A citation-based method for searching scientific literature

A Krogh, B Larsson, G von Heijne, E L Sonnhammer. J Mol Biol 2001
Times Cited: 7745







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



Times Cited
  Times     Co-cited
Similarity


SignalP 4.0: discriminating signal peptides from transmembrane regions.
Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Nat Methods 2011
22

SignalP 5.0 improves signal peptide predictions using deep neural networks.
José Juan Almagro Armenteros, Konstantinos D Tsirigos, Casper Kaae Sønderby, Thomas Nordahl Petersen, Ole Winther, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Nat Biotechnol 2019
18

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
18

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
15

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
15

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
12

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
11


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
11

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
9

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
9

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
8

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
8



MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
8

ModelFinder: fast model selection for accurate phylogenetic estimates.
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, Lars S Jermiin. Nat Methods 2017
7

A combined transmembrane topology and signal peptide prediction method.
Lukas Käll, Anders Krogh, Erik L L Sonnhammer. J Mol Biol 2004
7

Improved microbial gene identification with GLIMMER.
A L Delcher, D Harmon, S Kasif, O White, S L Salzberg. Nucleic Acids Res 1999
7

A hidden Markov model for predicting transmembrane helices in protein sequences.
E L Sonnhammer, G von Heijne, A Krogh. Proc Int Conf Intell Syst Mol Biol 1998
7

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
6

Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
O Emanuelsson, H Nielsen, S Brunak, G von Heijne. J Mol Biol 2000
6

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
6

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
6



New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Stéphane Guindon, Jean-François Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk, Olivier Gascuel. Syst Biol 2010
6

Improved prediction of signal peptides: SignalP 3.0.
Jannick Dyrløv Bendtsen, Henrik Nielsen, Gunnar von Heijne, Søren Brunak. J Mol Biol 2004
6

RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Staerfeldt, Torbjørn Rognes, David W Ussery. Nucleic Acids Res 2007
6

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
5


PredGPI: a GPI-anchor predictor.
Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio. BMC Bioinformatics 2008
338
5

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.
Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin. Nucleic Acids Res 2018
452
5

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
5

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.
Lukas Zimmermann, Andrew Stephens, Seung-Zin Nam, David Rau, Jonas Kübler, Marko Lozajic, Felix Gabler, Johannes Söding, Andrei N Lupas, Vikram Alva. J Mol Biol 2018
814
5

UniProt: the universal protein knowledgebase.
The UniProt Consortium. Nucleic Acids Res 2018
809
5


Apollo: Democratizing genome annotation.
Nathan A Dunn, Deepak R Unni, Colin Diesh, Monica Munoz-Torres, Nomi L Harris, Eric Yao, Helena Rasche, Ian H Holmes, Christine G Elsik, Suzanna E Lewis. PLoS Comput Biol 2019
58
8

Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation.
Jolene Ramsey, Helena Rasche, Cory Maughmer, Anthony Criscione, Eleni Mijalis, Mei Liu, James C Hu, Ry Young, Jason J Gill. PLoS Comput Biol 2020
26
19


Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server.
Lukas Käll, Anders Krogh, Erik L L Sonnhammer. Nucleic Acids Res 2007
886
5

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
5

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Nancy Y Yu, James R Wagner, Matthew R Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S Cenk Sahinalp, Martin Ester, Leonard J Foster,[...]. Bioinformatics 2010
5


Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
5

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.
Konstantinos D Tsirigos, Christoph Peters, Nanjiang Shu, Lukas Käll, Arne Elofsson. Nucleic Acids Res 2015
396
4

Proteinortho: detection of (co-)orthologs in large-scale analysis.
Marcus Lechner, Sven Findeiss, Lydia Steiner, Manja Marz, Peter F Stadler, Sonja J Prohaska. BMC Bioinformatics 2011
617
4


trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
4

MycoCosm portal: gearing up for 1000 fungal genomes.
Igor V Grigoriev, Roman Nikitin, Sajeet Haridas, Alan Kuo, Robin Ohm, Robert Otillar, Robert Riley, Asaf Salamov, Xueling Zhao, Frank Korzeniewski,[...]. Nucleic Acids Res 2014
575
4


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.