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  1. Article ; Online: PyPredT6: A python-based prediction tool for identification of Type VI effector proteins.

    Sen, Rishika / Nayak, Losiana / De, Rajat K

    Journal of bioinformatics and computational biology

    2019  Volume 17, Issue 3, Page(s) 1950019

    Abstract: Prediction of effector proteins is of paramount importance due to their crucial role as first-line invaders while establishing a pathogen-host interaction, often leading to infection of the host. Prediction of T6 effector proteins is a new challenge ... ...

    Abstract Prediction of effector proteins is of paramount importance due to their crucial role as first-line invaders while establishing a pathogen-host interaction, often leading to infection of the host. Prediction of T6 effector proteins is a new challenge since the discovery of T6 Secretion System and the unique nature of the particular secretion system. In this paper, we have first designed a Python-based standalone tool, called PyPredT6, to predict T6 effector proteins. A total of 873 unique features has been extracted from the peptide and nucleotide sequences of the experimentally verified effector proteins. Based on these features and using machine learning algorithms, we have performed
    MeSH term(s) Algorithms ; Bacterial Proteins/metabolism ; Bacterial Secretion Systems/metabolism ; Computational Biology/methods ; Host-Pathogen Interactions ; Machine Learning ; Programming Languages ; Software ; Vibrio cholerae/metabolism ; Vibrio cholerae/pathogenicity ; Yersinia pestis/metabolism ; Yersinia pestis/pathogenicity
    Chemical Substances Bacterial Proteins ; Bacterial Secretion Systems
    Language English
    Publishing date 2019-07-09
    Publishing country Singapore
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2115015-1
    ISSN 1757-6334 ; 0219-7200
    ISSN (online) 1757-6334
    ISSN 0219-7200
    DOI 10.1142/S0219720019500197
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Precision medicine with electronic medical records: from the patients and for the patients.

    Nayak, Losiana / Ray, Indrani / De, Rajat K

    Annals of translational medicine

    2016  Volume 4, Issue Suppl 1, Page(s) S61

    Language English
    Publishing date 2016-11-19
    Publishing country China
    Document type Journal Article ; Comment
    ZDB-ID 2893931-1
    ISSN 2305-5847 ; 2305-5839
    ISSN (online) 2305-5847
    ISSN 2305-5839
    DOI 10.21037/atm.2016.10.40
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Wnt signal transduction pathways: modules, development and evolution.

    Nayak, Losiana / Bhattacharyya, Nitai P / De, Rajat K

    BMC systems biology

    2016  Volume 10 Suppl 2, Page(s) 44

    Abstract: Background: Wnt signal transduction pathway (Wnt STP) is a crucial intracellular pathway mainly due to its participation in important biological processes, functions, and diseases, i.e., embryonic development, stem-cell management, and human cancers ... ...

    Abstract Background: Wnt signal transduction pathway (Wnt STP) is a crucial intracellular pathway mainly due to its participation in important biological processes, functions, and diseases, i.e., embryonic development, stem-cell management, and human cancers among others. This is why Wnt STP is one of the highest researched signal transduction pathways. Study and analysis of its origin, expansion and gradual development to the present state as found in humans is one aspect of Wnt research. The pattern of development and evolution of the Wnt STP among various species is not clear till date. A phylogenetic tree created from Wnt STPs of multiple species may address this issue.
    Results: In this respect, we construct a phylogenetic tree from modules of Wnt STPs of diverse species. We term it as the 'Module Tree'. A module is nothing but a self-sufficient minimally-dependent subset of the original Wnt STP. Authenticity of the module tree is tested by comparing it with the two reference trees.
    Conclusions: The module tree performs better than an alternative phylogenetic tree constructed from pathway topology of Wnt STPs. Moreover, an evolutionary emergence pattern of the Wnt gene family is created and the module tree is tallied with it to showcase the significant resemblances.
    MeSH term(s) Animals ; Evolution, Molecular ; Humans ; Models, Biological ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Wnt Signaling Pathway
    Chemical Substances RNA, Ribosomal, 18S
    Language English
    Publishing date 2016-08-01
    Publishing country England
    Document type Journal Article
    ISSN 1752-0509
    ISSN (online) 1752-0509
    DOI 10.1186/s12918-016-0299-7
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  4. Article: Computational neuroscience and neuroinformatics: Recent progress and resources

