Contact Details Assistant

Address: ****AN, Maastricht, Netherlands

Mobile: +31-687******; email: ************@*****.***

Rajinder Gupta

Curriculum Vitae

Personal information

Full name Gupta, Rajinder

Date of birth 04/04/1989, Jammu, India

ORCID ID https://orcid.org/0000-0003-3342-2122

GitHub ID https://github.com/rajinder4489

Current position

May 2016 –

present

Ph.D., Department of Toxicogenomics, FHML, Maastricht University, Maastricht, Netherlands

Mentors: Prof. Dr. Jos Kleinjans and Dr. Florian Caiment. Research

Research experience

Sep, 2014 – Apr,

2016

Junior Research Fellow in Computational Biology department Supervisor: Mr. Shrikant Mantri

National Agri Food Biotechnology Institute, Mohali, Punjab, India Methods skills

RNA-Seq data

analyses

FastQC, Fastp, ALFA, CellNet, Bowtie2, RSEM, DESeq2, EdgeR, Pathview, gene and transcript expression, Pathways, Ontologies Machine learning Various algorithms, dynamic Bayesian networks Programming Perl, R, Shell/Bash

Database MySQL

Version control GitHub, Source Tree

Cloud computing Amazon Web service (basics)

OS Linux, Windows

Miscellaneous APIs, natural language processing, literature mining, tool development, knowledge of Bioinformatics databases and tools

Education

2012-2014 M. Tech. Computational Biology, Jaypee University of Information and Technology, Solan, India

Master’s thesis: Top down approach to annotate heterogeneous biological networks through network motifs. Supervisor: Dr. Tiratha Raj Singh (JUIT), July 2013 – May 2014

Mini-project: Development of a datawarehouse Insulin, highlighting its structure variations, polymorphism, availability, regulation. Supervisor: Dr. Dipankar Sengupta (JUIT), October 2012 – December 2012

Address: 6227AN, Maastricht, Netherlands

Mobile: +31-687******; email: ************@*****.*** 2007-2011 B. Tech. Biotechnology, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Pune, India

Bachelor’s thesis: Molecular insight in modulation of immune responses with plant based fractions. Supervisor Dr. Anamika Khajuria (IIIM, Jammu), December 2010

– May 2011

Mini-project: Preclinical methodology to evaluate immune response in mice. Supervisor Dr. Anamika Khajuria (IIIM, Jammu), June 2008 – July 2008 2007 HSC, JKBOSE, Jammu, India

Physics, Chemistry, Mathematics, and Biology

2005 SSC, JKBOSE, Jammu, India

Academic and research training

Awards

2018 Best poster award, EU-ToxRisk General Assembly 2014 Vice Chancellor’s Gold Medal for topping the class in M. Tech. 2014 Runners up, poster presentation, Biorythm

Teaching

Teaching experience

2017 Tutor; Human Genetics, Reproduction and Prenatal Development 2018 Tutor, Brain, Behaviour and Movement

2018 Tutor, Human Genetics, Reproduction and Prenatal Development Research dissemination

Journal publications

1. Gupta, Rajinder, Yannick Schrooders, Duncan Hauser, Marcel van Herwijnen, Wiebke Albrecht, Bas Ter Braak, Tim Brecklinghaus et al. "Comparing in vitro human liver models to in vivo human liver using RNA-Seq." Archives of Toxicology (2020): 1-17. 2. Gupta, Rajinder, Yannick Schrooders, Marcha Verheijen, Adrian Roth, Jos Kleinjans, and Florian Caiment. "FuSe: A tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts." Bioinformatics (2020). 3. Gupta, Rajinder, and Shrikant S. Mantri. "Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over." Frontiers in Genetics 7 (2016): 46. 4. Attoff, Kristina, Ylva Johansson, Andrea Cediel Ulloa, Jessica Lundqvist, Rajinder Gupta, Florian Caiment, Anda Gliga, Anna Forsby “Acrylamide alters CREB and retinoic acid signaling pathways during differentiation of the human neuroblastoma SH-SY5Y cell line.” Sci Rep 10, 16714 (2020). https://doi.org/10.1038/s41598-020-73698-6 5. Gurjar, Anoop Kishor Singh, Abhijeet Singh Panwar, Rajinder Gupta, and Shrikant S. Mantri. "PmiRExAt: plant miRNA expression atlas database and web applications." Database 2016 (2016).

