Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: PharmacoGx

https://packages.ecosyste.ms/registries/bioconductor.org/packages/PharmacoGx

Analysis of Large-Scale Pharmacogenomic Data
1 version
Latest release: about 1 year ago
2 dependent packages
22,093 downloads total

Papers Mentioning PharmacoGx 26

10.1371/journal.pcbi.1006596

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer
Cited by: 43
Author(s): Deena M.A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra E. Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Pinjiang Cao, Lincoln Stein, Julie M. Wilson, John M.S. Bartlett, Ming‐Sound Tsao, Neesha C. Dhani, David W. Hedley, Steven Gallinger, Benjamin Haibe‐Kains
Software Mentions: 9
Published: almost 6 years ago

10.1002/cam4.2493

Integrated transcriptomics reveals master regulators of lung adenocarcinoma and novel repositioning of drug candidates
Cited by: 12
Author(s): Marco Antônio De Bastiani, Fábio Klamt
Software Mentions: 8
Published: about 5 years ago

10.1186/s12885-017-3689-3

GRcalculator: an online tool for calculating and mining dose–response data
Cited by: 57
Author(s): Nicholas Clark, Marc Hafner, Michal Kouril, Liz Williams, Jeremy Muhlich, Marcin Pilarczyk, Mario Niepel, Peter K. Sorger, Mario Medvedovic
Software Mentions: 7
Published: about 7 years ago

10.1186/s13058-019-1098-z

A subgroup of microRNAs defines PTEN-deficient, triple-negative breast cancer patients with poorest prognosis and alterations in RB1, MYC, and Wnt signaling
Cited by: 33
Author(s): Dong‐Yu Wang, Deena M.A. Gendoo, Yaacov Ben‐David, James R. Woodgett, Eldad Zacksenhaus
Software Mentions: 6
Published: almost 6 years ago

10.3390/ijms20164037

Consistent Biomarkers and Related Pathogenesis Underlying Asthma Revealed by Systems Biology Approach
Cited by: 18
Author(s): Xiner Nie, Jinyi Wei, Youjin Hao, Jingxin Tao, Yinghong Li, Mingwei Liu, Bo-Ying Xu, Bo Li
Software Mentions: 6
Published: about 5 years ago

10.1002/cam4.4161

Integrated pan‐cancer of AURKA expression and drug sensitivity analysis reveals increased expression of AURKA is responsible for drug resistance
Cited by: 12
Author(s): Noushin Miralaei, Ahmad Majd, Kamran Ghaedi, Maryam Peymani, Masoomeh Safaei
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-018-23195-8

Personalised drug repositioning for Clear Cell Renal Cell Carcinoma using gene expression
Cited by: 13
Author(s): Karel K.M. Koudijs, Anton G.T. Terwisscha van Scheltinga, Stefan Böhringer, Kirsten J. M. Schimmel, Henk‐Jan Guchelaar
Software Mentions: 5
Published: over 6 years ago

10.3389/fbioe.2020.00348

Analysis of Gene Signatures of Tumor Microenvironment Yields Insight Into Mechanisms of Resistance to Immunotherapy
Cited by: 4
Author(s): Ben Wang, Mengmeng Liu, Zhujie Ran, Xin Li, Jie Li, Yunsheng Ou
Software Mentions: 4
Published: over 4 years ago

10.26508/lsa.202101135

UVB mutagenesis differs in Nras- and Braf-mutant mouse models of melanoma
Cited by: 7
Author(s): Robert L. Bowman, Rebecca C. Hennessey, Tirzah J. Weiss, David Tallman, Emma R. Crawford, Brandon Murphy, Amy Webb, Souhui Zhang, Krista M. La Perle, Craig J. Burd, Ross L. Levine, A. Hunter Shain
Software Mentions: 4
Published: over 3 years ago

10.3389/fphar.2019.00109

A Comparative Study of Cluster Detection Algorithms in Protein–Protein Interaction for Drug Target Discovery and Drug Repurposing
Cited by: 23
Author(s): Ma Jun, Jenny Wang, Laleh Soltan Ghoraie, Xin Men, Benjamin Haibe‐Kains, Peng Dai
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-50224-x

Network-based method for drug target discovery at the isoform level
Cited by: 6
Author(s): Ma Jun, Jenny Wang, Laleh Soltan Ghoraie, Xin Men, Linna Liu, Peng Dai
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-019-3028-6

Influence of batch effect correction methods on drug induced differential gene expression profiles
Cited by: 12
Author(s): Wei Zhou, Karel K.M. Koudijs, Stefan Böhringer
Software Mentions: 3
Published: about 5 years ago

