A citation-based method for searching scientific literature

M Desmond Ramirez, Autum N Pairett, M Sabrina Pankey, Jeanne M Serb, Daniel I Speiser, Andrew J Swafford, Todd H Oakley. Genome Biol Evol 2016
Times Cited: 63







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



Times Cited
  Times     Co-cited
Similarity


Shedding new light on opsin evolution.
Megan L Porter, Joseph R Blasic, Michael J Bok, Evan G Cameron, Thomas Pringle, Thomas W Cronin, Phyllis R Robinson. Proc Biol Sci 2012
160
47

Metazoan opsin evolution reveals a simple route to animal vision.
Roberto Feuda, Sinead C Hamilton, James O McInerney, Davide Pisani. Proc Natl Acad Sci U S A 2012
105
42

The opsins.
Akihisa Terakita. Genome Biol 2005
325
34

Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain.
Detlev Arendt, Kristin Tessmar-Raible, Heidi Snyman, Adriaan W Dorresteijn, Joachim Wittbrodt. Science 2004
237
30

Evolution of opsins and phototransduction.
Yoshinori Shichida, Take Matsuyama. Philos Trans R Soc Lond B Biol Sci 2009
216
26

Co-expression of xenopsin and rhabdomeric opsin in photoreceptors bearing microvilli and cilia.
Oliver Vöcking, Ioannis Kourtesis, Sharat Chandra Tumu, Harald Hausen. Elife 2017
25
60

The comb jelly opsins and the origins of animal phototransduction.
Roberto Feuda, Omar Rota-Stabelli, Todd H Oakley, Davide Pisani. Genome Biol Evol 2014
38
36

Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones.
María Soledad Ramirez, Gang Xie, German M Traglia, Shannon L Johnson, Karen W Davenport, David van Duin, Azam Ramazani, Federico Perez, Michael R Jacobs, David J Sherratt,[...]. Genome Biol Evol 2016
20
70

Unconventional Roles of Opsins.
Nicole Y Leung, Craig Montell. Annu Rev Cell Dev Biol 2017
54
25

A novel Go-mediated phototransduction cascade in scallop visual cells.
D Kojima, A Terakita, T Ishikawa, Y Tsukahara, A Maeda, Y Shichida. J Biol Chem 1997
97
19


Spectral Tuning of Phototaxis by a Go-Opsin in the Rhabdomeric Eyes of Platynereis.
Martin Gühmann, Huiyong Jia, Nadine Randel, Csaba Verasztó, Luis A Bezares-Calderón, Nico K Michiels, Shozo Yokoyama, Gáspár Jékely. Curr Biol 2015
38
31


The origins of novel protein interactions during animal opsin evolution.
David C Plachetzki, Bernard M Degnan, Todd H Oakley. PLoS One 2007
76
17

Jellyfish vision starts with cAMP signaling mediated by opsin-G(s) cascade.
Mitsumasa Koyanagi, Kosuke Takano, Hisao Tsukamoto, Kohzoh Ohtsu, Fumio Tokunaga, Akihisa Terakita. Proc Natl Acad Sci U S A 2008
97
17

Eye evolution and its functional basis.
Dan-E Nilsson. Vis Neurosci 2013
94
15

The evolution of eyes and visually guided behaviour.
Dan-Eric Nilsson. Philos Trans R Soc Lond B Biol Sci 2009
101
15

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
15

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.
Daniel I Speiser, M Sabrina Pankey, Alexander K Zaharoff, Barbara A Battelle, Heather D Bracken-Grissom, Jesse W Breinholt, Seth M Bybee, Thomas W Cronin, Anders Garm, Annie R Lindgren,[...]. BMC Bioinformatics 2014
43
23

Evolution and functional diversity of jellyfish opsins.
Hiroshi Suga, Volker Schmid, Walter J Gehring. Curr Biol 2008
84
15

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
15

Evolution of eyes and photoreceptor cell types.
Detlev Arendt. Int J Dev Biol 2003
224
14

The Dynamic Evolutionary History of Pancrustacean Eyes and Opsins.
Miriam J Henze, Todd H Oakley. Integr Comp Biol 2015
53
16

Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems.
M A Yoshida, A Ogura, K Ikeo, S Shigeno, T Moritaki, G C Winters, A B Kohn, L L Moroz. Integr Comp Biol 2015
34
26

Ocular and extraocular expression of opsins in the rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa).
Jan Bielecki, Alexander K Zaharoff, Nicole Y Leung, Anders Garm, Todd H Oakley. PLoS One 2014
16
56



Amphioxus homologs of Go-coupled rhodopsin and peropsin having 11-cis- and all-trans-retinals as their chromophores.
Mitsumasa Koyanagi, Akihisa Terakita, Kaoru Kubokawa, Yoshinori Shichida. FEBS Lett 2002
86
14

Phototransduction motifs and variations.
King-Wai Yau, Roger C Hardie. Cell 2009
249
12

