failed analyze industries interface types technologies ibm throughput cancer translate genomic mechanisms accordingly therapy competing aggressive cells computational intuitive despite molecular prospective inform clinic watson renders cohorts clinicians elucidate men

Project "PrECISE" data sheet

The following table provides information about the project.

Coordinator	TECHNIKON FORSCHUNGS- UND PLANUNGSGESELLSCHAFT MBH Organization address address: BURGPLATZ 3A city: VILLACH postcode: 9500 website: https://urldefense.com/v3/__https://technikon.com__;!!DOxrgLBm!XQj8lX3wvrhxnrAflv0OBz99-qlU79olpwsKnLk7T4NxnEuLngVJcmEmxcnyX1OKvqUsEW_8DocHehV2MbBX$ contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Austria [AT]
Project website	https://precise-project.eu/
Total cost	5˙695˙712 €
EC max contribution	3˙090˙312 € (54%)
Programme	1. H2020-EU.3.1.1. (Understanding health, wellbeing and disease)
Code Call	H2020-PHC-2015-two-stage
Funding Scheme	RIA
Starting year	2016
Duration (year-month-day)	from 2016-01-01 to 2018-12-31

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	TECHNIKON FORSCHUNGS- UND PLANUNGSGESELLSCHAFT MBH TECHNIKON FORSCHUNGS- UND PLANUNGSGESELLSCHAFT MBH Organization address address: BURGPLATZ 3A city: VILLACH postcode: 9500 website: https://urldefense.com/v3/__https://technikon.com__;!!DOxrgLBm!XQj8lX3wvrhxnrAflv0OBz99-qlU79olpwsKnLk7T4NxnEuLngVJcmEmxcnyX1OKvqUsEW_8DocHehV2MbBX$ contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	AT (VILLACH)	coordinator	358˙125.00
2	UNIVERSITAETSKLINIKUM AACHEN UNIVERSITAETSKLINIKUM AACHEN Organization address address: Pauwelsstrasse 30 city: AACHEN postcode: 52074 website: www.ukaachen.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (AACHEN)	participant	620˙937.00
3	BAYLOR COLLEGE OF MEDICINE BAYLOR COLLEGE OF MEDICINE Organization address address: ONE BAYLOR PLAZA T119 city: HOUSTON TX postcode: 77030 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	US (HOUSTON TX)	participant	561˙250.00
4	TECHNISCHE UNIVERSITAT DARMSTADT TECHNISCHE UNIVERSITAT DARMSTADT Organization address address: KAROLINENPLATZ 5 city: DARMSTADT postcode: 64289 website: www.tu-darmstadt.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (DARMSTADT)	participant	539˙375.00
5	INSTITUT CURIE INSTITUT CURIE Organization address address: rue d'Ulm 26 city: PARIS postcode: 75231 website: www.curie.fr contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	FR (PARIS)	participant	535˙625.00
6	ASTRIDBIO TECHNOLOGIES KFT ASTRIDBIO TECHNOLOGIES KFT Organization address address: ALSO KIKOTO SOR 11D city: SZEGED postcode: 6726 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	HU (SZEGED)	participant	475˙000.00
7	EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH Organization address address: Raemistrasse 101 city: ZUERICH postcode: 8092 website: https://www.ethz.ch/de.html contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CH (ZUERICH)	participant	0.00
8	IBM RESEARCH GMBH IBM RESEARCH GMBH Organization address address: SAEUMERSTRASSE 4 city: RUESCHLIKON postcode: 8803 website: www.zurich.ibm.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CH (RUESCHLIKON)	participant	0.00
9	UNIVERSITAT ZURICH UNIVERSITAT ZURICH Organization address address: RAMISTRASSE 71 city: ZURICH postcode: 8006 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CH (ZURICH)	participant	0.00

Map

Project objective

Despite of their great promise, high-throughput technologies in cancer research have often failed to translate to major therapeutic advances in the clinic. One challenge has been tumour heterogeneity, where multiple competing subclones coexist within a single tumour. Genomic heterogeneity renders it difficult to identify all driving molecular alterations, and thus results in therapies that only target subsets of aggressive tumour cells. Another challenge lies in the integration of multiple types of molecular data into mathematical disease models that can make actionable clinical statements.

