Utsang Kumar

@bubhopal.ac.in

Department of Biochemistry and Genetics
Department of Biochemistry and Genetics, Barkatullah University

Utsang Kumar


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https://researchid.co/utsangkumar

EDUCATION

M.Sc. Genetics
Ph.D. Genetics (Pursuing)

RESEARCH, TEACHING, or OTHER INTERESTS

Agricultural and Biological Sciences, Virology, Biochemistry, Genetics and Molecular Biology, Pharmacology
9

Scopus Publications

255

Scholar Citations

5

Scholar h-index

3

Scholar i10-index

Scopus Publications

  • Insights into genetic architecture and disease associations of genes associated with different human blood group systems using codon usage bias
    Utsang Kumar, Shailja Singhal, Azmat Ali Khan, Amer M. Alanazi, Pankaj Gurjar, Rekha Khandia
    Journal of Biomolecular Structure and Dynamics, 2026
    The differential use of synonymous codons of an amino acid is an imperative evolutionary phenomenon, termed codon usage bias, that functions across various levels of organisms. It is accustomed to providing an understanding of a gene's differential architecture driven by functional regulation of gene expression. Numerous synonymous mutations are linked to various diseases, demonstrating that silent mutations can be deleterious. We employed bioinformatics methods to examine codon usage trends in 263 coding sequences of 44 blood group systems. The blood group systems were categorized into two groups based on association with a sort of neurodegenerative disorder. We performed a CUB study to investigate how multiple components, such as selection, mutation and biased nucleotide composition are accountable for the evolution of the transcripts of the blood group antigens. The compositional analysis implicated blood group genes were GC-rich. RSCU analysis showed G/C-ending codon choice among synonymous codons. Also, a distinct codon choice was found in both blood groups for serine and proline. Moreover, the leucine-coding CTG codon was found the most overrepresented in all the genes, indicating selectional pressure substantially impacts overall codon usage. This was also supported by biplot analysis. Additionally, CpC and GpG overrepresentation is in concordance with the results concerning neurodegenerative disorders where CpC has been attributed to non-CpG methylation and linked to several neurodegenerative ailments. Both the Z-test analysis and rare codon choice showed a substantial difference in codon usage by the genes of both groups.
  • Codon usage bias and nucleotide bias are not influenced by the 5′ flanking but by 3′ and intronic region composition in SCID-associated genes
    Yichun Zou, Quan Shi, Rekha Khandia, Utsang Kumar, Sami A. Al-HUSSAIN, Pankaj Gurjar, Magdi E.A. Zaki
    International Journal of Biological Macromolecules, 2025
  • Reverse vaccinology and applications as prophylactics
    Utsang Kumar, Shailja Singhal, Kishore Shende, Rekha Khandia
    Pathogenic Viruses and Armamentarium Design, 2024
  • Compositional constraints and selection forces dictate codon usage in human bocavirus
    Rekha Khandia, Shailja Singhal, Utsang Kumar, Kishore Shende, Megha Katare Pandey, Sergey Nikolaevich Povetkin, Igor Vladimirovich Rzhepakovsky, Ashwin Raut, Athanosius Alexiou, Kuldeep Dhama, George Zouganelis, Azmat Ali Khan
    Journal of King Saud University Science, 2023
    Human bocavirus (HBoV), of the genus Bocaparvovirus, is a small, non-enveloped linear single-stranded DNA virus of the Parvoviridae family. The virus is known to cause severe life-threatening respiratory tract infections in pediatric patients. Considering its deleterious impacts on respiratory, gastrointestinal, and hematological health, we prompted to investigate codon usage patterns, parity, neutrality, Nc-GC3 analysis, gene expression, Intrinsic codon bias index (ICDI), Codon bias index (CBI), Relative codon deoptimization index (RCDI), Translational selection (P2), and measure independent of length and composition (MILC) to investigate the role of evolutionary constraints such as selection and mutation and molecular patterns present in HBoV. 805 HBoV sequences were investigated using various software and statistical tools. The present study demonstrated the predominant governance of selection forces over mutational forces in determining codon usage. The compositional parameters were pivotal in deciding the dinucleotide occurrence and frequently used codons. Since the HBoV genomes were A-and T-nucleotide-rich, A/T ending codons and ApAdinucleotides were overrepresented. Despite the A/T richness, at the non-neutral positions of the codon, the G/C nucleotide content was found to be the highest, again underscoring the selective forces that drive a high percentage of G/C nucleotide. At the non-neutral codon positions, with an increase in GC nucleotide, codon bias also increased, while at the third position of the codon, with an increase in GC content, it was decreased. Overall, there is a low codon bias in HBoV. A total of nine A/T ending codons were overrepresented, while nineteen G/C ending codons were underrepresented. Interestingly, instead of CTG, a commonly overrepresented codon, AGA was the most overrepresented codon. AGA and CGG encoding for arginine showed average maximum and minimum RSCU values in the HBoV genome. The collective inference from the neutrality plot, Nc-GC3 curve, and P2 analysis indicated the prevalence of selection force over mutation force. With that, our study offers a novel perspective on the different molecular patterns present in HBoV, and the results might be implicated in designing efficacious therapeutic modalities against HBoV.
