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Informatics approaches for the rational selection of personalized cancer drug combinations

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Publications

Informatics Approaches for Predicting, Understanding, and Testing Cancer Drug Combinations

Author(s): Jing Tang
Published in: Kinase Signaling Networks, Issue 1636, 2017, Page(s) 485-506
DOI: 10.1007/978-1-4939-7154-1_30

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, Issue 78/9, 2018, Page(s) 2407-2418, ISSN 0008-5472
DOI: 10.1158/0008-5472.can-17-3644

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,
Published in: Cell Chemical Biology, Issue 25/2, 2018, Page(s) 224-229.e2, ISSN 2451-9456
DOI: 10.1016/j.chembiol.2017.11.009

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, Issue 2018, 2018, ISSN 1758-0463
DOI: 10.1093/database/bay083

Making Sense of the Epigenome Using Data Integration Approaches

Author(s): Emma Cazaly, Joseph Saad, Wenyu Wang, Caroline Heckman, Miina Ollikainen, Jing Tang
Published in: Frontiers in Pharmacology, Issue 10, 2019, ISSN 1663-9812
DOI: 10.3389/fphar.2019.00126

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
Published in: PLOS Computational Biology, Issue 15/5, 2019, Page(s) e1006752, ISSN 1553-7358
DOI: 10.1371/journal.pcbi.1006752

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, Issue 47/W1, 2019, Page(s) W43-W51, ISSN 0305-1048
DOI: 10.1093/nar/gkz337

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, Issue 50, 2019, Page(s) 67-80, ISSN 2352-3964
DOI: 10.1016/j.ebiom.2019.10.051

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, Issue 5/1, 2019, ISSN 2056-7189
DOI: 10.1038/s41540-019-0098-z

Multi-parametric single cell evaluation defines distinct drug responses in healthy hematological cells that are retained in corresponding malignant cell types

Author(s): Muntasir M. Majumder, Aino-Maija Leppä, Monica Hellesøy, Paul Dowling, Alina Malyutina, Reidun Kopperud, Despina Bazou, Emma Andersson, Alun Parsons, Jing Tang, Olli Kallioniemi, Satu Mustjoki, Peter O'Gorman, Krister Wennerberg, Kimmo Porkka, Bjørn T. Gjertsen, Caroline A. Heckman
Published in: Haematologica, 2019, Page(s) haematol.2019.217414, ISSN 0390-6078
DOI: 10.3324/haematol.2019.217414

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling

Author(s): E I Andersson, S Pützer, B Yadav, O Dufva, S Khan, L He, L Sellner, A Schrader, G Crispatzu, M Oleś, H Zhang, S Adnan-Awad, S Lagström, D Bellanger, J P Mpindi, S Eldfors, T Pemovska, P Pietarinen, A Lauhio, K Tomska, C Cuesta-Mateos, E Faber, S Koschmieder, T H Brümmendorf, S Kytölä, E-R Savolainen, T Siitonen, P Ellonen, O Kallioniemi, K Wennerberg, W Ding, M-H Stern, W Huber, S Anders, J
Published in: Leukemia, Issue 32/3, 2018, Page(s) 774-787, ISSN 0887-6924
DOI: 10.1038/leu.2017.252

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Author(s): Michael P. Menden, Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, Yuanfang Guan, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, Tin Nguyen, Mikhail Zaslavskiy, In Sock Jang, Zara Ghazoui, Mehmet Eren Ahsen, Robert Vogel, Elias Chaibub Neto, Thea Norman, Eric K. Y. Tang, Mathew J. Garnett, Giovanni Y. Di Veroli, Stephen Fawell, Gustavo Stolovitzky, Justin Guinney, Jonathan R. Dry
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-09799-2

SynergyFinder: a web application for analyzing drug combination dose–response matrix data

Author(s): Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang
Published in: Bioinformatics, Issue 33/15, 2017, Page(s) 2413-2415, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btx162

Systematic drug sensitivity testing reveals synergistic growth inhibition by dasatinib or mTOR inhibitors with paclitaxel in ovarian granulosa cell tumor cells

Author(s): Ulla-Maija Haltia, Noora Andersson, Bhagwan Yadav, Anniina Färkkilä, Evgeny Kulesskiy, Matti Kankainen, Jing Tang, Ralf Bützow, Annika Riska, Arto Leminen, Markku Heikinheimo, Olli Kallioniemi, Leila Unkila-Kallio, Krister Wennerberg, Tero Aittokallio, Mikko Anttonen
Published in: Gynecologic Oncology, Issue 144/3, 2017, Page(s) 621-630, ISSN 0090-8258
DOI: 10.1016/j.ygyno.2016.12.016