We aim to develop predictive computational technology that can exploit molecular and clinical data to improve our understanding of disease mechanisms and to inform clinicians about optimized strategies for therapeutic intervention. We propose to focus on prostate cancer, a leading cause of cancer death amongst men in Europe, but also prone to over-treatment. Our approach combines the exploitation of genomic, transcriptomic, proteomic, and clinical data in primary and metastatic tumours, prospective cohorts of well characterized prostate cancer patients, drug screenings in cell lines, and the use of the Watson technology, a last generation cognitive computer developed at IBM.

The translational objective of this study is to develop technology for identifying disease mechanisms and produce treatment recommendations for individual patients based on a therapeutic biomarker panel. The proposed software framework will be accessible through a graphical interface that will facilitate its dissemination and use by researchers, clinicians, and biomedical industries. The framework will provide intuitive tools to deposit, share, analyze, and visualize molecular and clinical data; as well as to infer prognosis, elucidate implicated mechanisms and recommend therapy accordingly. This software framework will serve as a proof of concept for future development by industrial partners in Europe.

Deliverables

List of deliverables.
Generate SWATH proteome profiles from sample punches prepared in D.6.2	Documents, reports	2020-03-25 14:53:42
1st Interim Progress Report	Documents, reports	2020-03-25 14:53:42
Network reconstruction algorithms for MS data	Other	2020-03-25 14:53:43
Re-implement methods	Other	2020-03-25 14:53:42
2nd Interim Progress Report	Documents, reports	2020-03-25 14:53:42
Generate amplicon sequencing profiles from sample punches prepared in D.6.2	Documents, reports	2020-03-25 14:53:42
Proteomic data sets in cancer cell lines	Documents, reports	2020-03-25 14:53:42
Data input and input interface	Other	2020-03-25 14:53:42
Robust cross-cohort clinical patient classifier	Documents, reports	2020-03-25 14:53:43
A complete catalogue of targeted profiles	Documents, reports	2020-03-25 14:53:42
Clonal classification of tumours	Documents, reports	2020-03-25 14:53:42
Targeted profiling of prospective cohort	Documents, reports	2020-03-25 14:53:42
Integrate methods, including ACSN and Watson	Other	2020-03-25 14:53:42
Generate cell line drug sensitivity/resistance validation assays	Documents, reports	2020-03-25 14:53:42
Catalogue of molecular alterations and dysregulated pathways	Documents, reports	2020-03-25 14:53:42
Identification of systematic alterations of networks for different prognosis and for different clonal composition	Other	2020-03-25 14:53:42
Final clone inference	Documents, reports	2020-03-25 14:53:42
Internal and external IT communication infrastructure and project website	Websites, patent fillings, videos etc.	2020-03-25 14:53:42
Project quality plan	Documents, reports	2020-03-25 14:53:42
Interactome of molecular interactions in prostate cancer	Other	2020-03-25 14:53:42
Generic model	Documents, reports	2020-03-25 14:53:42
First data-driven reconstruction of context-specific network	Other	2020-03-25 14:53:42
Computational pipeline to extract prior network information at the proteomic level	Other	2020-03-25 14:53:42
Targeted ultra-deep sequencing of cancer-gene loci	Documents, reports	2020-03-25 14:53:42
Data Management Plan	Documents, reports	2020-03-25 14:53:42
Final regulatory network inference	Documents, reports	2020-03-25 14:53:42
Ultra-deep sequencing of prognostic biomarkers	Documents, reports	2020-03-25 14:53:42
Design and integrate pathway visualization	Other	2020-03-25 14:53:41

Take a look to the deliverables list in detail: detailed list of PrECISE deliverables.

