I am currently affiliated as an Assistant Professor in the Department of Data Sciences, Centre of Biomedical Research, Lucknow, India.

Academic Profile

PostDoc (University Hospital Erlangen, Germany)
PostDoc (University of Würzburg, Germany)
PostDoc (University of Düsseldorf, Germany)

PhD in Bioinformatics (University of Würzburg, Germany)

Scientific Staff (University Hospital Heidelberg, Germany)

MSc in Bioinformatics (UIET, CSJM University, India)

Teaching & Research Experience

Postdoctoral Research Experience: 8 years
Research Experience (including PhD): 16 years
Teaching Experience : 5 years

Research Guidance (MSc, PhD)

PhD co-supervision: 1
MSc Dissertation: 5, guiding 1
Internships: 20+

• Our research primarily focuses on developing solutions for complex diseases by understanding their underlying mechanisms and identifying diagnostic and prognostic biomarkers. Our goal is to translate these findings into clinical practice to improve patient outcomes through personalized medicine, enabling more accurate diagnoses, targeted therapies, and better disease management. 

  Vision
  By combining OMICS, systems biology, and artificial intelligence, we will enhance our understanding of disease pathology, improve diagnostic accuracy, and develop patient-specific treatments. Computational modeling will be pivotal in advancing our comprehension and treatment of complex diseases.

  Aim
  To achieve this vision, we integrate prior scientific knowledge with diverse multi-omics, clinical, and healthcare data to elucidate disease mechanisms. We then create dynamic network models and validate our predictions through in-silico and in-vivo studies, in collaboration with experimental partners and clinicians.

  We primarily work along three lines of research-

  Integrating multi-omics data (genomics, transcriptomics, and metabolomics) with AI/ML: we focus on reconstructing dynamic pathway models, performing GWAS, metabolic modeling, and variant analysis to identify key mechanisms driving disease progression. By incorporating medical image classification techniques, we enhance our ability to analyze imaging data alongside multi-omics data. These approaches enable us to classify diseases more accurately and develop targeted diagnostic and therapeutic strategies. 

  Evolutionary approaches for understanding disease: exploring why humans might have evolved to be susceptible to certain diseases, studying the evolution of disease-associated genes, and applying evolutionary theories to fill gaps in disease maps.

  Investigation of infection mechanisms: examining pathogen-host interactions, co-evolution, cell-cell communication, cell signaling and regulation, and the non-linear dynamics of disease progression.

Publications

1.                Osmanoglu Ö, Gupta SK, Almasi A, Yagci S, Srivastava M, Araujo GH, Nagy Z, Balkenhol J, Dandekar T: Signaling network analysis reveals fostamatinib as a potential drug to control platelet hyperactivation during SARS-CoV-2 infection. Frontiers in Immunology 2023, 14.

2.                Cui M, Gupta SK, Bauer P: Role of the plant-specific calcium-binding C2-DOMAIN Abscisic Acid-Related (CAR) protein family in environmental signaling. European Journal of Cell Biology 2023:151322.

3.                Trivedi M, Singh S, Pandey T, Gupta SK, Verma RS, Pandey R: Sesquiterpenoids isolated from davana (Artemisia pallens Wall. ex DC) mitigates parkinsonism in Caenorhabditis elegans disease model. Biochemical and Biophysical Research Communications 2022.

4.                Gupta SK, Osmanoglu Ö, Minocha R, Bandi SR, Bencurova E, Srivastava M, Dandekar T: Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information. Frontiers in Medicine 2022, 9.

5.             Gupta SK, Minocha R, Thapa PJ, Srivastava M, Dandekar T: Role of the Pangolin in Origin of SARS-CoV-2: An Evolutionary Perspective. International Journal of Molecular Sciences 2022, 23:9115.

6.                Balkenhol J, Bencurova E, Gupta SK, Schmidt H, Heinekamp T, Brakhage A, Pottikkadavath A, Dandekar T: Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study. Computational and Structural Biotechnology Journal 2022.

7.                Akhoon BA, Gupta SK, Dhar MK: Dissecting the Genome, Secretome, and Effectome repertoires of Monilinia spp., The Causal Agent of Brown Rot Disease: A Comparative Analysis. 2022.

8.                Gupta SK, Srivastava M, Osmanoglu Ö, Xu Z, Brakhage AA, Dandekar T: Aspergillus fumigatus versus Genus Aspergillus: Conservation, adaptive evolution and specific virulence genes. Microorganisms 2021, 9:2014.

9.             Gupta SK, Srivastava M, Minocha R, Akash A, Dangwal S, Dandekar T: Alveolar Regeneration in COVID-19 Patients: A Network Perspective. International Journal of Molecular Sciences 2021, 22:11279.

10.             Gupta SK, Ponte-Sucre A, Bencurova E, Dandekar T: An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. Computational and structural biotechnology journal 2021, 19:5292-5308.

