A citation-based method for searching scientific literature

Emma Persson, Miguel Castresana-Aguirre, Davide Buzzao, Dimitri Guala, Erik L L Sonnhammer. J Mol Biol 2021
Times Cited: 4







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



Times Cited
  Times     Co-cited
Similarity


HumanNet v2: human gene networks for disease research.
Sohyun Hwang, Chan Yeong Kim, Sunmo Yang, Eiru Kim, Traver Hart, Edward M Marcotte, Insuk Lee. Nucleic Acids Res 2019
65
50

iRefIndex: a consolidated protein interaction database with provenance.
Sabry Razick, George Magklaras, Ian M Donaldson. BMC Bioinformatics 2008
354
50

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork,[...]. Nucleic Acids Res 2021
374
50

PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters.
Wei Su, Meng-Lu Liu, Yu-He Yang, Jia-Shu Wang, Shi-Hao Li, Hao Lv, Fu-Ying Dao, Hui Yang, Hao Lin. J Mol Biol 2021
15
25

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive.
Yana Rose, Jose M Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi Bhikadiya, Li Chen, Alexander S Rose, Sebastian Bittrich, Stephen K Burley,[...]. J Mol Biol 2021
20
25

PolarProtDb: A Database of Transmembrane and Secreted Proteins showing Apical-Basal Polarity.
András Zeke, László Dobson, Levente István Szekeres, Tamás Langó, Gábor E Tusnády. J Mol Biol 2021
2
50

aScan: A Novel Method for the Study of Allele Specific Expression in Single Individuals.
Federico Zambelli, Matteo Chiara, Erika Ferrandi, Pietro Mandreoli, Marco Antonio Tangaro, Giulio Pavesi, Graziano Pesole. J Mol Biol 2021
1
100

MEDUSA: Prediction of Protein Flexibility from Sequence.
Yann Vander Meersche, Gabriel Cretin, Alexandre G de Brevern, Jean-Christophe Gelly, Tatiana Galochkina. J Mol Biol 2021
8
25

RiPPMiner-Genome: A Web Resource for Automated Prediction of Crosslinked Chemical Structures of RiPPs by Genome Mining.
Priyesh Agrawal, Sana Amir, Deepak, Drishtee Barua, Debasisa Mohanty. J Mol Biol 2021
5
25

BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins.
Giovanni Madeo, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio. J Mol Biol 2021
3
33





Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.
Andrew I Jewett, David Stelter, Jason Lambert, Shyam M Saladi, Otello M Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M Bashusqeh, Tom Keyes,[...]. J Mol Biol 2021
13
25


interferENZY: A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis.
Maria Filipa Pinto, Antonio Baici, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro, Annalisa Pastore, Fernando Rocha, Pedro M Martins. J Mol Biol 2021
2
50

MPTherm-pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins.
A Kulandaisamy, Jan Zaucha, Dmitrij Frishman, M Michael Gromiha. J Mol Biol 2021
5
25

ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins.
R Prabakaran, Puneet Rawat, Sandeep Kumar, M Michael Gromiha. J Mol Biol 2021
5
25

ncRNAVar: A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases.
Wenliang Zhang, Binghui Zeng, Minglei Yang, Huan Yang, Jianbo Wang, Yongjie Deng, Haiyue Zhang, Guocai Yao, Song Wu, Weizhong Li. J Mol Biol 2021
5
25

ModFlex: Towards Function Focused Protein Modeling.
Mayya Sedova, Lukasz Jaroszewski, Mallika Iyer, Zhanwen Li, Adam Godzik. J Mol Biol 2021
1
100

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences.
Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A Andrade-Navarro. J Mol Biol 2021
1
100


FunRich enables enrichment analysis of OMICs datasets.
Pamali Fonseka, Mohashin Pathan, Sai V Chitti, Taeyoung Kang, Suresh Mathivanan. J Mol Biol 2021
36
25

Constrained Standardization of Count Data from Massive Parallel Sequencing.
Joris Van Houtven, Bart Cuypers, Pieter Meysman, Jef Hooyberghs, Kris Laukens, Dirk Valkenborg. J Mol Biol 2021
1
100

Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data.
Patricia Mirela-Bota, Joaquim Aguirre-Plans, Alberto Meseguer, Cristiano Galletti, Joan Segura, Joan Planas-Iglesias, Javi Garcia-Garcia, Emre Guney, Baldo Oliva, Narcis Fernandez-Fuentes. J Mol Biol 2021
2
50

GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite.
Ruth Barshir, Simon Fishilevich, Tsippi Iny-Stein, Ofer Zelig, Yaron Mazor, Yaron Guan-Golan, Marilyn Safran, Doron Lancet. J Mol Biol 2021
3
33


geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome.
C Gómez-Martín, E Aparicio-Puerta, J M Medina, Guillermo Barturen, J L Oliver, M Hackenberg. J Mol Biol 2021
1
100

GeneMANIA update 2018.
Max Franz, Harold Rodriguez, Christian Lopes, Khalid Zuberi, Jason Montojo, Gary D Bader, Quaid Morris. Nucleic Acids Res 2018
248
25

KEGG: integrating viruses and cellular organisms.
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe. Nucleic Acids Res 2021
596
25

Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
Robin M Meyers, Jordan G Bryan, James M McFarland, Barbara A Weir, Ann E Sizemore, Han Xu, Neekesh V Dharia, Phillip G Montgomery, Glenn S Cowley, Sasha Pantel,[...]. Nat Genet 2017
642
25

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Edward L Huttlin, Raphael J Bruckner, Jose Navarrete-Perea, Joe R Cannon, Kurt Baltier, Fana Gebreab, Melanie P Gygi, Alexandra Thornock, Gabriela Zarraga, Stanley Tam,[...]. Cell 2021
66
25

The COVID-19 Drug and Gene Set Library.
Maxim V Kuleshov, Daniel J Stein, Daniel J B Clarke, Eryk Kropiwnicki, Kathleen M Jagodnik, Alon Bartal, John E Evangelista, Jason Hom, Minxuan Cheng, Allison Bailey,[...]. Patterns (N Y) 2020
39
25

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
863
25

Correction to 'The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets'.
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork,[...]. Nucleic Acids Res 2021
37
25

The DisGeNET knowledge platform for disease genomics: 2019 update.
Janet Piñero, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I Furlong. Nucleic Acids Res 2020
438
25

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
273
25

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
Christian Haenig, Nir Atias, Alexander K Taylor, Arnon Mazza, Martin H Schaefer, Jenny Russ, Sean-Patrick Riechers, Shushant Jain, Maura Coughlin, Jean-Fred Fontaine,[...]. Cell Rep 2020
14
25

A reference map of the human binary protein interactome.
Katja Luck, Dae-Kyum Kim, Luke Lambourne, Kerstin Spirohn, Bridget E Begg, Wenting Bian, Ruth Brignall, Tiziana Cafarelli, Francisco J Campos-Laborie, Benoit Charloteaux,[...]. Nature 2020
223
25



Systematic Evaluation of Molecular Networks for Discovery of Disease Genes.
Justin K Huang, Daniel E Carlin, Michael Ku Yu, Wei Zhang, Jason F Kreisberg, Pablo Tamayo, Trey Ideker. Cell Syst 2018
99
25

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A Fulcher, Timothy A Holland, Ingrid M Keseler, Anamika Kothari, Aya Kubo,[...]. Nucleic Acids Res 2014
630
25

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.
Danielle Welter, Jacqueline MacArthur, Joannella Morales, Tony Burdett, Peggy Hall, Heather Junkins, Alan Klemm, Paul Flicek, Teri Manolio, Lucia Hindorff,[...]. Nucleic Acids Res 2014
25

Prioritizing candidate disease genes by network-based boosting of genome-wide association data.
Insuk Lee, U Martin Blom, Peggy I Wang, Jung Eun Shim, Edward M Marcotte. Genome Res 2011
420
25

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Jonas Schulte-Schrepping, Nico Reusch, Daniela Paclik, Kevin Baßler, Stephan Schlickeiser, Bowen Zhang, Benjamin Krämer, Tobias Krammer, Sophia Brumhard, Lorenzo Bonaguro,[...]. Cell 2020
501
25

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.
Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett,[...]. Nucleic Acids Res 2018
38
25

The ConsensusPathDB interaction database: 2013 update.
Atanas Kamburov, Ulrich Stelzl, Hans Lehrach, Ralf Herwig. Nucleic Acids Res 2013
506
25

The Human Phenotype Ontology in 2021.
Sebastian Köhler, Michael Gargano, Nicolas Matentzoglu, Leigh C Carmody, David Lewis-Smith, Nicole A Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M Brower,[...]. Nucleic Acids Res 2021
106
25


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.