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: GEOmetadb
https://packages.ecosyste.ms/registries/bioconductor.org/packages/GEOmetadb
A compilation of metadata from NCBI GEO
1 version
Latest release: about 1 year ago
71,563 downloads total
Papers Mentioning GEOmetadb 27
10.1093/bib/bbv080
Public data and open source tools for multi-assay genomic investigation of diseaseCited by: 47
Author(s): Lavanya Kannan, Marcel Ramos, Angela Re, Nehmé El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe‐Kains, Levi Waldron
Software Mentions: 15
Published: about 9 years ago
10.1186/s12864-021-07381-z
Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencingCited by: 11
Author(s): Benjamin P. Kellman, Hratch Baghdassarian, Tiziano Pramparo, Isaac Shamie, Vahid H. Gazestani, Arjana Begzati, Shangzhong Li, Srinivasa Nalabolu, Sarah Murray, Linda Lopez, Karen Pierce, Eric Courchesne, Nathan E. Lewis
Software Mentions: 11
Published: almost 4 years ago
10.1186/1756-0500-5-282
Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray resultsCited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: over 12 years ago
10.3390/ijms19061808
Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte DifferentiationCited by: 8
Author(s): Mahmoud Ahmed, Jin Seok Hwang, Trang Huyen Lai, Sahib Zada, Huynh Quoc Nguyen, Trang Min Pham, Miyong Yun, Deok Ryong Kim
Software Mentions: 7
Published: over 6 years ago
10.1186/s12859-018-2338-4
Data-driven human transcriptomic modules determined by independent component analysisCited by: 23
Author(s): Weizhuang Zhou, Russ B. Altman
Software Mentions: 6
Published: about 6 years ago
10.1186/s12859-019-2643-6
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_Cited by: 8
Author(s): Marco Moretto, Paolo Sonego, Ana B. Villasenõr-Altamirano, Kristof Engelen
Software Mentions: 6
Published: almost 6 years ago
10.1038/s41598-020-57716-1
Ontology-driven integrative analysis of omics data through OnassisCited by: 9
Author(s): Eugenia Galeota, Kamal Kishore, Mattia Pelizzola
Software Mentions: 6
Published: almost 5 years ago
10.18632/oncotarget.6679
Computational selection of antibody-drug conjugate targets for breast cancerCited by: 13
Author(s): François Fauteux, Jonathan D. Hill, María Jaramillo, Youlian Pan, Sieu Phan, Fazel Famili, Maureen D. O'Connor‐McCourt
Software Mentions: 4
Published: almost 9 years ago
10.1186/s12864-019-6390-x
High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasisCited by: 8
Author(s): Nirupama Benis, Jerry M. Wells, M.A. Smits, Soumya K. Kar, Bart van der Hee, Vítor A. P. Martins dos Santos, María Suárez-Diez, Dirkjan Schokker
Software Mentions: 4
Published: almost 5 years ago
10.1093/bioinformatics/btu027
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metricsCited by: 15
Author(s): Marta Rosikiewicz, Marc Robinson‐Rechavi
Software Mentions: 4
Published: almost 11 years ago
10.1186/1471-2164-11-574
Heading Down the Wrong Pathway: on the Influence of Correlation within Gene SetsCited by: 74
Author(s): Daniel M. Gatti, William T. Barry, Andrew B. Nobel, Ivan Rusyn, Fred A. Wright
Software Mentions: 3
Published: about 14 years ago
10.1186/1471-2105-11-421
Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray databaseCited by: 35
Author(s): Wei‐Chung Cheng, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen, Wun‐Yi Shu, Yun‐Shien Lee, Tzu‐Hao Wang, Ji-Hong Hong, Chia-Yang Li, Ian C. Hsu
Software Mentions: 3
Published: about 14 years ago
10.7717/peerj.5743
Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synoviumCited by: 6
Author(s): Shilpa Harshan, Poulami Dey, Srivatsan Ragunathan
Software Mentions: 3
Published: about 6 years ago
10.3390/microarrays5030023
Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public RepositoriesCited by: 9
Author(s): Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
Software Mentions: 3
Published: about 8 years ago
10.3389/fbioe.2015.00038
Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome AnalysesCited by: 33
Author(s): Takeshi Ara, Mitsuo Enomoto, Masanori Arita, Chiaki Ikeda, Kota Kera, Manabu Yamada, Takaaki Nishioka, Tasuku Ikeda, Yoshito Nihei, Daisuke Shibata, Shigehiko Kanaya, Nozomu Sakurai
Software Mentions: 3
Published: over 9 years ago
10.21203/rs.3.rs-100914/v1
Sex differences in viral entry protein expression, host responses to SARS-CoV-2, and in vitro responses to sex steroid hormone treatment in COVID-19Cited by: 5
Author(s): Mengying Sun, Rama Shankar, Meehyun Ko, Christopher Daniel Chang, Shan-Ju Yeh, Shilong Li, Ke Liu, Guoli Zhou, Jing Xing, Austin VanVelsen, Tyler VanVelsen, Shreya Paithankar, Benjamin Y. Feng, Krista Young, Michael Strug, Lauren Turco, Zichen Wang, Eric E. Schadt, Rong Chen, Xiaohong Li, Tomiko Oskotsky, Marina Sirota, Benjamin S. Glicksberg, Girish N. Nadkarni, Adam J. Moeser, Li Li, Seungtaek Kim, Jiayu Zhou, Bin Chen
Software Mentions: 3
Published: about 4 years ago
10.1093/database/bav099
<i>NeuroTransDB</i>: highly curated and structured transcriptomic metadata for neurodegenerative diseasesCited by: 7
Author(s): Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, A Namasivayam, Matthew J. Page, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 2
Published: almost 10 years ago
10.1093/database/bay063
PtRFdb: a database for plant transfer RNA-derived fragmentsCited by: 28
Author(s): Nikita Gupta, Ajeet Singh, Shafaque Zahra, Shailesh Kumar
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41388-018-0588-2
LCE: an open web portal to explore gene expression and clinical associations in lung cancerCited by: 70
Author(s): Ling Cai, Shing-Jong Lin, Luc Girard, Yunyun Zhou, Lin Yang, Bo Ci, Qinbo Zhou, Danni Luo, Bo Yao, Jing Tang, Jeffrey D. Allen, Kenneth E. Huffman, Adi F. Gazdar, John V. Heymach, Ignacio I. Wistuba, Guanghua Xiao, John D. Minna, Yang Xie
Software Mentions: 2
Published: almost 6 years ago
10.1093/database/bay135
AtFusionDB: a database of fusion transcripts in<i>Arabidopsis thaliana</i>Cited by: 6
Author(s): Ajeet Singh, Shafaque Zahra, Durdam Das, Shailesh Kumar
Software Mentions: 2
Published: almost 6 years ago
10.1093/database/bay145
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysisCited by: 18
Author(s): Guocai Chen, Juan Camilo Ramírez, Nan Deng, Xing Qiu, Canglin Wu, W. Jim Zheng, Hulin Wu
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pbio.2002477
Wide-Open: Accelerating public data release by automating detection of overdue datasetsCited by: 10
Author(s): Maxim Grechkin, Hoifung Poon, Bill Howe
Software Mentions: 2
Published: over 7 years ago
10.1186/1471-2164-10-S3-S15
Improving gene expression similarity measurement using pathway-based analytic dimensionCited by: 4
Author(s): Changwon Keum, Jung Hoon Woo, Won Seok Oh, Sue-Nie Park, Kyoung Tai No
Software Mentions: 2
Published: almost 15 years ago
10.1186/s12859-017-1888-1
ALE: automated label extraction from GEO metadataCited by: 19
Author(s): Cory B. Giles, Chase A. Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz, Jonathan D. Wren
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pcbi.1002090
An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading ProteinsCited by: 52
Author(s): Greet De Baets, Joke Reumers, Javier Delgado, Joaquı́n Dopazo, Joost Schymkowitz, Frédéric Rousseau
Software Mentions: 1
Published: over 13 years ago
10.12688/f1000research.8182.2
A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology researchCited by: 18
Author(s): Darawan Rinchai, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Damien Chaussabel
Software Mentions: 1
Published: over 8 years ago
10.1155/2015/318064
MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq StudiesCited by: 4
Author(s): Pankaj Kumar, Anna Halama, Shahina Hayat, Anja M. Billing, Manish Gupta, Noha A. Yousri, Gregory Smith, Karsten Suhre
Software Mentions: 1
Published: almost 10 years ago