Reconstructing the eyes of Urbilateria.
D Arendt, J Wittbrodt. Philos Trans R Soc Lond B Biol Sci 2001
107
12

Unique system of photoreceptors in sea urchin tube feet.
Esther M Ullrich-Lüter, Sam Dupont, Enrique Arboleda, Harald Hausen, Maria Ina Arnone. Proc Natl Acad Sci U S A 2011
60
13

Phototransduction and the evolution of photoreceptors.
Gordon L Fain, Roger Hardie, Simon B Laughlin. Curr Biol 2010
140
12

Opsin evolution in the Ambulacraria.
S D'Aniello, J Delroisse, A Valero-Gracia, E K Lowe, M Byrne, J T Cannon, K M Halanych, M R Elphick, J Mallefet, S Kaul-Strehlow,[...]. Mar Genomics 2015
21
38

Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution.
Michaela Liegertová, Jiří Pergner, Iryna Kozmiková, Peter Fabian, Antonio R Pombinho, Hynek Strnad, Jan Pačes, Čestmír Vlček, Petr Bartůněk, Zbyněk Kozmik. Sci Rep 2015
23
34

Extraordinary diversity of visual opsin genes in dragonflies.
Ryo Futahashi, Ryouka Kawahara-Miki, Michiyo Kinoshita, Kazutoshi Yoshitake, Shunsuke Yajima, Kentaro Arikawa, Takema Fukatsu. Proc Natl Acad Sci U S A 2015
88
12

Cnidocyte discharge is regulated by light and opsin-mediated phototransduction.
David C Plachetzki, Caitlin R Fong, Todd H Oakley. BMC Biol 2012
47
17

Stable transgenesis in the marine annelid Platynereis dumerilii sheds new light on photoreceptor evolution.
Benjamin Backfisch, Vinoth Babu Veedin Rajan, Ruth M Fischer, Claudia Lohs, Enrique Arboleda, Kristin Tessmar-Raible, Florian Raible. Proc Natl Acad Sci U S A 2013
56
14

The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway.
David C Plachetzki, Caitlin R Fong, Todd H Oakley. Proc Biol Sci 2010
50
16

A gonad-expressed opsin mediates light-induced spawning in the jellyfish Clytia.
Gonzalo Quiroga Artigas, Pascal Lapébie, Lucas Leclère, Noriyo Takeda, Ryusaku Deguchi, Gáspár Jékely, Tsuyoshi Momose, Evelyn Houliston. Elife 2018
39
20

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
12

Homologs of vertebrate Opn3 potentially serve as a light sensor in nonphotoreceptive tissue.
Mitsumasa Koyanagi, Eiichiro Takada, Takashi Nagata, Hisao Tsukamoto, Akihisa Terakita. Proc Natl Acad Sci U S A 2013
84
11

UV-sensitive photoreceptor protein OPN5 in humans and mice.
Daisuke Kojima, Suguru Mori, Masaki Torii, Akimori Wada, Rika Morishita, Yoshitaka Fukada. PLoS One 2011
105
11


An extended family of novel vertebrate photopigments is widely expressed and displays a diversity of function.
Wayne I L Davies, T Katherine Tamai, Lei Zheng, Josephine K Fu, Jason Rihel, Russell G Foster, David Whitmore, Mark W Hankins. Genome Res 2015
75
11

Characterisation and localisation of the opsin protein repertoire in the brain and retinas of a spider and an onychophoran.
Bo Joakim Eriksson, David Fredman, Gerhard Steiner, Axel Schmid. BMC Evol Biol 2013
35
20

Molecular analysis of the amphioxus frontal eye unravels the evolutionary origin of the retina and pigment cells of the vertebrate eye.
Pavel Vopalensky, Jiri Pergner, Michaela Liegertova, Elia Benito-Gutierrez, Detlev Arendt, Zbynek Kozmik. Proc Natl Acad Sci U S A 2012
83
11

Here, There and Everywhere: The Radiolar Eyes of Fan Worms (Annelida, Sabellidae).
Michael J Bok, María Capa, Dan-Eric Nilsson. Integr Comp Biol 2016
24
29

Development of pigment-cup eyes in the polychaete Platynereis dumerilii and evolutionary conservation of larval eyes in Bilateria.
Detlev Arendt, Kristin Tessmar, Maria-Ines Medeiros de Campos-Baptista, Adriaan Dorresteijn, Joachim Wittbrodt. Development 2002
125
11

Cephalochordate melanopsin: evolutionary linkage between invertebrate visual cells and vertebrate photosensitive retinal ganglion cells.
Mitsumasa Koyanagi, Kaoru Kubokawa, Hisao Tsukamoto, Yoshinori Shichida, Akihisa Terakita. Curr Biol 2005
159
11

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, Takashi Miyata. Nucleic Acids Res 2002
11


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.