A citation-based method for searching scientific literature

Christopher I Keeling, Erin O Campbell, Philip D Batista, Victor A Shegelski, Stephen A L Trevoy, Dezene P W Huber, Jasmine K Janes, Felix A H Sperling. Mol Ecol Resour 2022
Times Cited: 1







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



Times Cited
  Times     Co-cited
Similarity


A chromosome-level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology.
Mengyao Chen, Yang Mei, Xu Chen, Xi Chen, Da Xiao, Kang He, Qiang Li, Mengmeng Wu, Su Wang, Fan Zhang,[...]. Mol Ecol Resour 2021
8
100

A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance.
Fanghao Wan, Chuanlin Yin, Rui Tang, Maohua Chen, Qiang Wu, Cong Huang, Wanqiang Qian, Omar Rota-Stabelli, Nianwan Yang, Shuping Wang,[...]. Nat Commun 2019
50
100

PILER: identification and classification of genomic repeats.
Robert C Edgar, Eugene W Myers. Bioinformatics 2005
349
100


OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li Li, Christian J Stoeckert, David S Roos. Genome Res 2003
100

Constitutive roles for inducible genes: evidence for the alteration in expression of the inducible hsp70 gene in Antarctic notothenioid fishes.
Sean P Place, Mackenzie L Zippay, Gretchen E Hofmann. Am J Physiol Regul Integr Comp Physiol 2004
77
100


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
890
100

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

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest.
Claude Rispe, Fabrice Legeai, Paul D Nabity, Rosa Fernández, Arinder K Arora, Patrice Baa-Puyoulet, Celeste R Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue,[...]. BMC Biol 2020
22
100


GeneID in Drosophila.
G Parra, E Blanco, R Guigó. Genome Res 2000
245
100

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.
Jae Young Choi, Zoe N Lye, Simon C Groen, Xiaoguang Dai, Priyesh Rughani, Sophie Zaaijer, Eoghan D Harrington, Sissel Juul, Michael D Purugganan. Genome Biol 2020
33
100

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.
Andrew Adey, Jacob O Kitzman, Joshua N Burton, Riza Daza, Akash Kumar, Lena Christiansen, Mostafa Ronaghi, Sasan Amini, Kevin L Gunderson, Frank J Steemers,[...]. Genome Res 2014
101
100

The role of lineage-specific gene family expansion in the evolution of eukaryotes.
Olivier Lespinet, Yuri I Wolf, Eugene V Koonin, L Aravind. Genome Res 2002
317
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
578
100

Understanding the biological basis of psychiatric disease: What's next?
Conor Liston, Angela Roberts, Kafui Dzirasa, Dan Geschwind, Susanne E Ahmari, Christian Lüscher. Cell 2022
3
100

A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation.
Yi-Ming Weng, Charlotte B Francoeur, Cameron R Currie, David H Kavanaugh, Sean D Schoville. Mol Ecol Resour 2021
4
100

Nanopore sequencing and assembly of a human genome with ultra-long reads.
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes,[...]. Nat Biotechnol 2018
780
100

Fast model-based estimation of ancestry in unrelated individuals.
David H Alexander, John Novembre, Kenneth Lange. Genome Res 2009
100

Firefly genomes illuminate parallel origins of bioluminescence in beetles.
Timothy R Fallon, Sarah E Lower, Ching-Ho Chang, Manabu Bessho-Uehara, Gavin J Martin, Adam J Bewick, Megan Behringer, Humberto J Debat, Isaac Wong, John C Day,[...]. Elife 2018
66
100

CAFE: a computational tool for the study of gene family evolution.
Tijl De Bie, Nello Cristianini, Jeffery P Demuth, Matthew W Hahn. Bioinformatics 2006
797
100


The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
100

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
767
100

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies.
Michael J Roach, Simon A Schmidt, Anthony R Borneman. BMC Bioinformatics 2018
278
100

Chromosome-level genome assembly of the predator Propylea japonica to understand its tolerance to insecticides and high temperatures.
Lijuan Zhang, Song Li, Junyu Luo, Pei Du, Linke Wu, Yarong Li, Xiangzhen Zhu, Li Wang, Shuai Zhang, Jinjie Cui. Mol Ecol Resour 2020
25
100