    Nayak, Losiana / Das, Ritankar / Dasgupta, Abhijit / De, Rajat K / Ghosh, Kuntal

    Journal of biosciences. 2018 Dec., v. 43, no. 5

    2018  

    Abstract: The human brain and its temporal behavior correlated with development, structure, and function is a complex natural system even for its own kind. Coding and automation are necessary for modeling, analyzing and understanding the 86.1 ± 8.1 billion neurons, ...

    Abstract The human brain and its temporal behavior correlated with development, structure, and function is a complex natural system even for its own kind. Coding and automation are necessary for modeling, analyzing and understanding the 86.1 ± 8.1 billion neurons, an almost equal number of non-neuronal glial cells, and the neuronal networks of the human brain comprising about 100 trillion connections. ‘Computational neuroscience’ which is heavily dependent on biology, physics, mathematics and computation addresses such problems while the archival, retrieval and merging of the huge amount of generated data in the form of clinical records, scientific literature, and specialized databases are carried out by ‘neuroinformatics’ approaches. Neuroinformatics is thus an interface between computer science and experimental neuroscience. This article provides an introduction to computational neuroscience and neuroinformatics fields along with their state-of-the-art tools, software, and resources. Furthermore, it describes a few innovative applications of these fields in predicting and detecting brain network organization, complex brain disorder diagnosis, large-scale 3D simulation of the brain, brain–computer, and brain-to-brain interfaces. It provides an integrated overview of the fields in a non-technical way, appropriate for broad general readership. Moreover, the article is an updated unified resource of the existing knowledge and sources for researchers stepping into these fields.
    Keywords automation ; brain ; computer software ; databases ; humans ; mathematics ; models ; neuroglia ; neurons ; neurophysiology ; physics ; prediction
    Language English
    Dates of publication 2018-12
    Size p. 1037-1054.
    Publishing place Springer India
    Document type Article
    Note Review
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
    DOI 10.1007/s12038-018-9813-y
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  5. Article ; Online: Computational neuroscience and neuroinformatics: Recent progress and resources.

    Nayak, Losiana / Dasgupta, Abhijit / Das, Ritankar / Ghosh, Kuntal / De, Rajat K

    Journal of biosciences

    2018  Volume 43, Issue 5, Page(s) 1037–1054

    Abstract: The human brain and its temporal behavior correlated with development, structure, and function is a complex natural system even for its own kind. Coding and automation are necessary for modeling, analyzing and understanding the 86.1 +/- 8.1 +/- billion ... ...

    Abstract The human brain and its temporal behavior correlated with development, structure, and function is a complex natural system even for its own kind. Coding and automation are necessary for modeling, analyzing and understanding the 86.1 +/- 8.1 +/- billion neurons, an almost equal number of non-neuronal glial cells, and the neuronal networks of the human brain comprising about 100 trillion connections. 'Computational neuroscience' which is heavily dependent on biology, physics, mathematics and computation addresses such problems while the archival, retrieval and merging of the huge amount of generated data in the form of clinical records, scientific literature, and specialized databases are carried out by 'neuroinformatics' approaches. Neuroinformatics is thus an interface between computer science and experimental neuroscience. This article provides an introduction to computational neuroscience and neuroinformatics fields along with their state-ofthe- art tools, software, and resources. Furthermore, it describes a few innovative applications of these fields in predicting and detecting brain network organization, complex brain disorder diagnosis, large-scale 3D simulation of the brain, brain- computer, and brain-to-brain interfaces. It provides an integrated overview of the fields in a non-technical way, appropriate for broad general readership. Moreover, the article is an updated unified resource of the existing knowledge and sources for researchers stepping into these fields.
    MeSH term(s) Brain/anatomy & histology ; Brain/diagnostic imaging ; Brain/physiology ; Computational Biology/methods ; Connectome/instrumentation ; Connectome/methods ; Databases, Factual ; Humans ; Nerve Net/anatomy & histology ; Nerve Net/diagnostic imaging ; Nerve Net/physiology ; Neural Networks (Computer) ; Neuroglia/cytology ; Neuroglia/physiology ; Neurons/cytology ; Neurons/physiology ; Neurosciences/methods ; Software
    Language English
    Publishing date 2018-12-12
    Publishing country India
    Document type Journal Article ; Review
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  6. Article ; Online: Disease co-morbidity and the human Wnt signaling pathway: a network-wise study.

