Informatics approaches for the rational selection of personalized cancer drug combinations

Publikacje

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

Autorzy: 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
Opublikowane w: npj Systems Biology and Applications, 2019, ISSN 2056-7189
Wydawca: Springer Nature
DOI: 10.1038/s41540-019-0098-z

DrugComb: an integrative cancer drug combination data portal

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

Using BERT to identify drug-target interactions from whole PubMed

Autorzy: Jehad Aldahdooh, Markus Vähä-Koskela, Jing Tang, Ziaurrehman Tanoli
Opublikowane w: BMC Bioinformatics, 2022, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-022-04768-x

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

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

Bipartite network models to design combination therapies in acute myeloid leukaemia

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

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

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

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

Autorzy: 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
Opublikowane w: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Wydawca: Oxford University Press
DOI: 10.1093/bib/bbab272

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

Autorzy: 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
Opublikowane w: Cell Chemical Biology, 2018, ISSN 2451-9448
Wydawca: 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

Autorzy: 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
Opublikowane w: Cell Reports Medicine, 2022, ISSN 2666-3791
Wydawca: 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

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

Harmonizing across datasets to improve the transferability of drug combination prediction

Autorzy: Hanrui Zhang, Ziyan Wang, Yiyang Nan, Bulat Zagidullin, Daiyao Yi, Jing Tang, Yuanfang Guan
Opublikowane w: Communications Biology, 2023, ISSN 2399-3642
Wydawca: 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.

Autorzy: Alina Malyutina; Muntasir Mamun Majumder; Wenyu Wang; Alberto Pessia; Caroline A. Heckman; Jing Tang; Jing Tang
Opublikowane w: PLoS Computational Biology, Numer 2, 2019, ISSN 1553-734X
Wydawca: Public Library of Science
DOI: 10.1371/journal.pcbi.1006752

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

Autorzy: Bulat Zagidullin; Ziyan Wang; Yuanfang Guan; Esa Pitkänen; Jing Tang
Opublikowane w: Briefings in Bioinformatics, Numer 5, 2021, ISSN 1467-5463
Wydawca: Oxford University Press
DOI: 10.1093/bib/bbab291

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

Autorzy: Shuyu Zheng, Jehad Aldahdooh, Tolou Shadbahr, Yinyin Wang, Dalal Aldahdooh, Jie Bao, Wenyu Wang, Jing Tang
Opublikowane w: Nucleic Acids Research, 2021, ISSN 1362-4962
Wydawca: 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

Autorzy: Alberto Pessia, Jing Tang
Opublikowane w: BIT Numerical Mathematics, 2021, ISSN 0006-3835
Wydawca: Lunds Universitet
DOI: 10.1007/s10543-020-00836-x

Combined gene essentiality scoring improves the prediction of cancer dependency maps

Autorzy: Wenyu Wang, Alina Malyutina, Alberto Pessia, Jani Saarela, Caroline A. Heckman, Jing Tang
Opublikowane w: eBioMedicine, 2019, ISSN 2352-3964
Wydawca: 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

Autorzy: 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
Opublikowane w: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Wydawca: Oxford University Press
DOI: 10.1093/bib/bbab350

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