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Article ; Online: HuCoPIA: An Atlas of Human vs. SARS-CoV-2 Interactome and the Comparative Analysis with Other

Duhan, Naveen / Kaundal, Rakesh

2023 Volume 15, Issue 2

Abstract: SARS-CoV-2, a novel betacoronavirus strain, has caused a pandemic that has claimed the lives of nearly 6.7M people worldwide. Vaccines and medicines are being developed around the world to reduce the disease spread, fatality rates, and control the new ... ...

Abstract	SARS-CoV-2, a novel betacoronavirus strain, has caused a pandemic that has claimed the lives of nearly 6.7M people worldwide. Vaccines and medicines are being developed around the world to reduce the disease spread, fatality rates, and control the new variants. Understanding the protein-protein interaction mechanism of SARS-CoV-2 in humans, and their comparison with the previous SARS-CoV and MERS strains, is crucial for these efforts. These interactions might be used to assess vaccination effectiveness, diagnose exposure, and produce effective biotherapeutics. Here, we present the HuCoPIA database, which contains approximately 100,000 protein-protein interactions between humans and three strains (SARS-CoV-2, SARS-CoV, and MERS) of betacoronavirus. The interactions in the database are divided into common interactions between all three strains and those unique to each strain. It also contains relevant functional annotation information of human proteins. The HuCoPIA database contains SARS-CoV-2 (41,173), SARS-CoV (31,997), and MERS (26,862) interactions, with functional annotation of human proteins like subcellular localization, tissue-expression, KEGG pathways, and Gene ontology information. We believe HuCoPIA will serve as an invaluable resource to diverse experimental biologists, and will help to advance the research in better understanding the mechanism of betacoronaviruses.
MeSH term(s)	Humans ; Coronaviridae ; SARS-CoV-2/genetics ; COVID-19 ; Ascomycota ; Databases, Factual
Language	English
Publishing date	2023-02-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15020492
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets.

Kataria, Raghav / Kaundal, Rakesh

Frontiers in plant science

2022 Volume 13, Page(s) 895480

Abstract: ... Triticum ... ...

Abstract	Triticum aestivum
Language	English
Publishing date	2022-06-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2022.895480
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deciphering the Host-Pathogen Interactome of the Wheat-Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat.

Kataria, Raghav / Kaundal, Rakesh

International journal of molecular sciences

2022 Volume 23, Issue 5

Abstract: Common bunt, caused by two fungal species, ...

Abstract	Common bunt, caused by two fungal species,
MeSH term(s)	Basidiomycota/genetics ; Plant Diseases/genetics ; Plant Diseases/microbiology ; Triticum/genetics ; Triticum/microbiology
Language	English
Publishing date	2022-02-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23052589
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: ranchSATdb

Duhan, Naveen / Kaur, Simardeep / Kaundal, Rakesh

Genes

2023 Volume 14, Issue 7

Abstract: Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal ... ...

Abstract	Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database,
MeSH term(s)	Animals ; Chromosome Mapping ; Polymorphism, Genetic ; Livestock/genetics ; Genome, Plant ; Animals, Domestic/genetics ; Databases, Genetic ; Microsatellite Repeats/genetics
Language	English
Publishing date	2023-07-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14071481
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat-Stem rust host-pathogen interactome.

Kataria, Raghav / Kaundal, Rakesh

Database : the journal of biological databases and curation

2022 Volume 2022

Abstract: The increasing infectious diseases in wheat immensely reduce crop yield and quality, thus affecting global wheat production. The evolution in phytopathogens hinders the understanding of the disease infection mechanisms. TRustDB is an open-access, ... ...

Abstract	The increasing infectious diseases in wheat immensely reduce crop yield and quality, thus affecting global wheat production. The evolution in phytopathogens hinders the understanding of the disease infection mechanisms. TRustDB is an open-access, comprehensive database that is specifically focused on the disease stem rust (also known as black rust) in Triticum aestivum, which is caused by the fungal pathogen Puccinia graminis (Pgt), strains 'Ug99' and '21-0'. The database aims at a broader focus of providing the researchers with comprehensive tools to predict the protein-protein interactions and avail the functional annotations of the proteins involved in the interactions that cause the disease. The network of the predicted interactome can also be visualized on the browser. Various modules for the functional annotations of the host and pathogen proteins such as subcellular localization, functional domains, gene ontology annotations, pathogen orthologs and effector proteins have been implemented. The host proteins that serve as transcription factors, along with the respective Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways are also available, which further enhance the understanding of the disease infection mechanisms and the defense responses of the host. The database is also linked with several other databases such as InterPro, KEGG pathways, Ensembl and National Center for Biotechnology Information (NCBI). TRustDB has a user-friendly web interface, which can be accessed through . Database URL http://bioinfo.usu.edu/trustdb/.
MeSH term(s)	Triticum/genetics ; Triticum/microbiology ; Computational Biology ; Basidiomycota/genetics ; Software ; Molecular Sequence Annotation ; Proteins/genetics
Chemical Substances	Proteins
Language	English
Publishing date	2022-11-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/baac068
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: ProFeatX: A parallelized protein feature extraction suite for machine learning.

