Article

Kumar , A. and Nimsarkar , P. and Singh, S. (2022) Probing the Interactions Responsible for the Structural Stability of Trypanothione Reductase Through Computer Simulation and Biophysical Characterization. Protein Journal. p. 10052.

Anjum, F. and Mohammad, T. and Asrani, P. and Shafie, A. and Singh, S. and Yadav, DK and Uversky, VN and Hassan, MI (2022) Identification of intrinsically disorder regions in non-structural proteins of SARS-CoV-2: New insights into drug and vaccine resistance. Molecular and Cellular Biochemisty, 24. pp. 1-13.

Soni , B. and Singh , S. (2022) Synthetic Perturbations in IL6 Biological Circuit Induces Dynamical Cellular Response. Molecules., 27 (1). p. 124.

Samarth, N. and Kabra , R. and Singh , S. (2021) Anthraquinolone and Quinolizine Derivatives as an alley of future treatment for COVID-19 : An In silico Machine Lea. Scientific Reprot., 11. p. 17915.

Soni , B. and Kabra , R. and Singh , S. (2021) Quantitative Insight into Immunopathology of SARS-CoV-2 Infection. Journal of Interferon and Cytokine Research., 41 (7). pp. 244-257.

Choudhury, A. and Mohammad, T. and Samarth, N. and Hussain, A. and Rehman , MT. and Islam, A. and Alajmi , MF. and Singh, S. and Hassan, MI. (2021) Structural genomics approach to investigate deleteriousimpact of nsSNPs in conserved telomere maintenance component 1. Scientific Report., 11 (1). p. 10202.

Ingale , P. and Lad , B. and Kabra, R. and Singh, S. (2021) Dissecting druggability of ABC transporter proteins in Mycobacterium species through network modeling. Journal of Biomolecular Structure and Dynamics, 23. pp. 1-10.

Soni , B. and Singh, S. (2021) COVID-19 co-infection mathematical model as guided through signaling structural framework. Computational and Structural Biotechnology Journal, 19. pp. 1672-1683.

Singh , S. and Chouhan, MS. and Deshmukh, B. and Ramteke , P. and Athavale, D. and Bhat, MK. (2020) Role of TNFα and leptin signaling in colon cancer incidence and tumor growth under obese phenotype. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1866 ( 16566). 165660. ISSN Volume 1866, Issue 5, 1 May 2020, 165660

Nimsarkar, P. and Ingale, P. and Singh, S. (2020) Systems Studies Uncover miR-146a as a Target in Leishmania major Infection Model. ACS Omega, 5 (21). pp. 12516-12526.

Chauhan, N. and Singh, S. (2020) Multiscale Process Modelling in Translational Systems Biology of Leishmania major: A Holistic view. Scientific Reports, 10 (785).

Singh, S. and Mishra, G.C. (2020) Systems Biology: “Cherry Picking” in a Treasure Trove. National Academy Science Letters, 1 (3).

Singh, S. and Singh, S. and Chouhan, M.S. and Deshmukh, B. and Ramteke, P. and Athavale, D. and Bhat, M.K. (2019) Role of TNFα and leptin signaling in colon cancer incidence and tumor growth under obese phenotype. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1866 (5).

Misra, P. and Singh, S. (2019) Site specific microbiome of Leishmania parasite and its cross-talk with immune milieu. Immunology Letters.

Chauhan, N. and Singh, S. (2019) Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania. Frontiear in Bioengineering And Biotechology.

Soni, B. and Singh, S. (2019) Cytokine Milieu in Infectious Disease: A Sword or a Boon? Journal of Interferon and Cytokine Research , 40 (1).

Vaidya, A. and Singh, S. and Limaye, L. and Kale, V. (2019) Chimeric feeders of mesenchymal stromal cells and stromal cells modified with constitutively active AKT expandhematopoietic stem cells. Regenerative Medicine, 14 (6). pp. 535-553.

Misra, P. and Singh, S. (2019) Role of cytokines in combinatorial immunotherapeutics of non-small cell lung cancer through systems perspective. Cancer Medicine.

Kumar, A. and Chauhan, N. and Singh, S. (2019) Understanding the Cross-Talk of Redox Metabolism and Fe-S Cluster Biogenesis in Leishmania Through Systems Biology Approach. Frontier in Celluller and Infection Microbiology , 15. p. 3389.

