A citation-based method for searching scientific literature

Jessen V Bredeson, Jessica B Lyons, Ibukun O Oniyinde, Nneka R Okereke, Olufisayo Kolade, Ikenna Nnabue, Christian O Nwadili, Eva Hřibová, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey J Barton, Anna V Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie N Egesi, Jonathan Featherston, Asrat Asfaw, Gordon G Simpson, Jaroslav Doležel, Prasad S Hendre, Allen Van Deynze, Pullikanti Lava Kumar, Jude E Obidiegwu, Ranjana Bhattacharjee, Daniel S Rokhsar. Nat Commun 2022
Times Cited: 5







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



Times Cited
  Times     Co-cited
Similarity


Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination.
Muluneh Tamiru, Satoshi Natsume, Hiroki Takagi, Benjamen White, Hiroki Yaegashi, Motoki Shimizu, Kentaro Yoshida, Aiko Uemura, Kaori Oikawa, Akira Abe,[...]. BMC Biol 2017
52
60

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
40


IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.
Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear. Mol Biol Evol 2020
40



The pineapple genome and the evolution of CAM photosynthesis.
Ray Ming, Robert VanBuren, Ching Man Wai, Haibao Tang, Michael C Schatz, John E Bowers, Eric Lyons, Ming-Li Wang, Jung Chen, Eric Biggers,[...]. Nat Genet 2015
233
40

Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers.
Gemma Arnau, Ranjana Bhattacharjee, Sheela Mn, Hana Chair, Roger Malapa, Vincent Lebot, Abraham K, Xavier Perrier, Dalila Petro, Laurent Penet,[...]. PLoS One 2017
18
40

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae).
Karolina Heyduk, Michael R McKain, Falak Lalani, James Leebens-Mack. Mol Phylogenet Evol 2016
38
20

The asparagus genome sheds light on the origin and evolution of a young Y chromosome.
Alex Harkess, Jinsong Zhou, Chunyan Xu, John E Bowers, Ron Van der Hulst, Saravanaraj Ayyampalayam, Francesco Mercati, Paolo Riccardi, Michael R McKain, Atul Kakrana,[...]. Nat Commun 2017
127
20

Altered Gene Regulatory Networks Are Associated With the Transition From C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae).
Karolina Heyduk, Michelle Hwang, Victor Albert, Katia Silvera, Tianying Lan, Kimberly Farr, Tien-Hao Chang, Ming-Tsair Chan, Klaus Winter, Jim Leebens-Mack. Front Plant Sci 2019
15
20

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
20

Crassulacean acid metabolism: a continuous or discrete trait?
Klaus Winter, Joseph A M Holtum, J Andrew C Smith. New Phytol 2015
56
20

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
20

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
20

Parallel recruitment of multiple genes into c4 photosynthesis.
Pascal-Antoine Christin, Susanna F Boxall, Richard Gregory, Erika J Edwards, James Hartwell, Colin P Osborne. Genome Biol Evol 2013
47
20

Reference genome sequence of the model plant Setaria.
Jeffrey L Bennetzen, Jeremy Schmutz, Hao Wang, Ryan Percifield, Jennifer Hawkins, Ana C Pontaroli, Matt Estep, Liang Feng, Justin N Vaughn, Jane Grimwood,[...]. Nat Biotechnol 2012
436
20

Shared origins of a key enzyme during the evolution of C4 and CAM metabolism.
Pascal-Antoine Christin, Monica Arakaki, Colin P Osborne, Andrea Bräutigam, Rowan F Sage, Julian M Hibberd, Steven Kelly, Sarah Covshoff, Gane Ka-Shu Wong, Lillian Hancock,[...]. J Exp Bot 2014
54
20


Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species, Yucca gloriosa.
Karolina Heyduk, Jeremy N Ray, Jim Leebens-Mack. Ann Bot 2021
4
25


The genetics of convergent evolution: insights from plant photosynthesis.
Karolina Heyduk, Jose J Moreno-Villena, Ian S Gilman, Pascal-Antoine Christin, Erika J Edwards. Nat Rev Genet 2019
41
20

C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes.
Pascal-Antoine Christin, Nicolas Salamin, Vincent Savolainen, Melvin R Duvall, Guillaume Besnard. Curr Biol 2007
133
20

