A citation-based method for searching scientific literature

Estienne C Swart, John R Bracht, Vincent Magrini, Patrick Minx, Xiao Chen, Yi Zhou, Jaspreet S Khurana, Aaron D Goldman, Mariusz Nowacki, Klaas Schotanus, Seolkyoung Jung, Robert S Fulton, Amy Ly, Sean McGrath, Kevin Haub, Jessica L Wiggins, Donna Storton, John C Matese, Lance Parsons, Wei-Jen Chang, Michael S Bowen, Nicholas A Stover, Thomas A Jones, Sean R Eddy, Glenn A Herrick, Thomas G Doak, Richard K Wilson, Elaine R Mardis, Laura F Landweber. PLoS Biol 2013
Times Cited: 136







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



Times Cited
  Times     Co-cited
Similarity


The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.
Xiao Chen, John R Bracht, Aaron David Goldman, Egor Dolzhenko, Derek M Clay, Estienne C Swart, David H Perlman, Thomas G Doak, Andrew Stuart, Chris T Amemiya,[...]. Cell 2014
101
45

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.
Jonathan A Eisen, Robert S Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R Wortman, Jonathan H Badger, Qinghu Ren, Paolo Amedeo, Kristie M Jones,[...]. PLoS Biol 2006
521
42

The DNA of ciliated protozoa.
D M Prescott. Microbiol Rev 1994
499
39

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
Jean-Marc Aury, Olivier Jaillon, Laurent Duret, Benjamin Noel, Claire Jubin, Betina M Porcel, Béatrice Ségurens, Vincent Daubin, Véronique Anthouard, Nathalie Aiach,[...]. Nature 2006
565
38

The draft assembly of the radically organized Stylonychia lemnae macronuclear genome.
Samuel H Aeschlimann, Franziska Jönsson, Jan Postberg, Nicholas A Stover, Robert L Petera, Hans-Joachim Lipps, Mariusz Nowacki, Estienne C Swart. Genome Biol Evol 2014
39
74

RNA-mediated epigenetic programming of a genome-rearrangement pathway.
Mariusz Nowacki, Vikram Vijayan, Yi Zhou, Klaas Schotanus, Thomas G Doak, Laura F Landweber. Nature 2008
174
27

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome.
Eileen P Hamilton, Aurélie Kapusta, Piroska E Huvos, Shelby L Bidwell, Nikhat Zafar, Haibao Tang, Michalis Hadjithomas, Vivek Krishnakumar, Jonathan H Badger, Elisabet V Caler,[...]. Elife 2016
89
29

Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement.
Wenwen Fang, Xing Wang, John R Bracht, Mariusz Nowacki, Laura F Landweber. Cell 2012
99
25

The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.
Olivier Arnaiz, Nathalie Mathy, Céline Baudry, Sophie Malinsky, Jean-Marc Aury, Cyril Denby Wilkes, Olivier Garnier, Karine Labadie, Benjamin E Lauderdale, Anne Le Mouël,[...]. PLoS Genet 2012
105
20

The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.
Mark M Slabodnick, J Graham Ruby, Sarah B Reiff, Estienne C Swart, Sager Gosai, Sudhakaran Prabakaran, Ewa Witkowska, Graham E Larue, Susan Fisher, Robert M Freeman,[...]. Curr Biol 2017
52
38

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.
Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger,[...]. Genome Biol 2011
81
23

Programmed Genome Rearrangements in the Ciliate Oxytricha.
V Talya Yerlici, Laura F Landweber. Microbiol Spectr 2014
39
43

Genomes on the edge: programmed genome instability in ciliates.
John R Bracht, Wenwen Fang, Aaron David Goldman, Egor Dolzhenko, Elizabeth M Stein, Laura F Landweber. Cell 2013
58
27

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination.
Estienne Carl Swart, Valentina Serra, Giulio Petroni, Mariusz Nowacki. Cell 2016
91
17

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
15

A functional role for transposases in a large eukaryotic genome.
Mariusz Nowacki, Brian P Higgins, Genevieve M Maquilan, Estienne C Swart, Thomas G Doak, Laura F Landweber. Science 2009
82
17

Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates.
Xiao Chen, Seolkyoung Jung, Leslie Y Beh, Sean R Eddy, Laura F Landweber. Genome Biol Evol 2015
18
72