Fernandes, S. and Tembe, S. and Singh, S. and Vardhan, S. and Nair, V. and Kale, V. and Limaye, L. (2019) . Development and characterization of human iPSC line NCCSi004-A from umbilicalcord blood (UCB) derived CD34(+)cells obtained from donor belonging to Indianethnic population. Stem Cell Research, 26 (35). p. 101392.

Athavale, D. and Chouhan, S. and Pandey, V. and Mayengbam, S.S. and Singh, S. and Bhat, M.K. (2018) Hepatocellular carcinoma-associated hypercholesterolemia: involvement ofproprotein-convertase-subtilisin-kexin type-9 (PCSK9). Cancer and Metabolism, 6 (16).

Bejugam , P.R. and Singh , S. (2018) Engineering riboswitch in L. major: From prediction to conceptualization. Elsevier International Journal of Biological Macromolecules, 115. pp. 98-115. ISSN Volume 115, August 2018, Pages 98-105

Choppara, S. and Ganga, S. and Manne, R. and Dutta, P. and Singh, S. and Santra, M.K. (2018) The SCF(FBXO46)ubiquitin ligase complex mediates degradation of the tumor suppressor FBXO31 and thereby prevents premature cellular senescence. Journal of Biological Chemistry , 293 (42). pp. 16291-163061.

Soni , B. and Nimsarkar , P. and Saha , B. and Mol , M. and Singh , S. (2018) Systems-synthetic biology in understanding the complexities and simple devices in immunology. Cytokine (108). pp. 60-66.

Kabra, R. and Chauhan, N. and Kumar, A. and Ingale, P. and Singh, S. (2018) Efflux pumps and antimicrobialresistance: Paradoxical components in systems genomics. Progress in Biophysics and Molecular Biology.

Taye, N. and Alam , A. and Ghorai, S. and Chatterji, D. and Parulekar , A. and Mogare, D. and Singh, S. and Sengupta, P. and Chatterjee, S. and Bhat , M. and Santra , M. and Salunkhe , P. and Finston, S. and Chattopadhyay, S. (2018) SMAR1 inhibits Wnt/β-catenin signaling and prevents colorectal cancer progression. Oncotarget, 9 (30). 21322-21336..

Malvi , P. and Chaube , B. and Singh , S.V. and Mohammad , N. and Vijayakumar , M.V. and Singh, S. and Chouhan, S. and Bhat , M.K. (2018) Elevated circulatory levels of leptin and resistin impair therapeutic efficacy of dacarbazine in melanoma under obese state. Cancer & Metabolism.

Sonar , K. and Kabra , R. and Singh, S. (2018) TryTransDB: A web-based resource for transport proteins in Trypanosomatidae. Scientific Report, 8 (4368).

Mol, M. and Kosey, D. and Boppana, R. and Singh , S. (2018) Transcription Factor Target Gene Network governs the Logical Abstraction Analysis of the Synthetic Circuit in Leishmaniasis. Scientific Report, 8 (1). p. 3464.

Mol , M. and Kabra , R. and Singh , S. (2018) Genome modularity and synthetic biology: Engineering systems. Progress in Biophysics and Molecular Biology, 132. pp. 43-51.

Kumar , A. and Saha , B. and Singh , S. (2017) Dataset generated for Dissection of mechanisms of Trypanothione Reductase and Tryparedoxin Peroxidase through dynamic networkanalysis and simulations in leishmaniasis. Data Brief. 2017 Oct 19;15:757-769, 15. pp. 757-769.

Mandlik , V. and Kabra , R. and Singh , S. (2017) System pharmacogenomics application in infectious diseases. Brief Funct Genomics .

Kumari , R. and Chouhan , S. and Singh , S. and Chhipa , R.R and Ajay , A.K. and Bhat , M.K (2017) Constitutively activated ERK sensitizes cancer cells to doxorubicin: Involvement of p53-EGFR-ERK pathway. Journal of Bioscience, 42 (1). pp. 31-41. ISSN 42(1):31-41.

Kosey , D. and Singh , S. (2017) Computational design of molecular motors as nanocircuits in Leishmaniasis [version 1; referees: 1 approved with reservations]. F1000 Research.

Kosey , D. and Singh , S. (2017) Computational design of molecular motors as nanocircuits in Leishmaniasis. Version 2. F1000Res. 2017 Jan 31.

