Michael Zuker. Nucleic Acids Res 2003
Times Cited: 8800
Times Cited: 8800
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
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
8
Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
7
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
C Tuerk, L Gold. Science 1990
C Tuerk, L Gold. Science 1990
7
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
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
6
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
6
DINAMelt web server for nucleic acid melting prediction.
Nicholas R Markham, Michael Zuker. Nucleic Acids Res 2005
Nicholas R Markham, Michael Zuker. Nucleic Acids Res 2005
6
RNAstructure: software for RNA secondary structure prediction and analysis.
Jessica S Reuter, David H Mathews. BMC Bioinformatics 2010
Jessica S Reuter, David H Mathews. BMC Bioinformatics 2010
6
ViennaRNA Package 2.0.
Ronny Lorenz, Stephan H Bernhart, Christian Höner Zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker. Algorithms Mol Biol 2011
Ronny Lorenz, Stephan H Bernhart, Christian Höner Zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker. Algorithms Mol Biol 2011
6
Aptamers as targeted therapeutics: current potential and challenges.
Jiehua Zhou, John Rossi. Nat Rev Drug Discov 2017
Jiehua Zhou, John Rossi. Nat Rev Drug Discov 2017
5
VARNA: Interactive drawing and editing of the RNA secondary structure.
Kévin Darty, Alain Denise, Yann Ponty. Bioinformatics 2009
Kévin Darty, Alain Denise, Yann Ponty. Bioinformatics 2009
5
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
J SantaLucia. Proc Natl Acad Sci U S A 1998
J SantaLucia. Proc Natl Acad Sci U S A 1998
5
UNAFold: software for nucleic acid folding and hybridization.
Nicholas R Markham, Michael Zuker. Methods Mol Biol 2008
Nicholas R Markham, Michael Zuker. Methods Mol Biol 2008
5
The Vienna RNA websuite.
Andreas R Gruber, Ronny Lorenz, Stephan H Bernhart, Richard Neuböck, Ivo L Hofacker. Nucleic Acids Res 2008
Andreas R Gruber, Ronny Lorenz, Stephan H Bernhart, Richard Neuböck, Ivo L Hofacker. Nucleic Acids Res 2008
5
WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
5
Clustal W and Clustal X version 2.0.
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
5
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
5
In vitro selection of RNA molecules that bind specific ligands.
A D Ellington, J W Szostak. Nature 1990
A D Ellington, J W Szostak. Nature 1990
5
5
4
miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
4
psRNATarget: a plant small RNA target analysis server (2017 release).
Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao. Nucleic Acids Res 2018
Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao. Nucleic Acids Res 2018
4
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Fredrik Ronquist, Maxim Teslenko, Paul van der Mark, Daniel L Ayres, Aaron Darling, Sebastian Höhna, Bret Larget, Liang Liu, Marc A Suchard, John P Huelsenbeck. Syst Biol 2012
Fredrik Ronquist, Maxim Teslenko, Paul van der Mark, Daniel L Ayres, Aaron Darling, Sebastian Höhna, Bret Larget, Liang Liu, Marc A Suchard, John P Huelsenbeck. Syst Biol 2012
4
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
D H Mathews, J Sabina, M Zuker, D H Turner. J Mol Biol 1999
D H Mathews, J Sabina, M Zuker, D H Turner. J Mol Biol 1999
4
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
4
NUPACK: Analysis and design of nucleic acid systems.
Joseph N Zadeh, Conrad D Steenberg, Justin S Bois, Brian R Wolfe, Marshall B Pierce, Asif R Khan, Robert M Dirks, Niles A Pierce. J Comput Chem 2011
Joseph N Zadeh, Conrad D Steenberg, Justin S Bois, Brian R Wolfe, Marshall B Pierce, Asif R Khan, Robert M Dirks, Niles A Pierce. J Comput Chem 2011
4
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Robert C Edgar. Nucleic Acids Res 2004
Robert C Edgar. Nucleic Acids Res 2004
4
Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data.
