A citation-based method for searching scientific literature

Ian M Rambo, Marguerite V Langwig, Pedro Leão, Valerie De Anda, Brett J Baker. Nat Microbiol 2022
Times Cited: 3







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



Times Cited
  Times     Co-cited
Similarity


Expanded diversity of Asgard archaea and their relationships with eukaryotes.
Yang Liu, Kira S Makarova, Wen-Cong Huang, Yuri I Wolf, Anastasia N Nikolskaya, Xinxu Zhang, Mingwei Cai, Cui-Jing Zhang, Wei Xu, Zhuhua Luo,[...]. Nature 2021
52
100

Complex archaea that bridge the gap between prokaryotes and eukaryotes.
Anja Spang, Jimmy H Saw, Steffen L Jørgensen, Katarzyna Zaremba-Niedzwiedzka, Joran Martijn, Anders E Lind, Roel van Eijk, Christa Schleper, Lionel Guy, Thijs J G Ettema. Nature 2015
575
100

Viruses of archaea: Structural, functional, environmental and evolutionary genomics.
Mart Krupovic, Virginija Cvirkaite-Krupovic, Jaime Iranzo, David Prangishvili, Eugene V Koonin. Virus Res 2018
110
100

Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes.
Fabai Wu, Daan R Speth, Alon Philosof, Antoine Crémière, Aditi Narayanan, Roman A Barco, Stephanie A Connon, Jan P Amend, Igor A Antoshechkin, Victoria J Orphan. Nat Microbiol 2022
10
66

CRISPRDetect: A flexible algorithm to define CRISPR arrays.
Ambarish Biswas, Raymond H J Staals, Sergio E Morales, Peter C Fineran, Chris M Brown. BMC Genomics 2016
154
66

Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea.
Jong-Geol Kim, So-Jeong Kim, Virginija Cvirkaite-Krupovic, Woon-Jong Yu, Joo-Han Gwak, Mario López-Pérez, Francisco Rodriguez-Valera, Mart Krupovic, Jang-Cheon Cho, Sung-Keun Rhee. Proc Natl Acad Sci U S A 2019
27
66

Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway.
Jia-Wei Zhang, Hong-Po Dong, Li-Jun Hou, Yang Liu, Ya-Fei Ou, Yan-Ling Zheng, Ping Han, Xia Liang, Guo-Yu Yin, Dian-Ming Wu,[...]. ISME J 2021
11
66


Asgard archaea illuminate the origin of eukaryotic cellular complexity.
Katarzyna Zaremba-Niedzwiedzka, Eva F Caceres, Jimmy H Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U Kjeldsen,[...]. Nature 2017
491
66

HH-suite3 for fast remote homology detection and deep protein annotation.
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
271
66

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs.
Clovis Galiez, Matthias Siebert, François Enault, Jonathan Vincent, Johannes Söding. Bioinformatics 2017
90
66


Unification of the globally distributed spindle-shaped viruses of the Archaea.
Mart Krupovic, Emmanuelle R J Quemin, Dennis H Bamford, Patrick Forterre, David Prangishvili. J Virol 2014
58
66

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
66

Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
772
66

SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts.
R Zhang, M Mirdita, E Levy Karin, C Norroy, C Galiez, J Söding. Bioinformatics 2021
17
66

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes.
Sofia Medvedeva, Jiarui Sun, Natalya Yutin, Eugene V Koonin, Takuro Nunoura, Christian Rinke, Mart Krupovic. Nat Microbiol 2022
3
66

Lytic archaeal viruses infect abundant primary producers in Earth's crust.
Janina Rahlff, Victoria Turzynski, Sarah P Esser, Indra Monsees, Till L V Bornemann, Perla Abigail Figueroa-Gonzalez, Frederik Schulz, Tanja Woyke, Andreas Klingl, Cristina Moraru,[...]. Nat Commun 2021
8
66

Global Organization and Proposed Megataxonomy of the Virus World.
Eugene V Koonin, Valerian V Dolja, Mart Krupovic, Arvind Varsani, Yuri I Wolf, Natalya Yutin, F Murilo Zerbini, Jens H Kuhn. Microbiol Mol Biol Rev 2020
194
66

A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses.
Daniel Tamarit, Eva F Caceres, Mart Krupovic, Reindert Nijland, Laura Eme, Nicholas P Robinson, Thijs J G Ettema. Nat Microbiol 2022
4
66

