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: QUBIC

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

An R package for qualitative biclustering in support of gene co-expression analyses
1 version
Latest release: about 1 year ago
2 dependent packages
23,156 downloads total

Papers Mentioning QUBIC 26

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Cited by: 650
Author(s): Xijin Ge, Eun Wo Son, Runan Yao
Software Mentions: 14
Published: about 6 years ago

10.1093/gigascience/giz064

TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer
Cited by: 6
Author(s): Amartya Singh, Gyan Bhanot, Hossein Khiabanian
Software Mentions: 10
Published: over 5 years ago

10.1186/s12859-017-1487-1

A systematic comparative evaluation of biclustering techniques
Cited by: 94
Author(s): Victor Alexandre Padilha, Ricardo J. G. B. Campello
Software Mentions: 10
Published: almost 8 years ago

10.1371/journal.pcbi.1006792

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis
Cited by: 25
Author(s): Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma
Software Mentions: 7
Published: almost 6 years ago

10.1186/1756-0381-5-8

A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data
Cited by: 24
Author(s): Li Li, Yang Guo, Wenwu Wu, Yinggang Shi, Jian Cheng, Shiheng Tao
Software Mentions: 7
Published: over 12 years ago

10.1371/journal.pone.0090801

Biclustering Methods: Biological Relevance and Application in Gene Expression Analysis
Cited by: 77
Author(s): Ali Oghabian, Sami Kilpinen, Sampsa Hautaniemi, Elena Czeizler
Software Mentions: 6
Published: almost 11 years ago

10.1186/s12859-019-3289-0

Identifying gene-specific subgroups: an alternative to biclustering
Cited by: 3
Author(s): Vincent Branders, Pierre Schaus, Pierre Dupont
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1002228

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters
Cited by: 7
Author(s): Thadeous J. Kacmarczyk, Peter Waltman, Ashley R. Bate, Patrick Eichenberger, Richard Bonneau
Software Mentions: 5
Published: about 13 years ago

10.1186/gb-2010-11-9-r96

Multi-species integrative biclustering
Cited by: 35
Author(s): Peter Waltman, Thadeous J. Kacmarczyk, Ashley R. Bate, Daniel B. Kearns, David J Reiss, Patrick Eichenberger, Richard Bonneau
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2105-12-497

Partition decoupling for multi-gene analysis of gene expression profiling data
Cited by: 10
Author(s): Rosemary Braun, Gregory Leibon, Scott D. Pauls, Daniel N. Rockmore
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0159923

BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes
Cited by: 8
Author(s): Amir Lakizadeh, Saeed Jalili
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0082890

SiBIC: A Web Server for Generating Gene Set Networks Based on Biclusters Obtained by Maximal Frequent Itemset Mining
Cited by: 1
Author(s): Keiichiro Takahashi, Ichigaku Takigawa, Hiroshi Mamitsuka
Software Mentions: 4
Published: about 11 years ago

10.1186/1748-7188-6-18

DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach
Cited by: 61
Author(s): Akdes Serin, Martin Vingron
Software Mentions: 3
Published: over 13 years ago

10.1186/1748-7188-8-4

Configurable pattern-based evolutionary biclustering of gene expression data
Cited by: 33
Author(s): Beatriz Pontes, Raúl Giráldez, Jesús S. Aguilar–Ruiz
Software Mentions: 3
Published: almost 12 years ago

10.7554/eLife.43036

The unfolded protein response and endoplasmic reticulum protein targeting machineries converge on the stress sensor IRE1
Cited by: 59
Author(s): Diego Acosta‐Alvear, G. Elif Karagöz, Florian Fröhlich, Li Han, Tobias C. Walther, Peter Walter
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2017.00780

Drawing Links from Transcriptome to Metabolites: The Evolution of Aroma in the Ripening Berry of Moscato Bianco (Vitis vinifera L.)
Cited by: 25
Author(s): L. Costantini, Christian Kappel, Massimiliano Trenti, J. Battilana, F. Emanuelli, M. Sordo, Marco Moretto, Carlos Camps, R. Larcher, Serge Delrot, S. Grando
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2229-12-138

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis
Cited by: 51
Author(s): Shan Wang, Yanbin Yin, Qin Ma, Xiaojia Tang, Dongyun Hao, Ying Xu
Software Mentions: 2
Published: over 12 years ago

10.1038/srep23466

UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data
Cited by: 34
Author(s): Zhenjia Wang, Guojun Li, R. W. Robinson, Xiuzhen Huang
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.ymeth.2018.02.004

Bi-clustering of metabolic data using matrix factorization tools
Cited by: 7
Author(s): Quan Gu, Kirill Veselkov
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2016.00444

Learning from Co-expression Networks: Possibilities and Challenges
Cited by: 223
Author(s): Elise A. R. Serin, Harm Nijveen, Henk W. M. Hilhorst, Wilco Ligterink
Software Mentions: 1
Published: over 8 years ago

10.1128/mSystems.00413-19

<i>MetaMed</i> : Linking Microbiota Functions with Medicine Therapeutics
Cited by: 1
Author(s): Han Zhao, Shaliu Fu, Yifei Yu, Zhanbing Zhang, Ping Li, Qin Ma, Jia Wei, Kang Ning, Shen Qu, Qi Liu
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-14-144

Biclustering for the comprehensive search of correlated gene expression patterns using clustered seed expansion
Cited by: 20
Author(s): Taegyun Yun, Gwan‐Su Yi
Software Mentions: 1
Published: almost 12 years ago

10.26508/lsa.202000904

A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study
Cited by: 1
Author(s): Mengran Wang, John Withers, Piero Ricchiuto, Ivan Voitalov, Michael O. McAnally, Helia N. Sanchez, Alif Saleh, Viatcheslav R. Akmaev, Dina Ghiassian
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0032660

QServer: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters
Cited by: 11
Author(s): Fengfeng Zhou, Qin Ma, Guojun Li, Ying Xu
Software Mentions: 1
Published: almost 13 years ago

10.1186/1754-6834-6-131

Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress
Cited by: 36
Author(s): Charlotte M. Wilson, Shihui Yang, Miguel Rodríguez, Qin Ma, C. M. Johnson, Lezlee Dice, Ying Xu, Steven D. Brown
Software Mentions: 1
Published: over 11 years ago

10.1038/srep23030

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses
Cited by: 20
Author(s): Bingqiang Liu, Chunkui Zhou, Guojun Li, Han-Yuan Zhang, Erliang Zeng, Qi Liu, Qin Ma
Software Mentions: 1
Published: almost 9 years ago