Informatics approaches for the rational selection of personalized cancer drug combinations

Informazioni relative al progetto

DrugComb

ID dell’accordo di sovvenzione: 716063

DOI 10.3030/716063

Progetto chiuso

Data della firma CE 3 Maggio 2017

Data di avvio 1 Giugno 2017

Data di completamento 31 Maggio 2023

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale € 1 500 000,00

Contributo UE € 1 500 000,00

Coordinato da

HELSINGIN YLIOPISTO
Finland

Pubblicazioni

Peer reviewed articles (17)

Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer

Autori: Jing Tang, Prson Gautam, Abhishekh Gupta, Liye He, Sanna Timonen, Yevhen Akimov, Wenyu Wang, Agnieszka Szwajda, Alok Jaiswal, Denes Turei, Bhagwan Yadav, Matti Kankainen, Jani Saarela, Julio Saez-Rodriguez, Krister Wennerberg, Tero Aittokallio
Pubblicato in: npj Systems Biology and Applications, 2019, ISSN 2056-7189
Editore: Springer Nature
DOI: 10.1038/s41540-019-0098-z

DrugComb: an integrative cancer drug combination data portal

Autori: Bulat Zagidullin, Jehad Aldahdooh, Shuyu Zheng, Wenyu Wang, Yinyin Wang, Joseph Saad, Alina Malyutina, Mohieddin Jafari, Ziaurrehman Tanoli, Alberto Pessia, Jing Tang
Pubblicato in: Nucleic Acids Research, 2019, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkz337

Using BERT to identify drug-target interactions from whole PubMed

Autori: Jehad Aldahdooh, Markus Vähä-Koskela, Jing Tang, Ziaurrehman Tanoli
Pubblicato in: BMC Bioinformatics, 2022, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-022-04768-x

SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets

Autori: Shuyu Zheng, Wenyu Wang, Jehad Aldahdooh, Alina Malyutina, Tolou Shadbahr, Ziaurrehman Tanoli, Alberto Pessia, Jing Tang
Pubblicato in: Genomics Proteomics Bioinformatics, 2022, ISSN 1672-0229
Editore: Kexue Chubaneshe/Science Press
DOI: 10.1016/j.gpb.2022.01.004

Bipartite network models to design combination therapies in acute myeloid leukaemia

Autori: Mohieddin Jafari, Mehdi Mirzaie, Jie Bao, Farnaz Barneh, Shuyu Zheng, Johanna Eriksson, Caroline A. Heckman, Jing Tang
Pubblicato in: Nature Communications, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-29793-5

Patient-Customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients

Autori: Liye He, Jing Tang, Emma I. Andersson, Sanna Timonen, Steffen Koschmieder, Krister Wennerberg, Satu Mustjoki, Tero Aittokallio
Pubblicato in: Cancer Research, 2018, ISSN 0008-5472
Editore: American Association for Cancer Research
DOI: 10.1158/0008-5472.can-17-3644

Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer

Autori: Liye He, Daria Bulanova, Jaana Oikkonen, Antti Häkkinen, Kaiyang Zhang, Shuyu Zheng, Wenyu Wang, Erdogan Pekcan Erkan, Olli Carpén, Titta Joutsiniemi, Sakari Hietanen, Johanna Hynninen, Kaisa Huhtinen, Sampsa Hautaniemi, Anna Vähärautio, Jing Tang, Krister Wennerberg, Tero Aittokallio
Pubblicato in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Editore: Oxford University Press
DOI: 10.1093/bib/bbab272

Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions

Autori: Jing Tang, Zia-Ur-Rehman Tanoli, Balaguru Ravikumar, Zaid Alam, Anni Rebane, Markus Vähä-Koskela, Gopal Peddinti, Arjan J van Adrichem, Janica Wakkinen, Alok Jaiswal, Ella Karjalainen, Prson Gautam, Liye He, Elina Parri, Suleiman Khan, Abhishekh Gupta, Mehreen Ali, Laxman Yetukuri, Anna-Lena Gustavsson, Brinton Seashore-Ludlow, Anne Hersey, Andrew R Leach, John P Overington, Gretchen Repasky, Kr
Pubblicato in: Cell Chemical Biology, 2018, ISSN 2451-9448
Editore: Cell Press
DOI: 10.1016/j.chembiol.2017.11.009