Patel , R. and Parray Mehraj ud din, P. and Singh, U.K. and Islam , A. and Venkatesu , P. and Singh , S. and Bohidar , H.B. (2016) Effect of 1,4-bis(3-dodecylimidazolium-1-yl) butane bromide on channel form of gramicidin vesicles. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 508. pp. 150-158.

Jalnapurkar , S. and Singh , S. and Devi , M.R. and Limaye , L.S. and Kale, V.P. (2016) Nitric oxide has contrasting age-dependent effects on the functionality of murine hematopoietic stem cells. Stem Cell Res Ther. 2016 Nov 22;7 (1):171. , 7 (1). p. 171.

Mandlik, V. and Patil, S. and Bopanna, R. and Basu, S. and Singh, S. (2016) Biological Activity of Coumarin Derivatives as Anti-Leishmanial Agents. PLOS ONE , DOI:10 (1371). pp. 1-15.

Soni, S. and Mandlik , V. and Bejugam, P.R. and Singh , S. (2016) Molecular clock calibrations and substitution rates as a theoretical framework for systems approaches in TLRs: A perspective for drug targeting in leishmaniasis. Gene Reports, 4. pp. 74-86. ISSN Volume 4, September 2016, Pages 74–86

Mandlik, V. and Singh , S. (2016) Molecular docking and molecular dynamics simulation study of inositol phosphorylceramide synthase – inhibitor complex in leishmaniasis: Insight into the structure based drug design [version 1; referees: 1 approved with reservations]. F1000 Research , 5 (1610). pp. 1-10.

Chouhan , S. and Singh , S. and Athavale, D. and Ramteke , P. and Pandey , V. and Joseph, J. and Mohan , R. and Shetty , P.K. and Bhat , M.K. (2016) Glucose induced activation of canonical Wnt signaling pathway in hepatocellular carcinoma is regulated by DKK4. Scientific Report (27558 ).

Patel , P. and Mandlik , V. and Singh , S. (2016) LmSmdB: an integrated database for metabolic and gene regulatory network in Leishmania major and Schistosoma mansoni. Genomic Data , 7. pp. 115-118.

Bejugam , P.R. and Singh, S. (2016) Computing Molecular Devices in L.major through Transcriptome Analysis: Structured Simulation Approach. PLoS One, 11 (2). e0148909-e0148909. ISSN 2016 Feb 22;11(2):e0148909

Mandlik , V. and Patil , S. and Bopanna , R. and Basu , S. and Singh, S. (2016) Biological Activity of Coumarin Derivatives as Anti-Leishmanial Agents. PLoS One, 11 (10). e0164585-e0164585.

Bandyopathyaya , S. and Chandel, H.S. and Singh, S. and Roy , S. and Krishnasastry , M.V. and Saha , B. (2015) Counteractive functions are encrypted in the residues of CD154. Human Immunology, 76 (9). pp. 673-680.

Umbarkar, P. and Singh , S. and Arkat, S. and Bodhankar, S.L. and Lohidasan , S. and Sitasawad , S.L. (2015) Monoamine oxidase-A is an important source of oxidative stress and promotes cardiac dysfunction, apoptosis, and fibrosis in diabetic cardiomyopathy. Free Radical Biol. Med., 87. pp. 263-273.

Mandlik , V. and Gurav , M. and Singh, S. (2015) Regulatory dynamics of network architecture and function in Tristable genetic circuit of Leishmania: A Mathematical biology Approach. J Biomol Struct Dyn. .

Moirangthem , R.D. and Singh , S. and Adsul , A. and Jalnapurkar, S. and Limaye , L.S. and Kale, V.P. (2015) Hypoxic niche-mediated regeneration of hematopoiesis in the engraftment window is dominantly affected by oxygen tension in the milieu. Stem Cells and Development.

Mol, M. and Kosey , D. and Singh , S. (2015) Nano Synthetic Devices in Leishmaniasis : A Bioinformatics Approach. Frontiers in Immunology, 6. p. 323.

Gangalum PR, P.R. and de Castro, W. and Vieira, L.Q. and Dey, R. and Rivas , L. and Singh , S. and Majumdar, S.. and Saha , B. (2015) Platelet-activating factor receptor contributes to antileishmanial function of miltefosine. Journal of Immunology , 194 (12). pp. 5961-5967.