  • Biotechnological, Agriculture, Industrial, and Biopharmaceutical Research in Bioinformatics
    Shailja Singhal, Utsang Kumar, Megha Katare Pandey, Rekha Khandia
    Bioinformatics and Computational Biology Technological Advancements Applications and Opportunities, 2023
    Bioinformatics is an interdisciplinary field, comprising various approaches and tools of computation and analysis to store, manage, and interpret biological data. Advancements in bioinformatics and the integration of multiple omics technologies have made the analysis and interpretation of biological complexity possible at a rapid pace, particularly in areas involving sequence data processing and drug design. Biotechnology is interconnected with bioinformatics in many ways like nucleotide sequence analysis, phylogenetic analysis, protein and DNA modeling, protein-protein and/or protein-ligand docking, metagenomics, and metabolomics including microbial, plant, animal, and human and studies. Bioinformatics allows for a wide range of technologies to be used for retrieving coding sequences of protein and mRNA from datasets repositories, 3D-structural modeling, and interpretation. CRISPR-Cas9-based genetic engineering for agricultural bacteria and many other agriculture bioinformatics that are used for crop improvement are all examples of bioinformatics’ potential. In order to gain a better understanding of biopharmaceutical activity and function, bioinformatics tools might help in the study of the evolutionary relationship of genes in the entire genome sequences of various microalgal species. The ability to investigate the phylogenetic and effective constituents of microbial populations that have prominent significance in industrial processes has massively increased due to advancements in bioinformatics. As a result, bioinformatics applications have increased in the corporate sector, where altered microbiomes play a vital role in producing food, probiotics, nutraceuticals, cosmetics, and enzymes exploration. Moreover, one of the bioinformatics applications includes codon usage bias (CUB) analysis. It is extensively used in cell biology, genetics, and functional expression of genes. CUB is one of the approaches used in novel drug discovery. Attenuation of viruses to prevent any health hazards while boosting a strong immune response is one of the novel approaches based on codon usage bias manipulation. Furthermore, several protein targets are created by heterologous expression of transgenic proteins, which involves rearranging the coding sequence(s) from the innate sequence(s) to optimize the protein translation in specific host machinery. Several studies based on the elucidation of codon usage patterns of emerging pathogens helped in establishing approaches to modify their genomes to mitigate virulence and reveal the pathogen’s replicative efficiency in human hosts for creating a clinically efficient vaccine.
  • An Insight into Codon Pattern Analysis of Autophagy Genes Associated with Virus Infection
    Shailja Singhal, Utsang Kumar, Taha Alqahtani, Igor Vladimirovich Rzhepakovsky, Rekha Khandia, Megha Pandey, Saud Alqahtani, Hanan Alharbi, Mohammad Amjad Kamal
    Current Pharmaceutical Design, 2023
    Introduction: Apoptosis and autophagy are the two fundamental processes involved in maintaining homeostasis, and a common stimulus may initiate the processes. Autophagy has been implicated in various diseases, including viral infections. Genetic manipulations leading to altered gene expression might be a strategy to check virus infection. Aim: Determination of molecular patterns, relative synonymous codon usage, codon preference, codon bias, codon pair bias, and rare codons so that genetic manipulation of autophagy genes may be done to curb viral infection. Method: Using various software, algorithms, and statistical analysis, insights into codon patterns were obtained. A total of 41 autophagy genes were envisaged as they are involved in virus infection. Results: The A/T and G/C ending codons are preferred by different genes. AAA-GAA and CAG-CTG codon pairs are the most abundant codon pairs. CGA, TCG, CCG, and GCG are rarely used codons. Conclusion: The information generated in the present study helps manipulate the gene expression level of virus infection-associated autophagy genes through gene modification tools like CRISPR. Codon deoptimization for reducing while codon pair optimization for enhancing is efficacious for HO-1 gene expression.
  • Insight into codon utilization pattern of tumor suppressor gene epb41l3 from different mammalian species indicates dominant role of selection force
    Utsang Kumar, Rekha Khandia, Shailja Singhal, Nidhi Puranik, Meghna Tripathi, Atul Kumar Pateriya, Raju Khan, Talha Bin Emran, Kuldeep Dhama, Ashok Munjal, Taha Alqahtani, Ali M. Alqahtani