Prokaryotic viperins produce diverse antiviral molecules.
Aude Bernheim, Adi Millman, Gal Ofir, Gilad Meitav, Carmel Avraham, Helena Shomar, Masha M Rosenberg, Nir Tal, Sarah Melamed, Gil Amitai,[...]. Nature 2021
52
33

A complete domain-to-species taxonomy for Bacteria and Archaea.
Donovan H Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J Mussig, Philip Hugenholtz. Nat Biotechnol 2020
381
33


Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.
Brett J Baker, Jimmy H Saw, Anders E Lind, Cassandre Sara Lazar, Kai-Uwe Hinrichs, Andreas P Teske, Thijs J G Ettema. Nat Microbiol 2016
71
33

Phylogenomics provides robust support for a two-domains tree of life.
Tom A Williams, Cymon J Cox, Peter G Foster, Gergely J Szöllősi, T Martin Embley. Nat Ecol Evol 2020
86
33

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.
Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear. Mol Biol Evol 2020
33

DISARM is a widespread bacterial defence system with broad anti-phage activities.
Gal Ofir, Sarah Melamed, Hila Sberro, Zohar Mukamel, Shahar Silverman, Gilad Yaakov, Shany Doron, Rotem Sorek. Nat Microbiol 2018
118
33

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
33


Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes.
Mart Krupovic, Jens H Kuhn, Fengbin Wang, Diana P Baquero, Valerian V Dolja, Edward H Egelman, David Prangishvili, Eugene V Koonin. J Virol 2021
9
33

CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems.
Victor A Padilha, Omer S Alkhnbashi, Shiraz A Shah, André C P L F de Carvalho, Rolf Backofen. Gigascience 2020
16
33

CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.
Ambarish Biswas, Joshua N Gagnon, Stan J J Brouns, Peter C Fineran, Chris M Brown. RNA Biol 2013
178
33

Novel Sulfolobus Virus with an Exceptional Capsid Architecture.
Haina Wang, Zhenqian Guo, Hongli Feng, Yufei Chen, Xiuqiang Chen, Zhimeng Li, Walter Hernández-Ascencio, Xin Dai, Zhenfeng Zhang, Xiaowei Zheng,[...]. J Virol 2018
16
33

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.
David Paez-Espino, I-Min A Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, Ernest Szeto, Manoj Pillay, Jinghua Huang, Victor M Markowitz, Torben Nielsen,[...]. Nucleic Acids Res 2017
101
33

CDD/SPARCLE: the conserved domain database in 2020.
Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song,[...]. Nucleic Acids Res 2020
819
33

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
Ryan R Wick, Louise M Judd, Claire L Gorrie, Kathryn E Holt. PLoS Comput Biol 2017
33

Systematic discovery of antiphage defense systems in the microbial pangenome.
Shany Doron, Sarah Melamed, Gal Ofir, Azita Leavitt, Anna Lopatina, Mai Keren, Gil Amitai, Rotem Sorek. Science 2018
356
33


Renewing Felsenstein's phylogenetic bootstrap in the era of big data.
F Lemoine, J-B Domelevo Entfellner, E Wilkinson, D Correia, M Dávila Felipe, T De Oliveira, O Gascuel. Nature 2018
218
33

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
33

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.
Dinghua Li, Ruibang Luo, Chi-Man Liu, Chi-Ming Leung, Hing-Fung Ting, Kunihiko Sadakane, Hiroshi Yamashita, Tak-Wah Lam. Methods 2016
524
33

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
A A Schäffer, L Aravind, T L Madden, S Shavirin, J L Spouge, Y I Wolf, E V Koonin, S F Altschul. Nucleic Acids Res 2001
949
33

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.
Jiarong Guo, Ben Bolduc, Ahmed A Zayed, Arvind Varsani, Guillermo Dominguez-Huerta, Tom O Delmont, Akbar Adjie Pratama, M Consuelo Gazitúa, Dean Vik, Matthew B Sullivan,[...]. Microbiome 2021
97
33


RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.
Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Cole H Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M Duarte,[...]. Nucleic Acids Res 2021
370
33

CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
33

Pfam: The protein families database in 2021.
Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A Salazar, Erik L L Sonnhammer, Silvio C E Tosatto, Lisanna Paladin, Shriya Raj, Lorna J Richardson,[...]. Nucleic Acids Res 2021
967
33

genoPlotR: comparative gene and genome visualization in R.
Lionel Guy, Jens Roat Kultima, Siv G E Andersson. Bioinformatics 2010
376
33


GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.
Donovan H Parks, Maria Chuvochina, Christian Rinke, Aaron J Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz. Nucleic Acids Res 2022
90
33


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.