A citation-based method for searching scientific literature

Guangchuang Yu, Li-Gen Wang, Qing-Yu He. Bioinformatics 2015
Times Cited: 658







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



Times Cited
  Times     Co-cited
Similarity


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
61

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
47

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
39

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
37


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
27

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
26

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
20

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
19

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
18

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
17

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.
Caryn S Ross-Innes, Rory Stark, Andrew E Teschendorff, Kelly A Holmes, H Raza Ali, Mark J Dunning, Gordon D Brown, Ondrej Gojis, Ian O Ellis, Andrew R Green,[...]. Nature 2012
802
16


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
14

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
13

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
13

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
12



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
992
11

MEME-ChIP: motif analysis of large DNA datasets.
Philip Machanick, Timothy L Bailey. Bioinformatics 2011
825
10

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
9

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
9

deepTools: a flexible platform for exploring deep-sequencing data.
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
890
9


An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.
M Ryan Corces, Alexandro E Trevino, Emily G Hamilton, Peyton G Greenside, Nicholas A Sinnott-Armstrong, Sam Vesuna, Ansuman T Satpathy, Adam J Rubin, Kathleen S Montine, Beijing Wu,[...]. Nat Methods 2017
441
8

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
8

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
8

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

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
7

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
978
7

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.
Lihua J Zhu, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin, David S Lapointe, Michael R Green. BMC Bioinformatics 2010
457
7

Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules.
Kelsey A Maher, Marko Bajic, Kaisa Kajala, Mauricio Reynoso, Germain Pauluzzi, Donnelly A West, Kristina Zumstein, Margaret Woodhouse, Kerry Bubb, Michael W Dorrity,[...]. Plant Cell 2018
83
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
6

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.
Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K Chanda. Nat Commun 2019
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
6

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.
Dan Dominissini, Sharon Moshitch-Moshkovitz, Schraga Schwartz, Mali Salmon-Divon, Lior Ungar, Sivan Osenberg, Karen Cesarkas, Jasmine Jacob-Hirsch, Ninette Amariglio, Martin Kupiec,[...]. Nature 2012
6

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
6

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
6

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
6

Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
6

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

A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.
Jia Meng, Zhiliang Lu, Hui Liu, Lin Zhang, Shaowu Zhang, Yidong Chen, Manjeet K Rao, Yufei Huang. Methods 2014
92
5

Selective inhibition of tumor oncogenes by disruption of super-enhancers.
Jakob Lovén, Heather A Hoke, Charles Y Lin, Ashley Lau, David A Orlando, Christopher R Vakoc, James E Bradner, Tong Ihn Lee, Richard A Young. Cell 2013
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

Master transcription factors and mediator establish super-enhancers at key cell identity genes.
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
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

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason. Genome Biol 2012
692
5

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes.
Zefu Lu, Brigitte T Hofmeister, Christopher Vollmers, Rebecca M DuBois, Robert J Schmitz. Nucleic Acids Res 2017
95
5

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


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.