Dr. Shailendra Gupta

To reveal those components and mechanisms that are determining the cell’s response to perturbations, we construct models of molecular networks with differential equations and boolean logic.

Research interest

In my research, I combine Bioinformatics and Systems Biology for translational research in systems medicine. I am working on the integrative workflows combining various computational methods with experimentation to understand phenomenon in molecular biology and medical problems.

In the current project, I am investigating the role of E2F signaling in tumor progression and metastasis using systems biology approaches. I am also developing computational methods to screen anti-metastatic drugs by investigating interactions between E2F1 and its cofactors.

One of my main research interests is to investigate the role of non-coding RNAs in the regulation of gene expression, signaling pathways and diseases. In particular I study functional mechanisms of post-transcriptional gene regulation by miRNAs and the role of miRNAs in the emergence and progression of human diseases, their interplay with the immune system along with their possible role as therapeutic targets or agents. Towards this, I am developing tools and workflows by integrating methods for miRNA target prediction, RNA secondary and 3D structure prediction, molecular dynamics simulations, and kinetic model interactions.

I am  also working on several strategies to design personalized cancer immunotherapy by combining Immune-informatics, structural biology and systems biology approaches. I have developed a workflow to utilize patient specific mutation profile, HLA profile and various parameters identified from heterogeneous tumor cell populations for immunotherapy personalization.

 

Projects

Research Projects

A systems methodology to assess the risk of tumor relapse in melanoma by the profiling of plasma extracellular vesicles - MelEVIR

The aim of the project is to develop, test and prepare for translation into clinical practice a systems-biology-based diagnostic tool for assessing the probability of tumor relapse in melanoma patients, based on the profiling of pEVs. In the methodology proposed, in vitro and clinical data are integrated using data-driven mathematical modeling. The insights obtained from patient data analysis, reconstruction of biochemical networks, and model simulations are used to a) select a set of microRNAs, long non-coding RNAs, and proteins present in pEVs of patients to be measured in a blood test as surrogates of immune system activity against MRD and b) assess the probability of tumor relapse in the close future.

More

Selected publications

A web platform for the network analysis of highthroughput data in melanoma and its use to investigate mechanisms of resistance to anti-PD1 immunotherapy

Dreyer FS, Cantone M, Eberhardt M, Jaitly T,Walter L, Wittmann J, Gupta SK , Khan FM, Wolkenhauer O, Pützer BM, Jäck HM, Heinzerling L, Vera J

Biochimica et Biophysica Acta;2018 Feb 23. pii: S0925-4439(18)30031-0.

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide.

Singh KP, Baweja L, Wolkenhauer O, Rahman Q, Gupta SK

J Comput Aided Mol Des. 2018;32(3):487-496.

Interaction of anthraquinones of Cassia occidentalis seeds with DNA and Glutathione.

Panigrahi GK, Verma N, Singh N, Asthana S, Gupta SK, Tripathi A, Das M

Toxicol Rep. 2018;5:164-172.

MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance.

Lai X, Gupta SK, Schmitz U, Marquardt S, Knoll S, Spitschak A, Wolkenhauer O, Pützer BM, Vera J

Theranostics. 2018 Jan 1;8(4):1106-1120.

Identification of Antineoplastic Targets with Systems Approaches, Using Resveratrol as an In-Depth Case Study.

Singh N, Freiesleben S, Wolkenhauer O, Shukla Y, Gupta SK

Curr Pharm Des. 2017;23(32):4773-4793.

Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures

Khan FM, Marquardt S, Gupta SK,Knoll S, Schmitz U,Spitschak A, Engelmann D, Vera J, Wolkenhauer O & Pützer BM

Nature Communications

Aryl Hydrocarbon Receptor Activation Contributes to Benzanthrone-Induced Hyperpigmentation via Modulation of Melanogenic Signaling Pathways.

Abbas S, Alam S, Singh KP, Kumar M, Gupta SK, Ansari KM.

Chem Res Toxicol. 2017 Feb 20;30(2):625-634.

