A citation-based method for searching scientific literature

Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
Times Cited: 7721

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

Times Cited
  Times     Co-cited

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

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

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

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

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

A general framework for weighted gene co-expression network analysis.
Bin Zhang, Steve Horvath. Stat Appl Genet Mol Biol 2005

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

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

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

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

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Mihaela Pertea, Daehwan Kim, Geo M Pertea, Jeffrey T Leek, Steven L Salzberg. Nat Protoc 2016

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013

cytoHubba: identifying hub objects and sub-networks from complex interactome.
Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin. BMC Syst Biol 2014

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

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

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

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

Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R.
Peter Langfelder, Bin Zhang, Steve Horvath. Bioinformatics 2008

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data.
Chengjie Chen, Hao Chen, Yi Zhang, Hannah R Thomas, Margaret H Frank, Yehua He, Rui Xia. Mol Plant 2020

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015

Inferring tumour purity and stromal and immune cell admixture from expression data.
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W Laird, Douglas A Levine,[...]. Nat Commun 2013

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

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

Regularization Paths for Generalized Linear Models via Coordinate Descent.
Jerome Friedman, Trevor Hastie, Rob Tibshirani. J Stat Softw 2010

NCBI GEO: archive for functional genomics data sets--update.
Tanya Barrett, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Michelle Holko,[...]. Nucleic Acids Res 2013

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Yupeng Wang, Haibao Tang, Jeremy D Debarry, Xu Tan, Jingping Li, Xiyin Wang, Tae-ho Lee, Huizhe Jin, Barry Marler, Hui Guo,[...]. Nucleic Acids Res 2012

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

The Molecular Signatures Database (MSigDB) hallmark gene set collection.
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015

Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA).
Magdalena Niemira, Francois Collin, Anna Szalkowska, Agnieszka Bielska, Karolina Chwialkowska, Joanna Reszec, Jacek Niklinski, Miroslaw Kwasniewski, Adam Kretowski. Cancers (Basel) 2019

Circos: an information aesthetic for comparative genomics.
Martin Krzywinski, Jacqueline Schein, Inanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, Marco A Marra. Genome Res 2009

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

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

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016

MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis.
Rainer Schwacke, Gabriel Y Ponce-Soto, Kirsten Krause, Anthony M Bolger, Borjana Arsova, Asis Hallab, Kristina Gruden, Mark Stitt, Marie E Bolger, Björn Usadel. Mol Plant 2019

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

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Damian Szklarczyk, Andrea Franceschini, Stefan Wyder, Kristoffer Forslund, Davide Heller, Jaime Huerta-Cepas, Milan Simonovic, Alexander Roth, Alberto Santos, Kalliopi P Tsafou,[...]. Nucleic Acids Res 2015

The Immune Landscape of Cancer.
Vésteinn Thorsson, David L Gibbs, Scott D Brown, Denise Wolf, Dante S Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, Galen F Gao, Christopher L Plaisier, James A Eddy,[...]. Immunity 2018

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.
David A Barbie, Pablo Tamayo, Jesse S Boehm, So Young Kim, Susan E Moody, Ian F Dunn, Anna C Schinzel, Peter Sandy, Etienne Meylan, Claudia Scholl,[...]. Nature 2009

PLINK: a tool set for whole-genome association and population-based linkage analyses.
Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A R Ferreira, David Bender, Julian Maller, Pamela Sklar, Paul I W de Bakker, Mark J Daly,[...]. Am J Hum Genet 2007

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation.
Luis López-Maury, Samuel Marguerat, Jürg Bähler. Nat Rev Genet 2008

The Pfam protein families database in 2019.
Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart,[...]. Nucleic Acids Res 2019

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.
Jinpu Jin, Feng Tian, De-Chang Yang, Yu-Qi Meng, Lei Kong, Jingchu Luo, Ge Gao. Nucleic Acids Res 2017

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

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.