A citation-based method for searching scientific literature

Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex Bateman, Marco Punta, Teresa K Attwood, Christian J A Sigrist, Nicole Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork, Ivica Letunic, Julian Gough, Matt Oates, Daniel Haft, Hongzhan Huang, Darren A Natale, Cathy H Wu, Christine Orengo, Ian Sillitoe, Huaiyu Mi, Paul D Thomas, Robert D Finn. Nucleic Acids Res 2015
Times Cited: 874







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



Times Cited
  Times     Co-cited
Similarity


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
16

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
15

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
14

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

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
10

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
9

Automated generation of heuristics for biological sequence comparison.
Guy St C Slater, Ewan Birney. BMC Bioinformatics 2005
9

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
9


OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li Li, Christian J Stoeckert, David S Roos. Genome Res 2003
8




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
7

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
7

The Pfam protein families database: towards a more sustainable future.
Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas,[...]. Nucleic Acids Res 2016
7

De novo identification of repeat families in large genomes.
Alkes L Price, Neil C Jones, Pavel A Pevzner. Bioinformatics 2005
7


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
7

PubChem Substance and Compound databases.
Sunghwan Kim, Paul A Thiessen, Evan E Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A Shoemaker,[...]. Nucleic Acids Res 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
7


KEGG for integration and interpretation of large-scale molecular data sets.
Minoru Kanehisa, Susumu Goto, Yoko Sato, Miho Furumichi, Mao Tanabe. Nucleic Acids Res 2012
7

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
6

HMMER web server: interactive sequence similarity searching.
Robert D Finn, Jody Clements, Sean R Eddy. Nucleic Acids Res 2011
6

CDD: NCBI's conserved domain database.
Aron Marchler-Bauer, Myra K Derbyshire, Noreen R Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y Geer, Renata C Geer, Jane He, Marc Gwadz, David I Hurwitz,[...]. Nucleic Acids Res 2015
6

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
625
6

Repbase Update, a database of eukaryotic repetitive elements.
J Jurka, V V Kapitonov, A Pavlicek, P Klonowski, O Kohany, J Walichiewicz. Cytogenet Genome Res 2005
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

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
6

Predicting drug-disease associations by using similarity constrained matrix factorization.
Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang, Feng Liu. BMC Bioinformatics 2018
86
6


LRSSL: predict and interpret drug-disease associations based on data integration using sparse subspace learning.
Xujun Liang, Pengfei Zhang, Lu Yan, Ying Fu, Fang Peng, Lingzhi Qu, Meiying Shao, Yongheng Chen, Zhuchu Chen. Bioinformatics 2017
57
10

Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm.
Huimin Luo, Jianxin Wang, Min Li, Junwei Luo, Xiaoqing Peng, Fang-Xiang Wu, Yi Pan. Bioinformatics 2016
140
6

SMART: recent updates, new developments and status in 2015.
Ivica Letunic, Tobias Doerks, Peer Bork. Nucleic Acids Res 2015
6

The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
6

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-Claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria J Martin, Karine Michoud, Claire O'Donovan, Isabelle Phan,[...]. Nucleic Acids Res 2003
6

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
6


Using RepeatMasker to identify repetitive elements in genomic sequences.
Maja Tarailo-Graovac, Nansheng Chen. Curr Protoc Bioinformatics 2009
857
5

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
5

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
5

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
5


PREDICT: a method for inferring novel drug indications with application to personalized medicine.
Assaf Gottlieb, Gideon Y Stein, Eytan Ruppin, Roded Sharan. Mol Syst Biol 2011
390
5


Enhancing the Promise of Drug Repositioning through Genetics.
Jayne-Louise E Pritchard, Tracy A O'Mara, Dylan M Glubb. Front Pharmacol 2017
36
13

Drug repositioning by integrating target information through a heterogeneous network model.
Wenhui Wang, Sen Yang, Xiang Zhang, Jing Li. Bioinformatics 2014
145
5




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.