A citation-based method for searching scientific literature

Ronny Lorenz, Stephan H Bernhart, Christian Höner Zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker. Algorithms Mol Biol 2011
Times Cited: 1937







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



Times Cited
  Times     Co-cited
Similarity


Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
11

Infernal 1.1: 100-fold faster RNA homology searches.
Eric P Nawrocki, Sean R Eddy. Bioinformatics 2013
973
11

The Vienna RNA websuite.
Andreas R Gruber, Ronny Lorenz, Stephan H Bernhart, Richard Neuböck, Ivo L Hofacker. Nucleic Acids Res 2008
9

RNAstructure: software for RNA secondary structure prediction and analysis.
Jessica S Reuter, David H Mathews. BMC Bioinformatics 2010
892
8

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
8

CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
8

miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
929
8

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
8

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
8


Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov. Nucleic Acids Res 2018
401
7

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.
Silvi Rouskin, Meghan Zubradt, Stefan Washietl, Manolis Kellis, Jonathan S Weissman. Nature 2014
478
6

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
6

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.
Padideh Danaee, Mason Rouches, Michelle Wiley, Dezhong Deng, Liang Huang, David Hendrix. Nucleic Acids Res 2018
20
30

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
6

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, Jonathan S Weissman. Science 2009
6


RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look.
Ramya Rangan, Ivan N Zheludev, Rachel J Hagey, Edward A Pham, Hannah K Wayment-Steele, Jeffrey S Glenn, Rhiju Das. RNA 2020
87
5


Predicting effective microRNA target sites in mammalian mRNAs.
Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel. Elife 2015
5

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
5





Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
5

VARNA: Interactive drawing and editing of the RNA secondary structure.
Kévin Darty, Alain Denise, Yann Ponty. Bioinformatics 2009
645
5

Accurate SHAPE-directed RNA structure determination.
Katherine E Deigan, Tian W Li, David H Mathews, Kevin M Weeks. Proc Natl Acad Sci U S A 2009
432
4

CONTRAfold: RNA secondary structure prediction without physics-based models.
Chuong B Do, Daniel A Woods, Serafim Batzoglou. Bioinformatics 2006
256
4

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.
Zhen Tan, Yinghan Fu, Gaurav Sharma, David H Mathews. Nucleic Acids Res 2017
24
16


MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
4


NONCODE 2016: an informative and valuable data source of long non-coding RNAs.
Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q Zhang,[...]. Nucleic Acids Res 2016
358
4

Structural imprints in vivo decode RNA regulatory mechanisms.
Robert C Spitale, Ryan A Flynn, Qiangfeng Cliff Zhang, Pete Crisalli, Byron Lee, Jong-Wha Jung, Hannes Y Kuchelmeister, Pedro J Batista, Eduardo A Torre, Eric T Kool,[...]. Nature 2015
374
4


Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
4


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
4

ModelFinder: fast model selection for accurate phylogenetic estimates.
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, Lars S Jermiin. Nat Methods 2017
4

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
4

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
4

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.
Sebastian Will, Tejal Joshi, Ivo L Hofacker, Peter F Stadler, Rolf Backofen. RNA 2012
175
4

RNAalifold: improved consensus structure prediction for RNA alignments.
Stephan H Bernhart, Ivo L Hofacker, Sebastian Will, Andreas R Gruber, Peter F Stadler. BMC Bioinformatics 2008
335
4

Local RNA base pairing probabilities in large sequences.
Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler. Bioinformatics 2006
138
4

UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
3


Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
Daniel Wrapp, Nianshuang Wang, Kizzmekia S Corbett, Jory A Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S Graham, Jason S McLellan. Science 2020
3


Genome-wide measurement of RNA secondary structure in yeast.
Michael Kertesz, Yue Wan, Elad Mazor, John L Rinn, Robert C Nutter, Howard Y Chang, Eran Segal. Nature 2010
504
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.