A citation-based method for searching scientific literature

Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit. BMC Bioinformatics 2011
Times Cited: 360







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



Times Cited
  Times     Co-cited
Similarity


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
40

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
33

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
32

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
22

Normalization of RNA-seq data using factor analysis of control genes or samples.
Davide Risso, John Ngai, Terence P Speed, Sandrine Dudoit. Nat Biotechnol 2014
686
20



The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
17

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
16


Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.
James H Bullard, Elizabeth Purdom, Kasper D Hansen, Sandrine Dudoit. BMC Bioinformatics 2010
938
12

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.
Antonio Colaprico, Tiago C Silva, Catharina Olsen, Luciano Garofano, Claudia Cava, Davide Garolini, Thais S Sabedot, Tathiane M Malta, Stefano M Pagnotta, Isabella Castiglioni,[...]. Nucleic Acids Res 2016
826
12

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
12

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
12

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth. Genome Biol 2014
11

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
10

Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010
9

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
8

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.
Yang Liao, Gordon K Smyth, Wei Shi. Nucleic Acids Res 2013
7

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
7

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
7

Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
7

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
7

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
7


A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.
Marie-Agnès Dillies, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin, Nicolas Servant, Céline Keime, Guillemette Marot, David Castel, Jordi Estelle,[...]. Brief Bioinform 2013
617
6

RNA-Seq differential expression analysis: An extended review and a software tool.
Juliana Costa-Silva, Douglas Domingues, Fabricio Martins Lopes. PLoS One 2017
165
6

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
6

Transcript length bias in RNA-seq data confounds systems biology.
Alicia Oshlack, Matthew J Wakefield. Biol Direct 2009
283
6

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
6

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
5

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
5


Moderated statistical tests for assessing differences in tag abundance.
Mark D Robinson, Gordon K Smyth. Bioinformatics 2007
487
5

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
613
5

MultiQC: summarize analysis results for multiple tools and samples in a single report.
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
5

Differential expression in RNA-seq: a matter of depth.
Sonia Tarazona, Fernando García-Alcalde, Joaquín Dopazo, Alberto Ferrer, Ana Conesa. Genome Res 2011
919
5

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
5

Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
5

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
5

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.
Jianfang Liu, Tara Lichtenberg, Katherine A Hoadley, Laila M Poisson, Alexander J Lazar, Andrew D Cherniack, Albert J Kovatich, Christopher C Benz, Douglas A Levine, Adrian V Lee,[...]. Cell 2018
752
5

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.
Andrew Paul Hutchins, Ralf Jauch, Mateusz Dyla, Diego Miranda-Saavedra. Cell Regen 2014
46
10



Human housekeeping genes, revisited.
Eli Eisenberg, Erez Y Levanon. Trends Genet 2013
587
5

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
4

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
4


Toward a Shared Vision for Cancer Genomic Data.
Robert L Grossman, Allison P Heath, Vincent Ferretti, Harold E Varmus, Douglas R Lowy, Warren A Kibbe, Louis M Staudt. N Engl J Med 2016
512
4



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.