Subhash C Basak

Subhash C Basak
University of Minnesota Duluth | UMD · Center for Water and the Environment, UMD-NRRI; Department. of Chemistry & Biochemistry

PhD

About

552
Publications
56,895
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
10,606
Citations
Additional affiliations
June 1987 - present
University of Minnesota Twin Cities
Position
  • Professor (Associate)
Description
  • Development of Topological Indices, Hierarchical QSAR, Quantitative Molecular Similarity Analysis (QMSA), QMSA Based Estimation of Properties, Invariants of DNA Sequences, Mathematical Proteomics, Relative Chirality Index (RCI), Differential QSAR
March 1987 - October 2015
Natural Resources Research Institute
Position
  • Research Associate
Description
  • Research Areas: Development of novel molecular descriptors; QSAR/ QSPR modeling; Quantitative molecular similarity analysis (QMSA); Chemical graph theory; Predictive toxicology; Mathematical chemistry; Mathematical proteomics; DNA/ RNA sequence analysis
December 1981 - November 2014
University of Minnesota Duluth
Position
  • Senior Researcher
Description
  • Develop topological Indices; Study TI Intercorrelation; Hierarchical QSAR; Molecular Similarity ; DNA descriptors; Mathematical Proteomics; Chirality Index; Predict modes of action (MOA) of chemicals from structure; Characterization of complex mixtures

Publications

Publications (552)
Article
Full-text available
During an emergency, such as a pandemic in which time and resources are extremely scarce, it is important to find effective and rapid solutions when searching for possible treatments. One possibility in this regard is the repurposing of available “on the market” drugs. This is a proof of the concept study showing the potential of a collaboration be...
Preprint
Full-text available
Human sleep and sleep disorders constitute a set of complex processes. Sleepwalking or somnambulism is one important problem of sleep disorder. In many parts of the world people do various activities while sleepwalking and they do not remember any of those when they wake up from sleep. Is the phenomenon of observing walking ghosts in night times re...
Article
Full-text available
The design for vaccines using in silico analysis of genomic data of different viruses has taken many different paths, but lack of any precise computational approach has constrained them to alignment methods and some alignment-free techniques. In this work, a precise computational approach has been established wherein two new mathematical parameters...
Preprint
Full-text available
This Bengali language article discusses the psychosocial as well as neurochemical basis of the vulnerability to and development of drug addiction with special reference to alcohol and opioid class of drugs.
Preprint
Full-text available
This article describes my more than four decades of not so straightforward journey through mathematical chemistry and QSAR research with descriptions of some valuable personal interactions and collaborations with Professors Milan Randic and Mircea Diudea.
Preprint
In this article, the authors reviewed results of their research in the prediction of toxicities, bioactivities and properties of chemicals using computed mathematical descriptors. Robust statistical methods have been used to develop high quality predictive quantitative structure-activity relationship (QSAR) models for the prediction of Ames’ mutage...
Technical Report
Full-text available
This review article on COVID-19 discusses the basic biology of the coronavirus, its pathological manifestations, risk factors for transmissions among humans, and practical methods of avoiding infection. A short history of the epidemics and pandemics over the past two millennia is presented. The article is based on COVID-19 data published by the Wor...
Article
Introduction: Coronaviruses comprise a group of enveloped, positive-sense single-stranded RNA viruses that infect humans as well as a wide range of animals. The study was performed on a set of 573 sequences belonging to SARS, MERS and SARS-CoV-2 (CoVID-19) viruses. The sequences were represented with alignment-free sequence descriptors and analyze...
Presentation
Full-text available
During the past half century or so, we have witnessed numerous applications of discrete mathematics in the characterization of chemical and biological systems. Two principal factors sustained such a growth: i) Novel applications of discrete mathematics to chemical and biological systems, and ii) Availability of high-speed computers and associated s...
Article
Full-text available
In our previous review published in 2017 on the Zika virus pandemic sweeping the Western World, we mentioned that understanding viral pandemics and vaccine preparedness is vital to combating new outbreaks. In this review, we discuss key updated aspects of the Zika virus in terms of its origin, present status, and prognosis. We also discuss developm...
