A citation-based method for searching scientific literature

John K Colbourne, Michael E Pfrender, Donald Gilbert, W Kelley Thomas, Abraham Tucker, Todd H Oakley, Shinichi Tokishita, Andrea Aerts, Georg J Arnold, Malay Kumar Basu, Darren J Bauer, Carla E Cáceres, Liran Carmel, Claudio Casola, Jeong-Hyeon Choi, John C Detter, Qunfeng Dong, Serge Dusheyko, Brian D Eads, Thomas Fröhlich, Kerry A Geiler-Samerotte, Daniel Gerlach, Phil Hatcher, Sanjuro Jogdeo, Jeroen Krijgsveld, Evgenia V Kriventseva, Dietmar Kültz, Christian Laforsch, Erika Lindquist, Jacqueline Lopez, J Robert Manak, Jean Muller, Jasmyn Pangilinan, Rupali P Patwardhan, Samuel Pitluck, Ellen J Pritham, Andreas Rechtsteiner, Mina Rho, Igor B Rogozin, Onur Sakarya, Asaf Salamov, Sarah Schaack, Harris Shapiro, Yasuhiro Shiga, Courtney Skalitzky, Zachary Smith, Alexander Souvorov, Way Sung, Zuojian Tang, Dai Tsuchiya, Hank Tu, Harmjan Vos, Mei Wang, Yuri I Wolf, Hideo Yamagata, Takuji Yamada, Yuzhen Ye, Joseph R Shaw, Justen Andrews, Teresa J Crease, Haixu Tang, Susan M Lucas, Hugh M Robertson, Peer Bork, Eugene V Koonin, Evgeny M Zdobnov, Igor V Grigoriev, Michael Lynch, Jeffrey L Boore. Science 2011
Times Cited: 785







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



Times Cited
  Times     Co-cited
Similarity


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
26

The genome of the freshwater water flea Daphnia magna: A potential use for freshwater molecular ecotoxicology.
Bo-Young Lee, Beom-Soon Choi, Min-Sub Kim, Jun Chul Park, Chang-Bum Jeong, Jeonghoon Han, Jae-Seong Lee. Aquat Toxicol 2019
47
44

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex.
Zhiqiang Ye, Sen Xu, Ken Spitze, Jana Asselman, Xiaoqian Jiang, Matthew S Ackerman, Jacqueline Lopez, Brent Harker, R Taylor Raborn, W Kelley Thomas,[...]. G3 (Bethesda) 2017
51
31

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
16

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
16

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting.
Xiaojun Zhang, Jianbo Yuan, Yamin Sun, Shihao Li, Yi Gao, Yang Yu, Chengzhang Liu, Quanchao Wang, Xinjia Lv, Xiaoxi Zhang,[...]. Nat Commun 2019
155
15


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
12

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model.
Brooks E Miner, Luc De Meester, Michael E Pfrender, Winfried Lampert, Nelson G Hairston. Proc Biol Sci 2012
153
12

The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion.
Damian Kao, Alvina G Lai, Evangelia Stamataki, Silvana Rosic, Nikolaos Konstantinides, Erin Jarvis, Alessia Di Donfrancesco, Natalia Pouchkina-Stancheva, Marie Sémon, Marco Grillo,[...]. Elife 2016
90
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
11

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
10

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
10

Clonal genome evolution and rapid invasive spread of the marbled crayfish.
Julian Gutekunst, Ranja Andriantsoa, Cassandra Falckenhayn, Katharina Hanna, Wolfgang Stein, Jeanne Rasamy, Frank Lyko. Nat Ecol Evol 2018
81
11

High mutational rates of large-scale duplication and deletion in Daphnia pulex.
Nathan Keith, Abraham E Tucker, Craig E Jackson, Way Sung, José Ignacio Lucas Lledó, Daniel R Schrider, Sarah Schaack, Jeffry L Dudycha, Matthew Ackerman, Andrew J Younge,[...]. Genome Res 2016
56
16



Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.
Luisa Orsini, Donald Gilbert, Ram Podicheti, Mieke Jansen, James B Brown, Omid Shams Solari, Katina I Spanier, John K Colbourne, Douglas B Rusch, Ellen Decaestecker,[...]. Sci Data 2016
62
12

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Brian J Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,[...]. Nat Protoc 2013
8


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
987
8



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
92
7

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
7

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler. Bioinformatics 2008
824
7

Gene finding in novel genomes.
Ian Korf. BMC Bioinformatics 2004
7


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
7


Population Genomics of Daphnia pulex.
Michael Lynch, Ryan Gutenkunst, Matthew Ackerman, Ken Spitze, Zhiqiang Ye, Takahiro Maruki, Zhiyuan Jia. Genetics 2017
29
20

BUSCO: Assessing Genome Assembly and Annotation Completeness.
Mathieu Seppey, Mosè Manni, Evgeny M Zdobnov. Methods Mol Biol 2019
677
6



edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
6


Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex.
Abraham E Tucker, Matthew S Ackerman, Brian D Eads, Sen Xu, Michael Lynch. Proc Natl Acad Sci U S A 2013
94
6

A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.
Marinela Dukić, Daniel Berner, Marius Roesti, Christoph R Haag, Dieter Ebert. BMC Genet 2016
32
18

InterProScan 5: genome-scale protein function classification.
Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka,[...]. Bioinformatics 2014
6

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
6


The opsins.
Akihisa Terakita. Genome Biol 2005
330
5


OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li Li, Christian J Stoeckert, David S Roos. Genome Res 2003
5

Identification of putative ecdysteroid and juvenile hormone pathway genes in the shrimp Neocaridina denticulata.
Yung Wa Sin, Nathan J Kenny, Zhe Qu, Ka Wo Chan, Katie W S Chan, Sam P S Cheong, Ricky W T Leung, Ting Fung Chan, William G Bendena, Ka Hou Chu,[...]. Gen Comp Endocrinol 2015
47
10

Methyl farnesoate synthesis is necessary for the environmental sex determination in the water flea Daphnia pulex.
Kenji Toyota, Hitoshi Miyakawa, Chizue Hiruta, Kenjiro Furuta, Yukiko Ogino, Tetsuro Shinoda, Norihisa Tatarazako, Shinichi Miyagawa, Joseph R Shaw, Taisen Iguchi. J Insect Physiol 2015
53
9

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective.
Jouni Kvist, Camila Gonçalves Athanàsio, Omid Shams Solari, James B Brown, John K Colbourne, Michael E Pfrender, Leda Mirbahai. Genome Biol Evol 2018
20
25

Gene Body Methylation Patterns in Daphnia Are Associated with Gene Family Size.
Jana Asselman, Dieter I M De Coninck, Michael E Pfrender, Karel A C De Schamphelaere. Genome Biol Evol 2016
25
20

The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments.
Luisa Orsini, Klaus Schwenk, Luc De Meester, John K Colbourne, Michael E Pfrender, Lawrence J Weider. Trends Ecol Evol 2013
59
8

De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia galeata.
Ann Kathrin Huylmans, Alberto López Ezquerra, John Parsch, Mathilde Cordellier. Genome Biol Evol 2016
26
19


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.