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: cran: pathfindR

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/pathfindR

Enrichment Analysis Utilizing Active Subnetworks
22 versions
Latest release: about 1 year ago
1,554 downloads last month

Papers Mentioning pathfindR 19

10.3389/fbioe.2020.00034

A Guide to Conquer the Biological Network Era Using Graph Theory
Cited by: 129
Author(s): Mikaela Koutrouli, Evangelos Karatzas, David Páez-Espino, Georgios A. Pavlopoulos
Software Mentions: 11
Published: almost 5 years ago

10.1155/2021/9920234

Bioinformatic Analysis Reveals Central Role for Tumor-Infiltrating Immune Cells in Uveal Melanoma Progression
Cited by: 6
Author(s): Mieszko Lachota, Anton Lennikov, Karl‐Johan Malmberg, Radosław Zagożdżon
Software Mentions: 8
Published: over 3 years ago

10.1038/s42003-021-02146-6

NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data
Cited by: 38
Author(s): Liyun He, José Dávila-Velderrain, Tomokazu Sumida, David A. Hafler, M Kellis, Alexander M. Kulminski
Software Mentions: 8
Published: over 3 years ago

10.1080/19336918.2021.1903684

A role for GLUT3 in glioblastoma cell invasion that is not recapitulated by GLUT1
Cited by: 16
Author(s): Catherine Libby, Sajina Gc, Gloria A. Benavides, Jennifer L. Fisher, Sarah Williford, Sixue Zhang, Anh Tran, Emily R. Gordon, Amber Jones, Kaysaw Tuy, William Flavahan, Juan Gordillo, Ashlee Long, Sara J. Cooper, Brittany N. Lasseigne, Corinne E. Augelli‐Szafran, Victor Darley‐Usmar, Anita B. Hjelmeland
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2019.00858

pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks
Cited by: 189
Author(s): Ege Ülgen, Özan Özışık, Uğur Sezerman
Software Mentions: 4
Published: about 5 years ago

10.1155/2020/3968279

Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma
Cited by: 1
Author(s): Ana Carolina de Moraes Mello, Martiela Vaz de Freitas, Laura Coutinho, Tiago Falcón, Úrsula da Silveira Matte
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms21207767

Biological and Clinical Changes in a Pediatric Series Treated with Off-Label JAK Inhibitors
Cited by: 15
Author(s): Alessia Pin, Alessandra Tesser, Serena Pastore, Valentina Moressa, Erica Valencic, Anna Arbo, Alessandra Maestro, Alberto Tommasini, Andrea Taddio
Software Mentions: 3
Published: about 4 years ago

10.3389/fgene.2020.589231

Analysis of Pan-omics Data in Human Interactome Network (APODHIN)
Cited by: 7
Author(s): Nupur Biswas, Krishna Kumar, Sarpita Bose, Raisa Bera, Saikat Chakrabarti
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12969-019-0313-x

10th Congress of International Society of Systemic Auto-Inflammatory Diseases (ISSAID)
Cited by: 21
Author(s):
Software Mentions: 3
Published: over 5 years ago

10.3390/e23010002

Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data
Cited by: 29
Author(s): Malik Yousef, Abhishek Kumar, Burcu Bakır-Güngör
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12920-021-00904-3

Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma
Cited by: 0
Author(s): Ege Ülgen, Özge Çan, Kaya Bilgüvar, Cemaliye Akyerli Boylu, Şirin Yüksel, Ayça Erşen Danyeli, Osman Uğur Sezerman, Mustafa Cengiz Yakıcıer, M. Necmettin Pamir, Koray Özduman
Software Mentions: 2
Published: almost 4 years ago

10.1002/cam4.3223

Progesterone at high doses reduces the growth of U87 and A172 glioblastoma cells: Proteomic changes regarding metabolism and immunity
Cited by: 7
Author(s): Meriç A. Altinöz, Yasemin Uçal, Muazzez C Yilmaz, İrem Kiris, Özan Özışık, Uğur Sezerman, Aysel Özpınar, İlhan Elmacı
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2021.697307

Naïve Regulatory T Cell Subset Is Altered in X-Linked Agammaglobulinemia
Cited by: 2
Author(s): Pavel V. Shelyakin, Ksenia R Lupyr, Evgeny S. Egorov, И.А. Кофиади, Dmitriy B. Staroverov, Sofya A. Kasatskaya, Valeriia V Kriukova, Irina A. Shagina, Ekaterina M. Merzlyak, Tatiana O Nakonechnaya, Elena A. Latysheva, Irina A. Manto, Musa Khaitov, Sergey Lukyanov, Dmitriy M. Chudakov, Olga V. Britanova
Software Mentions: 2
Published: over 3 years ago

10.3389/fvets.2021.666767

Whole-Genome Comparative Analysis Reveals Association Between Salmonella Genomic Variation and Egg Production Systems
Cited by: 2
Author(s): Hamid Reza Sodagari, Shafi Sahibzada, Ian D. Robertson, Ihab Habib, Penghao Wang
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-84538-6

Pharmacological inhibition of tumor anabolism and host catabolism as a cancer therapy
Cited by: 7
Author(s): Alejandro Schcolnik‐Cabrera, Alma Chávez‐Blanco, Guadalupe Domínguez-Gómez, Mandy Juárez, Ariana Vargas‐Castillo, Rafael I. Ponce‐Toledo, Donna Lai, Hua Su, Armando R. Tovar, Nimbe Torres, Delia Pérez-Montiel, José Díaz‐Chávez, Alfonso Dueñas‐González
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms21217992

Transcriptomic Changes in Endothelial Cells Triggered by Na,K-ATPase Inhibition: A Search for Upstream Na+i/K+i Sensitive Genes
Cited by: 3
Author(s): Е. А. Климанова, S. V. Sidorenko, P A Abramicheva, Аrtem M. Tverskoi, Sergei N. Orlov, О.Д. Лопина
Software Mentions: 1
Published: about 4 years ago

10.7717/peerj-cs.336

CogNet: classification of gene expression data based on ranked active-subnetwork-oriented KEGG pathway enrichment analysis
Cited by: 19
Author(s): Malik Yousef, Ege Ülgen, Uğur Sezerman
Software Mentions: 1
Published: almost 4 years ago

10.3390/biomedicines8120574

Mutations and Copy Number Alterations in IDH Wild-Type Glioblastomas Are Shaped by Different Oncogenic Mechanisms
Cited by: 3
Author(s): Ege Ülgen, Sıla Karacan, Umut Gerlevik, Özge Çan, Kaya Bilgüvar, Yavuz Oktay, Cemaliye Boylu Akyerli, Şirin Yüksel, Ayça Erşen Danyeli, Tarık Tıhan, Osman Uğur Sezerman, Mustafa Cengiz Yakıcıer, M. Necmettin Pamir, Koray Özduman
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-67875-w

Association study based on topological constraints of protein–protein interaction networks
Cited by: 3
Author(s): Haobo Guo, Hong Qin
Software Mentions: 1
Published: over 4 years ago