A citation-based method for searching scientific literature

Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
Times Cited: 8365

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

Times Cited
  Times     Co-cited

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

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

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

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

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

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

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

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

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012

Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010

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

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

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

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

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

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

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

Differential analysis of gene regulation at transcript resolution with RNA-seq.
Cole Trapnell, David G Hendrickson, Martin Sauvageau, Loyal Goff, John L Rinn, Lior Pachter. Nat Biotechnol 2013

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

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

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

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

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

GeneWise and Genomewise.
Ewan Birney, Michele Clamp, Richard Durbin. Genome Res 2004

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

Using RepeatMasker to identify repetitive elements in genomic sequences.
Maja Tarailo-Graovac, Nansheng Chen. Curr Protoc Bioinformatics 2009

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

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

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

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

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Genis Parra, Keith Bradnam, Ian Korf. Bioinformatics 2007

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

The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002

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

Repbase Update, a database of repetitive elements in eukaryotic genomes.
Weidong Bao, Kenji K Kojima, Oleksiy Kohany. Mob DNA 2015

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

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.