Guevara-Barrientos, David / Kaundal, Rakesh

Computational and structural biotechnology journal

2022 Volume 21, Page(s) 796–801

Abstract: Machine learning algorithms have been successfully applied in proteomics, genomics and transcriptomics. and have helped the biological community to answer complex questions. However, most machine learning methods require lots of data, with every data ... ...

Abstract	Machine learning algorithms have been successfully applied in proteomics, genomics and transcriptomics. and have helped the biological community to answer complex questions. However, most machine learning methods require lots of data, with every data point having the same vector size. The biological sequence data, such as proteins, are amino acid sequences of variable length, which makes it essential to extract a definite number of features from all the proteins for them to be used as input into machine learning models. There are numerous methods to achieve this, but only several tools let researchers encode their proteins using multiple schemes without having to use different programs or, in many cases, code these algorithms themselves, or even come up with new algorithms. In this work, we created ProFeatX, a tool that contains 50 encodings to extract protein features in an efficient and fast way supporting desktop as well as high-performance computing environment. It can also encode concatenated features for protein-protein interactions. The tool has an easy-to-use web interface, allowing non-experts to use feature extraction techniques, as well as a stand-alone version for advanced users. ProFeatX is implemented in C++ and available on GitHub at https://github.com/usubioinfo/profeatx. The web server is available at http://bioinfo.usu.edu/profeatx/.
Language	English
Publishing date	2022-12-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.12.044
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: WeCoNET: a host-pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms.

Kataria, Raghav / Kaundal, Rakesh

Plant methods

2022 Volume 18, Issue 1, Page(s) 73

Abstract: Background: Triticum aestivum is the most important staple food grain of the world. In recent years, the outbreak of a major seed-borne disease, common bunt, in wheat resulted in reduced quality and quantity of the crop. The disease is caused by two ... ...

Abstract	Background: Triticum aestivum is the most important staple food grain of the world. In recent years, the outbreak of a major seed-borne disease, common bunt, in wheat resulted in reduced quality and quantity of the crop. The disease is caused by two fungal pathogens, Tilletia caries and Tilletia laevis, which show high similarity to each other in terms of life cycle, germination, and disease symptoms. The host-pathogen protein-protein interactions play a crucial role in initiating the disease infection mechanism as well as in plant defense responses. Due to the availability of limited information on Tilletia species, the elucidation of infection mechanisms is hampered. Results: We constructed a database WeCoNET ( http://bioinfo.usu.edu/weconet/ ), providing functional annotations of the pathogen proteins and various tools to exploit host-pathogen interactions and other relevant information. The database implements a host-pathogen interactomics tool to predict protein-protein interactions, followed by network visualization, BLAST search tool, advanced 'keywords-based' search module, etc. Other features in the database include various functional annotations of host and pathogen proteins such as gene ontology terms, functional domains, and subcellular localization. The pathogen proteins that serve as effector and secretory proteins have also been incorporated in the database, along with their respective descriptions. Additionally, the host proteins that serve as transcription factors were predicted, and are available along with the respective transcription factor family and KEGG pathway to which they belong. Conclusion: WeCoNET is a comprehensive, efficient resource to the molecular biologists engaged in understanding the molecular mechanisms behind the common bunt infection in wheat. The data integrated into the database can also be beneficial to the breeders for the development of common bunt-resistant cultivars.
Language	English
Publishing date	2022-06-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2203723-8
ISSN	1746-4811
ISSN	1746-4811
DOI	10.1186/s13007-022-00897-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deciphering the complete human-monkeypox virus interactome: Identifying immune responses and potential drug targets.

Kataria, Raghav / Kaur, Simardeep / Kaundal, Rakesh

Frontiers in immunology

2023 Volume 14, Page(s) 1116988

Abstract: Monkeypox virus (MPXV) is a dsDNA virus, belonging to Poxviridae family. The outbreak of monkeypox disease in humans is critical in European and Western countries, owing to its origin in African regions. The highest number of cases of the disease were ... ...