Chapter
Human civilization has always been combating different pathogens that have caused epidemics or pandemics at various points of time, which has ultimately taken away millions of lives worldwide. Among all the disease-causing pathogens, viruses are notably pathogenic. Their relatively smaller size and comparatively higher rate of mutation make them mo...
Article
Full-text available
SARS-CoV-2 infection has become a worldwide pandemic and spreading very fast to the people across the globe. To combat the situation, vaccine design is the essential solution. Mutation in the virus genome plays an important role in limiting the working life of a vaccine. In this study, we have identified several mutated clusters in the structural p...
Conference Paper
Viral epidemics have posed a problem for quick development of drugs and vaccines to control the menace. A case in point is the Ebola viral disease with high fatality ratio in Africa. It is making a comeback in the Democratic Republic of Congo (DRC), after its rampage in West Africa in 2014-16 that has spawned fears of leading to a pandemic. Vaccine...
Article
Full-text available
Recent decades have witnessed the emergence of many viral diseases some of which have resulted in epidemics and global pandemics. Design of drugs and vaccines for such diseases is expensive and time consuming. In this article we propose a new computer-assisted method for the fast design of a new class of vaccines, the peptide vaccines, based on the...
Conference Paper
Full-text available
Welcome From Chairs Dear colleagues worldwide, we are glad to invite you to MOL2NET-05, International Conference on Multidisciplinary Sciences, ISSN: 2624-5078, MDPI SciForum, Basel, Switzerland, 2019. MOL2NET is a year-round conference series with multiple associated workshops worldwide running and open to submissions almost all the year, please r...
Data
All the data for qR values of SARS-CoV-2 sequences are given. The analysis from this data is presented in the publication,'New Computational Analysis to Identify Mutational Changes in SARS-CoV-2'. This file contain data for a total of 1674 sequences.
Conference Paper
Full-text available
The ongoing rapid spread of COVID-19 disease from its first detection in Wuhan, China in late 2019 was declared a pandemic by World Health Organization on 11th March, 2020. It is believed that to combat this deadly virus, now designated as SARS-CoV-2, designing and developing a proper vaccine is the best solution. For developing a sustainable vacci...
Conference Paper
Full-text available
Graphical Abstract Abstract. We consider a novel approach to mathematically define a graphing method to represent amino acid sequences of proteins in two-dimensional plane and characterize them numerically. The amino acids are represented by their relative magnitude of their hydrophobicity.
Conference Paper
Full-text available
The currently surging SARS-COV-2 (or CoVID-19) is challenging the public health authorities worldwide. As of now there is no approved vaccine or drug available for the control of the viral disease. Therefore, non-pharmaceutical interventions (NPIs) are being used around the world to manage the spread of CoVID-19. In this article we used a computer-...
Chapter
With the increasing frequency of viral epidemics, vaccines to augment the human immune response system have been the medium of choice to combat viral infections. The tragic consequences of the Zika virus pandemic in South and Central America a few years ago brought the issues into sharper focus. While traditional vaccine development is time-consumi...
Technical Report
Full-text available
Rapid response to emerging viral epidemics - the new CoronaVirus epidemic from Wuhan, China
Presentation
Full-text available
In this presentation, the algorithms for designing peptide vaccines have been proposed. A new algorithm has been described which automates the selection of suitable peptide stretches as peptide-vaccine targets, to a large extent. Suitable comparisons have also been made regarding its results to justify its ability to predict the regions in the sequ...
Article
In this report we consider a data set, which consists of 310 Zika virus genome sequences taken from different continents, Africa, Asia and South America. The sequences, which were compiled from GenBank, were derived from the host cells of different mammalian species (Simiiformes, Aedes opok, Aedes africanus, Aedes luteocephalus, Aedes dalzieli, Aed...
Article
Full-text available
Traditional vaccines have seen spectacular successes in eradicating smallpox and have come close to eradicating poliomyelitis also. However, they have been short in combating viral epidemics which are now occurring with increasing frequency; the reasons are primarily due to rapid mutations in RNA viruses. Alternative procedures are to be found in t...