Address: 6227AN, Maastricht, Netherlands

Mobile: +31-687******; email: ************@*****.*** 6. Sehgal, Manika, Rajinder Gupta, Ahmed Moussa, and Tiratha Raj Singh. "An integrative approach for mapping differentially expressed genes and network components using novel parameters to elucidate key regulatory genes in colorectal cancer." Plos one 10, no. 7 (2015): e0133901.

Manuscripts

1. Vidya Chandrasekaran, Rajinder Gupta, Elisabeth Feifel, Georg Kern, Judith Lechner, Florian Caiment, Jos CS Kleinjans, Gerhard Gstraunthaler, Paul Jennings and Anja Wilmes

“Generation and characterisation of iPSC-derived renal proximal tubule-like cells with extended stability” Major revision at Scientific Reports 2. Gupta, Rajinder, Jos Kleinjans, Florian Caiment “Identifying the transcriptomics biomarkers for hepatocellular carcinoma (HCC) using machine learning” Submitted to Scientific Reports 3. Gupta, Rajinder, Jos Kleinjans, Florian Caiment “Unravelling the protein complex assembly using transcriptomics and dynamic Bayesian networks” Under preparation Invited talks

July 2020 FuSe: A tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts

Event: International Webinar on Biotechnology, Bioinformatics And Natural Products in Health Care at the Department of Biotechnology & Bioinformatics, Sambalpur University, Jyoti Vihar, Odisha, India

Aug, 2018 Comparing in vitro human liver models to in vivo human liver using RNA- Seq

Event: EUROTOX 2018

Conference talks

Feb 2019 Comparing in vitro human liver models to in vivo human liver using RNA- Seq.

Event: EU-ToxRisk, General Assembly

Conference posters

Nov, 2019 FuSe: Moving RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts

Event: byteMAL, 2019

Mar, 2019 Improving the interpretation of omics analyses Event: Revolutionizing Next-Generation Sequencing, Antwerp Feb, 2019 Comparing different in vitro liver models using RNA-Seq Event: EU-ToxRisk, General Assembly

Nov, 2018 Improving the interpretation of omics analyses Event: GROW Science Day, UM

Feb, 2018 Sequencing EU-ToxRisk human in vitro cell models for comparing expression of signaling pathways at baseline

Event: EU-ToxRisk, General Assembly

Nov, 2017 The importance of isozymes in pathway analyses Event: GROW Science Day, UM

Address: 6227AN, Maastricht, Netherlands

Mobile: +31-687******; email: ************@*****.*** Mar, 2016 Connections: Universal Bio-molecular relationship database Event: National Symposium on Computational Systems Biology, JUIT, Solan Feb, 2014 Deciphering Biological networks: Clues for cure Event: Biorhythm under the aegis of Department of Biotechnology India Oct, 2013 Identification and analysis of network motifs in human disease specific pathways applying top down Systems Biology approach

Event: Virtual Conference, Bioinformatics to Systems Biology Sep, 2013 Annotation of Biological Networks through Network Motifs using Top Down approach

Event: 3rd IFIP International Conference of Bioinformatics, MANIT, Bhopal Workshops

6-9, Mar, 2018 Modelling and Extrapolation

Event: EU-ToxRisk Summer School, Konstanz

19-21, Sep, 2016 AOP training course

Event: EU-ToxRisk Summer School, Vienna

3-5, Dec 2015 Foss: solution for application development Event: National Institute of Electronics and Information Technology, Chandigarh 22-24, Dec 2014 Fundamentals of Systems Biology

Event: National Network for Mathematical and Computational Biology, University of Delhi

Spoken languages

English Professional

Dutch Basic (A1)

Hindi Native

Contact details of references

1. Prof dr. Jos Kleinjans

Professor, Head of department, Toxicogenomics

Maastricht University

Email: *.*********@********************.**

Tel: +31-43-388****

Website: https://toxicogenomics-um.nl/staff/Jos-Kleinjans 2. Dr. Florian Caiment

Assistant Professor, Toxicogenomics

Maastricht University

Email: *******.*******@********************.**

Tel: +31-43-388****

Website: https://toxicogenomics-um.nl/staff/Florian-Caiment

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