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.



Research Projects


Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as non-alcoholic fatty liver disease (NAFLD), has a complex pathogenesis that requires an in-depth understanding of diagnostic and prognostic molecular patterns to develop effective clinical treatment strategies. Here, we present the MASLD Map, a comprehensive, web-based to investigate and simulate molecular processes involved in MASLD progression.


MelAutim - Systems medicine investigation of melanoma and autoimmunity in the context of immune therapies

The MelAutim project aims to uncover the molecular and cellular mechanisms for the interaction of cancer and autoimmunity. In particular, it aims to identify factors that are involved in the development of new or the exacerbation of existing autoimmune diseases during immunotherapy.


AIR: Atlas of Inflammation Resolution

The AIR is to provide an interactive platform connecting scientific and medical communities.


iPlacenta: A Systems Biology Approach towards Phenotype-Specific Interactomes for Placental Function

Pre-eclampsia (PE) is a complex disorder occurring during pregnancy and the postpartum affecting almost 5-8% of all pregnancies and often occurs with other complications. Its pathology is largely unknown. To improve the diagnosis and treatment outcomes, a deeper understanding of the determinants of pathophysiology is urgently needed.


A systems methodology to assess the risk of tumor relapse in melanoma - 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.



The TriplexRNA is a database of cooperating microRNAs and their mutual targets.

The database collects predicted and experimentally validated RNA triplexes, and provides an interactive interface for highligting targets of concerted RNA regulation within known disease pathways.


Selected publications

Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy.

Lischer C, Eberhardt M, ... , Gupta S, Singh KP, ... , Wolkenhauer O, ... , Vera J

Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model.

Singh S, Yadav S, Cavallo C, Mourya D, Singh I, Kumar V, Shukla S, Shukla P, Chaudhary R, Maurya GP, Müller RLJ, Rohde L, Mishra A, Wolkenhauer O, Gupta S, Tripathi A.

The Atlas of Inflammation-Resolution (AIR)

Serhan CN, Gupta SK, ... , Smita S, Schopohl P, Hoch M, Gjorgevikj D, Khan FM, Brauer D, ... , Wolkenhauer O

Drug Repositioning Inferred from E2F1-Coregulator Interactions Studies for the Prevention and Treatment of Metastatic Cancers.

Goody D, Gupta SK, Engelmann D, Spitschak A, Marquardt S, Mikkat S, Meier C, Hauser C, Gundlach JP, Egberts JH, Martin H, Schumacher T, Trauzold A, Wolkenhauer O, Logotheti S, Pützer BM.

Theranostics. 2019 Feb 20;9(5):1490-1509.

Large-scale knowledge graph representations of disease processes

Hoch M, Wolkenhauer O, Gupta S

Exploring Thiazolopyridine AV25R: Unraveling of Biological Activities, Selective Anti-Cancer Properties and In Silico Target and Binding Prediction in Hematological Neoplasms

Ladwig A, Gupta S, Ehlers P, Sekora A, Alammar M, Koczan D, Wolkenhauer O, Junghanss C, Langer P, Murua Escobar H

Molecules (Special Issue Small Molecules in
Targeted Cancer Therapy)

Logic-based modeling and drug repurposing for the prediction of novel therapeutic targets and combination regimens against E2F1-driven melanoma progression

Singh N, Khan FM, Bala L, Vera J, Wolkenhauer O, Pützer B, Logotheti S, Gupta SK

NaviCenta – The disease map for placental research

Scheel J, Hoch M, Wolfien M, Gupta S

Cell-Type-Specific Gene Regulatory Networks of Pro-Inflammatory and Pro-Resolving Lipid Mediator Biosynthesis in the Immune System

Hoch M, Jannik R, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Valerio C, Gupta S

Network analyses reveal new insights into the effect of multicomponent Tr14 compared to single-component diclofenac in an acute inflammation model

Hoch M, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Gupta S

Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence

Vera J, Lai X, Baur A, Erdmann M, Gupta S, Guttà C, Heinzerling L, Heppt MV, Kazmierczak PM, Kunz M, Lischer C, Pützer BM, Rehm M, Ostalecki C, Retzlaff J, Witt S, Wolkenhauer O, Berking C

Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps

Hoch M, Smita S, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Gupta S

Single extracellular vesicle analysis in human amniotic fluid shows evidence of phenotype alterations in preeclampsia

Gebara N, Scheel J, Skovronova R, Grange C, Marozio L, Gupta S, Giorgione V, Caicci F, Benedetto C, Khalil A, Bussolati B

bioRxiv (2022)

Overexpression of microRNAs miR-25-3p, miR-185-5p and miR-132-3p in Late Onset Fetal Growth Restriction, Validation of Results and Study of the Biochemical Pathways Involved

Loscalzo G, Scheel J, Ibañez-Cabellos J S, García-Lopez E, Gupta S, García-Gimenez J L, Mena-Mollá S, Perales-Marín A, Morales-Roselló J

IJMS (2021)

COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms

Ostaszewski M, Niarakis A, Mazein A, Wolkenhauer O et al.