Investigation of the Molecular Mechanisms of Antioxidant Damage and Immune Response Downregulation in Liver of Coilia nasus Under Starvation Stress.
Meiyao Wang, Gangchun Xu, Yongkai Tang, Shengyan Su, Yinping Wang, Zhixiang Zhu. Front Endocrinol (Lausanne) 2021
1
100

Improved reference genome of Aedes aegypti informs arbovirus vector control.
Benjamin J Matthews, Olga Dudchenko, Sarah B Kingan, Sergey Koren, Igor Antoshechkin, Jacob E Crawford, William J Glassford, Margaret Herre, Seth N Redmond, Noah H Rose,[...]. Nature 2018
221
100

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
Brian J Haas, Arthur L Delcher, Stephen M Mount, Jennifer R Wortman, Roger K Smith, Linda I Hannick, Rama Maiti, Catherine M Ronning, Douglas B Rusch, Christopher D Town,[...]. Nucleic Acids Res 2003
913
100

A paralogous decoy protects Phytophthora sojae apoplastic effector PsXEG1 from a host inhibitor.
Zhenchuan Ma, Lin Zhu, Tianqiao Song, Yang Wang, Qi Zhang, Yeqiang Xia, Min Qiu, Yachun Lin, Haiyang Li, Liang Kong,[...]. Science 2017
118
100


Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest.
Christopher I Keeling, Macaire M S Yuen, Nancy Y Liao, T Roderick Docking, Simon K Chan, Greg A Taylor, Diana L Palmquist, Shaun D Jackman, Anh Nguyen, Maria Li,[...]. Genome Biol 2013
182
100

Plant transposable elements: where genetics meets genomics.
Cédric Feschotte, Ning Jiang, Susan R Wessler. Nat Rev Genet 2002
563
100

HiCUP: pipeline for mapping and processing Hi-C data.
Steven Wingett, Philip Ewels, Mayra Furlan-Magaril, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Simon Andrews. F1000Res 2015
257
100

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.
T Rhyker Ranallo-Benavidez, Kamil S Jaron, Michael C Schatz. Nat Commun 2020
197
100

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.
Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei. Nucleic Acids Res 2011
100

Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology.
Adam C English, Stephen Richards, Yi Han, Min Wang, Vanesa Vee, Jiaxin Qu, Xiang Qin, Donna M Muzny, Jeffrey G Reid, Kim C Worley,[...]. PLoS One 2012
583
100

The pheromone frontalin and its dual function in the invasive bark beetle Dendroctonus valens.
Zhudong Liu, Bingbing Xu, Zhenwang Miao, Jianghua Sun. Chem Senses 2013
15
100

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
100

Genetic Diversity and Thermal Performance in Invasive and Native Populations of African Fig Flies.
Aaron A Comeault, Jeremy Wang, Silas Tittes, Kristin Isbell, Spencer Ingley, Allen H Hurlbert, Daniel R Matute. Mol Biol Evol 2020
10
100


High and rising economic costs of biological invasions worldwide.
Christophe Diagne, Boris Leroy, Anne-Charlotte Vaissière, Rodolphe E Gozlan, David Roiz, Ivan Jarić, Jean-Michel Salles, Corey J A Bradshaw, Franck Courchamp. Nature 2021
81
100

The genome of the model beetle and pest Tribolium castaneum.
Stephen Richards, Richard A Gibbs, George M Weinstock, Susan J Brown, Robin Denell, Richard W Beeman, Richard Gibbs, Richard W Beeman, Susan J Brown, Gregor Bucher,[...]. Nature 2008
919
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

TreeFam: a curated database of phylogenetic trees of animal gene families.
Heng Li, Avril Coghlan, Jue Ruan, Lachlan James Coin, Jean-Karim Hériché, Lara Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund,[...]. Nucleic Acids Res 2006
361
100

Infernal 1.1: 100-fold faster RNA homology searches.
Eric P Nawrocki, Sean R Eddy. Bioinformatics 2013
100

Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data.
Xingtan Zhang, Shengcheng Zhang, Qian Zhao, Ray Ming, Haibao Tang. Nat Plants 2019
115
100

GeneWise and Genomewise.
Ewan Birney, Michele Clamp, Richard Durbin. Genome Res 2004
100

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012
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.