A citation-based method for searching scientific literature

Rory Stark, Marta Grzelak, James Hadfield. Nat Rev Genet 2019
Times Cited: 263







List of co-cited articles
437 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
21

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
20

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
17

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
16

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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
11

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
11

Highly parallel direct RNA sequencing on an array of nanopores.
Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd, Mark Bruce, Nadia Pantic, Tigist Admassu, Phillip James, Anthony Warland,[...]. Nat Methods 2018
316
9


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
8

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
8


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
8

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

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
8

Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
8

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

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
895
7

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
7

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
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

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
7

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
6

Opportunities and challenges in long-read sequencing data analysis.
Shanika L Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E Ritchie, Quentin Gouil. Genome Biol 2020
140
6

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
302
5

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
5

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

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
855
5

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
698
5

Nanopore native RNA sequencing of a human poly(A) transcriptome.
Rachael E Workman, Alison D Tang, Paul S Tang, Miten Jain, John R Tyson, Roham Razaghi, Philip C Zuzarte, Timothy Gilpatrick, Alexander Payne, Joshua Quick,[...]. Nat Methods 2019
104
5


Single-Cell RNA-Seq Technologies and Related Computational Data Analysis.
Geng Chen, Baitang Ning, Tieliu Shi. Front Genet 2019
155
5

Single-cell RNA sequencing technologies and bioinformatics pipelines.
Byungjin Hwang, Ji Hyun Lee, Duhee Bang. Exp Mol Med 2018
364
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

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
5

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
5

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

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.
Samuel G Rodriques, Robert R Stickels, Aleksandrina Goeva, Carly A Martin, Evan Murray, Charles R Vanderburg, Joshua Welch, Linlin M Chen, Fei Chen, Evan Z Macosko. Science 2019
384
4

Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
4

The sequence read archive.
Rasko Leinonen, Hideaki Sugawara, Martin Shumway. Nucleic Acids Res 2011
4

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
4

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
4


Alternative isoform regulation in human tissue transcriptomes.
Eric T Wang, Rickard Sandberg, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F Kingsmore, Gary P Schroth, Christopher B Burge. Nature 2008
4

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.
Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E Mason, Nicholas D Socci, Doron Betel. Genome Biol 2013
387
4

RSeQC: quality control of RNA-seq experiments.
Liguo Wang, Shengqin Wang, Wei Li. Bioinformatics 2012
875
4

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Jiarui Ding, Xian Adiconis, Sean K Simmons, Monika S Kowalczyk, Cynthia C Hession, Nemanja D Marjanovic, Travis K Hughes, Marc H Wadsworth, Tyler Burks, Lan T Nguyen,[...]. Nat Biotechnol 2020
108
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.