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.


Academic background

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

Selected publications

The Atlas of Inflammation-Resolution (AIR)

Charles N. Serhan, Shailendra K. Gupta, ... , Olaf Wolkenhauer

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

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


  • 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.

Teaching Experience

2014 – To date Lectures on the construction of molecular interaction networks, network based analysis and graph theory to the Masters students in summer/ winter semesters
2013 – To date Supervising / Co-supervising of Masters and Ph.D. students