Kalanchoë PPC1 Is Essential for Crassulacean Acid Metabolism and the Regulation of Core Circadian Clock and Guard Cell Signaling Genes.
Susanna F Boxall, Nirja Kadu, Louisa V Dever, Jana Kneřová, Jade L Waller, Peter J D Gould, James Hartwell. Plant Cell 2020
27
20

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae).
Michael R McKain, Joel R McNeal, P Roxanne Kellar, Luis E Eguiarte, J Chris Pires, Jim Leebens-Mack. Am J Bot 2016
32
20



Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
Todd P Michael, Todd C Mockler, Ghislain Breton, Connor McEntee, Amanda Byer, Jonathan D Trout, Samuel P Hazen, Rongkun Shen, Henry D Priest, Christopher M Sullivan,[...]. PLoS Genet 2008
360
20

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
20

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.
María José Nueda, Sonia Tarazona, Ana Conesa. Bioinformatics 2014
167
20

Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules.
Sergei A Filichkin, Ghislain Breton, Henry D Priest, Palitha Dharmawardhana, Pankaj Jaiswal, Samuel E Fox, Todd P Michael, Joanne Chory, Steve A Kay, Todd C Mockler. PLoS One 2011
115
20

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.
France Denoeud, Lorenzo Carretero-Paulet, Alexis Dereeper, Gaëtan Droc, Romain Guyot, Marco Pietrella, Chunfang Zheng, Adriana Alberti, François Anthony, Giuseppe Aprea,[...]. Science 2014
290
20

Ecophysiology of Yucca brevifolia, an arborescent monocot of the Mojave sesert.
Stanley D Smith, Terry L Hartsock, Park S Nobel. Oecologia 1983
9
20

MetaCycle: an integrated R package to evaluate periodicity in large scale data.
Gang Wu, Ron C Anafi, Michael E Hughes, Karl Kornacker, John B Hogenesch. Bioinformatics 2016
204
20


Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext).
Travis C Glenn, Roger A Nilsen, Troy J Kieran, Jon G Sanders, Natalia J Bayona-Vásquez, John W Finger, Todd W Pierson, Kerin E Bentley, Sandra L Hoffberg, Swarnali Louha,[...]. PeerJ 2019
86
20

Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album.
Ching Man Wai, Sean E Weise, Philip Ozersky, Todd C Mockler, Todd P Michael, Robert VanBuren. PLoS Genet 2019
25
20

Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare.
Dominik Brilhaus, Andrea Bräutigam, Tabea Mettler-Altmann, Klaus Winter, Andreas P M Weber. Plant Physiol 2016
48
20


Molecular evolution of key metabolic genes during transitions to C4 and CAM photosynthesis.
Eric W Goolsby, Abigail J Moore, Lillian P Hancock, Jurriaan M De Vos, Erika J Edwards. Am J Bot 2018
11
20


Phytozome: a comparative platform for green plant genomics.
David M Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas Putnam,[...]. Nucleic Acids Res 2012
20

Transcript, protein and metabolite temporal dynamics in the CAM plant Agave.
Paul E Abraham, Hengfu Yin, Anne M Borland, Deborah Weighill, Sung Don Lim, Henrique Cestari De Paoli, Nancy Engle, Piet C Jones, Ryan Agh, David J Weston,[...]. Nat Plants 2016
78
20

Evolution of l-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales.
Hester Sheehan, Tao Feng, Nathanael Walker-Hale, Samuel Lopez-Nieves, Boas Pucker, Rui Guo, Won C Yim, Roshani Badgami, Alfonso Timoneda, Lijun Zhao,[...]. New Phytol 2020
25
20


Bacterial- and plant-type phosphoenolpyruvate carboxylase polypeptides interact in the hetero-oligomeric Class-2 PEPC complex of developing castor oil seeds.
Sam Gennidakis, Srinath Rao, Katie Greenham, R Glen Uhrig, Brendan O'Leary, Wayne A Snedden, Chaofu Lu, William C Plaxton. Plant J 2007
46
20

Maize global transcriptomics reveals pervasive leaf diurnal rhythms but rhythms in developing ears are largely limited to the core oscillator.
Kevin R Hayes, Mary Beatty, Xin Meng, Carl R Simmons, Jeffrey E Habben, Olga N Danilevskaya. PLoS One 2010
46
20

Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs.
Xianjun Lai, Claire Bendix, Lang Yan, Yang Zhang, James C Schnable, Frank G Harmon. BMC Genomics 2020
12
20

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
20



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.