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Article ; Online: PRECISION ONCOLOGY WITH ELECTRONIC MEDICAL RECORDS

Losiana Nayak / Rajat K. De

European Medical Journal Innovations, Vol 2, Iss 1, Pp 64-

2018 Volume 72

Abstract: Electronic medical record (EMR)-based precision oncology is a vision that is so far limited to a few pilot and basket studies, with the goal being the design of a proper treatment for cancer patients in real time, based on the panomics knowledge of the ... ...

Abstract	Electronic medical record (EMR)-based precision oncology is a vision that is so far limited to a few pilot and basket studies, with the goal being the design of a proper treatment for cancer patients in real time, based on the panomics knowledge of the patient, and that of similar types of patients. It aims to deliver better treatment outcomes through the design of rational drug combinations, a lower number of futile therapies, reduced patient discomfort, and a healthy human society with a reduced risk of cancer. The concept of precision oncology began with a few cancer awareness programmes and preventative screenings almost a decade ago. However, the technique took an astronomical leap with the start of the Precision Medicine Initiative Cohort Program and Cancer Moonshot programme very recently. Both projects have invested heavily towards several goals, including the merging of cancer registries and EMR to find the best treatment options for a cancer patient, an idea which, if extended globally, will generate unprecedented possibilities for precision oncology. EMR serve as a broad platform merging a variety of patient information and expert advice to facilitate co-ordinated cancer care. In this article, a summary of the recent EMR-based precision oncology practices for prevention, diagnosis, prognosis, prediction, and their associated concerns and limitations is presented. Though the path of precision oncology is unchartered, the usefulness of real-time information derived from EMR or electronic health records will lead to better precision decision-based oncotherapies.
Keywords	electronic health records (ehr) ; electronic medical record (emr) ; individualised medicine ; panomics ; precision cancer medicine ; precision decision ; stratified medicine ; Medical technology ; R855-855.5
Subject code	027
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	European Medical Journal
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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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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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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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
Database	NAL-Catalogue (AGRICOLA)

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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 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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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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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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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Article ; Online: A comprehensive mechanistic basis of prostate cancer advancement & its personalized implementation-bridging the gap

Journal of Men's Health, Vol 17, Iss 3, Pp 18-

present state and future prospect

2021 Volume 35

Abstract: Despite significant achievements in prostate cancer mechanistic understanding and its targeted therapies, currently there exists several major challenges that mainly arises during the therapy of advanced prostate cancer. Present prostate cancer precision ...

Abstract	Despite significant achievements in prostate cancer mechanistic understanding and its targeted therapies, currently there exists several major challenges that mainly arises during the therapy of advanced prostate cancer. Present prostate cancer precision medicine strategy principally suffers from several practical concerns, particularly in point of therapeutic resistance, tumor heterogeneity, complex clinical & pathological behavior and an extensive genomic perturbation landscape. Prostate Cancer Systems-Medicine Initiative is a global trans-disciplinary movement taken from corresponding scientific domains to critically determine the nature of this major existing challenges and its corresponding most possible solutions by systematically accumulating the present existing knowledge. Basically, it explains the importance of broad spectrum cancer hallmark based integrative approaches for development of combination therapy associated strategic measures for metastatic castration resistant prostate cancer. The major findings of this initiative can be summarized by identification of 136 therapeutic resistance mediators, 103 prostate cancer driver oncogenes and 8 progression pathways along with 5 terrain factors which centrally drives the basic events in prostate cancer pathogenesis, its further metastatic propagation and ultimate therapeutic resistance. In addition, it also attempts to summarize the critical features and basic challenging aspects of current therapeutic options.
Keywords	precision medicine ; therapy resistance ; cancer hallmarks ; terrain factors ; castration resistant prostate cancer (crpc) ; bone metastasis ; androgen receptor (ar) ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	MRE Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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