A citation-based method for searching scientific literature

Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R Ecker, Dario Cantu, David R Rank, Michael C Schatz. Nat Methods 2016
Times Cited: 919

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

Times Cited
  Times     Co-cited

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

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

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
Chen-Shan Chin, David H Alexander, Patrick Marks, Aaron A Klammer, James Drake, Cheryl Heiner, Alicia Clum, Alex Copeland, John Huddleston, Evan E Eichler,[...]. Nat Methods 2013

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

Gene finding in novel genomes.
Ian Korf. BMC Bioinformatics 2004

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

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

OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li Li, Christian J Stoeckert, David S Roos. Genome Res 2003

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

Infernal 1.1: 100-fold faster RNA homology searches.
Eric P Nawrocki, Sean R Eddy. Bioinformatics 2013

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

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

CAFE: a computational tool for the study of gene family evolution.
Tijl De Bie, Nello Cristianini, Jeffery P Demuth, Matthew W Hahn. Bioinformatics 2006

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
Olga Dudchenko, Sanjit S Batra, Arina D Omer, Sarah K Nyquist, Marie Hoeger, Neva C Durand, Muhammad S Shamim, Ido Machol, Eric S Lander, Aviva Presser Aiden,[...]. Science 2017

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

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

De novo assembly of haplotype-resolved genomes with trio binning.
Sergey Koren, Arang Rhie, Brian P Walenz, Alexander T Dilthey, Derek M Bickhart, Sarah B Kingan, Stefan Hiendleder, John L Williams, Timothy P L Smith, Adam M Phillippy. Nat Biotechnol 2018

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies.
Michael J Roach, Simon A Schmidt, Anthony R Borneman. BMC Bioinformatics 2018

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

GenomeScope: fast reference-free genome profiling from short reads.
Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz. Bioinformatics 2017

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

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

De novo identification of repeat families in large genomes.
Alkes L Price, Neil C Jones, Pavel A Pevzner. Bioinformatics 2005

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

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

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. Nat Methods 2021

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

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

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

RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Staerfeldt, Torbjørn Rognes, David W Ussery. Nucleic Acids Res 2007

Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.
T Rhyker Ranallo-Benavidez, Kamil S Jaron, Michael C Schatz. Nat Commun 2020

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

Synteny and collinearity in plant genomes.
Haibao Tang, John E Bowers, Xiyin Wang, Ray Ming, Maqsudul Alam, Andrew H Paterson. Science 2008

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

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

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons.
David Ellinghaus, Stefan Kurtz, Ute Willhoeft. BMC Bioinformatics 2008

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015

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.