A citation-based method for searching scientific literature

Thomas D Schmittgen, Kenneth J Livak. Nat Protoc 2008
Times Cited: 13921







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



Times Cited
  Times     Co-cited
Similarity



MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
5

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
4

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
4

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
3

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
3



PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, Stephane Rombauts. Nucleic Acids Res 2002
3

Melanin pigmentation in mammalian skin and its hormonal regulation.
Andrzej Slominski, Desmond J Tobin, Shigeki Shibahara, Jacobo Wortsman. Physiol Rev 2004
2

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
2


ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
2

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.
Tianzhen Zhang, Yan Hu, Wenkai Jiang, Lei Fang, Xueying Guan, Jiedan Chen, Jinbo Zhang, Christopher A Saski, Brian E Scheffler, David M Stelly,[...]. Nat Biotechnol 2015
748
2

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.
Fuguang Li, Guangyi Fan, Cairui Lu, Guanghui Xiao, Changsong Zou, Russell J Kohel, Zhiying Ma, Haihong Shang, Xiongfeng Ma, Jianyong Wu,[...]. Nat Biotechnol 2015
492
2

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
2

An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants.
Vinod Shanker Dubey, Ritu Bhalla, Rajesh Luthra. J Biosci 2003
90
2

MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Oliver Thimm, Oliver Bläsing, Yves Gibon, Axel Nagel, Svenja Meyer, Peter Krüger, Joachim Selbig, Lukas A Müller, Seung Y Rhee, Mark Stitt. Plant J 2004
2

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
2

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.
Yoshihiro Kawahara, Melissa de la Bastide, John P Hamilton, Hiroyuki Kanamori, W Richard McCombie, Shu Ouyang, David C Schwartz, Tsuyoshi Tanaka, Jianzhong Wu, Shiguo Zhou,[...]. Rice (N Y) 2013
857
2

Guideline to reference gene selection for quantitative real-time PCR.
Aleksandar Radonić, Stefanie Thulke, Ian M Mackay, Olfert Landt, Wolfgang Siegert, Andreas Nitsche. Biochem Biophys Res Commun 2004
2


Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.
Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman. Genome Biol 2002
2

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
2

Neurohumoral features of myocardial stunning due to sudden emotional stress.
Ilan S Wittstein, David R Thiemann, Joao A C Lima, Kenneth L Baughman, Steven P Schulman, Gary Gerstenblith, Katherine C Wu, Jeffrey J Rade, Trinity J Bivalacqua, Hunter C Champion. N Engl J Med 2005
2

Clinical Features and Outcomes of Takotsubo (Stress) Cardiomyopathy.
Christian Templin, Jelena R Ghadri, Johanna Diekmann, L Christian Napp, Dana R Bataiosu, Milosz Jaguszewski, Victoria L Cammann, Annahita Sarcon, Verena Geyer, Catharina A Neumann,[...]. N Engl J Med 2015
2

Transformation of agrobacterium using the freeze-thaw method.
Detlef Weigel, Jane Glazebrook. CSH Protoc 2006
122
2

Sulforhodamine B colorimetric assay for cytotoxicity screening.
Vanicha Vichai, Kanyawim Kirtikara. Nat Protoc 2006
2

Identification of jumonjiC domain containing gene family among the Oryza species and their expression analysis in FL478, a salt tolerant rice genotype.
Soni Chowrasia, Alok Kumar Panda, Hukam C Rawal, Harmeet Kaur, Tapan Kumar Mondal. Plant Physiol Biochem 2018
6
33

psRNATarget: a plant small RNA target analysis server.
Xinbin Dai, Patrick Xuechun Zhao. Nucleic Acids Res 2011
2

Long noncoding RNAs: functional surprises from the RNA world.
Jeremy E Wilusz, Hongjae Sunwoo, David L Spector. Genes Dev 2009
2


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
2

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

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data.
Jiyuan An, John Lai, Melanie L Lehman, Colleen C Nelson. Nucleic Acids Res 2013
127
2

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón, Montserrat Robles. Bioinformatics 2005
2



TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data.
Chengjie Chen, Hao Chen, Yi Zhang, Hannah R Thomas, Margaret H Frank, Yehua He, Rui Xia. Mol Plant 2020
978
2

Detecting and characterizing circular RNAs.
William R Jeck, Norman E Sharpless. Nat Biotechnol 2014
2

Natural RNA circles function as efficient microRNA sponges.
Thomas B Hansen, Trine I Jensen, Bettina H Clausen, Jesper B Bramsen, Bente Finsen, Christian K Damgaard, Jørgen Kjems. Nature 2013
2

Circular RNAs are a large class of animal RNAs with regulatory potency.
Sebastian Memczak, Marvin Jens, Antigoni Elefsinioti, Francesca Torti, Janna Krueger, Agnieszka Rybak, Luisa Maier, Sebastian D Mackowiak, Lea H Gregersen, Mathias Munschauer,[...]. Nature 2013
2

Regulation of circRNA biogenesis.
Ling-Ling Chen, Li Yang. RNA Biol 2015
858
2

Plant salt-tolerance mechanisms.
Ulrich Deinlein, Aaron B Stephan, Tomoaki Horie, Wei Luo, Guohua Xu, Julian I Schroeder. Trends Plant Sci 2014
514
2

Methanotrophs and copper.
Jeremy D Semrau, Alan A DiSpirito, Sukhwan Yoon. FEMS Microbiol Rev 2010
332
2

The biosynthesis of methanobactin.
Grace E Kenney, Laura M K Dassama, Maria-Eirini Pandelia, Anthony S Gizzi, Ryan J Martinie, Peng Gao, Caroline J DeHart, Luis F Schachner, Owen S Skinner, Soo Y Ro,[...]. Science 2018
41
4

Metals and Methanotrophy.
Jeremy D Semrau, Alan A DiSpirito, Wenyu Gu, Sukhwan Yoon. Appl Environ Microbiol 2018
50
4

Differences in cytotoxicity versus pro-inflammatory potency of different PM fractions in human epithelial lung cells.
Maurizio Gualtieri, Johan Øvrevik, Jørn A Holme, M Grazia Perrone, Ezio Bolzacchini, Per E Schwarze, Marina Camatini. Toxicol In Vitro 2010
136
2

Neutrophil recruitment and function in health and inflammation.
Elzbieta Kolaczkowska, Paul Kubes. Nat Rev Immunol 2013
2

Deficient neuron-microglia signaling results in impaired functional brain connectivity and social behavior.
Yang Zhan, Rosa C Paolicelli, Francesco Sforazzini, Laetitia Weinhard, Giulia Bolasco, Francesca Pagani, Alexei L Vyssotski, Angelo Bifone, Alessandro Gozzi, Davide Ragozzino,[...]. Nat Neurosci 2014
607
2


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.