Publications

List of publications.
year	authors and title	journal	last update
2018	H. Alexander Ebhardt, Alex Root, Yansheng Liu, Nicholas Paul Gauthier, Chris Sander, Ruedi Aebersold Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer published pages: , ISSN: 2056-7189, DOI: 10.1038/s41540-018-0064-1	npj Systems Biology and Applications 4/1	2020-03-25
2019	Jonas BÃ©al, Arnau Montagud, Pauline Traynard, Emmanuel Barillot, Laurence Calzone Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients published pages: , ISSN: 1664-042X, DOI: 10.3389/fphys.2018.01965	Frontiers in Physiology 9	2020-03-25
2018	Yang, Sikun; Koeppl, Heinz Collapsed Variational Inference for Nonparametric Bayesian Group Factor Analysis published pages: , ISSN: , DOI: 10.5281/zenodo.1966176	3	2020-03-25
2018	Angeliki Kalamara, Luis Tobalina, Julio Saez-Rodriguez How to find the right drug for each patient? Advances and challenges in pharmacogenomics published pages: 53-62, ISSN: 2452-3100, DOI: 10.1016/j.coisb.2018.07.001	Current Opinion in Systems Biology 10	2020-03-25
2018	Arnau Montagud, Jonas BÃ©al, Pauline Traynard, Luis Tobalina, Julio SÃ¡ez-RodrÃguez, Emmanuel Barillot and Laurence Calzone Patient-specific prostate logical models allow clinical stratification of patients and personalized drug treatment published pages: , ISSN: , DOI: 10.5281/zenodo.2416618		2020-03-25
2018	Yang, Sikun; Koeppl, Heinz Dependent Relational Gamma Process Models for Longitudinal Networks published pages: , ISSN: , DOI: 10.5281/zenodo.1314290	10	2020-03-25
2018	Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei Logical versus kinetic modeling of biological networks: applications in cancer research published pages: , ISSN: 2211-3398, DOI: 10.5281/zenodo.1243004	Current Opinion in Chemical Engineering 21 22-31 1	2020-03-25
2018	Dmytro Ustianenko, Hua-Sheng Chiu, Thomas Treiber, Sebastien M. Weyn-Vanhentenryck, Nora Treiber, Gunter Meister, Pavel Sumazin, Chaolin Zhang LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs published pages: 271-283.e5, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2018.06.029	Molecular Cell 71/2	2020-03-25
2017	Linzner, Dominik; Koepply, Heinz Inferring network statistics from high-dimensional undersampled time-course data published pages: , ISSN: , DOI: 10.5281/zenodo.841159	ISMB 2017 / CMSB 2017	2020-03-25
2017	Pauline Traynard, Luis Tobalina, Federica Eduati, Laurence Calzone, Julio Saez-Rodriguez Logic Modeling in Quantitative Systems Pharmacology published pages: 499-511, ISSN: 2163-8306, DOI: 10.1002/psp4.12225	CPT: Pharmacometrics & Systems Pharmacology 6/8	2020-03-25
2018	Oskooei, Ali; Born, Jannis; Manica, Matteo; Subramanian, Vigneshwari; Saez-Rodriguez, Julio; Rodriguez- Martinez, Maria PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks published pages: , ISSN: , DOI: 10.5281/zenodo.1967104	7	2020-03-25
2017	Mathis, Roland; Manica, Matteo; Rodriguez Martinez, Maria DeepGRN: Deciphering gene deregulation in cancer development using deep learning published pages: , ISSN: , DOI: 10.5281/zenodo.841163	2	2020-03-25
2017	Jonas BÃ©al, Arnau Montagud, Pauline Traynard, Emmanuel Barillot and Laurence Calzone Instantiation of Patient-Specific Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients published pages: , ISSN: , DOI: 10.5281/zenodo.2417118		2020-03-25
