SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
Germany
+49 381 498-7571
olaf.wolkenhauer@uni-rostock.de

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

MASLD Map

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.

TriplexRNA

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

DOI: https://doi.org/10.1136%2Fjitc-2023-008104

Pubmed: https://pubmed.ncbi.nlm.nih.gov/38724462

URL: https://jitc.bmj.com/content/12/5/e008104.long

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.

DOI: https://doi.org/10.1038%2Fs41540-024-00349-1

Pubmed: https://pubmed.ncbi.nlm.nih.gov/38431714

URL: https://www.nature.com/articles/s41540-024-00349-1

The Atlas of Inflammation-Resolution (AIR)

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

Molecular Aspects of Medicine 2020

DOI: https://doi.org/10.1016/j.mam.2020.100894

Pubmed: https://pubmed.ncbi.nlm.nih.gov/32893032/

URL: https://www.sciencedirect.com/science/article/pii/S0098299720300960

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.

DOI: 10.7150/thno.29546

Pubmed: 30867845

URL: http://www.thno.org/v09p1490.htm

Regulatory Role of IL-6 in Immune-Related Adverse Events During Checkpoint Inhibitor Treatment in Melanoma

Krishna Pal Singh, Anuj Singh, Olaf Wolkenhauer, Shailendra Kumar Gupta

DOI: https://doi.org/10.20944/preprints202409.0006.v1

Large-scale knowledge graph representations of disease processes

Hoch M, Wolkenhauer O, Gupta S

Current Opinion in Systems Biology

DOI: https://doi.org/10.1016/j.coisb.2024.100517

URL: https://www.sciencedirect.com/science/article/pii/S2452310024000131

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)

DOI: https://doi.org/10.3390/molecules28248120

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

BMC Chemistry

NaviCenta – The disease map for placental research

Scheel J, Hoch M, Wolfien M, Gupta S

Placenta

DOI: https://doi.org/10.1016/j.placenta.2023.09.007

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

International Journal of Molecular Sciences

DOI: 10.3390/ijms24054342

URL: https://www.mdpi.com/1422-0067/24/5/4342

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

BMC Journal of Inflammation

DOI: https://doi.org/10.1186/s12950-023-00335-0

Pubmed: 36973809

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

Briefings in Bioinformatics (2022)

DOI: 10.1093/bib/bbac433

URL: https://academic.oup.com/bib/article-abstract/23/6/bbac433/6761961?redirectedFrom=fulltext

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

npj Systems Biology and Applications (2022)

DOI: 10.1038/s41540-022-00222-z

URL: https://www.nature.com/articles/s41540-022-00222-z

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)

DOI: https://doi.org/10.1101/2022.02.14.480331

URL: https://www.biorxiv.org/content/10.1101/2022.02.14.480331v1

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)

DOI: https://doi.org/10.3390/ijms23010293

URL: https://www.mdpi.com/1422-0067/23/1/293

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

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

Molecular Systems Biology 2021

DOI: https://doi.org/10.1038/s41597-020-0477-8

Placental mitochondrial function as a driver of angiogenesis and placental dysfunction

Correia Y, Scheel J, Gupta S, Wang K

De Gruyter BioChem (2021)

DOI: https://doi.org/10.1515/hsz-2021-0121

URL: https://www.degruyter.com/document/doi/10.1515/hsz-2021-0121/html

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.

DOI: http://dx.doi.org/10.7150/thno.44176

URL: https://www.thno.org/v10p9620.htm

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

DOI: https://doi.org/10.1186/s12859-020-03656-6

Pubmed: 32703153

URL: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03656-6

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.

DOI: 1038/s41598-019-51649-0

Pubmed: 31673088

URL: https://www.nature.com/articles/s41598-019-51649-0

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

Annals of the Rheumatic Diseases 2019;78:1496.

DOI: http://dx.doi.org/10.1136/annrheumdis-2019-eular.5084

URL: https://ard.bmj.com/content/annrheumdis/78/Suppl_2/1496.1.full.pdf

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

DOI: https://doi.org/10.1111/srt.12622

Pubmed: 30030916

URL: https://onlinelibrary.wiley.com/doi/full/10.1111/srt.12622

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.

DOI: https://doi.org/10.1016/j.bbadis.2018.01.020

Pubmed: 29410200

URL: https://www.sciencedirect.com/science/article/pii/S0925443918300310

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.

