A citation-based method for searching scientific literature

José M Alonso, Anna N Stepanova, Thomas J Leisse, Christopher J Kim, Huaming Chen, Paul Shinn, Denise K Stevenson, Justin Zimmerman, Pascual Barajas, Rosa Cheuk, Carmelita Gadrinab, Collen Heller, Albert Jeske, Eric Koesema, Cristina C Meyers, Holly Parker, Lance Prednis, Yasser Ansari, Nathan Choy, Hashim Deen, Michael Geralt, Nisha Hazari, Emily Hom, Meagan Karnes, Celene Mulholland, Ral Ndubaku, Ian Schmidt, Plinio Guzman, Laura Aguilar-Henonin, Markus Schmid, Detlef Weigel, David E Carter, Trudy Marchand, Eddy Risseeuw, Debra Brogden, Albana Zeko, William L Crosby, Charles C Berry, Joseph R Ecker. Science 2003
Times Cited: 3826







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



Times Cited
  Times     Co-cited
Similarity






An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics.
Mario G Rosso, Yong Li, Nicolai Strizhov, Bernd Reiss, Koen Dekker, Bernd Weisshaar. Plant Mol Biol 2003
575
8

A high-throughput Arabidopsis reverse genetics system.
Allen Sessions, Ellen Burke, Gernot Presting, George Aux, John McElver, David Patton, Bob Dietrich, Patrick Ho, Johana Bacwaden, Cynthia Ko,[...]. Plant Cell 2002
694
8

GATEWAY vectors for Agrobacterium-mediated plant transformation.
Mansour Karimi, Dirk Inzé, Ann Depicker. Trends Plant Sci 2002
7

GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database.
Nils Kleinboelting, Gunnar Huep, Andreas Kloetgen, Prisca Viehoever, Bernd Weisshaar. Nucleic Acids Res 2012
255
7

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7

NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
6


Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
5

An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets.
Debbie Winter, Ben Vinegar, Hardeep Nahal, Ron Ammar, Greg V Wilson, Nicholas J Provart. PLoS One 2007
5

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

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
5

A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling.
Anna V Klepikova, Artem S Kasianov, Evgeny S Gerasimov, Maria D Logacheva, Aleksey A Penin. Plant J 2016
292
5

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
5

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
5

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
5

Genome-wide analysis of the ERF gene family in Arabidopsis and rice.
Toshitsugu Nakano, Kaoru Suzuki, Tatsuhito Fujimura, Hideaki Shinshi. Plant Physiol 2006
4

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
4

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
4

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

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
4

Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis.
Tomasz Czechowski, Mark Stitt, Thomas Altmann, Michael K Udvardi, Wolf-Rüdiger Scheible. Plant Physiol 2005
4


Glucosinolate metabolites required for an Arabidopsis innate immune response.
Nicole K Clay, Adewale M Adio, Carine Denoux, Georg Jander, Frederick M Ausubel. Science 2009
667
4


AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.
Mihaly Varadi, Stephen Anyango, Mandar Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon,[...]. Nucleic Acids Res 2022
510
4

Local, efflux-dependent auxin gradients as a common module for plant organ formation.
Eva Benková, Marta Michniewicz, Michael Sauer, Thomas Teichmann, Daniela Seifertová, Gerd Jürgens, Jirí Friml. Cell 2003
4

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
3



The Arabidopsis Phosphatidylinositol Phosphate 5-Kinase PIP5K3 is a key regulator of root hair tip growth.
Hiroaki Kusano, Christa Testerink, Joop E M Vermeer, Tomohiko Tsuge, Hiroaki Shimada, Atsuhiro Oka, Teun Munnik, Takashi Aoyama. Plant Cell 2008
142
3

Involvement of Arabidopsis thaliana phospholipase Dzeta2 in root hydrotropism through the suppression of root gravitropism.
Yukimi Y Taniguchi, Masatoshi Taniguchi, Tomohiko Tsuge, Atsuhiro Oka, Takashi Aoyama. Planta 2010
27
11

Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression.
Yoh Sakuma, Kyonoshin Maruyama, Feng Qin, Yuriko Osakabe, Kazuo Shinozaki, Kazuko Yamaguchi-Shinozaki. Proc Natl Acad Sci U S A 2006
412
3

Genome-wide analysis of ZmDREB genes and their association with natural variation in drought tolerance at seedling stage of Zea mays L.
Shengxue Liu, Xianglan Wang, Hongwei Wang, Haibo Xin, Xiaohong Yang, Jianbing Yan, Jiansheng Li, Lam-Son Phan Tran, Kazuo Shinozaki, Kazuko Yamaguchi-Shinozaki,[...]. PLoS Genet 2013
138
3



DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression.
Yoh Sakuma, Qiang Liu, Joseph G Dubouzet, Hiroshi Abe, Kazuo Shinozaki, Kazuko Yamaguchi-Shinozaki. Biochem Biophys Res Commun 2002
918
3

Abscisic acid biosynthesis and catabolism.
Eiji Nambara, Annie Marion-Poll. Annu Rev Plant Biol 2005
3

Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants.
David Wilson-Sánchez, Silvia Rubio-Díaz, Rafael Muñoz-Viana, José Manuel Pérez-Pérez, Sara Jover-Gil, María Rosa Ponce, José Luis Micol. Plant J 2014
28
10


Biogenesis and homeostasis of chloroplasts and other plastids.
Paul Jarvis, Enrique López-Juez. Nat Rev Mol Cell Biol 2013
381
3


Functional specialization amongst the Arabidopsis Toc159 family of chloroplast protein import receptors.
Sybille Kubis, Ramesh Patel, Jonathan Combe, Jocelyn Bédard, Sabina Kovacheva, Kathryn Lilley, Alexander Biehl, Dario Leister, Gabino Ríos, Csaba Koncz,[...]. Plant Cell 2004
152
3

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.
Chia-Yi Cheng, Vivek Krishnakumar, Agnes P Chan, Françoise Thibaud-Nissen, Seth Schobel, Christopher D Town. Plant J 2017
420
3

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