A citation-based method for searching scientific literature

Eric Bonnet, Laurence Calzone, Tom Michoel. PLoS Comput Biol 2015
Times Cited: 53







List of co-cited articles
420 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
Charles J Vaske, Stephen C Benz, J Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M Stuart. Bioinformatics 2010
480
33

Similarity network fusion for aggregating data types on a genomic scale.
Bo Wang, Aziz M Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg. Nat Methods 2014
657
33

More Is Better: Recent Progress in Multi-Omics Data Integration Methods.
Sijia Huang, Kumardeep Chaudhary, Lana X Garmire. Front Genet 2017
298
32


WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
26

JOINT AND INDIVIDUAL VARIATION EXPLAINED (JIVE) FOR INTEGRATED ANALYSIS OF MULTIPLE DATA TYPES.
Eric F Lock, Katherine A Hoadley, J S Marron, Andrew B Nobel. Ann Appl Stat 2013
174
26

An integrated approach to uncover drivers of cancer.
Uri David Akavia, Oren Litvin, Jessica Kim, Felix Sanchez-Garcia, Dylan Kotliar, Helen C Causton, Panisa Pochanard, Eyal Mozes, Levi A Garraway, Dana Pe'er. Cell 2010
330
24

Pattern discovery and cancer gene identification in integrated cancer genomic data.
Qianxing Mo, Sijian Wang, Venkatraman E Seshan, Adam B Olshen, Nikolaus Schultz, Chris Sander, R Scott Powers, Marc Ladanyi, Ronglai Shen. Proc Natl Acad Sci U S A 2013
214
22

Methods of integrating data to uncover genotype-phenotype interactions.
Marylyn D Ritchie, Emily R Holzinger, Ruowang Li, Sarah A Pendergrass, Dokyoon Kim. Nat Rev Genet 2015
448
22

Bayesian consensus clustering.
Eric F Lock, David B Dunson. Bioinformatics 2013
109
22

Bayesian joint analysis of heterogeneous genomics data.
Priyadip Ray, Lingling Zheng, Joseph Lucas, Lawrence Carin. Bioinformatics 2014
38
31

Bayesian correlated clustering to integrate multiple datasets.
Paul Kirk, Jim E Griffin, Richard S Savage, Zoubin Ghahramani, David L Wild. Bioinformatics 2012
116
20

Patient-specific data fusion defines prognostic cancer subtypes.
Yinyin Yuan, Richard S Savage, Florian Markowetz. PLoS Comput Biol 2011
59
20


Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.
Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle. Mol Syst Biol 2018
260
18

Analysis of a Gibbs sampler method for model-based clustering of gene expression data.
Anagha Joshi, Yves Van de Peer, Tom Michoel. Bioinformatics 2008
34
26

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.
Shihua Zhang, Chun-Chi Liu, Wenyuan Li, Hui Shen, Peter W Laird, Xianghong Jasmine Zhou. Nucleic Acids Res 2012
176
16

Multi-omics approaches to disease.
Yehudit Hasin, Marcus Seldin, Aldons Lusis. Genome Biol 2017
670
16

Module networks revisited: computational assessment and prioritization of model predictions.
Anagha Joshi, Riet De Smet, Kathleen Marchal, Yves Van de Peer, Tom Michoel. Bioinformatics 2009
62
15



A pathway-based data integration framework for prediction of disease progression.
José A Seoane, Ian N M Day, Tom R Gaunt, Colin Campbell. Bioinformatics 2014
43
18

A statistical framework for genomic data fusion.
Gert R G Lanckriet, Tijl De Bie, Nello Cristianini, Michael I Jordan, William Stafford Noble. Bioinformatics 2004
225
13

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
13


Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme.
Kristian Ovaska, Marko Laakso, Saija Haapa-Paananen, Riku Louhimo, Ping Chen, Viljami Aittomäki, Erkka Valo, Javier Núñez-Fontarnau, Ville Rantanen, Sirkku Karinen,[...]. Genome Med 2010
121
13

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
13

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
13

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
13

mixOmics: An R package for 'omics feature selection and multiple data integration.
Florian Rohart, Benoît Gautier, Amrit Singh, Kim-Anh Lê Cao. PLoS Comput Biol 2017
998
13

Network-based integration of multi-omics data for prioritizing cancer genes.
Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Luca Häfliger, Jonas Behr, Hesam Montazeri, Michael N Hall, Niko Beerenwinkel. Bioinformatics 2018
73
13

Multi-omics Data Integration, Interpretation, and Its Application.
Indhupriya Subramanian, Srikant Verma, Shiva Kumar, Abhay Jere, Krishanpal Anamika. Bioinform Biol Insights 2020
201
13

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.
Wenyuan Li, Shihua Zhang, Chun-Chi Liu, Xianghong Jasmine Zhou. Bioinformatics 2012
73
11

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.
Eran Segal, Michael Shapira, Aviv Regev, Dana Pe'er, David Botstein, Daphne Koller, Nir Friedman. Nat Genet 2003
985
11

Cluster analysis and display of genome-wide expression patterns.
M B Eisen, P T Spellman, P O Brown, D Botstein. Proc Natl Acad Sci U S A 1998
11

A multivariate approach to the integration of multi-omics datasets.
Chen Meng, Bernhard Kuster, Aedín C Culhane, Amin Moghaddas Gholami. BMC Bioinformatics 2014
126
11

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery.
Hiromi W L Koh, Damian Fermin, Christine Vogel, Kwok Pui Choi, Rob M Ewing, Hyungwon Choi. NPJ Syst Biol Appl 2019
41
14

MOLI: multi-omics late integration with deep neural networks for drug response prediction.
Hossein Sharifi-Noghabi, Olga Zolotareva, Colin C Collins, Martin Ester. Bioinformatics 2019
76
11

Validating module network learning algorithms using simulated data.
Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper, Kathleen Marchal,[...]. BMC Bioinformatics 2007
25
20

Module network inference from a cancer gene expression data set identifies microRNA regulated modules.
Eric Bonnet, Marianthi Tatari, Anagha Joshi, Tom Michoel, Kathleen Marchal, Geert Berx, Yves Van de Peer. PLoS One 2010
35
14

Group sparse canonical correlation analysis for genomic data integration.
Dongdong Lin, Jigang Zhang, Jingyao Li, Vince D Calhoun, Hong-Wen Deng, Yu-Ping Wang. BMC Bioinformatics 2013
48
10


Integrative subtype discovery in glioblastoma using iCluster.
Ronglai Shen, Qianxing Mo, Nikolaus Schultz, Venkatraman E Seshan, Adam B Olshen, Jason Huse, Marc Ladanyi, Chris Sander. PLoS One 2012
127
9

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer.
Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan. PLoS Comput Biol 2015
43
11

Extensions of sparse canonical correlation analysis with applications to genomic data.
Daniela M Witten, Robert J Tibshirani. Stat Appl Genet Mol Biol 2009
213
9

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.
Jeremiah J Faith, Boris Hayete, Joshua T Thaden, Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J Collins, Timothy S Gardner. PLoS Biol 2007
877
9

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data.
Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S Morris, Bradley M Broom, Ganiraju Manyam, Kim-Anh Do. Bioinformatics 2013
87
9

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
9


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.