    Nayak, Losiana / Tunga, Harinandan / De, Rajat K

    Omics : a journal of integrative biology

    2013  Volume 17, Issue 6, Page(s) 318–337

    Abstract: The human Wnt signaling pathway contains 57 genes communicating among themselves by 70 experimentally established associations, as given in the KEGG/PATHWAY database. It is responsible for a variety of crucial biological functions such as regulation of ... ...

    Abstract The human Wnt signaling pathway contains 57 genes communicating among themselves by 70 experimentally established associations, as given in the KEGG/PATHWAY database. It is responsible for a variety of crucial biological functions such as regulation of cell fate determination, proliferation, differentiation, migration, and apoptosis. Abnormal behavior of its members causes numerous types of human cancers, dramatic changes in bone mass density that lead to diseases such as osteoporosis-pseudo-glioma syndrome, Van-Buchem disease, skeletal malformation, autosomal dominant sclerosteosis, and osteoporosis type I syndromes. So far, single genes have been investigated for their disease-causing properties, and single diseases have been traced backwards to discover foul-play of the system pathways. Differential expression of the whole genome has been mapped by microarray. But how all the genes involved in a pathway affect each other in single/multiple disease state(s) and whether the presence of one disease state makes a person prone to another kind of disease(s) (i.e., co-morbidity among diseases associated with a certain important biological pathway) is still unknown. We have developed a human Wnt signaling pathway diseasome and analyzed it for finding answers to such questions. Data used in constructing the diseasome can be downloaded from the publicly accessible webserver http://www.isical.ac.in/-rajat/diseasome/index.php.
    MeSH term(s) Comorbidity ; Computational Biology/methods ; Computer Simulation ; Databases, Genetic ; Gene Regulatory Networks ; Genetic Association Studies ; Humans ; Models, Biological ; Wnt Proteins/genetics ; Wnt Proteins/metabolism ; Wnt Signaling Pathway/physiology
    Chemical Substances Wnt Proteins
    Language English
    Publishing date 2013-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2012.0053
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  7. Article: Modularized study of human calcium signalling pathway.

    Nayak, Losiana / De, Rajat K

    Journal of biosciences

    2007  Volume 32, Issue 5, Page(s) 1009–1017

    Abstract: Signalling pathways are complex biochemical networks responsible for regulation of numerous cellular functions. These networks function by serial and successive interactions among a large number of vital biomolecules and chemical compounds. For ... ...

