A citation-based method for searching scientific literature

Guangtu Gao, Susana Magadan, Geoffrey C Waldbieser, Ramey C Youngblood, Paul A Wheeler, Brian E Scheffler, Gary H Thorgaard, Yniv Palti. G3 (Bethesda) 2021
Times Cited: 14







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



Times Cited
  Times     Co-cited
Similarity


The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.
Camille Berthelot, Frédéric Brunet, Domitille Chalopin, Amélie Juanchich, Maria Bernard, Benjamin Noël, Pascal Bento, Corinne Da Silva, Karine Labadie, Adriana Alberti,[...]. Nat Commun 2014
531
42

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
35

The Atlantic salmon genome provides insights into rediploidization.
Sigbjørn Lien, Ben F Koop, Simen R Sandve, Jason R Miller, Matthew P Kent, Torfinn Nome, Torgeir R Hvidsten, Jong S Leong, David R Minkley, Aleksey Zimin,[...]. Nature 2016
528
35

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
28

Response to selection for bacterial cold water disease resistance in rainbow trout.
T D Leeds, J T Silverstein, G M Weber, R L Vallejo, Y Palti, C E Rexroad, J Evenhuis, S Hadidi, T J Welch, G D Wiens. J Anim Sci 2010
67
28

Sex-dependent dominance maintains migration supergene in rainbow trout.
Devon E Pearse, Nicola J Barson, Torfinn Nome, Guangtu Gao, Matthew A Campbell, Alicia Abadía-Cardoso, Eric C Anderson, David E Rundio, Thomas H Williams, Kerry A Naish,[...]. Nat Ecol Evol 2019
90
28

Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that long-range LD is a major contributing factor.
Roger L Vallejo, Rafael M O Silva, Jason P Evenhuis, Guangtu Gao, Sixin Liu, James E Parsons, Kyle E Martin, Gregory D Wiens, Daniela A L Lourenco, Timothy D Leeds,[...]. J Anim Breed Genet 2018
39
28

Circos: an information aesthetic for comparative genomics.
Martin Krzywinski, Jacqueline Schein, Inanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, Marco A Marra. Genome Res 2009
21

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
21

Flavobacterium psychrophilum infections in salmonid fish.
A Nematollahi, A Decostere, F Pasmans, F Haesebrouck. J Fish Dis 2003
213
21


Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum.
David Marancik, Guangtu Gao, Bam Paneru, Hao Ma, Alvaro G Hernandez, Mohamed Salem, Jianbo Yao, Yniv Palti, Gregory D Wiens. Front Genet 2015
44
21

Second-generation PLINK: rising to the challenge of larger and richer datasets.
Christopher C Chang, Carson C Chow, Laurent Cam Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee. Gigascience 2015
21

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
21


Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon.
Nicola J Barson, Tutku Aykanat, Kjetil Hindar, Matthew Baranski, Geir H Bolstad, Peder Fiske, Céleste Jacq, Arne J Jensen, Susan E Johnston, Sten Karlsson,[...]. Nature 2015
261
21

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
21

Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture.
Roger L Vallejo, Timothy D Leeds, Guangtu Gao, James E Parsons, Kyle E Martin, Jason P Evenhuis, Breno O Fragomeni, Gregory D Wiens, Yniv Palti. Genet Sel Evol 2017
82
21

The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout.
Y Palti, G Gao, S Liu, M P Kent, S Lien, M R Miller, C E Rexroad, T Moen. Mol Ecol Resour 2015
87
21

Rainbow trout resistance to bacterial cold water disease: two new quantitative trait loci identified after a natural disease outbreak on a French farm.
C Fraslin, S Brard-Fudulea, J D'Ambrosio, A Bestin, M Charles, P Haffray, E Quillet, F Phocas. Anim Genet 2019
8
37

A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing.
Guangtu Gao, Torfinn Nome, Devon E Pearse, Thomas Moen, Kerry A Naish, Gary H Thorgaard, Sigbjørn Lien, Yniv Palti. Front Genet 2018
24
21

Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing.
Sixin Liu, Guangtu Gao, Ryan M Layer, Gary H Thorgaard, Gregory D Wiens, Timothy D Leeds, Kyle E Martin, Yniv Palti. Front Genet 2021
5
60

Versatile and open software for comparing large genomes.
Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg. Genome Biol 2004
14

DNA fingerprinting confirms isogenicity of androgenetically derived rainbow trout lines.
W P Young, P A Wheeler, R D Fields, G H Thorgaard. J Hered 1996
81
14

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.
Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shu-Qi Zhao, Liping Wei, Ge Gao. Nucleic Acids Res 2007
14

Crosstalk among lncRNAs, microRNAs and mRNAs in the muscle 'degradome' of rainbow trout.
Bam Paneru, Ali Ali, Rafet Al-Tobasei, Brett Kenney, Mohamed Salem. Sci Rep 2018
23
14

Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes.
Ali Ali, Caird E Rexroad, Gary H Thorgaard, Jianbo Yao, Mohamed Salem. Front Genet 2014
35
14

Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.
Rafet Al-Tobasei, Bam Paneru, Mohamed Salem. PLoS One 2016
60
14


Rainbow trout resistance to bacterial cold-water disease is moderately heritable and is not adversely correlated with growth.
J T Silverstein, R L Vallejo, Y Palti, T D Leeds, C E Rexroad, T J Welch, G D Wiens, V Ducrocq. J Anim Sci 2009
71
14

Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead (Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment.
Mackenzie R Gavery, Krista M Nichols, Barry A Berejikian, Christopher P Tatara, Giles W Goetz, Jon T Dickey, Donald M Van Doornik, Penny Swanson. Genes (Basel) 2019
16
14

Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout.
Devon E Pearse, Nicola J Barson, Torfinn Nome, Guangtu Gao, Matthew A Campbell, Alicia Abadía-Cardoso, Eric C Anderson, David E Rundio, Thomas H Williams, Kerry A Naish,[...]. Nat Ecol Evol 2020
3
66

RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout (Oncorhynchus mykiss).
Matthew C Hale, Garrett J McKinney, Frank P Thrower, Krista M Nichols. Comp Biochem Physiol Part D Genomics Proteomics 2016
20
14

Genome-wide identification of loci associated with growth in rainbow trout.
Ali Ali, Rafet Al-Tobasei, Daniela Lourenco, Tim Leeds, Brett Kenney, Mohamed Salem. BMC Genomics 2020
12
16

Alternative splicing: a pivotal step between eukaryotic transcription and translation.
Alberto R Kornblihtt, Ignacio E Schor, Mariano Alló, Gwendal Dujardin, Ezequiel Petrillo, Manuel J Muñoz. Nat Rev Mol Cell Biol 2013
517
14


T Cell Receptor Alpha Chain Genes in the Teleost Ballan Wrasse (Labrus bergylta) Are Subjected to Somatic Hypermutation.
Sumaira Bilal, Kai Kristoffer Lie, Øystein Sæle, Ivar Hordvik. Front Immunol 2018
11
18

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome.
Kris A Christensen, Jong S Leong, Dionne Sakhrani, Carlo A Biagi, David R Minkley, Ruth E Withler, Eric B Rondeau, Ben F Koop, Robert H Devlin. PLoS One 2018
42
14

Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
Jay Ghurye, Arang Rhie, Brian P Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M Phillippy, Sergey Koren. PLoS Comput Biol 2019
145
14

The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome.
Kris A Christensen, Eric B Rondeau, David R Minkley, Dionne Sakhrani, Carlo A Biagi, Anne-Marie Flores, Ruth E Withler, Scott A Pavey, Terry D Beacham, Theresa Godin,[...]. PLoS One 2020
10
20

Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array.
Agustín Barría, Kris A Christensen, Grazyella Yoshida, Ana Jedlicki, Jong S Leong, Eric B Rondeau, Jean P Lhorente, Ben F Koop, William S Davidson, José M Yáñez. Front Genet 2019
20
14

Chromosome evolution in the Salmonidae (Pisces): an update.
R Phillips, P Ráb. Biol Rev Camb Philos Soc 2001
143
14

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
14

The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids.
Ayaka Yano, Barbara Nicol, Elodie Jouanno, Edwige Quillet, Alexis Fostier, René Guyomard, Yann Guiguen. Evol Appl 2013
142
14

The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males.
Fernando Ayllon, Erik Kjærner-Semb, Tomasz Furmanek, Vidar Wennevik, Monica F Solberg, Geir Dahle, Geir Lasse Taranger, Kevin A Glover, Markus Sällman Almén, Carl J Rubin,[...]. PLoS Genet 2015
93
14

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
14

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).
Robert Kofler, Ram Vinay Pandey, Christian Schlötterer. Bioinformatics 2011
434
14

The zebrafish reference genome sequence and its relationship to the human genome.
Kerstin Howe, Matthew D Clark, Carlos F Torroja, James Torrance, Camille Berthelot, Matthieu Muffato, John E Collins, Sean Humphray, Karen McLaren, Lucy Matthews,[...]. Nature 2013
14

Epithelial Cadherin Determines Resistance to Infectious Pancreatic Necrosis Virus in Atlantic Salmon.
Thomas Moen, Jacob Torgersen, Nina Santi, William S Davidson, Matthew Baranski, Jørgen Ødegård, Sissel Kjøglum, Bente Velle, Matthew Kent, Krzysztof P Lubieniecki,[...]. Genetics 2015
69
14

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.
Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan,[...]. BMC Genomics 2017
73
14


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.