The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata).
Feng Gao, Alan Warren, Qianqian Zhang, Jun Gong, Miao Miao, Ping Sun, Dapeng Xu, Jie Huang, Zhenzhen Yi, Weibo Song. Sci Rep 2016
173
13

Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina.
Weibo Zheng, Chundi Wang, Ying Yan, Feng Gao, Thomas G Doak, Weibo Song. Genome Biol Evol 2018
17
76

RNA-Mediated Epigenetic Programming of Genome Rearrangements.
Mariusz Nowacki, Keerthi Shetty, Laura F Landweber. Annu Rev Genomics Hum Genet 2011
51
23

DNA elimination in ciliates: transposon domestication and genome surveillance.
Douglas L Chalker, Meng-Chao Yao. Annu Rev Genet 2011
96
12


High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus.
Ruanlin Wang, Jie Xiong, Wei Wang, Wei Miao, Aihua Liang. Sci Rep 2016
30
40

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
12



Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors.
Xiao Chen, Yaohan Jiang, Feng Gao, Weibo Zheng, Timothy J Krock, Naomi A Stover, Chao Lu, Laura A Katz, Weibo Song. Mol Ecol Resour 2019
32
37

Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns.
Guénola Ricard, Rob M de Graaf, Bas E Dutilh, I Duarte, Theo A van Alen, Angela Ham van Hoek, Brigitte Boxma, Georg W M van der Staay, Seung Yeo Moon-van der Staay, Wei-Jen Chang,[...]. BMC Genomics 2008
27
40

RNA-mediated epigenetic regulation of DNA copy number.
Mariusz Nowacki, Joanna E Haye, Wenwen Fang, Vikram Vijayan, Laura F Landweber. Proc Natl Acad Sci U S A 2010
50
22

Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila.
Joseph N Fass, Nikhil A Joshi, Mary T Couvillion, Josephine Bowen, Martin A Gorovsky, Eileen P Hamilton, Eduardo Orias, Kyungah Hong, Robert S Coyne, Jonathan A Eisen,[...]. G3 (Bethesda) 2011
55
20

Genome remodeling in ciliated protozoa.
Carolyn L Jahn, Lawrence A Klobutcher. Annu Rev Microbiol 2002
129
11

PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia.
Céline Baudry, Sophie Malinsky, Matthieu Restituito, Aurélie Kapusta, Sarah Rosa, Eric Meyer, Mireille Bétermier. Genes Dev 2009
126
11

Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena.
Kazufumi Mochizuki, Noah A Fine, Toshitaka Fujisawa, Martin A Gorovsky. Cell 2002
443
11


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
11

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages.
E Gentekaki, M Kolisko, V Boscaro, K J Bright, F Dini, G Di Giuseppe, Y Gong, C Miceli, L Modeo, R E Molestina,[...]. Mol Phylogenet Evol 2014
55
18

WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
10


Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.
John R Bracht, David H Perlman, Laura F Landweber. Genome Biol 2012
32
31

Estimating the timing of early eukaryotic diversification with multigene molecular clocks.
Laura Wegener Parfrey, Daniel J G Lahr, Andrew H Knoll, Laura A Katz. Proc Natl Acad Sci U S A 2011
414
10

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
10

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.
Laurent Duret, Jean Cohen, Claire Jubin, Philippe Dessen, Jean-François Goût, Sylvain Mousset, Jean-Marc Aury, Olivier Jaillon, Benjamin Noël, Olivier Arnaiz,[...]. Genome Res 2008
63
15




Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates.
Ying Yan, Xyrus X Maurer-Alcalá, Rob Knight, Sergei L Kosakovsky Pond, Laura A Katz. mBio 2019
24
41

The revised classification of eukaryotes.
Sina M Adl, Alastair G B Simpson, Christopher E Lane, Julius Lukeš, David Bass, Samuel S Bowser, Matthew W Brown, Fabien Burki, Micah Dunthorn, Vladimir Hampl,[...]. J Eukaryot Microbiol 2012
798
9

Microarray analyses of gene expression during the Tetrahymena thermophila life cycle.
Wei Miao, Jie Xiong, Josephine Bowen, Wei Wang, Yifan Liu, Olga Braguinets, Jorg Grigull, Ronald E Pearlman, Eduardo Orias, Martin A Gorovsky. PLoS One 2009
135
9

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax.
Ke Xu, Thomas G Doak, Hans J Lipps, Jingmei Wang, Estienne C Swart, Wei-Jen Chang. Gene 2012
28
32


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.