A citation-based method for searching scientific literature

Frédéric Chaux-Jukic, Samuel O'Donnell, Rory J Craig, Stephan Eberhard, Olivier Vallon, Zhou Xu. Nucleic Acids Res 2021
Times Cited: 1







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



Times Cited
  Times     Co-cited
Similarity


A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism.
Patrice A Salomé, Sabeeha S Merchant. Plant Cell 2019
5
100

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
100


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
100

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
Andrea Pauli, Eivind Valen, Michael F Lin, Manuel Garber, Nadine L Vastenhouw, Joshua Z Levin, Lin Fan, Albin Sandelin, John L Rinn, Aviv Regev,[...]. Genome Res 2012
531
100

Initial sequencing and comparative analysis of the mouse genome.
Robert H Waterston, Kerstin Lindblad-Toh, Ewan Birney, Jane Rogers, Josep F Abril, Pankaj Agarwal, Richa Agarwala, Rachel Ainscough, Marina Alexandersson, Peter An,[...]. Nature 2002
100


Alignathon: a competitive assessment of whole-genome alignment methods.
Dent Earl, Ngan Nguyen, Glenn Hickey, Robert S Harris, Stephen Fitzgerald, Kathryn Beal, Igor Seledtsov, Vladimir Molodtsov, Brian J Raney, Hiram Clawson,[...]. Genome Res 2014
48
100


Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.
Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern, Stephan Waack. BMC Bioinformatics 2006
475
100

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.
Michael F Lin, Irwin Jungreis, Manolis Kellis. Bioinformatics 2011
543
100

Whole-Genome Annotation with BRAKER.
Katharina J Hoff, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke. Methods Mol Biol 2019
81
100

Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii.
Rory J Craig, Katharina B Böndel, Kazuharu Arakawa, Takashi Nakada, Takuro Ito, Graham Bell, Nick Colegrave, Peter D Keightley, Rob W Ness. Mol Ecol 2019
4
100

Tyrosine Recombinase Retrotransposons and Transposons.
Russell T M Poulter, Margi I Butler. Microbiol Spectr 2015
13
100

Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii.
Rob W Ness, Andrew D Morgan, Radhakrishnan B Vasanthakrishnan, Nick Colegrave, Peter D Keightley. Genome Res 2015
52
100

The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Sabeeha S Merchant, Simon E Prochnik, Olivier Vallon, Elizabeth H Harris, Steven J Karpowicz, George B Witman, Astrid Terry, Asaf Salamov, Lillian K Fritz-Laylin, Laurence Maréchal-Drouard,[...]. Science 2007
100

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
100

Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii.
Rob W Ness, Andrew D Morgan, Nick Colegrave, Peter D Keightley. Genetics 2012
69
100

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.
Brant C Faircloth, Michael G Branstetter, Noor D White, Seán G Brady. Mol Ecol Resour 2015
102
100

Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
Paul Cliften, Priya Sudarsanam, Ashwin Desikan, Lucinda Fulton, Bob Fulton, John Majors, Robert Waterston, Barak A Cohen, Mark Johnston. Science 2003
624
100



The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage.
Jonathan Featherston, Yoko Arakaki, Erik R Hanschen, Patrick J Ferris, Richard E Michod, Bradley J S C Olson, Hisayoshi Nozaki, Pierre M Durand. Mol Biol Evol 2018
13
100

Comparative genomics as a tool to understand evolution and disease.
Jessica Alföldi, Kerstin Lindblad-Toh. Genome Res 2013
68
100

Evolutionary rates and expression level in Chlamydomonas.
Cristina E Popescu, Tudor Borza, Joseph P Bielawski, Robert W Lee. Genetics 2006
31
100

Linking high GC content to the repair of double strand breaks in prokaryotic genomes.
Jake L Weissman, William F Fagan, Philip L F Johnson. PLoS Genet 2019
7
100

QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
100

Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan.
Takashi Nakada, Haruka Shinkawa, Takuro Ito, Masaru Tomita. J Plant Res 2010
25
100