10.12688/f1000research.9611.3

Revisiting inconsistency in large pharmacogenomic studies
Cited by: 42
Author(s): Zhaleh Safikhani, Петр Смирнов, Mark Freeman, Nehmé El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai J. Birkbak, Christos Hatzis, Leming Shi, Andrew H. Beck, Hugo J.W.L. Aerts, John Quackenbush, Benjamin Haibe‐Kains
Software Mentions: 3
Published: about 7 years ago

10.1038/s41597-019-0174-7

Creating reproducible pharmacogenomic analysis pipelines
Cited by: 5
Author(s): Anthony Mammoliti, Alexander Smirnov, Zhaleh Safikhani, Wail Ba-Alawi, Benjamin Haibe‐Kains
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-39891-y

The impact of estimated tumour purity on gene expression-based drug repositioning of Clear Cell Renal Cell Carcinoma samples
Cited by: 6
Author(s): Karel K.M. Koudijs, Anton G.T. Terwisscha van Scheltinga, Stefan Böhringer, Kirsten J. M. Schimmel, Henk‐Jan Guchelaar
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-61236-3

MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma
Cited by: 9
Author(s): Christopher B. Lietz, Cassandra Garbutt, William T. Barry, Vikram Deshpande, Yen‐Lin Chen, Santiago Lozano-Calderón, Yao‐Yu Wang, Brian Lawney, David Ebb, Gregory M. Coté, Zhenfeng Duan, Francis J. Hornicek, Edwin Choy, G. Petur Nielsen, Benjamin Haibe‐Kains, John Quackenbush, Dimitrios Spentzos
Software Mentions: 2
Published: over 4 years ago

10.18632/oncotarget.26725

AXL knockdown gene signature reveals a drug repurposing opportunity for a class of antipsychotics to reduce growth and metastasis of triple-negative breast cancer
Cited by: 30
Author(s): Marie-Anne Goyette, Rebecca Cusseddu, Islam Elkholi, Afnan Abu-Thuraia, Nehmé El-Hachem, Benjamin Haibe‐Kains, Jean-Philippe Gratton, Jean‐François Côté
Software Mentions: 2
Published: over 5 years ago

10.3390/genes10100770

A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity
Cited by: 3
Author(s): Sean M. Santos, Mert Icyuz, Ilya Pound, Doreen William, Jingyu Guo, Brett A. McKinney, Michael Niederweis, John W. Rodgers, John L. Hartman
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-59656-2

Assessment of modelling strategies for drug response prediction in cell lines and xenografts
Cited by: 26
Author(s): Roman Kurilov, Benjamin Haibe‐Kains, Benedikt Brors
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-06996-y

GMIEC: a shiny application for the identification of gene-targeted drugs for precision medicine
Cited by: 0
Author(s): Guidantonio Malagoli Tagliazucchi, Cristian Taccioli
Software Mentions: 1
Published: about 4 years ago

10.12688/f1000research.8705.1

Assessment of pharmacogenomic agreement
Cited by: 33
Author(s): Zhaleh Safikhani, Nehme El‐Hachem, Rene Quevedo, Петр Смирнов, Anna Goldenberg, Nicolai J. Birkbak, Christopher E. Mason, Christos Hatzis, Leming Shi, Hugo J.W.L. Aerts, John Quackenbush, Benjamin Haibe‐Kains
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1006743

Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features
Cited by: 4
Author(s): David A. Knowles, Gina Bouchard, Sylvia K. Plevritis
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2020.00185

Computational Methods for the Integrative Analysis of Genomics and Pharmacological Data
Cited by: 8
Author(s): Jimmy Caroli, Martina Dori, Silvio Bicciato
Software Mentions: 1
Published: over 4 years ago

10.18632/oncotarget.10010

Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies
Cited by: 42
Author(s): Nikita Pozdeyev, Minjae Yoo, Ryan S. Mackie, Rebecca E. Schweppe, Aik Choon Tan, Bryan R. Haugen
Software Mentions: 1
Published: over 8 years ago

10.1186/s40170-019-0201-3

A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
Cited by: 6
Author(s): Sean M. Santos, John L. Hartman
Software Mentions: 1
Published: about 5 years ago

10.1093/bioinformatics/btz158

Dr.VAE: improving drug response prediction via modeling of drug perturbation effects
Cited by: 113
Author(s): Ladislav Rampášek, Daniel Hidru, Петр Смирнов, Benjamin Haibe‐Kains, Anna Goldenberg
Software Mentions: 1
Published: over 5 years ago