    Cancers, 2021
    Uneven codon usage within genes as well as among genomes is a usual phenomenon across organisms. It plays a significant role in the translational efficiency and evolution of a particular gene. EPB41L3 is a tumor suppressor protein-coding gene, and in the present study, the pattern of codon usage was envisaged. The full-length sequences of the EPB41L3 gene for the human, brown rat, domesticated cattle, and Sumatran orangutan available at the NCBI were retrieved and utilized to analyze CUB patterns across the selected mammalian species. Compositional properties, dinucleotide abundance, and parity analysis showed the dominance of A and G whilst RSCU analysis indicated the dominance of G/C-ending codons. The neutrality plot plotted between GC12 and GC3 to determine the variation between the mutation pressure and natural selection indicated the dominance of selection pressure (R = 0.926; p < 0.00001) over the three codon positions across the gene. The result is in concordance with the codon adaptation index analysis and the ENc-GC3 plot analysis, as well as the translational selection index (P2). Overall selection pressure is the dominant pressure acting during the evolution of the EPB41L3 gene.
  • Current scenario of the pandemic covid-19: An overview
    , Utsang Kumar, Shailja Singhal, , Rekha Khandia, , Ashok Munjal, and
    Journal of Experimental Biology and Agricultural Sciences, 2020
    The novel coronavirus disease-19 (COVID-19) caused by the SARS-CoV-2 is an emerging disease with deadly consequences, extended its stride over the globe commenced from the epicenter, Wuhan wet market, China led to declare globally as pandemic disease. Several non-specific features of the disease like prolonged incubation period, asymptomatic yet contagious, longer illness duration, and conveyance post clinical recovery feature makes prevention difficult and is the key reason for its rapid spread across the world. Covid-19 shows varied manifestations with the majority of reported cases having mild or even no symptoms. However, the infection led to a destructive footprint in the pulmonary system, specifically, lungs are most prone to damage, making them incapable of conducting respiratory functions and thus, resulting in acute respiratory distress syndrome (ARDS), multi-organ dysfunction, and loss of life. Up to the present, there is no worldwide-approved treatment for COVID-19 and only repurposed drugs are employed for the hospitalized patient, necessitating an urgent need to develop effective therapeutics. Hence, effective control of disease spread through screening and isolation of contacts is crucial in the community. The contagion effect of the COVID-19 outbreak has brought major challenges to health systems as well as global economy worldwide. Development of rapid diagnostic test and effective vaccine as well as minimizing the exposure of the human population to possible animal reservoirs is measures needed to curb future impact. The outbreak of SARS-CoV in 2003 followed by MERS-CoV within a decade, indicates the threat of novel infectious diseases resulting from RNA viruses, will continue to present a serious global health threat, as epitomized by COVID-19. Therefore, this review is attempting to provide an overview of the current scenario of COVID-19 in terms of epidemiology, pathophysiology, diagnosis, prevention, and treatment, especially focusing on public health impact.
  • Analysis of nipah virus codon usage and adaptation to hosts
    Rekha Khandia, Shailja Singhal, Utsang Kumar, Afzal Ansari, Ruchi Tiwari, Kuldeep Dhama, Jayashankar Das, Ashok Munjal, Raj Kumar Singh
    Frontiers in Microbiology, 2019
    A recent outbreak of Nipah virus (NiV) in India has caused 17 deaths in people living in districts of Kerala state. Its zoonotic nature, as well as high rate of human-to-human transmission, has led researchers worldwide to work toward understanding the different aspects of the NiV. We performed a codon usage analysis, based on publicly available nucleotide sequences of NiV and its host adaptation, along with other members of the Henipavirus genus in ten hosts. NiV genome encodes nine open reading frames; and overall, no significant bias in codon usage was observed. Aromaticity of proteins had no impact on codon usage. An analysis of preferred codons used by NiV and the tRNA pool in human cells indicated that NiV prefers codons from a suboptimal anticodon tRNA pool. We observed that codon usage by NiV is mainly constrained by compositional and selection pressures, not by mutational forces. Parameters that define NiV and host relatedness in terms of codon usage were analyzed, with a codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index calculations; which indicated that, of all hosts analyzed, NiV was best adapted to African green monkeys. A comparative analysis based on the relative codon deoptimization index (RCDI) for host adaptation of NiV, Hendra virus (HeV), Cedar virus (CedV), and Hendra like Mojiang virus (MojV) revealed that except for dogs and ferrets, all evaluated hosts were more susceptible to HeV than NiV.

