A citation-based method for searching scientific literature

Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
Times Cited: 14612







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



Times Cited
  Times     Co-cited
Similarity


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
21

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
14

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
14

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
14

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
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
11

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
10


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
10

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
10

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg. Genome Biol 2013
9


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
8

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
8

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
7





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
7

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
7

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
6

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
6

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.
Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K Chanda. Nat Commun 2019
5

RSeQC: quality control of RNA-seq experiments.
Liguo Wang, Shengqin Wang, Wei Li. Bioinformatics 2012
854
5

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
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
5

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
5

Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
5

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
5

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
4


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
3

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
919
3



GENCODE reference annotation for the human and mouse genomes.
Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong,[...]. Nucleic Acids Res 2019
636
3


REVIGO summarizes and visualizes long lists of gene ontology terms.
Fran Supek, Matko Bošnjak, Nives Škunca, Tomislav Šmuc. PLoS One 2011
3

The UCSC Genome Browser database: 2019 update.
Maximilian Haeussler, Ann S Zweig, Cath Tyner, Matthew L Speir, Kate R Rosenbloom, Brian J Raney, Christopher M Lee, Brian T Lee, Angie S Hinrichs, Jairo Navarro Gonzalez,[...]. Nucleic Acids Res 2019
286
3

A general framework for weighted gene co-expression network analysis.
Bin Zhang, Steve Horvath. Stat Appl Genet Mol Biol 2005
3

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.
Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shu-Qi Zhao, Liping Wei, Ge Gao. Nucleic Acids Res 2007
3

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
3


Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.
Moran N Cabili, Cole Trapnell, Loyal Goff, Magdalena Koziol, Barbara Tazon-Vega, Aviv Regev, John L Rinn. Genes Dev 2011
3

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012
3

NF-κB signaling in inflammation.
Ting Liu, Lingyun Zhang, Donghyun Joo, Shao-Cong Sun. Signal Transduct Target Ther 2017
3

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19.
Daniel Blanco-Melo, Benjamin E Nilsson-Payant, Wen-Chun Liu, Skyler Uhl, Daisy Hoagland, Rasmus Møller, Tristan X Jordan, Kohei Oishi, Maryline Panis, David Sachs,[...]. Cell 2020
3

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.
Charlotte Soneson, Michael I Love, Mark D Robinson. F1000Res 2015
888
3


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.