Jing Tang

发表

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.

Evan O. Paull, Joshua M. Stuart, Adam A. Margolin, 2017, Cell systems.

Network pharmacology applications to map the unexplored target space and therapeutic potential of natural products.

T. Aittokallio, K. Wennerberg, N. Saarinen, 2015, Natural product reports.

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

Elina Parri, Krister Wennerberg, Tero Aittokallio, 2017, Cell chemical biology.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Matti Pirinen, Jukka Corander, Krister Wennerberg, 2016, Nature Communications.

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

Sanna Timonen, Krister Wennerberg, Tero Aittokallio, 2019, npj Systems Biology and Applications.

Network Pharmacology Strategies Toward Multi-Target Anticancer Therapies: From Computational Models to Experimental Design Principles

Tero Aittokallio, Jing Tang, T. Aittokallio, 2014, Current pharmaceutical design.

A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data

Robert J. Allaway, D. Gerhard, P. Aloy, 2020, bioRxiv.

Landscapes Using an Interaction Potency Model

T. Aittokallio, K. Wennerberg, Jing Tang, 2022 .

Bipartite network models to design combination therapies in acute myeloid leukaemia

C. Heckman, Jing Tang, F. Barneh, 2022, Nature Communications.

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

Krister Wennerberg, Andrea Zaliani, Jing Tang, 2020, bioRxiv.

DrugRepo: A novel approach to repurpose a huge collection of compounds based on chemical and genomic features

M. Vähä-Koskela, Jing Tang, Ziaurrehman Tanoli, 2022, bioRxiv.

Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

Jing Tang, Shuyu Zheng, Péter Poczai, 2020, Frontiers in Genetics.

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

M. Hall, K. Wennerberg, M. Hajdúch, 2021, Briefings Bioinform..

Anti-cancer Drug Synergy Prediction in Understudied Tissues using Transfer Learning

Z. Li, Xiaoqian Jiang, W. J. Zheng, 2020, bioRxiv.

Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation

Zhongming Zhao, Xiaoqian Jiang, S. Savitz, 2020, Research square.

DrugRepo: A novel approach to repurpose a huge collection of compounds based on chemical and genomic features

M. Vähä-Koskela, Jing Tang, Ziaurrehman Tanoli, 2022, bioRxiv.

Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro

S. Ludwig, Jing Tang, L. Brunotte, 2020, bioRxiv.

Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells

T. Aittokallio, K. Wennerberg, A. Jaiswal, 2017, Genome Medicine.

JAK1/2 and BCL2 inhibitors synergize to counteract bone marrow stromal cell-induced protection of AML.

T. Aittokallio, D. Tamborero, O. Kallioniemi, 2015, Blood.

User instructions and tutorials of the synergyfinder package

T. Aittokallio, K. Wennerberg, Jing Tang, 2016 .

Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity?

Jing Tang, N. Ansari-Pour, R. Karbalaei, 2019, bioRxiv.

Do signaling networks and whole-transcriptome gene expression profiles orchestrate the same symphony?

Jing Tang, N. Ansari-Pour, M. Mirzaie, 2019 .

PGMG: A Pharmacophore-Guided Deep Learning Approach for Bioactive Molecular Generation

Jing Tang, Hui Zhu, Renyi Zhou, 2022, ArXiv.

RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection

K. Borgwardt, Jing Tang, K. Avican, 2020, Nature Communications.

Research and Applications Anticancer drug synergy prediction in understudied tissues using transfer learning

Jing Tang, Shuyu Zheng, Yejin Kim, 2021 .

A gene essentiality signature for studying the mechanism of action of drugs

Jing Tang, Ziaurrehman Tanoli, Shangke Huang, 2022, bioRxiv.

Loss-of-function mutations with circadian rhythm regulator Per1/Per2 lead to premature ovarian insufficiency†

Peixin Yang, Jing Tang, Ying Xu, 2018, Biology of reproduction.

Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles.

Krister Wennerberg, Tero Aittokallio, Laura Turunen, 2015, Chemistry & biology.

From drug response profiling to target addiction scoring in cancer cell models

Krister Wennerberg, Tero Aittokallio, Agnieszka Szwajda, 2015, Disease Models & Mechanisms.

Seasonal Variation in the Brain μ-Opioid Receptor Availability

L. Nummenmaa, J. Hirvonen, J. Hietala, 2020, The Journal of Neuroscience.

Seasonal variation in brain mu-opioid receptor availability

L. Nummenmaa, J. Hirvonen, J. Hietala, 2020, bioRxiv.

Corrigendum to “Searching for drug synergy in complex dose–response landscapes using an interaction potency model” [Comput. Struct. Biotechnol. J. 13 (2015) 504–513]

Krister Wennerberg, Tero Aittokallio, Jing Tang, 2017, Computational and structural biotechnology journal.