Chakraborty, S. and Srivastava , A. and Jha , M.K. and Nair, A. and Pandey , S.P and Srivastava , N. and Kumari , S. and Singh , S. and Krishnasastry M.V.; Saha B. , M.V. and Saha , B. (2015) Inhibition of CD40-Induced N-Ras Activation Reduces Leishmania major Infection. Journal of Immunology , 194. pp. 3852-3860. ISSN Journal of Immunology

Singh, S. and Mandlik , V. and Shinde, S. (2015) Molecular dynamics simulations and statistical coupling analysis of GPI12 in L. major: functional co-evolution and conservedness reveals potential drug–target sites. Molecular BioSystems, 11 (3). pp. 958-968.

Singh , S. and Ghode, S and Moirangthem , R.D. and Devi, M. and Limaye , L.S. and Kale , V. (2015) Phenotypic and functional characterization of a marrow-derived stromal cell line, M210B4 and its comparison with primary marrow stromal cells. Biomedical Research Journal, 2 (1). pp. 120-133.

Shinde, S. and Milsee , M. and Singh, S. (2014) Regulatory networks, genes and glycerophospholipid biosynthesis pathway in schistosomiasis: A systems biology view for pharmacological intervention. Gene, 550 (2). pp. 214-222.

Shinde , S. and Mol, M. and Jamdar, V. and Singh , S. (2014) Molecular modeling and molecular dynamics simulations of GPI 14 in Leishmania major: Insight into the catalytic site for active site directed drug design. Journal of Theoretical Biology, 351. pp. 37-46.

Mandlik , V. and Shinde , S. and Singh , S. and UNSPECIFIED (2014) Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation. BMC Evolutionary Biology , 14 (142). pp. 1-10.

Mandlik , V and Limbachiya , D and Shinde , S and Mol, M. and Singh, S. (2013) Synthetic circuit of inositol phosphorylceramide synthase in Leishmania: a chemical biology approach. J Chem Biol , 6. pp. 51-62.

Mandlik , V and Shinde , S and Chaudhary , A and Singh, S. (2012) Biological network modeling identifies IPCS in Leishmania as a therapeutic target. Integrative Biology, 4 (9). pp. 1130-1142.

Hasan , S.S. and Singh , S. and Parikh , R.Y. and HDharne, M.S. and Patole , M.S. and Prasad , B.L. and Prasad , B.L. (2008) Bacterial synthesis of copper/copper oxide nanoparticles. J Nanosci Nanotechnol. 2008 Jun;8(6):3191-6, 8 (6). pp. 3191-3196.

Book Section

Singh , S. (2021) Metagenomic Systems Biology (Edited Book). In: Metagenomic Systems Biology Integrative Analysis of the Microbiome. Springer Nature. ISBN 978-981-15-8561-6

Misra , P. and Singh, S. (2020) Vaccine Design, Nanoparticle Vaccines and Biomaterial Applications. In: Systems and Synthetic Immunology. In: Systems and Synthetic Immunology pp 1-52. Springer.

Singh, S. (2018) Synthetic Biology: Omics Tools and their Application,. In: Synthetic Biology : Omics Tools and Their Applications. Springer.

Mandlik, V. and Bejugam , P.P. and Singh , S. (2015) Application of Artificial Neural Networks in Modern Drug Discovery Chapter – 6 published in Artificial Neural Network for Drug Design, Delivery and Disposition. In: Artificial Neural Network for Drug Design, Delivery and Disposition. Elsevier.

Mol., M. and Singh , S. (2014) Computational Design of Biological Systems: From Systems to Synthetic Biology. In: Frontiers in Computational Chemistry. Benthum Science, pp. 158-196. ISBN 978-1-60805-865-5 ISSN :2352-944X

Mol., M. and Singh , S. (2014) In silico Approaches for Dealing With Gene Regulatory Networks to Understand Molecular Mechanisms of Immunity in Infectious Disease. In: Genomics and Drug Discovery. Benthum Science, pp. 1-20. (In Press)

Singh , S. (2013) Gene Regulatory Network: A New Paradigm in Bioinformatics. In: Biotechnology Volume 6: Bioinformatics and Computational Biology. Bioinformatics and Computational Biology , 6 . Studium Press LLC, U.S.A., pp. 1-11. ISBN 9781626990210

Singh, S. (2012) Quantum pharmacology for infectious diseases: a molecular connectivity approach. In: Quantum pharmacology. Benthum Science, pp. 249-254.

Other

Singh , S. (2020) Systems and Synthetic Immunology. Springer.