A citation-based method for searching scientific literature

Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Times Cited: 8953







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



Times Cited
  Times     Co-cited
Similarity


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
42

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
24

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
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

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
20

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
18


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
13

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
13

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
12

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
11

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
9

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
9

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
8



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
7


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
7

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
7

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
7

deepTools: a flexible platform for exploring deep-sequencing data.
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
863
6




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

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
6

Super-enhancers in the control of cell identity and disease.
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
6

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
5

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
5

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
5

Software for computing and annotating genomic ranges.
Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T Morgan, Vincent J Carey. PLoS Comput Biol 2013
5

JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Oriol Fornes, Jaime A Castro-Mondragon, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip A Richmond, Bhavi P Modi, Solenne Correard, Marius Gheorghe, Damir Baranašić,[...]. Nucleic Acids Res 2020
285
5

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
5

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
5

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
5

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
5

MEME SUITE: tools for motif discovery and searching.
Timothy L Bailey, Mikael Boden, Fabian A Buske, Martin Frith, Charles E Grant, Luca Clementi, Jingyuan Ren, Wilfred W Li, William S Noble. Nucleic Acids Res 2009
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
4

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
4

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna,[...]. Nat Genet 2011
4

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
4

BUSCO: Assessing Genome Assembly and Annotation Completeness.
Mathieu Seppey, Mosè Manni, Evgeny M Zdobnov. Methods Mol Biol 2019
316
4

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
4

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
4

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
4

Improved vectors and genome-wide libraries for CRISPR screening.
Neville E Sanjana, Ophir Shalem, Feng Zhang. Nat Methods 2014
4

Genome engineering using the CRISPR-Cas9 system.
F Ann Ran, Patrick D Hsu, Jason Wright, Vineeta Agarwala, David A Scott, Feng Zhang. Nat Protoc 2013
4

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Stephen G Landt, Georgi K Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E Bernstein, Peter Bickel, James B Brown, Philip Cayting,[...]. Genome Res 2012
970
4

Differential analysis of RNA-seq incorporating quantification uncertainty.
Harold Pimentel, Nicolas L Bray, Suzette Puente, Páll Melsted, Lior Pachter. Nat Methods 2017
501
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.