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Mark B Gerstein, Zhi John Lu, Eric L Van Nostrand, Chao Cheng, Bradley I Arshinoff, Tao Liu, Kevin Y Yip, Rebecca Robilotto, Andreas Rechtsteiner, Kohta Ikegami,[...]. Science 2010
662
100

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.
Simon E Prochnik, James Umen, Aurora M Nedelcu, Armin Hallmann, Stephen M Miller, Ichiro Nishii, Patrick Ferris, Alan Kuo, Therese Mitros, Lillian K Fritz-Laylin,[...]. Science 2010
316
100

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.
Robert M Waterhouse, Mathieu Seppey, Felipe A Simão, Mosè Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V Kriventseva, Evgeny M Zdobnov. Mol Biol Evol 2018
736
100

Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production.
Melissa S Roth, Shawn J Cokus, Sean D Gallaher, Andreas Walter, David Lopez, Erika Erickson, Benjamin Endelman, Daniel Westcott, Carolyn A Larabell, Sabeeha S Merchant,[...]. Proc Natl Acad Sci U S A 2017
65
100

Spontaneous dominant mutations in chlamydomonas highlight ongoing evolution by gene diversification.
Alix Boulouis, Dominique Drapier, Hélène Razafimanantsoa, Katia Wostrikoff, Nicolas J Tourasse, Kevin Pascal, Jacqueline Girard-Bascou, Olivier Vallon, Francis-André Wollman, Yves Choquet. Plant Cell 2015
17
100

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
100



Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs.
Adrian A Valli, Bruno A C M Santos, Silvia Hnatova, Andrew R Bassett, Attila Molnar, Betty Y Chung, David C Baulcombe. Genome Res 2016
23
100

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.
Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas,[...]. Genome Biol 2012
142
100

Inferring the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii.
Katharina B Böndel, Susanne A Kraemer, Toby Samuels, Deirdre McClean, Josianne Lachapelle, Rob W Ness, Nick Colegrave, Peter D Keightley. PLoS Biol 2019
11
100

Chlamydomonas reinhardtii at the crossroads of genomics.
Arthur R Grossman, Elizabeth E Harris, Charles Hauser, Paul A Lefebvre, Diego Martinez, Dan Rokhsar, Jeff Shrager, Carolyn D Silflow, David Stern, Olivier Vallon,[...]. Eukaryot Cell 2003
93
100

WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
100

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds.
Andrea Del Cortona, Christopher J Jackson, François Bucchini, Michiel Van Bel, Sofie D'hondt, Pavel Škaloud, Charles F Delwiche, Andrew H Knoll, John A Raven, Heroen Verbruggen,[...]. Proc Natl Acad Sci U S A 2020
17
100

UpSet: Visualization of Intersecting Sets.
Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister. IEEE Trans Vis Comput Graph 2014
455
100

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
Michael F Lin, Joseph W Carlson, Madeline A Crosby, Beverley B Matthews, Charles Yu, Soo Park, Kenneth H Wan, Andrew J Schroeder, L Sian Gramates, Susan E St Pierre,[...]. Genome Res 2007
108
100

Molecular evolutionary analysis of a gender-limited MID ortholog from the homothallic species Volvox africanus with male and monoecious spheroids.
Kayoko Yamamoto, Hiroko Kawai-Toyooka, Takashi Hamaji, Yuki Tsuchikane, Toshiyuki Mori, Fumio Takahashi, Hiroyuki Sekimoto, Patrick J Ferris, Hisayoshi Nozaki. PLoS One 2017
10
100


trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
100

Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes in Volvocine Algal Mating Haplotypes.
Takashi Hamaji, Yuko Mogi, Patrick J Ferris, Toshiyuki Mori, Shinya Miyagishima, Yukihiro Kabeya, Yoshiki Nishimura, Atsushi Toyoda, Hideki Noguchi, Asao Fujiyama,[...]. G3 (Bethesda) 2016
12
100

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
Katharina J Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke. Bioinformatics 2016
368
100

The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity.
Erik R Hanschen, Tara N Marriage, Patrick J Ferris, Takashi Hamaji, Atsushi Toyoda, Asao Fujiyama, Rafik Neme, Hideki Noguchi, Yohei Minakuchi, Masahiro Suzuki,[...]. Nat Commun 2016
63
100


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.