Anticancer drug synergy prediction in understudied tissues using transfer learning

Zhao Li, Xiaoqian Jiang, Jing Tang, 2020, J. Am. Medical Informatics Assoc..

Drug repurposing for COVID-19 using graph neural network and harmonizing multiple evidence

Zhongming Zhao, Xiaoqian Jiang, Jing Tang, 2020, Scientific Reports.

Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS‐CoV‐2 infection in vitro

S. Ludwig, Jing Tang, L. Brunotte, 2021, British journal of pharmacology.

Unsupervised Learning and Multipartite Network Models: A Promising Approach for Understanding Traditional Medicine

Ali Amiryousefi, Mohieddin Jafari, Yinyin Wang, 2020, Frontiers in Pharmacology.

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

Jing Tang, A. Pessia, Wenyu Wang, 2021, bioRxiv.

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

T. Aittokallio, K. Wennerberg, S. Hautaniemi, 2021, Briefings Bioinform..

Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis

Tao Xu, Krister Wennerberg, Tero Aittokallio, 2014, J. Chem. Inf. Model..

Making Sense of the Epigenome Using Data Integration Approaches

Wenyu Wang, Jing Tang, Joseph Saad, 2019, Front. Pharmacol..

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

Tero Aittokallio, Jing Tang, Aleksandr Ianevski, 2017, Bioinform..

Corrigendum to “Searching for drug synergy in complex dose–response landscapes using an interaction potency model” [Comput. Struct. Biotechnol. J. 13 (2015) 504–513]

Krister Wennerberg, Tero Aittokallio, Jing Tang, 2017, Computational and structural biotechnology journal.

Exploration of databases and methods supporting drug repurposing: a comprehensive survey

Krister Wennerberg, Andreas Scherer, Jing Tang, 2020, Briefings Bioinform..

Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation

Jing Tang, Zhongming Zhao, Yejin Kim, 2020, Research square.

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

S. Mustjoki, O. Kallioniemi, K. Wennerberg, 2019, Haematologica.

Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways

Tao Xu, Krister Wennerberg, Tero Aittokallio, 2013, PLoS Comput. Biol..

Toward more realistic drug^target interaction predictions

Tapio Pahikkala, Antti Airola, Tero Aittokallio, 2014 .

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

Sanna Timonen, Krister Wennerberg, Tero Aittokallio, 2018, Cancer research.

Combined gene essentiality scoring improves the prediction of cancer dependency maps

C. Heckman, Jing Tang, A. Pessia, 2019, EBioMedicine.

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

Jukka Corander, Jing Tang, Jukka Sirén, 2008, BMC Bioinformatics.

Prediction of human population responses to toxic compounds by a collaborative competition

Ana L. Teixeira, Eleni G. Christodoulou, Jeffrey T. Chang, 2015, Nature Biotechnology.

What is synergy? The Saariselkä agreement revisited

Jing Tang, Krister Wennerberg, Tero Aittokallio, 2015, Front. Pharmacol..

Bayesian analysis of population structure based on linked molecular information.

Jukka Corander, Jing Tang, J. Corander, 2007, Mathematical biosciences.

Network-based modeling of herb combinations in traditional Chinese medicine

Jing Tang, Linxiao Chen, Mohieddin Jafari, 2021, bioRxiv.

Using BERT to identify drug-target interactions from whole PubMed

M. Vähä-Koskela, Jing Tang, Ziaurrehman Tanoli, 2021, bioRxiv.

Methods for High-Throughput Drug Combination Screening and Synergy Scoring

Krister Wennerberg, Tero Aittokallio, Laura Turunen, 2016, bioRxiv.

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

Jing Tang, Jing Tang, 2017, Methods in molecular biology.

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

Jing Tang, Wenyu Wang, Shuyu Zheng, 2021, bioRxiv.

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

Amir K. Foroushani, Yuanfang Guan, Jaewoo Kang, 2019, Nature Communications.

DrugRepo: a novel approach to repurposing drugs based on chemical and genomic features

M. Vähä-Koskela, Jing Tang, Ziaurrehman Tanoli, 2022, Scientific Reports.

Identification of Celecoxib-Targeted Proteins Using Label-Free Thermal Proteome Profiling on Rat Hippocampus

M. Baumann, Jing Tang, K. Gilany, 2021, Molecular Pharmacology.

Identification of Celecoxib-Targeted Proteins Using Label-Free Thermal Proteome Profiling on Rat Hippocampus

M. Baumann, Jing Tang, K. Gilany, 2020, Molecular Pharmacology.

A gene essentiality signature enables predicting the mechanism of action of drugs

Jing Tang, Ziaurrehman Tanoli, Shangke Huang, 2023, bioRxiv.