RECENT SCHOLAR PUBLICATIONS

  • Plasmonic dual-silver decorated dielectric nanoantenna arrays for enhanced surface-enhanced Raman scattering (SERS) sensors
    RP Singh, N Nagabhooshanam, Y Thakur, D Nathiya, MDA Praveena, ...
    Current Applied Physics 84, 136-144 , 2026
    2026
  • Enrichment of algae harvesting and actions of potassium carbonate on hydrogen production from dairy wastewater via supercritical water gasification: performance measures
    AM Krishnan, N Nagabhooshanam, Y Thakur, A Kulshreshta, ...
    Journal of Chemical Technology & Biotechnology 101 (1), 60-67 , 2026
    2026
  • Influence of natural fiber and Isocyanate processing on functional behaviour of polyester composites
    SGA Hasan, N Nagabhooshanam, Y Thakur, A Kulshreshta, ...
    Journal of Mechanical Science and Technology, 1-6 , 2025
    2025
    Citations: 1
  • Combinations of Lauric acid phase change material and hybrid nanofluid on energy storage and thermal behaviour of solar heat exchanger
    VR Veeraraj, N Nagabhooshanam, Y Thakur, A Kulshreshta, ...
    Applied Thermal Engineering, 128560 , 2025
    2025
    Citations: 5
  • AI-driven discovery of alloyed plasmonic nanodisks for broadband solar absorption and charge carrier multiplication
    RP Singh, N Nagabhooshanam, Y Thakur, D Nathiya, A Praveena, ...
    Plasmonics, 1-14 , 2025
    2025
    Citations: 33
  • Codon usage bias and nucleotide bias are not influenced by the 5′ flanking but by 3′ and intronic region composition in SCID-associated genes
    Y Zou, Q Shi, R Khandia, U Kumar, SA Al-Hussain, P Gurjar, MEA Zaki
    International Journal of Biological Macromolecules 308, 142182 , 2025
    2025
    Citations: 1
  • Insights into genetic architecture and disease associations of genes associated with different human blood group systems using codon usage bias
    U Kumar, S Singhal, AA Khan, AM Alanazi, P Gurjar, R Khandia
    Journal of Biomolecular Structure and Dynamics, 1-21 , 2025
    2025
    Citations: 1
  • Reverse vaccinology and applications as prophylactics
    U Kumar, S Singhal, K Shende, R Khandia
    Pathogenic Viruses and Armamentarium Design, 127-143 , 2024
    2024
    Citations: 2
  • Pathogenic viruses and armamentarium design
    A Kumar, K Pant
    Elsevier , 2024
    2024
    Citations: 2
  • Homogenizer
    U Kumar, S Singhal, R Khandia
    IN Patent 411899-001 , 2024
    2024
  • 26 Biotechnological, Agriculture
    S Singhal, U Kumar, MK Pandey, R Khandia
    Bioinformatics and Computational Biology: Technological Advancements … , 2023
    2023
  • Biotechnological, Agriculture, Industrial, and Biopharmaceutical Research in Bioinformatics
    S Singhal, U Kumar, M Katare, R Khandia
    https://www.taylorfrancis.com/chapters/edit/10.1201/9781003331247-29 … , 2023
    2023
    Citations: 1
  • An insight into codon pattern analysis of autophagy genes associated with virus infection
    S Singhal, U Kumar, T Alqahtani, IV Rzhepakovsky, R Khandia, M Pandey, ...
    Current Pharmaceutical Design 29 (14), 1105-1120 , 2023
    2023
    Citations: 4
  • Compositional constraints and selection forces dictate codon usage in human bocavirus
    R Khandia, S Singhal, U Kumar, K Shende, MK Pandey, SN Povetkin, ...
    Journal of King Saud University-Science 35 (6), 102726 , 2023
    2023
    Citations: 6
  • A Filter to Visualize Green Fluorescent Objects
    R Khandia, U Kumar, S Singhal
    IN Patent 470,113 , 2022
    2022
  • Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force
    U Kumar, R Khandia, S Singhal, N Puranik, M Tripathi, AK Pateriya, ...
    Cancers 13 (11), 2739 , 2021
    2021
    Citations: 30
  • CURRENT SCENARIO OF THE PANDEMIC COVID-19: AN OVERVIEW
    U Kumar, S Singhal, R Khandia, A Munjal
    Journal of Experimental Biology and Agricultural Sciences 8 (Spl-1-SARS-CoV … , 2020
    2020
    Citations: 7
  • Analysis of Nipah virus codon usage and adaptation to hosts
    R Khandia, S Singhal, U Kumar, A Ansari, R Tiwari, K Dhama, J Das, ...
    Frontiers in microbiology 10, 886 , 2019
    2019
    Citations: 162

