A citation-based method for searching scientific literature

Richard E Green, Edward L Braun, Joel Armstrong, Dent Earl, Ngan Nguyen, Glenn Hickey, Michael W Vandewege, John A St John, Salvador Capella-Gutiérrez, Todd A Castoe, Colin Kern, Matthew K Fujita, Juan C Opazo, Jerzy Jurka, Kenji K Kojima, Juan Caballero, Robert M Hubley, Arian F Smit, Roy N Platt, Christine A Lavoie, Meganathan P Ramakodi, John W Finger, Alexander Suh, Sally R Isberg, Lee Miles, Amanda Y Chong, Weerachai Jaratlerdsiri, Jaime Gongora, Christopher Moran, Andrés Iriarte, John McCormack, Shane C Burgess, Scott V Edwards, Eric Lyons, Christina Williams, Matthew Breen, Jason T Howard, Cathy R Gresham, Daniel G Peterson, Jürgen Schmitz, David D Pollock, David Haussler, Eric W Triplett, Guojie Zhang, Naoki Irie, Erich D Jarvis, Christopher A Brochu, Carl J Schmidt, Fiona M McCarthy, Brant C Faircloth, Federico G Hoffmann, Travis C Glenn, Toni Gabaldón, Benedict Paten, David A Ray. Science 2014
Times Cited: 198







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



Times Cited
  Times     Co-cited
Similarity


The genome of the green anole lizard and a comparative analysis with birds and mammals.
Jessica Alföldi, Federica Di Palma, Manfred Grabherr, Christina Williams, Lesheng Kong, Evan Mauceli, Pamela Russell, Craig B Lowe, Richard E Glor, Jacob D Jaffe,[...]. Nature 2011
399
21

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.
Zhuo Wang, Juan Pascual-Anaya, Amonida Zadissa, Wenqi Li, Yoshihito Niimura, Zhiyong Huang, Chunyi Li, Simon White, Zhiqiang Xiong, Dongming Fang,[...]. Nat Genet 2013
255
20

Whole-genome analyses resolve early branches in the tree of life of modern birds.
Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y W Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard,[...]. Science 2014
903
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
545
17

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
15


The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.
H Bradley Shaffer, Patrick Minx, Daniel E Warren, Andrew M Shedlock, Robert C Thomson, Nicole Valenzuela, John Abramyan, Chris T Amemiya, Daleen Badenhorst, Kyle K Biggar,[...]. Genome Biol 2013
204
13


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
13

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
12

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
12




Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator.
Qiu-Hong Wan, Sheng-Kai Pan, Li Hu, Ying Zhu, Peng-Wei Xu, Jin-Quan Xia, Hui Chen, Gen-Yun He, Jing He, Xiao-Wei Ni,[...]. Cell Res 2013
70
14

The African coelacanth genome provides insights into tetrapod evolution.
Chris T Amemiya, Jessica Alföldi, Alison P Lee, Shaohua Fan, Hervé Philippe, Iain Maccallum, Ingo Braasch, Tereza Manousaki, Igor Schneider, Nicolas Rohner,[...]. Nature 2013
408
10

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
Ingo Braasch, Andrew R Gehrke, Jeramiah J Smith, Kazuhiko Kawasaki, Tereza Manousaki, Jeremy Pasquier, Angel Amores, Thomas Desvignes, Peter Batzel, Julian Catchen,[...]. Nat Genet 2016
316
9

Genome analysis of the platypus reveals unique signatures of evolution.
Wesley C Warren, LaDeana W Hillier, Jennifer A Marshall Graves, Ewan Birney, Chris P Ponting, Frank Grützner, Katherine Belov, Webb Miller, Laura Clarke, Asif T Chinwalla,[...]. Nature 2008
458
9

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.
Todd A Castoe, A P Jason de Koning, Kathryn T Hall, Daren C Card, Drew R Schield, Matthew K Fujita, Robert P Ruggiero, Jack F Degner, Juan M Daza, Wanjun Gu,[...]. Proc Natl Acad Sci U S A 2013
176
9

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes.
R Alexander Pyron, Frank T Burbrink, John J Wiens. BMC Evol Biol 2013
677
9

