SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
+49 381 498-7571
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.
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.
The AIR is to provide an interactive platform connecting scientific and medical communities.
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.
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.
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.
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
accepted for publication in Briefings in Bioinformatics
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
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
Placental mitochondrial function as a driver of angiogenesis and placental dysfunction
Correia Y, Scheel J, Gupta S, Wang K
De Gruyter BioChem (2021)
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
Sci Rep. 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
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
Systems Medicine - Integrative, Qualitative, and Computational Approaches
Wolkenhauer O (Editor-in-Chief)
Academic Press 2020
ISBN 13 (online): 978-0-12-816078-7
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
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
- 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.