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: PADOG

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

Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
1 version
Latest release: 10 months ago
2 dependent packages
36,137 downloads total

Papers Mentioning PADOG 19

GeneWalk identifies relevant gene functions for a biological context using network representation learning
Cited by: 26
Author(s): Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger, L. Stirling Churchman
Software Mentions: 14
Published: over 3 years ago

10.1093/bib/bbz158

Toward a gold standard for benchmarking gene set enrichment analysis
Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pone.0079217

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
Cited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Software Mentions: 12
Published: over 10 years ago

10.1186/s13059-019-1790-4

Identifying significantly impacted pathways: a comprehensive review and assessment
Cited by: 113
Author(s): Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen, Sorin Drăghici
Software Mentions: 12
Published: almost 5 years ago

10.1038/srep18871

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
Cited by: 37
Author(s): Xinran Dong, Yun Huang, Xiao Wang, Weidong Tian
Software Mentions: 12
Published: over 8 years ago

10.1074/mcp.TIR120.002155

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis
Cited by: 129
Author(s): Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Kim Nguyen, Antonio Fabregat, Henning Hermjakob
Software Mentions: 11
Published: over 3 years ago

10.1186/s40246-019-0226-2

Size matters: how sample size affects the reproducibility and specificity of gene set analysis
Cited by: 28
Author(s): Farhad Maleki, Katie Ovens, Ian McQuillan, Anthony Kusalik
Software Mentions: 10
Published: almost 5 years ago

10.1186/1471-2105-13-136

Down-weighting overlapping genes improves gene set analysis
Cited by: 120
Author(s): Adi L. Tarca, Sorin Drăghici, Gaurav Bhatti, Roberto Romero
Software Mentions: 9
Published: about 12 years ago

10.3389/fphys.2013.00278

Methods and approaches in the topology-based analysis of biological pathways
Cited by: 162
Author(s): Cristina Mitrea, Zeinab Taghavi, Behzad Bokanizad, Samer Najeeb Hanoudi, Rebecca Tagett, Michèle Donato, Călin Voichiţa, Sorin Drăghici
Software Mentions: 9
Published: over 11 years ago

10.1371/journal.pone.0118573

Transcriptomics of Maternal and Fetal Membranes Can Discriminate between Gestational-Age Matched Preterm Neonates with and without Cognitive Impairment Diagnosed at 18–24 Months
Cited by: 16
Author(s): Athina Pappas, Tinnakorn Chaiworapongsa, Roberto Romero, Steven J. Korzeniewski, Josef C. Cortez, Gaurav Bhatti, Nardhy Gomez-López, Sonia S. Hassan, Seetha Shankaran, Adi L. Tarca
Software Mentions: 6
Published: over 9 years ago

10.1186/s12864-015-2188-7

Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples
Cited by: 16
Author(s): Xiangtian Yu, Tao Zeng, Guojun Li
Software Mentions: 5
Published: over 8 years ago

10.3934/Neuroscience.2019.4.333

Identification of biomarkers associated with Parkinson’s disease by gene expression profiling studies and bioinformatics analysis
Cited by: 10
Author(s): Marios G. Krokidis
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-017-1571-6

Avoiding the pitfalls of gene set enrichment analysis with SetRank
Cited by: 87
Author(s): Cédric Simillion, Robin Liechti, Heidi E. L. Lischer, Vassilios Ioannidis, Rémy Bruggmann
Software Mentions: 4
Published: over 7 years ago

10.1155/2019/8912961

Curcumin Inhibits ERK/c-Jun Expressions and Phosphorylation against Endometrial Carcinoma
Cited by: 25
Author(s): Zhenxue Zhang, Pengfei Yi, Changchun Tu, Jiejie Zhan, Liping Jiang, Fanglin Zhang
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.9695

Identifying disease-associated signaling pathways through a novel effector gene analysis
Cited by: 1
Author(s): Zhenshen Bao, Bing Zhang, Li Li, Qinyu Ge, Wanjun Gu, Ya Mei Bai
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-019-2635-6

FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods
Cited by: 5
Author(s): Fatemeh Mansoori, Maseud Rahgozar, Kaveh Kavousi
Software Mentions: 3
Published: over 5 years ago

10.1186/s12918-018-0646-y

Integrating proteomic and phosphoproteomic data for pathway analysis in breast cancer
Cited by: 6
Author(s): Jie Ren, Bo Wang, Jing Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.00631

CARMAL Is a Long Non-coding RNA Locus That Regulates MFGE8 Expression
Cited by: 2
Author(s): Sébastien Soubeyrand, Majid Nikpay, Paulina Lau, Adam Turner, Huy-Dung Hoang, Tommy Alain, Ruth McPherson
Software Mentions: 1
Published: about 4 years ago

10.1038/srep14563

Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach
Cited by: 12
Author(s): Tunahan Çakır
Software Mentions: 1
Published: almost 9 years ago