Conference Paper
Full-text available
In this paper, we have described the algorithms based on mathematical and computational modelling, that are essential for designing peptide vaccines
Poster
Full-text available
We describe a methodology to fine tune conserved segents of the Ebola GP2 protein with ASA profiles and HLA profiles of the local population. This methodology automates the selection process giving a wider range of acceptable vaccine targets. More work on this line is continuing for a highly pathogenic viral disease.
Technical Report
Full-text available
This technical report the development and use of mathematical chemodescriptors and proteomics based biodescriptors in the prediction of toxicity of chemicals.
Article
Full-text available
Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and ef...
Conference Paper
Full-text available
USA-Europe Data Analysis Training School (USEDAT) is a Multi-center Trans-Atlantic initiative offering hands-on training focused in both Introduction to Experimental Data Recording (NMR, MS, IR, 2DGE, EEG, etc.) and/or posterior Computational Data Analysis (Machine Learning, Complex Networks, etc.). We made emphasis on applications in for Cheminfor...
Article
In this paper we used two sets of calculated molecular descriptors to predict blood-brain barrier (BBB) entry of a collection of 415 chemicals. First set of 579 descriptors were calculated by Schrodinger and TopoCluj software. Polly and Triplet software were used to calculate the second set of 198 descriptors. Random forest modelling and a two-deep...
Article
In this paper we used two sets of calculated molecular descriptors to predict blood-brain barrier (BBB) entry of a collection of 415 chemicals. First set of 579 descriptors were calculated by Schrodinger and TopoCluj software. Polly and Triplet software were used to calculate the second set of 198 descriptors. Random forest modelling and a two-deep...
Book
Full-text available
ABSTRACT: (https://novapublishers.com/shop/zika-virus-basic-biology-symptoms-transmission-immunology-and-anti-zika-drug-discovery/) The bubonic plague, smallpox, HIV/AIDS, malaria, and influenza are some of the worst epidemics/pandemics that afflicted human beings from antiquity to modern times, killing millions of people. The mosquito-borne human-...
Book
Full-text available
Conference: Proceedings of the conference MOL2NET International Conference on Multidisciplinary Sciences (4th edition), 2018 is part of a year-round worldwide conference series hosted by MDPI Sciforum, Basel, Switzerland. This conference series has had organized more than 20 associated workshop series in universities worldwide: USA, France, Portuga...
Conference Paper
Full-text available
Abstract. The recent emergence of a highly lethal zoonotic virus, the Nipah virus, has raised concerns of a possible pandemic with high fatality ratios. While the similarities of the Malaysian and Bangladesh strains of the virus have been commented upon by various authors, the significant differences, if any, between the two strains that have led t...
Article
We briefly review the situations arising out of epidemics that erupt rather suddenly, threatening life and livelihoods of humans. Ebola, Zika and the Nipah virus outbreaks are recent examples where the viral epidemics have led to considerably high degree of fatalities or debilitating consequences. The problems are accentuated by a lack of drugs or...
Article
Background: In view of many current mosquito-borne diseases there is a need for the design of novel repellents. Objective: The objective of this article is to review the research of results carried out by the authors in the computer-assisted design of novel mosquito repellents. Method: Two methods in the computational design of repellents have...
Chapter
The exponential growth in database of bio-molecular sequences have spawned many approaches towards storage, retrieval, classification and analyses requirements. Alignment-free techniques such as graphical representations and numerical characterisation (GRANCH) methods have enabled some detailed analyses of large sequences and found a number of diff...
Preprint
Full-text available
9 The Nipah virus disease is a lethal infection that has led to 40% to 75% fatalities in Malaysia, 10 Bangladesh and India. The reports of human-to-human transmission documented in Bangladesh 11 has raised the specter of pandemic potential and has caused the World Health Organization to list 12 the Nipah virus as one of the pathogens to be consider...
Article
Introduction: Among the mosquito-borne human-infecting flavivirus species that include Zika, West Nile, yellow fever, Japanese encephalitis and Dengue viruses, the Zika virus is found to be closest to Dengue virus, sharing the same clade in the Flavivirus phylogenetic tree. We consider these five flaviviruses and on closer examination in our analys...
Article
Applications of nanomaterials in biomedical, industrial, and consumer goods areas are expanding rapidly because of their unique physicochemical properties. Hazard assessment of nanosubstances is necessary for the protection of human and ecological health. We studied the proteomics patterns of three cell lines: co-culture of Caco-2 and HT29-MTX cell...