Placental mitochondrial function as a driver of angiogenesis and placental dysfunction

Correia Y, Scheel J, Gupta S, Wang K

LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1

Logotheti S, Marquardt S, Gupta SK, Richter C, Edelhäuser BAH, Engelmann D, Brenmoehl J, Söhnchen C, Murr N, Alpers M, Singh KP, Wolkenhauer O, Heckl D, Spitschak A, Pützer BM

Theranostics 2020; 10(21):9620-9643.

An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma

Singh N, Eberhardt M, Wolkenhauer O, Vera J, Gupta SK

BMC Bioinformatics 2020, 21 (1), 1-17

C. elegans protein interaction network analysis probes RNAi validated pro-longevity effect of nhr-6, a human homolog of tumor suppressor Nr4a1

Akhoon BA, Gupta SK, Tiwari S, Rathor L, Pant A, Singh N, Gupta SK, Dandekar T, Pandey R

2019 Oct 31;9(1):15711.

A systems appraoch to investigate inflammation resolution by multicomponent medicinal product TR14

Schopohl P, Smita S, Khan F, Gebhardt T, Hoch M, Brauer D, Cesnulevicius D, Schultz M, Wolkenhauer O, Gupta S

Recent advancement in the early detection of melanoma using computerized tools: An image analysis perspective

Singh N, Gupta SK

Skin Res Technol. 2019;25(2):129-141

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

Jalili M, Salehzadeh-Yazdi A, Gupta S, Wolkenhauer O, Yaghmaie M, Resendis-Antonio O and Alimoghaddam K

Frontiers in Physiology

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

Inflammation Resolution and Chronic Diseases

Tripathi A, Dwivedi A, Gupta S, Poojan S (eds.)

ISBN 13 (print): 978-981-97-0156-8

ISBN 13 (online): 978-981-97-0157-5

DOI: https://doi.org/10.1007/978-981-97-0157-5

URL: https://link.springer.com/book/10.1007/978-981-97-0157-5

Mechanistic Understanding of Inflammation Resolution Using the Atlas of Inflammation Resolution (AIR)

Müller RLJ, Cavallo C, Gupta SS, Hoch M, Gupta S

In: Tripathi, A., Dwivedi, A., Gupta, S., Poojan, S. (eds) Inflammation Resolution and Chronic Diseases. Springer, Singapore.

ISBN 13 (print): 978-981-97-0156-8

ISBN 13 (online): 978-981-97-0157-5

DOI: https://doi.org/10.1007/978-981-97-0157-5_13

URL: https://link.springer.com/chapter/10.1007/978-981-97-0157-5_13

Are Multi-Component Drugs Better in Resolving the Inflammation Compared to the Single-Component Drugs?

Cavallo C, Hoch M, Gupta S

In: Tripathi, A., Dwivedi, A., Gupta, S., Poojan, S. (eds) Inflammation Resolution and Chronic Diseases. Springer, Singapore.

ISBN 13 (print): 978-981-97-0156-8

ISBN 13 (online): 978-981-97-0157-5

DOI: https://doi.org/10.1007/978-981-97-0157-5_10

URL: https://link.springer.com/chapter/10.1007/978-981-97-0157-5_10

Inflammation Resolution Mediators: Future Prospects

Müller RLJ, Hoch M, Gupta S

In: Tripathi, A., Dwivedi, A., Gupta, S., Poojan, S. (eds) Inflammation Resolution and Chronic Diseases. Springer, Singapore.

ISBN 13 (print): 9789819701568

ISBN 13 (online): 9789819701575

DOI: https://doi.org/10.1007/978-981-97-0157-5_9

URL: https://link.springer.com/book/10.1007/978-981-97-0157-5

Systems Medicine - Integrative, Qualitative, and Computational Approaches

Wolkenhauer O (Editor-in-Chief)

Academic Press 2020

Network Biology Approaches in Ophthalmological Diseases: A Case Study of Glaucoma

Choudhari JK, Chatterjee T, Gupta SK, Garcia-Garcia JG, Vera J

In Systems Medicine: Integrative, qualitative and computational approaches (2020)

Envisioning the Application of Systems Biology in Cancer Immunology

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

In: Rezaei N. (eds) Cancer Immunology. Springer, Cham. (2020)

ISBN 13 (print): 978-3-030-30844-5

ISBN 13 (online): 978-3-030-30845-2

DOI: https://doi.org/10.1007/978-3-030-30845-2_27

URL: https://link.springer.com/chapter/10.1007/978-3-030-30845-2_27

Computational Biology of Non-Coding RNA

Lai X, Gupta SK, Vera J (eds.)

Springer (2019), part of the Methods in Molecular Biology book series (MIMB, volume 1912)

ISBN 13 (print): 9781493989812

ISBN 13 (online): 9781493989829

DOI: https://doi.org/10.1007/978-1-4939-8982-9

Integrative workflow for network analysis

Faiz M. Khan, Shailendra K. Gupta, Olaf Wolkenhauer


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

E2F1-induced autocrine IL-6 inflammatory loop mediates cancer-immune cell crosstalk that regulates metastatic properties in melanoma

Dhar P, Singh KP, Gupta S, Peringot D, Spitschak A, Pützer BM

AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6814.

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


  • 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.