    Abstract Signalling pathways are complex biochemical networks responsible for regulation of numerous cellular functions. These networks function by serial and successive interactions among a large number of vital biomolecules and chemical compounds. For deciphering and analysing the underlying mechanism of such networks,a modularized study is quite helpful. Here we propose an algorithm for modularization of calcium signalling pathway of H. sapiens . The idea that "a node whose function is dependent on maximum number of other nodes tends to be the center of a sub network" is used to divide a large signalling network into smaller sub networks. Inclusion of node(s) into sub networks(s) is dependent on the outdegree of the node(s). Here outdegree of a node refers to the number of relations of the considered node lying outside the constructed sub network. Node(s) having more than c relations lying outside the expanding sub network have to be excluded from it. Here c is a specified variable based on user preference, which is finally fixed during adjustments of created sub networks, so that certain biological significance can be conferred on them.
    MeSH term(s) Algorithms ; Amino Acid Motifs ; Animals ; Calcium/chemistry ; Calcium/metabolism ; Calcium/physiology ; Calcium Signaling/physiology ; Humans ; Models, Molecular
    Chemical Substances Calcium (SY7Q814VUP)
    Language English
    Publishing date 2007-10-03
    Publishing country India
    Document type Journal Article ; Review
    ZDB-ID 756157-x
    ISSN 0250-5991
    ISSN 0250-5991
    DOI 10.1007/s12038-007-0100-6
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  8. Article ; Online: An algorithm for modularization of MAPK and calcium signaling pathways: comparative analysis among different species.

    Nayak, Losiana / De, Rajat K

    Journal of biomedical informatics

    2007  Volume 40, Issue 6, Page(s) 726–749

    Abstract: Signaling pathways are large complex biochemical networks. It is difficult to analyze the underlying mechanism of such networks as a whole. In the present article, we have proposed an algorithm for modularization of signal transduction pathways. Unlike ... ...

    Abstract Signaling pathways are large complex biochemical networks. It is difficult to analyze the underlying mechanism of such networks as a whole. In the present article, we have proposed an algorithm for modularization of signal transduction pathways. Unlike studying a signaling pathway as a whole, this enables one to study the individual modules (less complex smaller units) easily and hence to study the entire pathway better. A comparative study of modules belonging to different species (for the same signaling pathway) has been made, which gives an overall idea about development of the signaling pathways over the taken set of species of calcium and MAPK signaling pathways. The superior performance, in terms of biological significance, of the proposed algorithm over an existing community finding algorithm of Newman [Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci USA 2006;103(23):8577-82] has been demonstrated using the aforesaid pathways of H. sapiens.
    MeSH term(s) Algorithms ; Animals ; Artificial Intelligence ; Calcium Signaling/physiology ; Computer Simulation ; Humans ; MAP Kinase Signaling System/physiology ; Models, Biological ; Species Specificity
    Language English
    Publishing date 2007-12
    Publishing country United States
    Document type Comparative Study ; Journal Article
    ZDB-ID 2057141-0
    ISSN 1532-0480 ; 1532-0464
    ISSN (online) 1532-0480
    ISSN 1532-0464
    DOI 10.1016/j.jbi.2007.05.007
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  9. Article: Modularized study of human calcium signalling pathway

    Nayak, Losiana / De, Rajat K

    Journal of biosciences. 2007 Aug., v. 32, no. Supplement 1

    2007  

    Abstract: Signalling pathways are complex biochemical networks responsible for regulation of numerous cellular functions. These networks function by serial and successive interactions among a large number of vital biomolecules and chemical compounds. For ... ...

    Abstract Signalling pathways are complex biochemical networks responsible for regulation of numerous cellular functions. These networks function by serial and successive interactions among a large number of vital biomolecules and chemical compounds. For deciphering and analysing the underlying mechanism of such networks, a modularized study is quite helpful. Here we propose an algorithm for modularization of calcium signalling pathway of H. sapiens. The idea that “a node whose function is dependant on maximum number of other nodes tends to be the center of a subnetwork” is used to divide a large signalling network into smaller subnetworks. Inclusion of node(s) into subnetworks(s) is dependant on the outdegree of the node(s). Here outdegree of a node refers to the number of relations of the considered node lying outside the constructed subnetwork. Node(s) having more than c relations lying outside the expanding subnetwork have to be excluded from it. Here c is a specified variable based on user preference, which is finally fixed during adjustments of created subnetworks, so that certain biological significance can be conferred on them.
    Keywords algorithms ; biochemical compounds ; calcium signaling ; chemical compounds ; humans
    Language English
    Dates of publication 2007-08
    Size p. 1009-1017.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
    DOI 10.1007/s12038-007-0100-6
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