A citation-based method for searching scientific literature

Yang Liao, Gordon K Smyth, Wei Shi. Bioinformatics 2014
Times Cited: 5392







List of co-cited articles
179 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
50

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
48

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
29

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
21

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
17

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


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

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
11

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
10

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
10

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
9

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
8


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
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


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

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

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
6

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

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
6

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.
Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A Grüning,[...]. Nucleic Acids Res 2018
952
6

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
785
6

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
6


RSeQC: quality control of RNA-seq experiments.
Liguo Wang, Shengqin Wang, Wei Li. Bioinformatics 2012
864
5



Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Steffen Durinck, Paul T Spellman, Ewan Birney, Wolfgang Huber. Nat Protoc 2009
5

MultiQC: summarize analysis results for multiple tools and samples in a single report.
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
989
5

Global quantification of mammalian gene expression control.
Björn Schwanhäusser, Dorothea Busse, Na Li, Gunnar Dittmar, Johannes Schuchhardt, Jana Wolf, Wei Chen, Matthias Selbach. Nature 2011
4

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
4

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
4

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
4

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
4

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
4

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
4


Cancer statistics, 2019.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2019
3

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
3

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.
Ruijie Liu, Aliaksei Z Holik, Shian Su, Natasha Jansz, Kelan Chen, Huei San Leong, Marnie E Blewitt, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie. Nucleic Acids Res 2015
159
3

A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Bradley E Bernstein, Tarjei S Mikkelsen, Xiaohui Xie, Michael Kamal, Dana J Huebert, James Cuff, Ben Fry, Alex Meissner, Marius Wernig, Kathrin Plath,[...]. Cell 2006
3



ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Jason D Buenrostro, Beijing Wu, Howard Y Chang, William J Greenleaf. Curr Protoc Mol Biol 2015
961
3

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
3

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

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.
John G Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W Vaimberg, Katherine F Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard,[...]. Nat Biotechnol 2016
3

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


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.