bioconductor: PFP | Projects | Ecosyste.ms: Papers

10.3390/ijms21082873

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
Cited by: 115
Author(s): Chen Chen, Jie Hou, John J. Tanner
Software Mentions: 4
Published: over 4 years ago

PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks
Cited by: 7
Author(s): Seyyede Fatemeh Seyyedsalehi, Mahdieh Soleymani, Hamid R. Rabiee, Mohammad R. K. Mofrad
Software Mentions: 4
Published: almost 4 years ago

10.1155/2014/641469

Computational Prediction of Protein Function Based on Weighted Mapping of Domains and GO Terms
Cited by: 3
Author(s): Zhaogang Teng, Maozu Guo, Qigen Dai, Chunyu Wang, Jin Li, Xiaoyan Liu
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-019-45072-8

Computational identification of protein-protein interactions in model plant proteomes
Cited by: 51
Author(s): Ziyun Ding, Daisuke Kihara
Software Mentions: 3
Published: over 5 years ago

10.1186/s13742-015-0083-4

The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches
Cited by: 15
Author(s): Ishita Khan, Wei Qing, Samuel Chapman, Dukka B. Kc, Daisuke Kihara
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2105-12-373

Quantification of protein group coherence and pathway assignment using functional association
Cited by: 10
Author(s): Meghana Chitale, Shriphani Palakodety, Daisuke Kihara
Software Mentions: 3
Published: about 13 years ago

10.1155/2008/619832

Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics
Cited by: 1,633
Author(s): Ana Conesa, Stefan Götz
Software Mentions: 3
Published: over 16 years ago

10.1186/s12859-017-1600-5

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology
Cited by: 44
Author(s): Wei Qing, Ishita Khan, Ziyun Ding, Satwica Yerneni
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-14-S3-S2

In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment
Cited by: 5
Author(s): Meghana Chitale, Ishita Khan, Daisuke Kihara
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2180-7-99

Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus
Cited by: 227
Author(s): Sarah K. Highlander, Kristina G. Hultén, Xiang Qin, Huaiyang Jiang, Shailaja Yerrapragada, Edward O. Mason, Yue Shang, Todd A. Williams, Régine M. Fortunov, Yamei Liu, Okezie Igboeli, Joseph F. Petrosino, Madhan R. Tirumalai, Akif Uzman, George E. Fox, Ana Marı́a Cárdenas, Donna M. Muzny, Lisa Hemphill, Yan Ding, Shannon Dugan, Peter R Blyth, Christian Buhay, Huyen Dinh, Alicia Hawes, Michael Holder, Christie Kovar, Sandra L. Lee, Wen Liu, Lynne V. Nazareth, Qiaoyan Wang, Jianling Zhou, Sheldon L. Kaplan, George M. Weinstock
Software Mentions: 2
Published: about 17 years ago

10.1186/1753-6561-6-S7-S5

Evaluation of function predictions by PFP, ESG, and PSI-BLAST for moonlighting proteins
Cited by: 20
Author(s): Ishita Khan, Meghana Chitale, Catherine Rayon, Daisuke Kihara
Software Mentions: 2
Published: about 12 years ago

10.1186/s13062-014-0030-9

Genome-scale identification and characterization of moonlighting proteins
Cited by: 39
Author(s): Ishita Khan, Yuqian Chen, Tiange Dong, Xioawei Hong, Rikiya Takeuchi, Hirotada Mori, Daisuke Kihara
Software Mentions: 2
Published: about 10 years ago

10.1186/1475-2875-13-315

Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility
Cited by: 49
Author(s): Arthur M. Talman, Judith Helena Prieto, Sara Marques, Ceereena Ubaida‐Mohien, Mara Lawniczak, Mark N. Wass, Tao Xu, Roland Frank, Andrea Ecker, Rebecca Limenitakis Stanway, Sanjeev Krishna, Michael J.E. Sternberg, George K. Christophides, David R. Graham, Rhoel R. Dinglasan, John R. Yates, Robert E. Sinden
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0086632