Michael J Axtell, Blake C Meyers. Plant Cell 2018
Michael J Axtell, Blake C Meyers. Plant Cell 2018
4
miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2014
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2014
4
QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences.
Oleg Kikin, Lawrence D'Antonio, Paramjeet S Bagga. Nucleic Acids Res 2006
Oleg Kikin, Lawrence D'Antonio, Paramjeet S Bagga. Nucleic Acids Res 2006
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
4
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski, Sudhir Kumar. Mol Biol Evol 2013
Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski, Sudhir Kumar. Mol Biol Evol 2013
4
ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.
Dean Laslett, Björn Canbäck. Bioinformatics 2008
Dean Laslett, Björn Canbäck. Bioinformatics 2008
4
SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands.
Regina Stoltenburg, Christine Reinemann, Beate Strehlitz. Biomol Eng 2007
Regina Stoltenburg, Christine Reinemann, Beate Strehlitz. Biomol Eng 2007
3
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.
Kazutaka Katoh, John Rozewicki, Kazunori D Yamada. Brief Bioinform 2019
Kazutaka Katoh, John Rozewicki, Kazunori D Yamada. Brief Bioinform 2019
3
Understanding nucleic acid-ion interactions.
Jan Lipfert, Sebastian Doniach, Rhiju Das, Daniel Herschlag. Annu Rev Biochem 2014
Jan Lipfert, Sebastian Doniach, Rhiju Das, Daniel Herschlag. Annu Rev Biochem 2014
3
Post-SELEX optimization of aptamers.
Shunxiang Gao, Xin Zheng, Binghua Jiao, Lianghua Wang. Anal Bioanal Chem 2016
Shunxiang Gao, Xin Zheng, Binghua Jiao, Lianghua Wang. Anal Bioanal Chem 2016
4
3
The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences.
P Stothard. Biotechniques 2000
P Stothard. Biotechniques 2000
3
The non-Watson-Crick base pairs and their associated isostericity matrices.
Neocles B Leontis, Jesse Stombaugh, Eric Westhof. Nucleic Acids Res 2002
Neocles B Leontis, Jesse Stombaugh, Eric Westhof. Nucleic Acids Res 2002
3
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
G C P van Zundert, J P G L M Rodrigues, M Trellet, C Schmitz, P L Kastritis, E Karaca, A S J Melquiond, M van Dijk, S J de Vries, A M J J Bonvin. J Mol Biol 2016
G C P van Zundert, J P G L M Rodrigues, M Trellet, C Schmitz, P L Kastritis, E Karaca, A S J Melquiond, M van Dijk, S J de Vries, A M J J Bonvin. J Mol Biol 2016
3
Recent Advances in SELEX Technology and Aptamer Applications in Biomedicine.
Zhenjian Zhuo, Yuanyuan Yu, Maolin Wang, Jie Li, Zongkang Zhang, Jin Liu, Xiaohao Wu, Aiping Lu, Ge Zhang, Baoting Zhang. Int J Mol Sci 2017
Zhenjian Zhuo, Yuanyuan Yu, Maolin Wang, Jie Li, Zongkang Zhang, Jin Liu, Xiaohao Wu, Aiping Lu, Ge Zhang, Baoting Zhang. Int J Mol Sci 2017
3
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
3
Sequence logos: a new way to display consensus sequences.
T D Schneider, R M Stephens. Nucleic Acids Res 1990
T D Schneider, R M Stephens. Nucleic Acids Res 1990
3
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA.
Matthew W Jones-Rhoades, David P Bartel. Mol Cell 2004
Matthew W Jones-Rhoades, David P Bartel. Mol Cell 2004
3
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
3
SELEX methods on the road to protein targeting with nucleic acid aptamers.
Payam Bayat, Rahim Nosrati, Mona Alibolandi, Houshang Rafatpanah, Khalil Abnous, Mostafa Khedri, Mohammad Ramezani. Biochimie 2018
Payam Bayat, Rahim Nosrati, Mona Alibolandi, Houshang Rafatpanah, Khalil Abnous, Mostafa Khedri, Mohammad Ramezani. Biochimie 2018
4
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.