A citation-based method for searching scientific literature

Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
Times Cited: 8152







List of co-cited articles
240 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
17


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
15

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
14

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


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
8

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

Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010
7

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

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

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

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
7

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón, Montserrat Robles. Bioinformatics 2005
7

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
6

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
6

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
6

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

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
6

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
6

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
5

A survey of best practices for RNA-seq data analysis.
Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J Gaffney, Laura L Elo, Xuegong Zhang,[...]. Genome Biol 2016
912
5

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
5

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

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
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

Gene ontology analysis for RNA-seq: accounting for selection bias.
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
4

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
4

Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
543
4

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
4


Accounting for technical noise in single-cell RNA-seq experiments.
Philip Brennecke, Simon Anders, Jong Kyoung Kim, Aleksandra A Kołodziejczyk, Xiuwei Zhang, Valentina Proserpio, Bianka Baying, Vladimir Benes, Sarah A Teichmann, John C Marioni,[...]. Nat Methods 2013
501
4

Differential expression in RNA-seq: a matter of depth.
Sonia Tarazona, Fernando García-Alcalde, Joaquín Dopazo, Alberto Ferrer, Ana Conesa. Genome Res 2011
919
4

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
4

Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz,[...]. Genome Biol 2020
142
4

mRNA-Seq whole-transcriptome analysis of a single cell.
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
4

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
4


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

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
4

Proteomics. Tissue-based map of the human proteome.
Mathias Uhlén, Linn Fagerberg, Björn M Hallström, Cecilia Lindskog, Per Oksvold, Adil Mardinoglu, Åsa Sivertsson, Caroline Kampf, Evelina Sjöstedt, Anna Asplund,[...]. Science 2015
3

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.
Stephen A Bustin, Vladimir Benes, Jeremy A Garson, Jan Hellemans, Jim Huggett, Mikael Kubista, Reinhold Mueller, Tania Nolan, Michael W Pfaffl, Gregory L Shipley,[...]. Clin Chem 2009
3


Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
215
3


Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Aaron T L Lun, Karsten Bach, John C Marioni. Genome Biol 2016
373
3

Normalizing single-cell RNA sequencing data: challenges and opportunities.
Catalina A Vallejos, Davide Risso, Antonio Scialdone, Sandrine Dudoit, John C Marioni. Nat Methods 2017
155
3


Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
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.