Abstract	Monkeypox virus (MPXV) is a dsDNA virus, belonging to Poxviridae family. The outbreak of monkeypox disease in humans is critical in European and Western countries, owing to its origin in African regions. The highest number of cases of the disease were found in the United States, followed by Spain and Brazil. Understanding the complete infection mechanism of diverse MPXV strains and their interaction with humans is important for therapeutic drug development, and to avoid any future epidemics. Using computational systems biology, we deciphered the genome-wide protein-protein interactions (PPIs) between 22 MPXV strains and human proteome. Based on phylogenomics and disease severity, 3 different strains of MPXV: Zaire-96-I-16, MPXV-UK_P2, and MPXV_USA_2022_MA001 were selected for comparative functional analysis of the proteins involved in the interactions. On an average, we predicted around 92,880 non-redundant PPIs between human and MPXV proteomes, involving 8014 host and 116 pathogen proteins from the 3 strains. The gene ontology (GO) enrichment analysis revealed 10,624 common GO terms in which the host proteins of 3 strains were highly enriched. These include significant GO terms such as platelet activation (GO:0030168), GABA-A receptor complex (GO:1902711), and metalloendopeptidase activity (GO:0004222). The host proteins were also significantly enriched in calcium signaling pathway (hsa04020), MAPK signaling pathway (hsa04010), and inflammatory mediator regulation of TRP channels (hsa04750). These significantly enriched GO terms and KEGG pathways are known to be implicated in immunomodulatory and therapeutic role in humans during viral infection. The protein hubs analysis revealed that most of the MPXV proteins form hubs with the protein kinases and AGC kinase C-terminal domains. Furthermore, subcellular localization revealed that most of the human proteins were localized in cytoplasm (29.22%) and nucleus (26.79%). A few drugs including Fostamatinib, Tamoxifen and others were identified as potential drug candidates against the monkeypox virus disease. This study reports the genome-scale PPIs elucidation in human-monkeypox virus pathosystem, thus facilitating the research community with functional insights into the monkeypox disease infection mechanism and augment the drug development.
MeSH term(s)	Humans ; Mpox (monkeypox) ; Monkeypox virus/genetics ; Protein Kinases ; Democratic Republic of the Congo ; Immunity
Chemical Substances	Protein Kinases (EC 2.7.-)
Language	English
Publishing date	2023-03-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1116988
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria.

Kataria, Raghav / Kaundal, Rakesh

International journal of molecular sciences

2021 Volume 22, Issue 15

Abstract: Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused ... ...

Abstract	Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused by
MeSH term(s)	Bacterial Proteins/metabolism ; Databases, Protein ; Host-Pathogen Interactions ; Medicago sativa/immunology ; Medicago sativa/metabolism ; Medicago sativa/microbiology ; Plant Diseases/immunology ; Plant Diseases/microbiology ; Protein Interaction Maps ; Pseudomonas syringae/pathogenicity
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2021-08-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22158342
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Article ; Online: WeCoNET

Raghav Kataria / Rakesh Kaundal

Plant Methods, Vol 18, Iss 1, Pp 1-

a host–pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms

2022 Volume 11

Abstract: Abstract Background Triticum aestivum is the most important staple food grain of the world. In recent years, the outbreak of a major seed-borne disease, common bunt, in wheat resulted in reduced quality and quantity of the crop. The disease is caused by ... ...

Abstract	Abstract Background Triticum aestivum is the most important staple food grain of the world. In recent years, the outbreak of a major seed-borne disease, common bunt, in wheat resulted in reduced quality and quantity of the crop. The disease is caused by two fungal pathogens, Tilletia caries and Tilletia laevis, which show high similarity to each other in terms of life cycle, germination, and disease symptoms. The host–pathogen protein–protein interactions play a crucial role in initiating the disease infection mechanism as well as in plant defense responses. Due to the availability of limited information on Tilletia species, the elucidation of infection mechanisms is hampered. Results We constructed a database WeCoNET ( http://bioinfo.usu.edu/weconet/ ), providing functional annotations of the pathogen proteins and various tools to exploit host–pathogen interactions and other relevant information. The database implements a host–pathogen interactomics tool to predict protein–protein interactions, followed by network visualization, BLAST search tool, advanced ‘keywords-based’ search module, etc. Other features in the database include various functional annotations of host and pathogen proteins such as gene ontology terms, functional domains, and subcellular localization. The pathogen proteins that serve as effector and secretory proteins have also been incorporated in the database, along with their respective descriptions. Additionally, the host proteins that serve as transcription factors were predicted, and are available along with the respective transcription factor family and KEGG pathway to which they belong. Conclusion WeCoNET is a comprehensive, efficient resource to the molecular biologists engaged in understanding the molecular mechanisms behind the common bunt infection in wheat. The data integrated into the database can also be beneficial to the breeders for the development of common bunt-resistant cultivars.
Keywords	Annotations ; Common bunt ; Effector proteins ; Interolog ; Protein–protein interactions ; Secretory proteins ; Plant culture ; SB1-1110 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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