11.           Gupta SK, Srivastava M, Osmanoglu Ö, Dandekar T: Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. Scientific reports 2020, 10:1-12.

12.       Srivastava M, Bencurova E, Gupta SK, Weiss E, Löffler J, Dandekar T: Aspergillus fumigatus challenged by human dendritic cells: metabolic and regulatory pathway responses testify a tight battle. Frontiers in cellular and infection microbiology 2019, 9:168.

13.          Akhoon BA, Gupta SK, Tiwari S, Rathor L, Pant A, Singh N, Gupta SK, Dandekar T, Pandey R: C. elegans protein interaction network analysis probes RNAi validated pro-longevity effect of nhr-6, a human homolog of tumor suppressor Nr4a1. Scientific reports 2019, 9:1-10.

14.           Berger S, Goekeri C, Gupta SK, Vera J, Dietert K, Behrendt U, Lienau J, Wienhold S-M, Gruber AD, Suttorp N: Delay in antibiotic therapy results in fatal disease outcome in murine pneumococcal pneumonia. Critical Care 2018, 22:1-11.

15.             Bencurova E, Gupta SK, Sarukhanyan E, Dandekar T: Identification of antifungal targets based on computer modeling. Journal of Fungi 2018, 4:81.

16.             Bencurova E, Gupta SK, Oskoueian E, Bhide M, Dandekar T: Omics and bioinformatics applied to vaccine development against Borrelia. Molecular Omics 2018, 14:330-340.

17.             Singh KP, Verma N, Akhoon BA, Bhatt V, Gupta SK, Gupta SK, Smita S: Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains. 3 Biotech 2016, 6:39.

18.           Liang C, Schaack D, Srivastava M, Gupta SK, Sarukhanyan E, Giese A, Pagels M, Romanov N, Pané-Farré J, Fuchs S: A Staphylococcus aureus proteome overview: shared and specific proteins and protein complexes from representative strains of all three clades. Proteomes 2016, 4:8.

19.            Kaltdorf M, Srivastava M, Gupta SK, Liang C, Binder J, Dietl A-M, Meir Z, Haas H, Osherov N, Krappmann S: Systematic identification of anti-fungal drug targets by a metabolic network approach. Frontiers in molecular biosciences 2016, 3:22.

20.             Gupta SK, Gross R, Dandekar T: An antibiotic target ranking and prioritization pipeline combining sequence, structure and network-based approaches exemplified for Serratia marcescens. Gene 2016, 591:268-278.

21.           Gupta SK, Bencurova E, Srivastava M, Pahlavan P, Balkenhol J, Dandekar T: Improving re-annotation of annotated eukaryotic genomes. In Big Data Analytics in Genomics. Springer, Cham; 2016: 171-195

22.             Singh AK, Kingston JJ, Gupta SK, Batra HV: Recombinant bivalent fusion protein rVE induces CD4+ and CD8+ T-cell mediated memory immune response for protection against Yersinia enterocolitica infection. Frontiers in microbiology 2015, 6:1407.

23.             Ranjbar MM, Gupta SK, Ghorban K, Nabian S, Sazmand A, Taheri M, Esfandyari S, Taheri M: Designing and modeling of complex DNA vaccine based on tropomyosin protein of Boophilus genus tick. Applied biochemistry and biotechnology 2015, 175:323-339.

24.           Gupta SK, Kupper M, Ratzka C, Feldhaar H, Vilcinskas A, Gross R, Dandekar T, Förster F: Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing. BMC genomics 2015, 16:1-21.

25.          Kupper M, Gupta SK, Feldhaar H, Gross R: Versatile roles of the chaperonin GroEL in microorganism–insect interactions. FEMS Microbiology Letters 2014, 353:1-10.

26.             Akhoon BA, Singh KP, Varshney M, Gupta SK, Shukla Y, Gupta SK: Understanding the mechanism of atovaquone drug resistance in Plasmodium falciparum cytochrome b mutation Y268S using computational methods. PloS one 2014, 9:e110041.

27.           Srivastava M, Gupta SK, Abhilash P, Singh N: Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches. Journal of molecular modeling 2012:1-9.

28.             Gupta SK, Srivastava M, Akhoon BA, Gupta SK, Grabe N: In silico accelerated identification of structurally conserved CD8+ and CD4+ T-cell epitopes in high-risk HPV types. Infection, Genetics and Evolution 2012.

29.             Baloria U, Akhoon BA, Gupta SK, Sharma S, Verma V: In silico proteomic characterization of human epidermal growth factor receptor 2 (HER-2) for the mapping of high affinity antigenic determinants against breast cancer. Amino acids 2012, 42:1349-1360.

30.             Srivastava M, Gupta S, Saxena A, Shittu L: A review of occurrence of fungal pathogens on significant brassicaceous vegetable crops and their control measures. Asian journal of Agricultural sciences 2011, 3:70-79.