DOI: https://doi.org/10.1007/s10822-018-0103-4

Pubmed: 29397519

URL: https://link.springer.com/article/10.1007%2Fs10822-018-0103-4

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.

DOI: https://doi.org/10.1016/j.toxrep.2017.12.024

Pubmed: 29326881

URL: https://www.sciencedirect.com/science/article/pii/S2214750017301464

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.

DOI: https://doi.org/10.7150/thno.19904

Pubmed: 29464002

URL: http://www.thno.org/v08p1106.htm

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.

DOI: https://doi.org/10.2174/1381612823666170710152918

Pubmed: 28699531

URL: http://www.eurekaselect.com/154061

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

DOI: 10.1038/s41467-017-00268-2

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.

DOI: https://doi.org/10.1021/acs.chemrestox.6b00364

Pubmed: 28029781

URL: https://pubs.acs.org/doi/10.1021/acs.chemrestox.6b00364

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

DOI: https://doi.org/10.3389/fphys.2016.00375

URL: http://journal.frontiersin.org/article/10.3389/fphys.2016.00375/full

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.

DOI: https://doi.org/10.1093/nar/gkv885

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.

DOI: https://doi.org/10.1016/j.biomaterials.2016.01.018

Pubmed: 26803409

URL: https://www.sciencedirect.com/science/article/pii/S014296121600020X?via%3Dihub

Personalized cancer immunotherapy using systems medicine approaches.

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

Briefings in Bioinformatics 2015.

DOI: http://dx.doi.org/10.1093/bib/bbv046

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.

DOI: http://dx.doi.org/10.1093/bib/bbv061

URL: http://database.oxfordjournals.org/content/2015/bau130.full

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.

DOI: http://dx.doi.org/10.1039/c5mb00245a

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

DOI: https://doi.org/10.1371/journal.pone.0110041

Pubmed: 25334024

URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110041

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.

DOI: 10.1002/path.4400

Pubmed: 25042645

URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/path.4400

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

DOI: https://doi.org/10.1016/j.tube.2013.08.001

URL: http://www.sciencedirect.com/science/article/pii/S1472979213001509

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,

DOI: http://dx.doi.org/10.1093/nar/gku465

URL: http://nar.oxfordjournals.org/content/early/2014/05/29/nar.gku465.full

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.

DOI: https://doi.org/10.1093/nar/gks657

URL: http://nar.oxfordjournals.org/content/early/2012/07/13/nar.gks657.abstract

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

DOI: https://doi.org/10.1016/j.meegid.2011.03.018

URL: http://www.sciencedirect.com/science/article/pii/S1567134811000992

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

DOI: https://doi.org/10.1016/j.meegid.2010.10.013

Pubmed: https://www.ncbi.nlm.nih.gov/pubmed/21094280

URL: http://www.sciencedirect.com/science/article/pii/S1567134810002947

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

DOI: https://doi.org/10.1016/j.seizure.2010.06.005

URL: http://www.sciencedirect.com/science/article/pii/S1059131110001196

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

DOI: http://dx.doi.org/10.2174/1875036201004010001

URL: https://benthamopen.com/ABSTRACT/TOBIOIJ-4-1

Downloads & more:

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

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

DOI: 10.4172/jpb.1000107

URL: https://www.omicsonline.org/hmg-coa-reductase-for-their-role-as-cancer-chemo-preventive-agents-jpb.1000107.php?aid=1410

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

ISBN 13 (online): 978-0-12-816078-7

URL: https://www.sciencedirect.com/referencework/9780128160787/systems-medicine

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)

DOI: https://doi.org/10.1016/B978-0-12-801238-3.11586-7

URL: https://www.sciencedirect.com/science/article/pii/B9780128012383115867?via%3Dihub

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

DOI: 10.1042/EBC20180005

Pubmed: 30366988

URL: http://essays.biochemistry.org/content/62/4/549

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

Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O

DOI: https://doi.org/10.1007/978-1-4939-7456-6_12

Pubmed: 29119509

URL: https://link.springer.com/search?facet-content-type=%22Book%22&package=12345&facet-start-year=2018&facet-end-year=2018

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.

DOI: https://doi.org/10.1158/1538-7445.AM2024-6814

URL: https://aacrjournals.org/cancerres/article/84/6_Supplement/6814/738162

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

DOI: https://doi.org/10.7287/peerj.preprints.2385v1

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.