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: SetRank

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

Advanced Gene Set Enrichment Analysis
3 versions
Latest release: over 8 years ago
176 downloads last month

Papers Mentioning SetRank 17

10.1186/s12864-020-06856-9

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data
Cited by: 28
Author(s): Antony Kaspi, Mark Ziemann
Software Mentions: 15
Published: over 4 years ago

Identification of Specific Circular RNA Expression Patterns and MicroRNA Interaction Networks in Mesial Temporal Lobe Epilepsy
Cited by: 10
Author(s): Lachlan G. Gray, James D. Mills, Ashton Curry‐Hyde, Sasha Devore, Daniel Friedman, Maria Thom, Catherine Scott, Roland D. Thijs, Eleonora Aronica, Orrin Devinsky, Michael Janitz
Software Mentions: 9
Published: about 4 years ago

10.3389/fimmu.2020.596173

The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment
Cited by: 4
Author(s): Trust Odia, Stephanus T. Malherbe, Stuart Meier, Elizna Maasdorp, Léanie Kleynhans, Nelita du Plessis, André G. Loxton, Daniel E. Zak, Ethan Thompson, Fergal J. Duffy, Helena Kuivaniemi, Katharina Ronacher, Jill Winter, Gerhard Walzl, Gerard Tromp
Software Mentions: 8
Published: almost 4 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

10.1186/s13148-019-0680-7

DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data
Cited by: 13
Author(s): Yujie He, Lot de Witte, Lotte C Houtepen, Danny M Nispeling, Zhida Xu, Qiong Yu, Yaqin Yu, Elly M. Hol, René S. Kahn, Marco P. Boks
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.19904

The hyaluronan-mediated motility receptor RHAMM promotes growth, invasiveness and dissemination of colorectal cancer
Cited by: 44
Author(s): Valentina Mele, Lena Sokol, Viktor Kölzer, Dennis Pfaff, Manuele Giuseppe Muraro, Irene Keller, Stefan Zahnd, Irene Centeno, Luigi Terracciano, Heather Dawson, Inti Zlobec, Giovanna Iezzi, Alessandro Lugli
Software Mentions: 2
Published: over 7 years ago

10.15252/emmm.201506089

Impaired liver regeneration in aged mice can be rescued by silencing Hippo core kinases MST1 and MST2
Cited by: 87
Author(s): G. Loforese, Thomas Malinka, Adrian Keogh, Felix Alexander Baier, Cédric Simillion, M. Montani, Thanos D. Halazonetis, Daniel Candinas, Deborah Stroka
Software Mentions: 2
Published: almost 8 years ago

10.3390/genes10110931

HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data
Cited by: 5
Author(s): Lydia Mok, Yongkang Kim, Sungyoung Lee, Sungkyoung Choi, Seungyeoun Lee, Jin Young Jang, Taesung Park
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-017-06634-w

Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver
Cited by: 47
Author(s): Rongrui Liang, Bo Han, Qian Li, Yǒulù Yuán, Jianguo Li, Dan Sun
Software Mentions: 2
Published: over 7 years ago

10.1126/science.aau4732

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children
Cited by: 263
Author(s): Jeanette L. Gehrig, Siddarth Venkatesh, Hung-Sheng Chang, Matthew C. Hibberd, Vanderlene L. Kung, Jiye Cheng, Robert Y. Chen, Sathish Subramanian, Carrie A. Cowardin, Martin Meier, David O’Donnell, Michael Talcott, Larry D. Spears, Clay F. Semenkovich, Bernard Henrissat, Richard J. Giannone, Robert L. Hettich, Olga Ilkayeva, Michael J. Muehlbauer, Christopher B. Newgard, Christopher Sawyer, Richard D. Head, Dmitry A. Rodionov, Aleksandr A. Arzamasov, Semen A. Leyn, Andrei L. Osterman, Iqbal Hossain, M Munirul Islam, Nuzhat Choudhury, Shafiqul Alam Sarker, Sayeeda Huq, Imteaz Mahmud, Ishita Mostafa, Mustafa Mahfuz, Michael J. Barratt, Tahmeed Ahmed, Jeffrey I. Gordon
Software Mentions: 2
Published: over 5 years ago

10.1007/s12015-017-9790-9

Gene Network Analysis of Interstitial Macrophages After Treatment with Induced Pluripotent Stem Cells Secretome (iPSC-cm) in the Bleomycin Injured Rat Lung
Cited by: 13
Author(s): Luca Tamò, Cédric Simillion, Youssef Hibaoui, Anis Féki, Mathias Gugger, Antje Prasse, B Jäger, Torsten Goldmann, Thomas Geiser, Amiq Gazdhar
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.52063

The genetic basis of aneuploidy tolerance in wild yeast
Cited by: 59
Author(s): James Hose, Leah E. Escalante, Katie J. Clowers, H Auguste Dutcher, DeElegant Robinson, Venera Bouriakov, Joshua J. Coon, Evgenia Shishkova, Audrey P. Gasch
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12885-021-08479-z

Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA)
Cited by: 3
Author(s): Mahmoud Hallal, Sophie Braga-Lagache, Jovana Jankovic, Cédric Simillion, Rémy Bruggmann, Anne-Christine Uldry, Ramanjaneyulu Allam, Manfred Heller, Nicolas Bonadies
Software Mentions: 1
Published: over 3 years ago

10.1186/s12859-019-2716-6

MGSEA – a multivariate Gene set enrichment analysis
Cited by: 9
Author(s): Khong-Loon Tiong, Chen‐Hsiang Yeang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12931-020-1275-8

Azithromycin has enhanced effects on lung fibroblasts from idiopathic pulmonary fibrosis (IPF) patients compared to controls
Cited by: 24
Author(s): Kristína Krempaská, Sandra Barnowski, Jacopo Gavini, Nina Hobi, Simone Ebener, Cédric Simillion, Andrea Stokes, Ronja Schliep, Lars Knudsen, Thomas Geiser, Manuela Funke-Chambour
Software Mentions: 1
Published: almost 5 years ago

10.7554/eLife.42037

Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling
Cited by: 143
Author(s): Philip V’kovski, Marlène Gerber, Jenna N. Kelly, Stephanie Pfaender, Nadine Ebert, Sophie Braga Lagache, Cédric Simillion, Jasmine Portmann, Hanspeter Stalder, Véronique Gaschen, Rémy Bruggmann, Michael Hubert Stoffel, Manfred Heller, Ronald Dijkman, Volker Thiel
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-017-14516-4

TREM-1 promotes intestinal tumorigenesis
Cited by: 31
Author(s): Leslie Saurer, Daniel Zysset, Silvia Rihs, Lukas F. Mager, Matteo Gusberti, Cédric Simillion, Alessandro Lugli, Inti Zlobec, Philippe Krebs, Christoph Mueller
Software Mentions: 1
Published: about 7 years ago