A citation-based method for searching scientific literature

Valentina Peona, Mozes P K Blom, Luohao Xu, Reto Burri, Shawn Sullivan, Ignas Bunikis, Ivan Liachko, Tri Haryoko, Knud A Jønsson, Qi Zhou, Martin Irestedt, Alexander Suh. Mol Ecol Resour 2021
Times Cited: 21







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



Times Cited
  Times     Co-cited
Similarity


Repbase Update, a database of repetitive elements in eukaryotic genomes.
Weidong Bao, Kenji K Kojima, Oleksiy Kohany. Mob DNA 2015
38

How complete are "complete" genome assemblies?-An avian perspective.
Valentina Peona, Matthias H Weissensteiner, Alexander Suh. Mol Ecol Resour 2018
43
33

Complex evolutionary trajectories of sex chromosomes across bird taxa.
Qi Zhou, Jilin Zhang, Doris Bachtrog, Na An, Quanfei Huang, Erich D Jarvis, M Thomas P Gilbert, Guojie Zhang. Science 2014
141
33

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

Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
494
28

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.
Luohao Xu, Gabriel Auer, Valentina Peona, Alexander Suh, Yuan Deng, Shaohong Feng, Guojie Zhang, Mozes P K Blom, Les Christidis, Stefan Prost,[...]. Nat Ecol Evol 2019
32
28

Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators.
Daniel W Bellott, Helen Skaletsky, Ting-Jan Cho, Laura Brown, Devin Locke, Nancy Chen, Svetlana Galkina, Tatyana Pyntikova, Natalia Koutseva, Tina Graves,[...]. Nat Genet 2017
65
28

RepeatModeler2 for automated genomic discovery of transposable element families.
Jullien M Flynn, Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G Clark, Cédric Feschotte, Arian F Smit. Proc Natl Acad Sci U S A 2020
142
28

Evolution of bird genomes-a transposon's-eye view.
Aurélie Kapusta, Alexander Suh. Ann N Y Acad Sci 2017
52
23

A unified classification system for eukaryotic transposable elements.
Thomas Wicker, François Sabot, Aurélie Hua-Van, Jeffrey L Bennetzen, Pierre Capy, Boulos Chalhoub, Andrew Flavell, Philippe Leroy, Michele Morgante, Olivier Panaud,[...]. Nat Rev Genet 2007
23

Piercing the dark matter: bioinformatics of long-range sequencing and mapping.
Fritz J Sedlazeck, Hayan Lee, Charlotte A Darby, Michael C Schatz. Nat Rev Genet 2018
172
23


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
23

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
23

Genetic variation and the de novo assembly of human genomes.
Mark J P Chaisson, Richard K Wilson, Evan E Eichler. Nat Rev Genet 2015
171
19

Phased diploid genome assembly with single-molecule real-time sequencing.
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz,[...]. Nat Methods 2016
706
19

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
19

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.
Wesley C Warren, LaDeana W Hillier, Chad Tomlinson, Patrick Minx, Milinn Kremitzki, Tina Graves, Chris Markovic, Nathan Bouk, Kim D Pruitt, Francoise Thibaud-Nissen,[...]. G3 (Bethesda) 2017
121
19

The genome of a songbird.
Wesley C Warren, David F Clayton, Hans Ellegren, Arthur P Arnold, Ladeana W Hillier, Axel Künstner, Steve Searle, Simon White, Albert J Vilella, Susan Fairley,[...]. Nature 2010
534
19

Comparative genomics reveals insights into avian genome evolution and adaptation.
Guojie Zhang, Cai Li, Qiye Li, Bo Li, Denis M Larkin, Chul Lee, Jay F Storz, Agostinho Antunes, Matthew J Greenwold, Robert W Meredith,[...]. Science 2014
502
19

Discovery and population genomics of structural variation in a songbird genus.
Matthias H Weissensteiner, Ignas Bunikis, Ana Catalán, Kees-Jan Francoijs, Ulrich Knief, Wieland Heim, Valentina Peona, Saurabh D Pophaly, Fritz J Sedlazeck, Alexander Suh,[...]. Nat Commun 2020
19
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
19

Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds.
Fidel Botero-Castro, Emeric Figuet, Marie-Ka Tilak, Benoit Nabholz, Nicolas Galtier. Mol Biol Evol 2017
34
19

Evolutionary analysis of the female-specific avian W chromosome.
Linnéa Smeds, Vera Warmuth, Paulina Bolivar, Severin Uebbing, Reto Burri, Alexander Suh, Alexander Nater, Stanislav Bureš, Laszlo Z Garamszegi, Silje Hogner,[...]. Nat Commun 2015
63
19

Massive gene amplification on a recently formed Drosophila Y chromosome.
Doris Bachtrog, Shivani Mahajan, Ryan Bracewell. Nat Ecol Evol 2019
29
19

Y and W Chromosome Assemblies: Approaches and Discoveries.
Marta Tomaszkiewicz, Paul Medvedev, Kateryna D Makova. Trends Genet 2017
46
19

Origins and functional evolution of Y chromosomes across mammals.
Diego Cortez, Ray Marin, Deborah Toledo-Flores, Laure Froidevaux, Angélica Liechti, Paul D Waters, Frank Grützner, Henrik Kaessmann. Nature 2014
270
19

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
19

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
19


Towards complete and error-free genome assemblies of all vertebrate species.
Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim,[...]. Nature 2021
58
19

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.
Takeshi Kawakami, Linnéa Smeds, Niclas Backström, Arild Husby, Anna Qvarnström, Carina F Mugal, Pall Olason, Hans Ellegren. Mol Ecol 2014
117
14

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.
Matthias H Weissensteiner, Andy W C Pang, Ignas Bunikis, Ida Höijer, Olga Vinnere-Petterson, Alexander Suh, Jochen B W Wolf. Genome Res 2017
44
14

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
14

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

Telomere-to-telomere assembly of a complete human X chromosome.
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon,[...]. Nature 2020
166
14

Ten things you should know about transposable elements.
Guillaume Bourque, Kathleen H Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L Levin, Todd S Macfarlan,[...]. Genome Biol 2018
246
14

Resolving the complexity of the human genome using single-molecule sequencing.
Mark J P Chaisson, John Huddleston, Megan Y Dennis, Peter H Sudmant, Maika Malig, Fereydoun Hormozdiari, Francesca Antonacci, Urvashi Surti, Richard Sandstrom, Matthew Boitano,[...]. Nature 2015
393
14

Direct determination of diploid genome sequences.
Neil I Weisenfeld, Vijay Kumar, Preyas Shah, Deanna M Church, David B Jaffe. Genome Res 2017
290
14

The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.
Jesper Boman, Carolina Frankl-Vilches, Michelly da Silva Dos Santos, Edivaldo H C de Oliveira, Manfred Gahr, Alexander Suh. Genes (Basel) 2019
6
50

The degeneration of Y chromosomes.
B Charlesworth, D Charlesworth. Philos Trans R Soc Lond B Biol Sci 2000
578
14

Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies.
Roy N Platt, Laura Blanco-Berdugo, David A Ray. Genome Biol Evol 2016
48
14

Conservation of the human telomere sequence (TTAGGG)n among vertebrates.
J Meyne, R L Ratliff, R K Moyzis. Proc Natl Acad Sci U S A 1989
585
14

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson,[...]. Nat Biotechnol 2019
269
14

Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds.
Luohao Xu, Simon Yung Wa Sin, Phil Grayson, Scott V Edwards, Timothy B Sackton. Genome Biol Evol 2019
19
15

Evolutionary stasis: the stable chromosomes of birds.
Hans Ellegren. Trends Ecol Evol 2010
145
14

Evolutionary signals of selection on cognition from the great tit genome and methylome.
Veronika N Laine, Toni I Gossmann, Kyle M Schachtschneider, Colin J Garroway, Ole Madsen, Koen J F Verhoeven, Victor de Jager, Hendrik-Jan Megens, Wesley C Warren, Patrick Minx,[...]. Nat Commun 2016
92
14

The long and the short of avian W chromosomes: no evidence for gradual W shortening.
Joanna Rutkowska, Malgorzata Lagisz, Shinichi Nakagawa. Biol Lett 2012
22
14


GeneWise and Genomewise.
Ewan Birney, Michele Clamp, Richard Durbin. Genome Res 2004
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.