MOST CITED SCHOLAR PUBLICATIONS

  • Analysis of Nipah virus codon usage and adaptation to hosts
    R Khandia, S Singhal, U Kumar, A Ansari, R Tiwari, K Dhama, J Das, ...
    Frontiers in microbiology 10, 886 , 2019
    2019
    Citations: 162
  • AI-driven discovery of alloyed plasmonic nanodisks for broadband solar absorption and charge carrier multiplication
    RP Singh, N Nagabhooshanam, Y Thakur, D Nathiya, A Praveena, ...
    Plasmonics, 1-14 , 2025
    2025
    Citations: 33
  • Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force
    U Kumar, R Khandia, S Singhal, N Puranik, M Tripathi, AK Pateriya, ...
    Cancers 13 (11), 2739 , 2021
    2021
    Citations: 30
  • CURRENT SCENARIO OF THE PANDEMIC COVID-19: AN OVERVIEW
    U Kumar, S Singhal, R Khandia, A Munjal
    Journal of Experimental Biology and Agricultural Sciences 8 (Spl-1-SARS-CoV … , 2020
    2020
    Citations: 7
  • Compositional constraints and selection forces dictate codon usage in human bocavirus
    R Khandia, S Singhal, U Kumar, K Shende, MK Pandey, SN Povetkin, ...
    Journal of King Saud University-Science 35 (6), 102726 , 2023
    2023
    Citations: 6
  • Combinations of Lauric acid phase change material and hybrid nanofluid on energy storage and thermal behaviour of solar heat exchanger
    VR Veeraraj, N Nagabhooshanam, Y Thakur, A Kulshreshta, ...
    Applied Thermal Engineering, 128560 , 2025
    2025
    Citations: 5
  • An insight into codon pattern analysis of autophagy genes associated with virus infection
    S Singhal, U Kumar, T Alqahtani, IV Rzhepakovsky, R Khandia, M Pandey, ...
    Current Pharmaceutical Design 29 (14), 1105-1120 , 2023
    2023
    Citations: 4
  • Reverse vaccinology and applications as prophylactics
    U Kumar, S Singhal, K Shende, R Khandia
    Pathogenic Viruses and Armamentarium Design, 127-143 , 2024
    2024
    Citations: 2
  • Pathogenic viruses and armamentarium design
    A Kumar, K Pant
    Elsevier , 2024
    2024
    Citations: 2
  • Influence of natural fiber and Isocyanate processing on functional behaviour of polyester composites
    SGA Hasan, N Nagabhooshanam, Y Thakur, A Kulshreshta, ...
    Journal of Mechanical Science and Technology, 1-6 , 2025
    2025
    Citations: 1
  • Codon usage bias and nucleotide bias are not influenced by the 5′ flanking but by 3′ and intronic region composition in SCID-associated genes
    Y Zou, Q Shi, R Khandia, U Kumar, SA Al-Hussain, P Gurjar, MEA Zaki
    International Journal of Biological Macromolecules 308, 142182 , 2025
    2025
    Citations: 1
  • Insights into genetic architecture and disease associations of genes associated with different human blood group systems using codon usage bias
    U Kumar, S Singhal, AA Khan, AM Alanazi, P Gurjar, R Khandia
    Journal of Biomolecular Structure and Dynamics, 1-21 , 2025
    2025
    Citations: 1