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

Jing Tang, Wenyu Wang, Alina Malyutina, 2019, bioRxiv.

TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples

Krister Wennerberg, Tero Aittokallio, Jing Tang, 2015, Bioinform..

A Bayesian Predictive Model for Clustering Data of Mixed Discrete and Continuous Type

Jukka Corander, Jing Tang, Jie Xiong, 2015, IEEE Transactions on Pattern Analysis and Machine Intelligence.

Combination Therapy with Fluoxetine and the Nucleoside Analog GS-441524 Exerts Synergistic Antiviral Effects against Different SARS-CoV-2 Variants In Vitro

S. Ludwig, Jing Tang, L. Brunotte, 2021, Pharmaceutics.

Harmonizing across datasets to improve the transferability of drug combination prediction

Y. Guan, Ziteng Wang, Jing Tang, 2023, Communications Biology.

DrugComb: an integrative cancer drug combination data portal

Wenyu Wang, Jing Tang, Mohieddin Jafari, 2019, Nucleic acids research.

Determining the Balance Between Drug Efficacy and Safety by the Network and Biological System Profile of Its Therapeutic Target

Feng Zhu, Yunxia Wang, Weiwei Xue, 2018, Front. Pharmacol..

DrugComb: an integrative cancer drug combination data portal

Jing Tang, Yinyin Wang, Joseph Saad, 2019, Nucleic Acids Res..

Predicting Meridian in Chinese traditional medicine using machine learning approaches

Mohieddin Jafari, Yinyin Wang, Yun Tang, 2019, bioRxiv.

Heterogeneous modulation of Bcl-2 family members and drug efflux mediate MCL-1 inhibitor resistance in multiple myeloma

S. Kubicek, J. Hannich, C. Heckman, 2021, Blood advances.

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

T. Aittokallio, J. Saez-Rodriguez, S. Timonen, 2019, npj Systems Biology and Applications.

Improving the consistency of functional genomics screens using molecular features - a multi-omics, pan-cancer study

C. Heckman, Jing Tang, A. Pessia, 2018, bioRxiv.

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

Balaguru Ravikumar, Krister Wennerberg, Tero Aittokallio, 2018, Database J. Biol. Databases Curation.

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

T. Aittokallio, J. Saez-Rodriguez, S. Timonen, 2019, npj Systems Biology and Applications.

User instructions and tutorial of the timma package

T. Aittokallio, K. Wennerberg, Jing Tang, 2015 .

Facilitating the design of combination therapy in cancer using multipartite network models: Emphasis on acute myeloid leukemia

Mehdi Mirzaie, Farnaz Barneh, Jing Tang, 2021, bioRxiv.

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

Tero Aittokallio, Jing Tang, Aleksandr Ianevski, 2020, Bioinformatics.

Facilitating the design of combination therapy for cancer using multipartite network models: Emphasis on acute myeloid leukaemia

Jing Tang, F. Barneh, M. Mirzaie, 2021 .

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach

Jukka Corander, Jing Tang, Christophe Fraser, 2009, PLoS Comput. Biol..

Bayesian Clustering of Fuzzy Feature Vectors Using a Quasi-Likelihood Approach

Bernard De Baets, Jukka Corander, Jing Tang, 2009, IEEE Transactions on Pattern Analysis and Machine Intelligence.

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

M. Hall, K. Wennerberg, M. Shen, 2020, bioRxiv.

DrugComb - an integrative cancer drug combination data portal

Jing Tang, A. Pessia, Wenyu Wang, 2019, bioRxiv.

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

T. Aittokallio, Jing Tang, Liye He, 2020, Bioinform..

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Suleiman A. Khan, Michael A. Goren, Donna E. Dillenberger, 2016, Nature Communications.

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

John P. Overington, Suleiman A. Khan, A. Leach, 2017, Cell chemical biology.

GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction

Kaili Wang, Jing Tang, Min Li, 2023, Bioinformatics.

T-BAPS: A Bayesian Statistical Tool for Comparison of Microbial Communities Using Terminal-restriction Fragment Length Polymorphism (T-RFLP) Data

Jukka Corander, Jing Tang, Jinglun Tao, 2007, Statistical applications in genetics and molecular biology.

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

Jing Tang, A. Pessia, Wenyu Wang, 2022, Genom. Proteom. Bioinform..

Loss-of-function mutations with circadian rhythm regulator Per1/Per2 lead to premature ovarian insufficiency

Peixin Yang, Jing Tang, Ying Xu, 2018, Biology of reproduction.