A citation-based method for searching scientific literature

Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez, Markus Müller. BMC Bioinformatics 2011
Times Cited: 4541







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



Times Cited
  Times     Co-cited
Similarity


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
15

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
12

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
8

Regularization Paths for Generalized Linear Models via Coordinate Descent.
Jerome Friedman, Trevor Hastie, Rob Tibshirani. J Stat Softw 2010
7

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
7

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
6

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
5

NCBI GEO: archive for functional genomics data sets--update.
Tanya Barrett, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Michelle Holko,[...]. Nucleic Acids Res 2013
5

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
5


Design and validation of a histological scoring system for nonalcoholic fatty liver disease.
David E Kleiner, Elizabeth M Brunt, Mark Van Natta, Cynthia Behling, Melissa J Contos, Oscar W Cummings, Linda D Ferrell, Yao-Chang Liu, Michael S Torbenson, Aynur Unalp-Arida,[...]. Hepatology 2005
3

Dermatologist-level classification of skin cancer with deep neural networks.
Andre Esteva, Brett Kuprel, Roberto A Novoa, Justin Ko, Susan M Swetter, Helen M Blau, Sebastian Thrun. Nature 2017
3

DrugBank 5.0: a major update to the DrugBank database for 2018.
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
3

Inferring tumour purity and stromal and immune cell admixture from expression data.
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W Laird, Douglas A Levine,[...]. Nat Commun 2013
3

Computational Radiomics System to Decode the Radiographic Phenotype.
Joost J M van Griethuysen, Andriy Fedorov, Chintan Parmar, Ahmed Hosny, Nicole Aucoin, Vivek Narayan, Regina G H Beets-Tan, Jean-Christophe Fillion-Robin, Steve Pieper, Hugo J W L Aerts. Cancer Res 2017
3

Radiomics: the bridge between medical imaging and personalized medicine.
Philippe Lambin, Ralph T H Leijenaar, Timo M Deist, Jurgen Peerlings, Evelyn E C de Jong, Janita van Timmeren, Sebastian Sanduleanu, Ruben T H M Larue, Aniek J G Even, Arthur Jochems,[...]. Nat Rev Clin Oncol 2017
3

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar,[...]. Nat Biotechnol 2019
3

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
Zefang Tang, Chenwei Li, Boxi Kang, Ge Gao, Cheng Li, Zemin Zhang. Nucleic Acids Res 2017
3

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.
Jun-Hao Li, Shun Liu, Hui Zhou, Liang-Hu Qu, Jian-Hua Yang. Nucleic Acids Res 2014
3

cytoHubba: identifying hub objects and sub-networks from complex interactome.
Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin. BMC Syst Biol 2014
3

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
3


Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response.
Peng Jiang, Shengqing Gu, Deng Pan, Jingxin Fu, Avinash Sahu, Xihao Hu, Ziyi Li, Nicole Traugh, Xia Bu, Bo Li,[...]. Nat Med 2018
725
3


Transparent Reporting of a multivariable prediction model for Individual Prognosis or Diagnosis (TRIPOD): explanation and elaboration.
Karel G M Moons, Douglas G Altman, Johannes B Reitsma, John P A Ioannidis, Petra Macaskill, Ewout W Steyerberg, Andrew J Vickers, David F Ransohoff, Gary S Collins. Ann Intern Med 2015
2

FibroScan-AST (FAST) score for the non-invasive identification of patients with non-alcoholic steatohepatitis with significant activity and fibrosis: a prospective derivation and global validation study.
Philip N Newsome, Magali Sasso, Jonathan J Deeks, Angelo Paredes, Jérôme Boursier, Wah-Kheong Chan, Yusuf Yilmaz, Sébastien Czernichow, Ming-Hua Zheng, Vincent Wai-Sun Wong,[...]. Lancet Gastroenterol Hepatol 2020
137
2

Age as a Confounding Factor for the Accurate Non-Invasive Diagnosis of Advanced NAFLD Fibrosis.
Stuart McPherson, Tim Hardy, Jean-Francois Dufour, Salvatore Petta, Manuel Romero-Gomez, Mike Allison, Claudia P Oliveira, Sven Francque, Luc Van Gaal, Jörn M Schattenberg,[...]. Am J Gastroenterol 2017
264
2

Accuracy of FibroScan Controlled Attenuation Parameter and Liver Stiffness Measurement in Assessing Steatosis and Fibrosis in Patients With Nonalcoholic Fatty Liver Disease.
Peter J Eddowes, Magali Sasso, Michael Allison, Emmanouil Tsochatzis, Quentin M Anstee, David Sheridan, Indra N Guha, Jeremy F Cobbold, Jonathan J Deeks, Valérie Paradis,[...]. Gastroenterology 2019
316
2