  • Biotechnological, Agriculture, Industrial, and Biopharmaceutical Research in Bioinformatics
    S Singhal, U Kumar, M Katare, R Khandia
    https://www.taylorfrancis.com/chapters/edit/10.1201/9781003331247-29 … , 2023
    2023
    Citations: 1
  • Plasmonic dual-silver decorated dielectric nanoantenna arrays for enhanced surface-enhanced Raman scattering (SERS) sensors
    RP Singh, N Nagabhooshanam, Y Thakur, D Nathiya, MDA Praveena, ...
    Current Applied Physics 84, 136-144 , 2026
    2026
  • Enrichment of algae harvesting and actions of potassium carbonate on hydrogen production from dairy wastewater via supercritical water gasification: performance measures
    AM Krishnan, N Nagabhooshanam, Y Thakur, A Kulshreshta, ...
    Journal of Chemical Technology & Biotechnology 101 (1), 60-67 , 2026
    2026
  • Homogenizer
    U Kumar, S Singhal, R Khandia
    IN Patent 411899-001 , 2024
    2024
  • 26 Biotechnological, Agriculture
    S Singhal, U Kumar, MK Pandey, R Khandia
    Bioinformatics and Computational Biology: Technological Advancements … , 2023
    2023
  • A Filter to Visualize Green Fluorescent Objects
    R Khandia, U Kumar, S Singhal
    IN Patent 470,113 , 2022
    2022

GRANT DETAILS

INSPIRE Award

RESEARCH OUTPUTS (PATENTS, SOFTWARE, PUBLICATIONS, PRODUCTS)

Patent - A filter to visualize green fluorescent objects
Patent No. 470113
Abstract:
The present invention provides the formation of cheap, ease of access, durable, almost negligible running and maintenance cost advanced material via a novel chemical and thermal treatment useful for visualization applications as in green fluorescent objects herein green fluorescent protein respectively. Present invention explains the novel use of colored cellophane wrapping sheet material as a filter to observe green fluorescent protein.. The novel use of the material broad application spectrum in various areas like medical, aerospace, electronics etc. A novel process for obtaining the advanced product is used in the form of filter for specific function like visualization of green fluorescent objects herein enhanced green fluorescent protein, means for monitoring gene expression, and protein localization in living cells.

Patent - Homogenizer
Patent No. 411899-001
Abstract:
The mini homogenizer with cabinet is an extremely useful lab instrument when you need to do sensitive work like, dealing with biological specimen that are very sensitive to things floating in the air and are prone to cross-contamination by several factors. It provides a clean atmosphere inside the cabinet, thereby, enabling you to work with small quantities of tissue. There is no need of any particular environment to operate this homogenizer.....

Industry, Institute, or Organisation Collaboration

InSc- Institute of Scholars, Bengaluru, India

INDUSTRY EXPERIENCE

CSIR-Central Drug Research Institute, Lucknow, India
(Laboratory Animals Handling and Management.)