A citation-based method for searching scientific literature

Marco Gerdol, Klevia Dishnica, Alejandro Giorgetti. Virus Res 2022
Times Cited: 11







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



Times Cited
  Times     Co-cited
Similarity



Nextstrain: real-time tracking of pathogen evolution.
James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher. Bioinformatics 2018
36

Indels in SARS-CoV-2 occur at template-switching hotspots.
Brianna Sierra Chrisman, Kelley Paskov, Nate Stockham, Kevin Tabatabaei, Jae-Yoon Jung, Peter Washington, Maya Varma, Min Woo Sun, Sepideh Maleki, Dennis P Wall. BioData Min 2021
12
27

GISAID's Role in Pandemic Response.
Shruti Khare, Céline Gurry, Lucas Freitas, Mark B Schultz, Gunter Bach, Amadou Diallo, Nancy Akite, Joses Ho, Raphael Tc Lee, Winston Yeo,[...]. China CDC Wkly 2021
66
27

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Raquel Viana, Sikhulile Moyo, Daniel G Amoako, Houriiyah Tegally, Cathrine Scheepers, Christian L Althaus, Ugochukwu J Anyaneji, Phillip A Bester, Maciej F Boni, Mohammed Chand,[...]. Nature 2022
297
27

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape.
Kevin R McCarthy, Linda J Rennick, Sham Nambulli, Lindsey R Robinson-McCarthy, William G Bain, Ghady Haidar, W Paul Duprex. Science 2021
292
27

Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.
Tyler N Starr, Allison J Greaney, Sarah K Hilton, Daniel Ellis, Katharine H D Crawford, Adam S Dingens, Mary Jane Navarro, John E Bowen, M Alejandra Tortorici, Alexandra C Walls,[...]. Cell 2020
869
27


Exploring human 40S ribosomal proteins binding to the 18S rRNA fragment containing major 3'-terminal domain.
Alexander V Gopanenko, Alexey A Malygin, Galina G Karpova. Biochim Biophys Acta 2015
7
28

Host-Virus Chimeric Events in SARS-CoV-2-Infected Cells Are Infrequent and Artifactual.
Bingyu Yan, Srishti Chakravorty, Carmen Mirabelli, Luopin Wang, Jorge L Trujillo-Ochoa, Daniel Chauss, Dhaneshwar Kumar, Michail S Lionakis, Matthew R Olson, Christiane E Wobus,[...]. J Virol 2021
18
18



bpRNA: large-scale automated annotation and analysis of RNA secondary structure.
Padideh Danaee, Mason Rouches, Michelle Wiley, Dezhong Deng, Liang Huang, David Hendrix. Nucleic Acids Res 2018
37
18

Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting.
Fran Robson, Khadija Shahed Khan, Thi Khanh Le, Clément Paris, Sinem Demirbag, Peter Barfuss, Palma Rocchi, Wai-Lung Ng. Mol Cell 2020
170
18


Assessment of potential SARS-CoV-2 virus integration into human genome reveals no significant impact on RT-qPCR COVID-19 testing.
Erica Briggs, William Ward, Sol Rey, Dylan Law, Katharine Nelson, Michael Bois, Nili Ostrov, Henry H Lee, Jon M Laurent, Paolo Mita. Proc Natl Acad Sci U S A 2021
7
28

Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2.
Katherine Laiton-Donato, Carlos Franco-Muñoz, Diego A Álvarez-Díaz, Hector Alejandro Ruiz-Moreno, José A Usme-Ciro, Diego Andrés Prada, Jhonnatan Reales-González, Sheryll Corchuelo, María T Herrera-Sepúlveda, Julian Naizaque,[...]. Infect Genet Evol 2021
56
18

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner. Nucleic Acids Res 2013
18

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
18

Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking.
Sander Granneman, Elisabeth Petfalski, Agata Swiatkowska, David Tollervey. EMBO J 2010
107
18

SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma.
Emanuele Andreano, Giulia Piccini, Danilo Licastro, Lorenzo Casalino, Nicole V Johnson, Ida Paciello, Simeone Dal Monego, Elisa Pantano, Noemi Manganaro, Alessandro Manenti,[...]. Proc Natl Acad Sci U S A 2021
151
18


SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum.
Kèvin Knoops, Marjolein Kikkert, Sjoerd H E van den Worm, Jessika C Zevenhoven-Dobbe, Yvonne van der Meer, Abraham J Koster, A Mieke Mommaas, Eric J Snijder. PLoS Biol 2008
631
18