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

Autori: Eugene F Douglass Jr 1 2, Robert J Allaway 3, Bence Szalai 4, Wenyu Wang, Tingzhong Tian 6, Adrià Fernández-Torras 7, Ron Realubit 1, Charles Karan 1, Shuyu Zheng, Alberto Pessia, Ziaurrehman Tanoli, Mohieddin Jafari, Fangping Wan 6, Shuya Li 6, Yuanpeng Xiong 8, Miquel Duran-Frigola 7, Martino Bertoni 7, Pau Badia-I-Mompel 7, Lídia Mateo 7, Oriol Guitart-Pla 7, Verena Chung 3; DREAM CTD-square
Pubblicato in: Cell Reports Medicine, 2022, ISSN 2666-3791
Editore: Cell press
DOI: 10.1016/j.xcrm.2021.100492

Drug Target Commons 2.0: a community platform for systematic analysis of drug–target interaction profiles

Autori: ZiaurRehman Tanoli, Zaid Alam, Markus Vähä-Koskela, Balaguru Ravikumar, Alina Malyutina, Alok Jaiswal, Jing Tang, Krister Wennerberg, Tero Aittokallio
Pubblicato in: Database (Oxford), 2018, ISSN 1758-0463
Editore: Oxford University Press
DOI: 10.1093/database/bay083

Harmonizing across datasets to improve the transferability of drug combination prediction

Autori: Hanrui Zhang, Ziyan Wang, Yiyang Nan, Bulat Zagidullin, Daiyao Yi, Jing Tang, Yuanfang Guan
Pubblicato in: Communications Biology, 2023, ISSN 2399-3642
Editore: Nature Publishing Group
DOI: 10.1038/s42003-023-04783-5

Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer.

Autori: Alina Malyutina; Muntasir Mamun Majumder; Wenyu Wang; Alberto Pessia; Caroline A. Heckman; Jing Tang; Jing Tang
Pubblicato in: PLoS Computational Biology, Numero 2, 2019, ISSN 1553-734X
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1006752

Comparative analysis of molecular fingerprints in prediction of drug combination effects.

Autori: Bulat Zagidullin; Ziyan Wang; Yuanfang Guan; Esa Pitkänen; Jing Tang
Pubblicato in: Briefings in Bioinformatics, Numero 5, 2021, ISSN 1467-5463
Editore: Oxford University Press
DOI: 10.1093/bib/bbab291

DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal

Autori: Shuyu Zheng, Jehad Aldahdooh, Tolou Shadbahr, Yinyin Wang, Dalal Aldahdooh, Jie Bao, Wenyu Wang, Jing Tang
Pubblicato in: Nucleic Acids Research, 2021, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkab438

A three-term recurrence relation for accurate evaluation of transition probabilities of the simple birth-and-death process

Autori: Alberto Pessia, Jing Tang
Pubblicato in: BIT Numerical Mathematics, 2021, ISSN 0006-3835
Editore: Lunds Universitet
DOI: 10.1007/s10543-020-00836-x

Combined gene essentiality scoring improves the prediction of cancer dependency maps

Autori: Wenyu Wang, Alina Malyutina, Alberto Pessia, Jani Saarela, Caroline A. Heckman, Jing Tang
Pubblicato in: eBioMedicine, 2019, ISSN 2352-3964
Editore: Elsevier BV
DOI: 10.1016/j.ebiom.2019.10.051

Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments

Autori: Ziaurrehman Tanoli, Jehad Aldahdooh, Farhan Alam, Yinyin Wang, Umair Seemab, Maddalena Fratelli, Petr Pavlis, Marian Hajduch, Florence Bietrix, Philip Gribbon, Andrea Zaliani, Matthew D Hall, Min Shen, Kyle Brimacombe, Evgeny Kulesskiy, Jani Saarela, Krister Wennerberg, Markus Vähä-Koskela, Jing Tang
Pubblicato in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Editore: Oxford University Press
DOI: 10.1093/bib/bbab350