Article
Quantitative bioactivity and toxicity assessment of chemical compounds plays a central role in drug discovery as it saves a substantial amount of resources. To this end, high-performance computing has enabled researchers and practitioners to leverage hundreds, or even thousands, of computed molecular descriptors for activity prediction of candidate...
Article
Graphical representation methods constitute a class of alignment-free techniques for comparative study of biomolecular sequences. In this brief commentary, we study how well some of these methods can discriminate among closely related genes.
Article
Full-text available
This article reviews the role of the emerging field of mathematical chemistry in new drug discovery and the protection of human as well as ecological health. It also gives, for the beginners to the field, information regarding mathematical chemistry workshops and conferences organized by Subhash C. Basak and his collaborators in India, USA, and Sou...
Presentation
Full-text available
Subhash Basak gave a four part presentation on the following four topics: Part 1: QSAR of mutagens Part 2: Integrated QSARs using chemo- and biodescriptors from 2DE Part 3:Mathematical nanotoxicoproteomics Part4: DNA/ RNA biodescriptors
Poster
This poster presented results of chemometrical analyses of the proteomics data from three types of cell lines exposed to multi-walled carbon nanotube (MWCNT) and TiO2 nanobelt (TiO2-NB)
Article
Full-text available
This article discusses the development of the concept of pharmacophore.
Book
Full-text available
We are glad to invite all colleagues worldwide to participate on a new edition of this International Conference Series. The official title of this conference series is MOL2NET International Conference Series on Multidisciplinary Sciences. MOL2NET (the conference running title) is the acronym of the lemma of the conference: From Molecules to Network...
Article
Full-text available
Background: Proper validation is an important aspect of QSAR modelling. External validation is one of the widely used validation methods in QSAR where the model is built on a subset of the data and validated on the rest of the samples. However, its effectiveness for datasets with a small number of samples but large number of predictors remains susp...
Book
Full-text available
Proceedings of the conference MOL2NET International Conference on Multidisciplinary Sciences (3rd edition), 2017. Year-Round conference series hosted by MDPI Sciforum, Basel, Switzerland. These conferences have more than 10 associated workshop series in universities of USA, Spain, China, Chile, Brazil, etc. These workshop series run in person and/o...
Book
Full-text available
Proceedings of MOL2NET International Conference on Multidisciplinary Sciences (2nd edition), 2016. Year-Round conferences series hosted by MDPI Sciforum, Basel, Switzerland with > 10 associated in person workshops in USA, Spain, China, Chile, Brazil, etc. Some of the workshops are SRI-08 St Thomas University (STU)- Miami Dade College (MDC), Miami,...
Chapter
Viral diseases and epidemics are occurring across the world with increasing frequency and with incidences of new and old viruses with renewed vigour. Traditional drugs and vaccines with their long developmental times and shortcomings are proving inadequate to curb the menace. Advancements in computer science and technology, in genetics and immunolo...
Article
Full-text available
A new theoretical method for the virus identifcation has been proposed. The 2D-Dynamic Representation of DNA/RNA Sequences has been applied to the prediction of influenza A virus subtypes. We have shown that the method can be successfully combined with novel supervised machine learning algorithms, such as C5.0. The descriptors of the 2D-Dynamic Rep...
Conference Paper
Full-text available
An increasing trend of viral diseases have led to search for faster response systems for preventives and therapeutics. While traditional vaccinations have led to spectacular successes against smallpox and polio viruses, the need for rapid response to new viral epidemics, like in the case of Ebola and Zika viruses, has called for new ways of tacklin...
Article
Dimensionality of a relatively big data set (95 compounds) observed for toxicity (mutagenicity) was explored in order to compute QSAR models. Distinct molecular descriptors were used. Dimensionality of data, using PCA, correlation plots and clustering, was evaluated. Analyzing data dimensionality allowed model optimization. Docking studies and PCA...
Conference Paper
During the past half century or so, we have witnessed numerous applications of discrete mathematics in the characterization of chemical and biological systems. Two principal factors sustained such a growth: i) Novel applications of discrete mathematics to chemical and biological systems, and ii) Availabilit