31.          Gupta SK, Srivastava M, Akhoon BA, Smita S, Schmitz U, Wolkenhauer O, Vera J, Gupta SK: Identification of immunogenic consensus T-cell epitopes in globally distributed influenza-A H1N1 neuraminidase. Infection, Genetics and Evolution 2011, 11:308-319.

32.             Gupta SK, Gupta SK, Smita S, Srivastava M, Lai X, Schmitz U, Rahman Q, Wolkenhauer O, Vera J: Computational analysis and modeling the effectiveness of ‘Zanamivir’targeting neuraminidase protein in pandemic H1N1 strains. Infection, Genetics and Evolution 2011, 11:1072-1082.

33.             Gupta SK, Baweja L, Gurbani D, Pandey AK, Dhawan A: Interaction of C60 fullerene with the proteins involved in DNA mismatch repair pathway. Journal of biomedical nanotechnology 2011, 7:179-180.

34.           Akhoon BA, Slathia PS, Sharma P, Gupta SK, Verma V: In silico identification of novel protective VSG antigens expressed by Trypanosoma brucei and an effort for designing a highly immunogenic DNA vaccine using IL-12 as adjuvant. Microbial pathogenesis 2011, 51:77-87.

35.            Akhoon BA, Gupta SK, Dhaliwal G, Srivastava M, Gupta SK: Virtual screening of specific chemical compounds by exploring E. coli NAD+-dependent DNA ligase as a target for antibacterial drug discovery. Journal of molecular modeling 2011, 17:265-273.

36.            Srivastava M, Akhoon BA, Gupta SK, Gupta SK: Development of resistance against blackleg disease in Brassica oleracea var. botrytis through In silico methods. Fungal Genetics and Biology 2010, 47:800-808.

37.             Gupta SK, Smita S, Sarangi AN, Srivastava M, Akhoon BA, Rahman Q, Gupta SK: In silico CD4+ T-cell epitope prediction and HLA distribution analysis for the potential proteins of Neisseria meningitidis Serogroup B—A clue for vaccine development. Vaccine 2010, 28:7092-7097.

38.           Gupta S, Akhoon B, Srivastava M, Gupta S: A novel algorithm to design an efficient siRNA by combining the pre proposed rules of siRNA designing. J Comput Sci Syst Biol 2010, 3:005-009.

39.             Akhoon BA, Gupta SK, Verma V, Dhaliwal G, Srivastava M, Gupta SK, Ahmad RF: In silico designing and optimization of anti-breast cancer antibody mimetic oligopeptide targeting HER-2 in women. Journal of Molecular Graphics and Modelling 2010, 28:664-669.

40.             Gupta SK, Singh A, Srivastava M, Gupta SK, Akhoon BA: In silico DNA vaccine designing against human papillomavirus (HPV) causing cervical cancer. Vaccine 2009, 28:120-131.

41.             Gupta S, Singh A, Srivastava M: Designing of drug for removal of methylation from Tcf21 gene in lung cancer. Online Journal of Bioinformatics 2009, 11:149-155.

Book Chapters

42.           Gupta SK, Minocha R, Akash A, Parkar S, Sirkinti L, Thapa PJ, Almasi A, Balkenhol J, Osmanoglu Ö, Pottikkadavath A, Dandekar T: From Proteins to Networks: Assembly, Interpretation, and Advances. In Bioinformatics and Computational Biology. Chapman and Hall/CRC; 2024: 199-224

43.             Gupta SK, Osmanoglu Ö, Srivastava M, Bencúrová E, Dandekar T: Pathogen and Host-Pathogen Protein Interactions Provide a Key to Identify Novel Drug Targets. Reference Module in Biomedical Sciences; Elsevier: Amsterdam, The Netherlands 2020.

44.             Gupta SK, Dandekar T: Bioinformatics in Leishmania Drug Design. In Drug Resistance in Leishmania Parasites. Springer, Cham; 2018: 297-317

45.             Gupta SK, Srivastava M, Smita S, Gupta T, Gupta SK: Methods to Identify Evolutionary Conserved Regulatory Elements Using Molecular Phylogenetics in Microbes. In Computational Biology and Bioinformatics. Chapman and Hall/CRC 2016.

46.             Smita S, Singh KP, Akhoon BA, Gupta SK, Gupta SK: Bioinformatics tools for interpretation of data used in molecular identification. In Analyzing Microbes. Springer, Berlin, Heidelberg; 2013: 209-243

Meeting report

47.             Akudibillah G, Boas SE, Carreres BM, Dallinga M, van Dijk A-J, Gupta SK, Hunt A, Jacobsen A, Kasbawati K, Merks RR: Scientific report: Training workshop interdisciplinary life sciences. In Book Scientific report: Training workshop interdisciplinary life sciences. PeerJ PrePrints; 2014.