2018	Yang, Sikun; Koeppl, Heinz A Poisson Gamma Probabilistic Model for Latent Node-group Memberships in Dynamic Networks published pages: , ISSN: , DOI: 10.5281/zenodo.1242987	AAAI 2018 - Association for the Advancement of Artificial Intelligence 2018 3	2020-03-25
2018	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) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, JosÃ© H. Fregnani, Adhemar Longatto-Filho, Rui M. Rei Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context published pages: 297-312.e12, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2018.03.064	Cell Reports 23/1	2020-03-25
2018	Traynard, Pauline; Tobalina, Luis; Eduati, Federica; Calzone, Laurence; Saez-Rodriguez, Julio Logic modeling in quantitative systems pharmacology (Poster) published pages: , ISSN: , DOI: 10.5281/zenodo.841126	1	2020-03-25
2018	LInzner, Dominik; Koeppl, Heinz Cluster Variatonal Approximations for Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data published pages: , ISSN: , DOI: 10.5281/zenodo.1966608	10	2020-03-25
2018	Gaelle Letort, Arnau Montagud, Gautier Stoll, Randy Heiland, Emmanuel Barillot, Paul Macklin, Andrei Zinovyev, Laurence Calzone PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling published pages: , ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty766	Bioinformatics	2020-03-25
2018	Cuklina, Jelena; Lee, Chloe; Williams, Evan G.; Sajic, Tatjana; Collins, Ben; Rodriguez-Martinez, Maria; Pedrioli, Patrick; Aebersold, Ruedi Batch effects in large-scale proteomic studies: diagnostics and correction published pages: , ISSN: , DOI: 10.5281/zenodo.1446001	10	2020-03-25
2018	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 Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers published pages: e201800042, ISSN: 2575-1077, DOI: 10.26508/lsa.201800042	Life Science Alliance 1/2	2020-03-25
2018	Al- Sayed, Sara; Koeppl, Heinz Network Reconstruction From Time-Course Perturbation Data Using Multivariate Gaussian Processes published pages: , ISSN: , DOI: 10.5281/zenodo.1488635	(MLSP 2018) 2018 IEEE International Workshop on Machine Learning for Signal Processing 2	2020-03-25
2019	Matteo Manica, Joris Cadow, Roland Mathis, MarÃa RodrÃguez MartÃnez PIMKL: Pathway-Induced Multiple Kernel Learning published pages: , ISSN: 2056-7189, DOI: 10.1038/s41540-019-0086-3	npj Systems Biology and Applications 5/1	2020-03-25
2017	Traynard, Pauline; Beal, Jonas; Tobalina, Luis; Barillot, Emmanuel; Saez-Rodriguez, Julio; Calzone, Laurence Incorporating patient-specific molecular data into a logic model of prostate cancer published pages: , ISSN: , DOI: 10.5281/zenodo.841116	ISMB 2017 9	2020-03-25
2017	Al-Sayed, Sara; Koeppl, Heinz Fast biological network reconstruction from high-dimensional time-course perturbation data using sparse multivariate Gaussian processes published pages: , ISSN: , DOI: 10.5281/zenodo.841132	ISMB 2017 5	2020-03-25
2017	Subramanian, Vigneshwari; Szalai, Bence; Tobalina, Luis; Saez-Rodriguez, Julio Application of network diffusion approaches to drug screenings: A perspective on multilayered networks derived from drugs and cell lines published pages: , ISSN: , DOI: 10.5281/zenodo.1066906	NETTAB 2017 4	2020-03-25
2017	Cuklina, Jelena; Wu, Yibo; Williams, Evan G.; Rodriguez Martinez, Maria; Aebersold, Ruedi Selection of stable biomarker signature for prediction of metabolic phenotypes published pages: , ISSN: , DOI: 10.5281/zenodo.841208	ISMB 2017 6	2020-03-25

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