The Architecture of SARS-CoV-2 Transcriptome.
Dongwan Kim, Joo-Yeon Lee, Jeong-Sun Yang, Jun Won Kim, V Narry Kim, Hyeshik Chang. Cell 2020
961
18

Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein.
Jian Lei, Yuri Kusov, Rolf Hilgenfeld. Antiviral Res 2018
294
18


Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination.
Yiyan Yang, Wei Yan, A Brantley Hall, Xiaofang Jiang. Mol Biol Evol 2021
24
18

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.
Yatish Turakhia, Bryan Thornlow, Angie S Hinrichs, Nicola De Maio, Landen Gozashti, Robert Lanfear, David Haussler, Russell Corbett-Detig. Nat Genet 2021
61
18

The architecture of the SARS-CoV-2 RNA genome inside virion.
Changchang Cao, Zhaokui Cai, Xia Xiao, Jian Rao, Juan Chen, Naijing Hu, Minnan Yang, Xiaorui Xing, Yongle Wang, Manman Li,[...]. Nat Commun 2021
42
18

Molecular Evolution of Human Coronavirus Genomes.
Diego Forni, Rachele Cagliani, Mario Clerici, Manuela Sironi. Trends Microbiol 2017
362
18


Ubiquitination of SARS-CoV-2 ORF7a promotes antagonism of interferon response.
Zengguo Cao, Hongjie Xia, Ricardo Rajsbaum, Xianzhu Xia, Hualei Wang, Pei-Yong Shi. Cell Mol Immunol 2021
36
18

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
18

The SARS-CoV-2 subgenome landscape and its novel regulatory features.
Dehe Wang, Ao Jiang, Jiangpeng Feng, Guangnan Li, Dong Guo, Muhammad Sajid, Kai Wu, Qiuhan Zhang, Yann Ponty, Sebastian Will,[...]. Mol Cell 2021
28
18

Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14+ monocytes.
Ziliang Zhou, Chunliu Huang, Zhechong Zhou, Zhaoxia Huang, Lili Su, Sisi Kang, Xiaoxue Chen, Qiuyue Chen, Suhua He, Xia Rong,[...]. iScience 2021
46
18

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms.
Nicholas C Huston, Han Wan, Madison S Strine, Rafael de Cesaris Araujo Tavares, Craig B Wilen, Anna Marie Pyle. Mol Cell 2021
84
18

Why do RNA viruses recombine?
Etienne Simon-Loriere, Edward C Holmes. Nat Rev Microbiol 2011
348
18


Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues.
Liguo Zhang, Alexsia Richards, M Inmaculada Barrasa, Stephen H Hughes, Richard A Young, Rudolf Jaenisch. Proc Natl Acad Sci U S A 2021
73
18

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
Nathan D Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L Matteson, Jaqueline Goes De Jesus, Bradley J Main, Amanda L Tan, Lauren M Paul, Doug E Brackney, Saran Grewal,[...]. Genome Biol 2019
289
18


NanoPack: visualizing and processing long-read sequencing data.
Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven. Bioinformatics 2018
620
18

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
18

Membrane rearrangements mediated by coronavirus nonstructural proteins 3 and 4.
Marne C Hagemeijer, Iryna Monastyrska, Janice Griffith, Peter van der Sluijs, Jarno Voortman, Paul M van Bergen en Henegouwen, Annelotte M Vonk, Peter J M Rottier, Fulvio Reggiori, Cornelis A M de Haan. Virology 2014
90
18


Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.
Erik Volz, Swapnil Mishra, Meera Chand, Jeffrey C Barrett, Robert Johnson, Lily Geidelberg, Wes R Hinsley, Daniel J Laydon, Gavin Dabrera, Áine O'Toole,[...]. Nature 2021
467
18

A new coronavirus associated with human respiratory disease in China.
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei,[...]. Nature 2020
18

Response to Parry et al.: Strong evidence for genomic integration of SARS-CoV-2 sequences and expression in patient tissues.
Liguo Zhang, Alexsia Richards, M Inmaculada Barrasa, Stephen H Hughes, Richard A Young, Rudolf Jaenisch. Proc Natl Acad Sci U S A 2021
4
50

No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues.
Rhys Parry, Robert J Gifford, Spyros Lytras, Stuart C Ray, Lachlan J M Coin. Proc Natl Acad Sci U S A 2021
14
18

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
18


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.