Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
Times Cited: 8825
Times Cited: 8825
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
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
33
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
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
28
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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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
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Yang Liao, Gordon K Smyth, Wei Shi. Bioinformatics 2014
Yang Liao, Gordon K Smyth, Wei Shi. Bioinformatics 2014
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fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
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HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
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Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
K J Livak, T D Schmittgen. Methods 2001
K J Livak, T D Schmittgen. Methods 2001
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
Bo Li, Colin N Dewey. BMC Bioinformatics 2011
Bo Li, Colin N Dewey. BMC Bioinformatics 2011
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Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
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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
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
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WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
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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
Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K Chanda. Nat Commun 2019
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
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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
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
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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
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
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
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
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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
Chengjie Chen, Hao Chen, Yi Zhang, Hannah R Thomas, Margaret H Frank, Yehua He, Rui Xia. Mol Plant 2020
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KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.
Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei. Nucleic Acids Res 2011
Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei. Nucleic Acids Res 2011
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clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
6
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
Neva C Durand, Muhammad S Shamim, Ido Machol, Suhas S P Rao, Miriam H Huntley, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
Neva C Durand, Muhammad S Shamim, Ido Machol, Suhas S P Rao, Miriam H Huntley, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
6
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
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
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
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
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
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
6
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
5
RepeatModeler2 for automated genomic discovery of transposable element families.
Jullien M Flynn, Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G Clark, Cédric Feschotte, Arian F Smit. Proc Natl Acad Sci U S A 2020
Jullien M Flynn, Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G Clark, Cédric Feschotte, Arian F Smit. Proc Natl Acad Sci U S A 2020
5
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
Mihaela Pertea, Daehwan Kim, Geo M Pertea, Jeffrey T Leek, Steven L Salzberg. Nat Protoc 2016
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
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
5
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
Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón, Montserrat Robles. Bioinformatics 2005
4
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
4
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
4
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Alexandros Stamatakis. Bioinformatics 2014
Alexandros Stamatakis. Bioinformatics 2014
4
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Kazutaka Katoh, Daron M Standley. Mol Biol Evol 2013
Kazutaka Katoh, Daron M Standley. Mol Biol Evol 2013
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MUMmer4: A fast and versatile genome alignment system.
Guillaume Marçais, Arthur L Delcher, Adam M Phillippy, Rachel Coston, Steven L Salzberg, Aleksey Zimin. PLoS Comput Biol 2018
Guillaume Marçais, Arthur L Delcher, Adam M Phillippy, Rachel Coston, Steven L Salzberg, Aleksey Zimin. PLoS Comput Biol 2018
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Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
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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
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
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KEGG: integrating viruses and cellular organisms.
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe. Nucleic Acids Res 2021
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe. Nucleic Acids Res 2021
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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
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
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Gene ontology analysis for RNA-seq: accounting for selection bias.
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
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DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.
Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang. Bioinformatics 2010
Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang. Bioinformatics 2010
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KEGG for linking genomes to life and the environment.
Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu,[...]. Nucleic Acids Res 2008
Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu,[...]. Nucleic Acids Res 2008
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Transcriptome assembly from long-read RNA-seq alignments with StringTie2.
Sam Kovaka, Aleksey V Zimin, Geo M Pertea, Roham Razaghi, Steven L Salzberg, Mihaela Pertea. Genome Biol 2019
Sam Kovaka, Aleksey V Zimin, Geo M Pertea, Roham Razaghi, Steven L Salzberg, Mihaela Pertea. Genome Biol 2019
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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
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
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TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
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.