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times.
Sudhir Kumar, Glen Stecher, Michael Suleski, S Blair Hedges. Mol Biol Evol 2017
9


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
556
8


Evolution and Diversity of Transposable Elements in Vertebrate Genomes.
Cibele G Sotero-Caio, Roy N Platt, Alexander Suh, David A Ray. Genome Biol Evol 2017
110
7

Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.
Alexander Suh, Gennady Churakov, Meganathan P Ramakodi, Roy N Platt, Jerzy Jurka, Kenji K Kojima, Juan Caballero, Arian F Smit, Kent A Vliet, Federico G Hoffmann,[...]. Genome Biol Evol 2014
42
16

Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
7

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria).
Ylenia Chiari, Vincent Cahais, Nicolas Galtier, Frédéric Delsuc. BMC Biol 2012
213
7

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
7

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
6

A high-resolution map of human evolutionary constraint using 29 mammals.
Kerstin Lindblad-Toh, Manuel Garber, Or Zuk, Michael F Lin, Brian J Parker, Stefan Washietl, Pouya Kheradpour, Jason Ernst, Gregory Jordan, Evan Mauceli,[...]. Nature 2011
696
6

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Adam Siepel, Gill Bejerano, Jakob S Pedersen, Angie S Hinrichs, Minmei Hou, Kate Rosenbloom, Hiram Clawson, John Spieth, Ladeana W Hillier, Stephen Richards,[...]. Genome Res 2005
6

A phylogenomic analysis of turtles.
Nicholas G Crawford, James F Parham, Anna B Sellas, Brant C Faircloth, Travis C Glenn, Theodore J Papenfuss, James B Henderson, Madison H Hansen, W Brian Simison. Mol Phylogenet Evol 2015
131
6

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
6

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.
John A St John, Edward L Braun, Sally R Isberg, Lee G Miles, Amanda Y Chong, Jaime Gongora, Pauline Dalzell, Christopher Moran, Bertrand Bed'hom, Arkhat Abzhanov,[...]. Genome Biol 2012
99
6

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing.
Richard O Prum, Jacob S Berv, Alex Dornburg, Daniel J Field, Jeffrey P Townsend, Emily Moriarty Lemmon, Alan R Lemmon. Nature 2015
644
6

Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals.
Giulia I M Pasquesi, Richard H Adams, Daren C Card, Drew R Schield, Andrew B Corbin, Blair W Perry, Jacobo Reyes-Velasco, Robert P Ruggiero, Michael W Vandewege, Jonathan A Shortt,[...]. Nat Commun 2018
50
12


Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.
Jeramiah J Smith, Shigehiro Kuraku, Carson Holt, Tatjana Sauka-Spengler, Ning Jiang, Michael S Campbell, Mark D Yandell, Tereza Manousaki, Axel Meyer, Ona E Bloom,[...]. Nat Genet 2013
397
6

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.
Edward S Rice, Satomi Kohno, John St John, Son Pham, Jonathan Howard, Liana F Lareau, Brendan L O'Connell, Glenn Hickey, Joel Armstrong, Alden Deran,[...]. Genome Res 2017
23
21

Dynamics of genome size evolution in birds and mammals.
Aurélie Kapusta, Alexander Suh, Cédric Feschotte. Proc Natl Acad Sci U S A 2017
159
5

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features.
Ryohei Seki, Cai Li, Qi Fang, Shinichi Hayashi, Shiro Egawa, Jiang Hu, Luohao Xu, Hailin Pan, Mao Kondo, Tomohiko Sato,[...]. Nat Commun 2017
38
13

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

Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
583
5

HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Glenn Hickey, Benedict Paten, Dent Earl, Daniel Zerbino, David Haussler. Bioinformatics 2013
55
9

Aligning multiple genomic sequences with the threaded blockset aligner.
Mathieu Blanchette, W James Kent, Cathy Riemer, Laura Elnitski, Arian F A Smit, Krishna M Roskin, Robert Baertsch, Kate Rosenbloom, Hiram Clawson, Eric D Green,[...]. Genome Res 2004
949
5



Repbase Update, a database of repetitive elements in eukaryotic genomes.
Weidong Bao, Kenji K Kojima, Oleksiy Kohany. Mob DNA 2015
5



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.