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Informatics approaches for the rational selection of personalized cancer drug combinations

Publications

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

Author(s): 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
Published in: npj Systems Biology and Applications, 2019, ISSN 2056-7189
Publisher: Springer Nature
DOI: 10.1038/s41540-019-0098-z

DrugComb: an integrative cancer drug combination data portal

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

Using BERT to identify drug-target interactions from whole PubMed

Author(s): Jehad Aldahdooh, Markus Vähä-Koskela, Jing Tang, Ziaurrehman Tanoli
Published in: BMC Bioinformatics, 2022, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04768-x

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

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

Bipartite network models to design combination therapies in acute myeloid leukaemia

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

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

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

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

Author(s): 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
Published in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab272

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

Author(s): 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
Published in: Cell Chemical Biology, 2018, ISSN 2451-9448
Publisher: 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

Author(s): 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
Published in: Cell Reports Medicine, 2022, ISSN 2666-3791
Publisher: 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

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

Harmonizing across datasets to improve the transferability of drug combination prediction

Author(s): Hanrui Zhang, Ziyan Wang, Yiyang Nan, Bulat Zagidullin, Daiyao Yi, Jing Tang, Yuanfang Guan
Published in: Communications Biology, 2023, ISSN 2399-3642
Publisher: 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.

Author(s): Alina Malyutina; Muntasir Mamun Majumder; Wenyu Wang; Alberto Pessia; Caroline A. Heckman; Jing Tang; Jing Tang
Published in: PLoS Computational Biology, Issue 2, 2019, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1006752

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

Author(s): Bulat Zagidullin; Ziyan Wang; Yuanfang Guan; Esa Pitkänen; Jing Tang
Published in: Briefings in Bioinformatics, Issue 5, 2021, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab291

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

Author(s): Shuyu Zheng, Jehad Aldahdooh, Tolou Shadbahr, Yinyin Wang, Dalal Aldahdooh, Jie Bao, Wenyu Wang, Jing Tang
Published in: Nucleic Acids Research, 2021, ISSN 1362-4962
Publisher: 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

Author(s): Alberto Pessia, Jing Tang
Published in: BIT Numerical Mathematics, 2021, ISSN 0006-3835
Publisher: Lunds Universitet
DOI: 10.1007/s10543-020-00836-x

Combined gene essentiality scoring improves the prediction of cancer dependency maps

Author(s): Wenyu Wang, Alina Malyutina, Alberto Pessia, Jani Saarela, Caroline A. Heckman, Jing Tang
Published in: eBioMedicine, 2019, ISSN 2352-3964
Publisher: 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

Author(s): 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
Published in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab350

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