A citation-based method for searching scientific literature

. Nucleic Acids Res 2019
Times Cited: 3610







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



Times Cited
  Times     Co-cited
Similarity


Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
10

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
7

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
7

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
7

The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.
Gil Stelzer, Naomi Rosen, Inbar Plaschkes, Shahar Zimmerman, Michal Twik, Simon Fishilevich, Tsippi Iny Stein, Ron Nudel, Iris Lieder, Yaron Mazor,[...]. Curr Protoc Bioinformatics 2016
7

UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
6

SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
6

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
6

DrugBank 5.0: a major update to the DrugBank database for 2018.
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
6

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
6

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 Pfam protein families database in 2019.
Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart,[...]. Nucleic Acids Res 2019
6

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
6

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
5

The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher,[...]. Nucleic Acids Res 2019
5


Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
5

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
5

PubChem in 2021: new data content and improved web interfaces.
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu,[...]. Nucleic Acids Res 2021
725
5

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
4

WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
4


The Phyre2 web portal for protein modeling, prediction and analysis.
Lawrence A Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J E Sternberg. Nat Protoc 2015
4

KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
4

The reactome pathway knowledgebase.
Bijay Jassal, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, Justin Cook, Marc Gillespie, Robin Haw,[...]. Nucleic Acids Res 2020
4

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
4



The EMBL-EBI search and sequence analysis tools APIs in 2019.
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
3


trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
3

Phylogeny-aware alignment with PRANK.
Ari Löytynoja. Methods Mol Biol 2014
313
3

The sequence read archive.
Rasko Leinonen, Hideaki Sugawara, Martin Shumway. Nucleic Acids Res 2011
3

Fast and sensitive taxonomic classification for metagenomics with Kaiju.
Peter Menzel, Kim Lee Ng, Anders Krogh. Nat Commun 2016
675
3

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Donovan H Parks, Michael Imelfort, Connor T Skennerton, Philip Hugenholtz, Gene W Tyson. Genome Res 2015
3

Centrifuge: rapid and sensitive classification of metagenomic sequences.
Daehwan Kim, Li Song, Florian P Breitwieser, Steven L Salzberg. Genome Res 2016
484
3

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
3

Pfam: the protein families database.
Robert D Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry,[...]. Nucleic Acids Res 2014
3

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
3

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
David Warde-Farley, Sylva L Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes,[...]. Nucleic Acids Res 2010
3


Unified rational protein engineering with sequence-based deep representation learning.
Ethan C Alley, Grigory Khimulya, Surojit Biswas, Mohammed AlQuraishi, George M Church. Nat Methods 2019
211
3

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Sandra Orchard, Mais Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro,[...]. Nucleic Acids Res 2014
3

The BioGRID interaction database: 2019 update.
Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, Jennifer Rust, Lorrie Boucher, Christie Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam,[...]. Nucleic Acids Res 2019
633
3

Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics.
Yunxia Wang, Song Zhang, Fengcheng Li, Ying Zhou, Ying Zhang, Zhengwen Wang, Runyuan Zhang, Jiang Zhu, Yuxiang Ren, Ying Tan,[...]. Nucleic Acids Res 2020
370
3

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies.
Jing Tang, Jianbo Fu, Yunxia Wang, Bo Li, Yinghong Li, Qingxia Yang, Xuejiao Cui, Jiajun Hong, Xiaofeng Li, Yuzong Chen,[...]. Brief Bioinform 2020
97
3


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
3



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.