A citation-based method for searching scientific literature

Gerton Lunter, Martin Goodson. Genome Res 2011
Times Cited: 700







List of co-cited articles
454 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
48

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
31


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
23

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
23

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
18

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
14


SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
12


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
11


Stacks: an analysis tool set for population genomics.
Julian Catchen, Paul A Hohenlohe, Susan Bassham, Angel Amores, William A Cresko. Mol Ecol 2013
10

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

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

ART: a next-generation sequencing read simulator.
Weichun Huang, Leping Li, Jason R Myers, Gabor T Marth. Bioinformatics 2012
549
9



Inference of population structure using multilocus genotype data.
J K Pritchard, M Stephens, P Donnelly. Genetics 2000
8

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
8

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

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
7

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R F Twigg, Andrew O M Wilkie, Gil McVean, Gerton Lunter. Nat Genet 2014
492
7

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
7

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
7

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
7

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.
Brant C Faircloth, John E McCormack, Nicholas G Crawford, Michael G Harvey, Robb T Brumfield, Travis C Glenn. Syst Biol 2012
442
6

Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
6


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
6

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
6

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
6

An extensive evaluation of read trimming effects on Illumina NGS data analysis.
Cristian Del Fabbro, Simone Scalabrin, Michele Morgante, Federico M Giorgi. PLoS One 2013
177
5

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
5

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
Susannah J Salter, Michael J Cox, Elena M Turek, Szymon T Calus, William O Cookson, Miriam F Moffatt, Paul Turner, Julian Parkhill, Nicholas J Loman, Alan W Walker. BMC Biol 2014
5

Adaptation from standing genetic variation.
Rowan D H Barrett, Dolph Schluter. Trends Ecol Evol 2008
841
5

The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
5

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Brian J Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,[...]. Nat Protoc 2013
5


An integrated map of genetic variation from 1,092 human genomes.
Goncalo R Abecasis, Adam Auton, Lisa D Brooks, Mark A DePristo, Richard M Durbin, Robert E Handsaker, Hyun Min Kang, Gabor T Marth, Gil A McVean. Nature 2012
5

ANGSD: Analysis of Next Generation Sequencing Data.
Thorfinn Sand Korneliussen, Anders Albrechtsen, Rasmus Nielsen. BMC Bioinformatics 2014
682
5

Fast model-based estimation of ancestry in unrelated individuals.
David H Alexander, John Novembre, Kenneth Lange. Genome Res 2009
5

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
5

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).
Robert Kofler, Ram Vinay Pandey, Christian Schlötterer. Bioinformatics 2011
342
5


ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Xavier Didelot, Daniel J Wilson. PLoS Comput Biol 2015
336
4

VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Daniel C Koboldt, Ken Chen, Todd Wylie, David E Larson, Michael D McLellan, Elaine R Mardis, George M Weinstock, Richard K Wilson, Li Ding. Bioinformatics 2009
741
4

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
4

The genomic basis of adaptive evolution in threespine sticklebacks.
Felicity C Jones, Manfred G Grabherr, Yingguang Frank Chan, Pamela Russell, Evan Mauceli, Jeremy Johnson, Ross Swofford, Mono Pirun, Michael C Zody, Simon White,[...]. Nature 2012
937
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.