Evolution of centrality measurements for the detection of essential proteins in biological networks

Mahdi Jalili, Ali Salehzadeh-Yazdi, Shailendra Gupta, Olaf Wolkenhauer, Marjan Yaghmaie, Osbaldo Resendis-Antonio and Kamran Alimoghaddam (2016)

Frontiers in Physiology

Ambient UV-B exposure reduces the binding of ofloxacin with bacterial DNA gyrase and induces DNA damage mediated apoptosis

Singh J, Dwivedi A, Mujtaba SF, Singh KP, Pal MK, Chopra D, Goyal S, Srivastav AK, Dubey D, Gupta SK, Haldar C, Ray RS

The International Journal of Biochemistry and Cell Biology. 2016. pii: S1357-2725(16)30001-2.

Epigenetic factor EPC1 is a master regulator of DNA damage response by interacting with E2F1 to silence death and activate metastasis-related gene signatures

Wang Y, Alla V, Goody D, Gupta SK, Spitschak A, Wolkenhauer O, Putzer B, Engelmann D

Nucleic Acids Research. 2016; 44(1):117-33.

Photoprotective efficiency of PLGA-curcumin nanoparticles versus curcumin through the involvement of ERK/AKT pathway under ambient UV-R exposure in HaCaT cell line

Chopra D, Ray L, Dwivedi A, Tiwari SK, Singh J, Singh KP, Kushwaha HN, Jahan S, Pandey A, Gupta SK, Chaturvedi RK, Pant AB, Ray RS, Gupta KC

Biomaterials. 2016; 84:25-41.

Personalized cancer immunotherapy using systems medicine approaches.

Gupta SK, Jaitly T, Schmitz U, Schuler G, Wolkenhauer O, Vera J

Briefings in Bioinformatics 2015.

The RNA world in the 21st century – a systems approach to finding non-coding keys to clinical questions

Schmitz U, NAderi-Meshkin H, Gupta SK, Wolkenhauer O, Vera J

Briefings in Bioinformatics 2015.

Naïve Bayes classifier predicts functional microRNA target interactions in colorectal cancer

Raheleh A, Schmitz U, Farazmand A, Gupta SK, Ahmadi H, Wolkenhauer O

Molecular BioSystems 2015; 11(8): 2126-34.

Understanding the mechanism of Atovaquone drug resistance in Plasmodium falciparum cytochrome b mutation Y268S using computational methods

Akhoon BA, Singh KP, Varshney M, Gupta SK, Shukla Y, Gupta SK

PLOS One 2014; 9(10):e110041

Association of RHAMM with E2F1 promotes tumour cell extravasation by transcriptional up-regulation of fibronectin

Meier C, Spitschak A, Abshagen K, Gupta S, Mor JM, Wolkenhauer O, Haier J, Vollmar B, Alla V, Pützer BM

Journal of Pathology. 2014; 234(3):351-64.

Ethnicity-tailored novel set of ESAT-6 peptides for differentiating active and latent tuberculosis

Singh SB, Biswas D, Rawat J, Sindhwani G, Patras A, Devrani S, Sarkar P, Mitra S, Gupta SK

Tuberculosis, Volume 93, Issue 6, 618 - 624

Cooperative gene regulation by microRNA pairs and their identification using a computational workflow

Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta S

Nucleic Acids Research 2014, 42 (12): 7539-7552,

Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs

Lai X, Schmitz U, Gupta S, Bhattacharya A, Kunz M, Wolkenhauer O, Vera J (2012)

Nucleic Acids Research, 40: 8818-8834.

Computational analysis and modeling the effectiveness of "Zanamivir" targeting neuraminidase protein in pandemic H1N1 strains

Gupta SK, Gupta SK, Smita S, Srivastava M, Lai X, Schmitz U, Rahman Q, Wolkenhauer O, Vera J (2011)

Infection, Genetics and Evolution 11: 1072 - 1082

Identification of immunogenic consensus T-cell epitopes in globally distributed influenza-A H1N1 neuraminidase

Gupta SK, Srivastava M, Akhoon BA, Smita S, Schmitz U, Wolkenhauer O, Vera J, Gupta SK (2011)

Infection, Genetics and Evolution 11: 308 - 319

Baccoside A suppresses epileptic-like seizure/convulsion in Caenorhabditis elegans

Pandey R, Gupta S, Tandon S, Wolkenhauer O, Vera J (2010)

Seizure 19: 439 - 442

Mining the proteome of Haemophilus ducreyi for identification of potential drug targets

Sarangi AN, Trivedi N, Rathi B, Gupta S

The Open Bioinformatics Journal, 4: 1-4, 2010

Geraniol and limonene interaction with 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase for their role as cancer chemo-preventive agents

Pattanayak M, Seth PK, Smita S, Gupta SK (2009)

Journal of Proteomics & Bioinformatics 2: 466-474

A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression.

Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O

Biochemical pathway modeling tools for drug target detection in Cancer and other complex diseases

Marin-Sanguino A, Gupta SK, Voit EO, Vera J

In Michael Johnson editor: Methods in Enzymology, Vol. 487,
Burlington: Academic Press, 2010, pp 319-370.

Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive

Eberhardt M, Lai X, Tomar N, Gupta SK, Schmech B, Steinkasserer A, Schuler G, Vera J

In: Systems Medicine, Methods in Molecular Biology (2016) 1386: 135-179.
Published by Springer.

ISBN 13 (print): 9781493932825

Envisioning the Application of Systems Biology in Cancer

J.Vera, S.Gupta, O.Wolkenhauer, G.Schuler (2015)

In Cancer Immunology, N.Rezaei (ed.), 429-449, Springer 2015

ISBN 13 (print): 9783662440063

Bioinformatics Analysis of High-Throughput Experiments

Gupta S, Schmitz U

in: Recent Trends in Biotechnology. Volume 2; Singh M P, Agrawal A, Sharma B (eds.); Nova Science Publishers 2011.

ISBN 13 (print): 9781617617973

Enriching biotechnology with recent bioinformatics tools and protocols

Gupta SK, Smita S, Rahman Q

in: Recent trends in Biotechnology; Singh MP, Agrawal A, Sharma B (eds.); Nova Science Publishers Inc. 2011.

ISBN 13 (print): 9781608761487

An integrative computational framework for personalized detection of tumor epitopes in melanoma immunotherapy

Jaitly T, Schaft N, Doerrie J, Gross S, Schuler-Thurner B, Wolkenhauer O, Schuler G, Taher L, Gupta S, Vera J

PeerJ Preprints 4:e2385v1

Predicting targets of synergistic microRNA regulation

Schmitz U, Gupta S, Lai X, Vera J, Wolkenhauer O

German Conference on Bioinformatics 2013, Göttingen, Germany

Venue: Göttingen, Germany

On the regulation of microRNA target hubs: a Systems Biology perspective

Lai X, Schmitz U, Gupta S, Kunz M, Wolkenhauer O, Vera J

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Venue: Heidelberg/Mannheim, Germany

MicroRNAs in malignant melanoma progression

Schmitz U, Bhattacharya A, Gupta S, Schultz J, Kunz M, Wolkenhauer O

German Conference on Bioinformatics, Braunschweig, Germany, September 2010

Venue: Braunschweig, Germany

Education and Work Experience

Employment and Appointments

2013 - to date

Postdoctoral Fellow, Department of Systems Biology & Bioinformatics, University of Rostock, Germany

2011 - to date

Senior Scientist (Bioinformatics), Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Lucknow India

2007 - 2011

Scientist (Bioinformatics), Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Lucknow India

2009 - 2010

Research Associate, Department of Systems Biology & Bioinformatics, University of Rostock, Germany

2006 - 2007

Senior Research Officer, Biomedical Information Centre, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow India

2005 - 2006

Director, The Bioinformatica Solutions, Society for Biological Research & Rural Development, Lucknow India

2004 - 2005

Senior Programmer, Biotech Park, Lucknow India

2002 - 2004

Research Assistant, Bioinformatics Centre, CSIR - Central Institute of Medicinal & Aromatic Plants, Lucknow India

Services

  • Consultancy services to Biologische Heilmittel Heel GmbH

Awards and Distinctions

  • Adjunct Professorship, Bioinformatics, Chhattisgarh Swami Vivekanand Technical University, Bhilai, India, November 2017
  • Awards to attend DFG-DAAD Seventh German Russian Week of the Young Researcher 2017
  • Award for the "Model of the Month" from the BioModels database on the model submitted on Cooperative gene regulation by microRNA pairs. July 2014
  • Young Scientist Award - 2011 by Council of Science & Technology, Govt. of Uttar Pradesh, India.
  • Promoted to Senior Scientist (Bioinformatics) based on the work assessment within the minimum residency period at CSIR - Indian Institute of Toxicology Research, Lucknow, India.
  • Best Faculty Member (Bioinformatics) award by subDIC Bioinformatics centre, National Institute of Technology, Raipur, Chhattisgarh, India.