A citation-based method for searching scientific literature

Samuel Marguerat, Jürg Bähler. Cell Mol Life Sci 2010
Times Cited: 267







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



Times Cited
  Times     Co-cited
Similarity


RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
55

Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
26

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
19

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
17

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
15


TopHat: discovering splice junctions with RNA-Seq.
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
13

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
13


Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010
12

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
John C Marioni, Christopher E Mason, Shrikant M Mane, Matthew Stephens, Yoav Gilad. Genome Res 2008
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

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
11

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
9

Gene ontology analysis for RNA-seq: accounting for selection bias.
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
9

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
9

Differential analysis of gene regulation at transcript resolution with RNA-seq.
Cole Trapnell, David G Hendrickson, Martin Sauvageau, Loyal Goff, John L Rinn, Lior Pachter. Nat Biotechnol 2013
8

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
8

RNA sequencing: advances, challenges and opportunities.
Fatih Ozsolak, Patrice M Milos. Nat Rev Genet 2011
8

Sequencing technologies - the next generation.
Michael L Metzker. Nat Rev Genet 2010
8


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
8

Next-generation transcriptome assembly.
Jeffrey A Martin, Zhong Wang. Nat Rev Genet 2011
661
7

Analyzing real-time PCR data by the comparative C(T) method.
Thomas D Schmittgen, Kenneth J Livak. Nat Protoc 2008
7

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
7

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

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
6

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
6

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.
Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang. Bioinformatics 2010
6

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
6

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

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
6


The transcriptional landscape of the yeast genome defined by RNA sequencing.
Ugrappa Nagalakshmi, Zhong Wang, Karl Waern, Chong Shou, Debasish Raha, Mark Gerstein, Michael Snyder. Science 2008
5

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
5

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
5

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
5


WEGO: a web tool for plotting GO annotations.
Jia Ye, Lin Fang, Hongkun Zheng, Yong Zhang, Jie Chen, Zengjin Zhang, Jing Wang, Shengting Li, Ruiqiang Li, Lars Bolund,[...]. Nucleic Acids Res 2006
5

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
5

REVIGO summarizes and visualizes long lists of gene ontology terms.
Fran Supek, Matko Bošnjak, Nives Škunca, Tomislav Šmuc. PLoS One 2011
5

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

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
5

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
5

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Brian J Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,[...]. Nat Protoc 2013
5

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.
Zheng Chang, Guojun Li, Juntao Liu, Yu Zhang, Cody Ashby, Deli Liu, Carole L Cramer, Xiuzhen Huang. Genome Biol 2015
131
5

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels.
Yu Peng, Henry C M Leung, Siu-Ming Yiu, Ming-Ju Lv, Xin-Guang Zhu, Francis Y L Chin. Bioinformatics 2013
83
6

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.
Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Shengkang Li,[...]. Bioinformatics 2014
448
5

From RNA-seq reads to differential expression results.
Alicia Oshlack, Mark D Robinson, Matthew D Young. Genome Biol 2010
390
4

Stem cell transcriptome profiling via massive-scale mRNA sequencing.
Nicole Cloonan, Alistair R R Forrest, Gabriel Kolle, Brooke B A Gardiner, Geoffrey J Faulkner, Mellissa K Brown, Darrin F Taylor, Anita L Steptoe, Shivangi Wani, Graeme Bethel,[...]. Nat Methods 2008
681
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.