The Discovery of phiAGATE, A Novel Phage Infecting Bacillus pumilus, Leads to New Insights into the Phylogeny of the Subfamily Spounavirinae
Cited by: 30
Author(s): Jakub Barylski, Grzegorz Nowicki, Anna Goździcka-Józefiak
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0078280

Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse
Cited by: 116
Author(s): Rebecca R. Bellone, Heather M. Holl, Vijayasaradhi Setaluri, Sulochana Devi, Nityanand Maddodi, Sheila Archer, Lynne S Sandmeyer, Arne Ludwig, Daniel W. Foerster, Mélanie Pruvost, Monika Reißmann, Ralf Bortfeldt, David L. Adelson, Seng Han Lim, Janelle Nelson, Bianca Haase, Martina Engensteiner, Tosso Leeb, G. W. Forsyth, Michael J. Mienaltowski, Padmanabhan Mahadevan, Michael Hofreiter, Johanna L. A. Paijmans, Gloria G. Fortes, Bruce H Grahn, Samantha A. Brooks
Software Mentions: 2
Published: about 11 years ago

10.1038/s41598-019-54405-6

NNTox: Gene Ontology-Based Protein Toxicity Prediction Using Neural Network
Cited by: 7
Author(s): Aashish Jain, Daisuke Kihara
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0004619

Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology
Cited by: 37
Author(s): Paolo Fontana, Alessandro Cestaro, Riccardo Velasco, Elide Formentin, Stefano Toppo
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0012382

GOPred: GO Molecular Function Prediction by Combined Classifiers
Cited by: 23
Author(s): Oemer Sinan Sarac, Volkan Atalay, Rengül Cetin-Atalay
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0000928

Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032
Cited by: 117
Author(s): Jason Gioia, Shailaja Yerrapragada, Xiang Qin, Huaiyang Jiang, Okezie Igboeli, Donna M. Muzny, Shannon Dugan-Rocha, Yan Ding, Alicia Hawes, Wen Li, Lesette Perez, Christie Kovar, Huyen Dinh, Sandra Lee, Lynne V. Nazareth, Peter R Blyth, Michael Holder, Christian Buhay, Madhan R. Tirumalai, Yamei Liu, Indrani Dasgupta, Lina Bokhetache, Masaya Fujita, Fathi Karouia, Prahathees Eswara Moorthy, Johnathan Siefert, Akif Uzman, Prince Buzumbo, Avani Verma, Hiba Zwiya, Brian D. McWilliams, Adeola Olowu, Kenneth D. Clinkenbeard, David Newcombe, Lisa Golebiewski, Joseph F. Petrosino, Wayne L. Nicholson, George E. Fox, Kasthuri Venkateswaran, Sarah K. Highlander, George M. Weinstock
Software Mentions: 1
Published: about 17 years ago

10.1186/1752-0509-6-S1-S19

A novel neural response algorithm for protein function prediction
Cited by: 5
Author(s): Hari Krishna Yalamanchili, Quan-Wu Xiao, Junwen Wang
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2180-10-69

GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems
Cited by: 10
Author(s): Fengfeng Zhou, Huiling Chen, Ying Xu
Software Mentions: 1
Published: almost 15 years ago

10.1016/j.heliyon.2019.e02734

In silico characterization of hypothetical proteins from Orientia tsutsugamushi str. Karp uncovers virulence genes
Cited by: 8
Author(s): Nikhat Imam, Aftab Alam, Rafat Ali, Mohd Faizan Siddiqui, Sher Ali, Md. Zubbair Malik, Romana Ishrat
Software Mentions: 1
Published: about 5 years ago

10.1186/s12875-020-01215-9

Development of type 2 diabetes mellitus quality indicators in general practice by a modified Delphi method in Beijing, China
Cited by: 3
Author(s): Jin Gao, Yun Wei, Liu Yan-li, Fei‐Yue Wang, Meirong Wang, Yan Zhao, Juan Du, Shijun Cui, Xiaoqin Lu
Software Mentions: 1
Published: over 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: PFP

Papers Mentioning PFP 27