Utility of transient elastography (fibroscan) and impact of bariatric surgery on nonalcoholic fatty liver disease (NAFLD) in morbidly obese patients.
Harshit Garg, Sandeep Aggarwal, Shalimar, Rajni Yadav, Siddhartha Datta Gupta, Lokesh Agarwal, Samagra Agarwal. Surg Obes Relat Dis 2018
52
3


Development of a simple noninvasive index to predict significant fibrosis in patients with HIV/HCV coinfection.
Richard K Sterling, Eduardo Lissen, Nathan Clumeck, Ricard Sola, Mendes Cassia Correa, Julio Montaner, Mark S Sulkowski, Francesca J Torriani, Doug T Dieterich, David L Thomas,[...]. Hepatology 2006
2

SLIM: Simultaneous Logic-in-Memory Computing Exploiting Bilayer Analog OxRAM Devices.
Sandeep Kaur Kingra, Vivek Parmar, Che-Chia Chang, Boris Hudec, Tuo-Hung Hou, Manan Suri. Sci Rep 2020
57
3

The NAFLD fibrosis score: a noninvasive system that identifies liver fibrosis in patients with NAFLD.
Paul Angulo, Jason M Hui, Giulio Marchesini, Ellisabetta Bugianesi, Jacob George, Geoffrey C Farrell, Felicity Enders, Sushma Saksena, Alastair D Burt, John P Bida,[...]. Hepatology 2007
2

A blood-based biomarker panel (NIS4) for non-invasive diagnosis of non-alcoholic steatohepatitis and liver fibrosis: a prospective derivation and global validation study.
Stephen A Harrison, Vlad Ratziu, Jérôme Boursier, Sven Francque, Pierre Bedossa, Zouher Majd, Geneviève Cordonnier, Fouad Ben Sudrik, Raphael Darteil, Roman Liebe,[...]. Lancet Gastroenterol Hepatol 2020
46
4

Sampling variability of liver biopsy in nonalcoholic fatty liver disease.
Vlad Ratziu, Frédéric Charlotte, Agnès Heurtier, Sophie Gombert, Philippe Giral, Eric Bruckert, André Grimaldi, Frédérique Capron, Thierry Poynard. Gastroenterology 2005
2



Clinical-grade computational pathology using weakly supervised deep learning on whole slide images.
Gabriele Campanella, Matthew G Hanna, Luke Geneslaw, Allen Miraflor, Vitor Werneck Krauss Silva, Klaus J Busam, Edi Brogi, Victor E Reuter, David S Klimstra, Thomas J Fuchs. Nat Med 2019
376
2

Incidence Estimate of Nonmelanoma Skin Cancer (Keratinocyte Carcinomas) in the U.S. Population, 2012.
Howard W Rogers, Martin A Weinstock, Steven R Feldman, Brett M Coldiron. JAMA Dermatol 2015
729
2

Utilizing Machine Learning for Image Quality Assessment for Reflectance Confocal Microscopy.
Kivanc Kose, Alican Bozkurt, Christi Alessi-Fox, Dana H Brooks, Jennifer G Dy, Milind Rajadhyaksha, Melissa Gill. J Invest Dermatol 2020
12
16

Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations.
David M Rissin, Cheuk W Kan, Todd G Campbell, Stuart C Howes, David R Fournier, Linan Song, Tomasz Piech, Purvish P Patel, Lei Chang, Andrew J Rivnak,[...]. Nat Biotechnol 2010
960
2

KEGG: integrating viruses and cellular organisms.
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe. Nucleic Acids Res 2021
596
2

The Molecular Signatures Database (MSigDB) hallmark gene set collection.
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
2

TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment.
Dongqing Sun, Jin Wang, Ya Han, Xin Dong, Jun Ge, Rongbin Zheng, Xiaoying Shi, Binbin Wang, Ziyi Li, Pengfei Ren,[...]. Nucleic Acids Res 2021
70
2

LinkedOmics: analyzing multi-omics data within and across 32 cancer types.
Suhas V Vasaikar, Peter Straub, Jing Wang, Bing Zhang. Nucleic Acids Res 2018
682
2

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
2

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Jeffrey T Leek, W Evan Johnson, Hilary S Parker, Andrew E Jaffe, John D Storey. Bioinformatics 2012
2

affy--analysis of Affymetrix GeneChip data at the probe level.
Laurent Gautier, Leslie Cope, Benjamin M Bolstad, Rafael A Irizarry. Bioinformatics 2004
2

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
2


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.