A citation-based method for searching scientific literature

Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
Times Cited: 12649







List of co-cited articles
269 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
26

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
19

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
17

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
15


HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
11

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
10


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
8


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
7

TopHat: discovering splice junctions with RNA-Seq.
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
7

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
7

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
Marc R Friedländer, Sebastian D Mackowiak, Na Li, Wei Chen, Nikolaus Rajewsky. Nucleic Acids Res 2012
7

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

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
7

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


The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
6

miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
882
6

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
6


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
5

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
5

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner. Nucleic Acids Res 2013
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


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
5

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
5

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
5

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, Jonathan S Weissman. Science 2009
5


The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
4

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
4

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
4

Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010
4

GREAT improves functional interpretation of cis-regulatory regions.
Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano. Nat Biotechnol 2010
4

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
4

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
4

InterProScan 5: genome-scale protein function classification.
Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka,[...]. Bioinformatics 2014
4

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
4

Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
4

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
4

miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2014
4

Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
4

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.
Julius Brennecke, Alexei A Aravin, Alexander Stark, Monica Dus, Manolis Kellis, Ravi Sachidanandam, Gregory J Hannon. Cell 2007
3

MicroRNA-100 regulates neovascularization by suppression of mammalian target of rapamycin in endothelial and vascular smooth muscle cells.
Sebastian Grundmann, Felix P Hans, Sheena Kinniry, Jennifer Heinke, Thomas Helbing, Franziska Bluhm, Joost P G Sluijter, Imo Hoefer, Gerard Pasterkamp, Christoph Bode,[...]. Circulation 2011
140
3


Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash. Nucleic Acids Res 2002
3

Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization.
Minna U Kaikkonen, Henri Niskanen, Casey E Romanoski, Emilia Kansanen, Annukka M Kivelä, Jarkko Laitalainen, Sven Heinz, Christopher Benner, Christopher K Glass, Seppo Ylä-Herttuala. Nucleic Acids Res 2014
32
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.