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Sandeep Kaushik is an Auxiliary (Assistant) Researcher equivalent to Assistant Professor in 3B's Research Group, University of Minho and works in the area(s) of Computational Biology and Bioinformatics. His current research interest is to develop a computational model for breast cancer using agent based modeling approach. His post-doctoral research experience in bioinformatics extends across past 7 years and includes analysis of NGS data (both transcriptomics and genomics), database scraping, website and web-based-tool development, molecular modeling and programming in R (Bioconductor), PERL and NetLogo languages. He has analysed RNA-seq data derived from mycobacteria (M. tuberculosis & M. smegmatis) and humans (vitiligo) along with plant (wheat) genomic data.
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Identification

Personal identification

Full name
Sandeep Kaushik

Citation names

  • Kaushik, Sandeep

Author identifiers

Ciência ID
8914-D444-D58E
ORCID iD
0000-0001-9649-1358
Google Scholar ID
y0BVHqEAAAAJ
Researcher Id
M-3840-2017
Scopus Author Id
56970619500

Email addresses

  • sandeep.kaushik.nii2012@gmail.com (Professional)
  • prince.kratos@gmail.com (Personal)

Telephones

Mobile phone
  • 919581649 (Personal)

Addresses

  • 3B's Resaerch Group, Head Qtrs of European Instt. of Excellence on, Tissue Engg. and Regenerative Medicine Avepark, 4805-017, Barco, Guimaraes, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Hindi (Mother tongue)
Education
Degree Classification
2012/01/31
Concluded
 Bioinformatics (Doktor (PhD))
Major in Molecular Dynamics Simulations, PERL programming
Jawaharlal Nehru University, India

National Institute of Immunology, India
"Computational analysis of the structural stability and substrate specificity of legume lectins" (THESIS/DISSERTATION)
 N A
2002 - 2004
Concluded
 Biotechnology (Master)
Major in Biotechnology
Jawaharlal Nehru University, India

Jawaharlal Nehru University School of Biotechnology, India
"Understanding the folding/unfolding of Ubiquitin" (THESIS/DISSERTATION)
 A-
1999 - 2002/06
Concluded
 Biochemistry (Hons) (Bachelor)
Major in Biochemistry
University of Delhi, India

Sri Venkateswara College, India
61 %
Affiliation

Science

Category
Host institution 		Employer
2017/03/01 - Current Auxiliary Researcher (Research) Biomaterials Biodegradables and Biomimetics, Portugal
2016/02/01 - 2016/07/31 Postdoc (Research) Genome Institute of Singapore, Singapore
2014/08/04 - 2015/12/06 Research Assistant (Research) National Research Center on Plant Biotechnology, India
2011/11/07 - 2014/07/15 Research Assistant (Research) Institute of Genomics and Integrative Biology CSIR, India
Outputs

Publications

Book chapter
  1. Kaushik, Sandeep. "Text Mining Resources for Bioinformatics". edited by Shoba Ranganathan; Michael Gribskov; Kenta Nakai; Christian Schönbach, 1083-1092. Academic Press, 2019.
    https://doi.org/10.1016/B978-0-12-809633-8.20499-8
  2. Kaushik, Sandeep. "Mutation Effects on 3D-Structural Reorganization Using HIV-1 Protease as a Case Study". edited by Shoba Ranganathan; Michael Gribskov; Kenta Nakai; Christian Schönbach, 706-721. Academic Press, 2019.
    https://doi.org/10.1016/B978-0-12-809633-8.20279-3
  3. Kaushik, Sandeep. "Phylogenetic Analysis: Early Evolution of Life". Elsevier, 2018.
    https://doi.org/10.1016/B978-0-12-809633-8.20171-4
  4. Kaushik, Sandeep. "Pharmacophore Development". Elsevier, 2018.
    https://doi.org/10.1016/B978-0-12-809633-8.20276-8
  5. Kaushik, Sandeep. "Pathway Informatics". Elsevier, 2018.
    https://doi.org/10.1016/B978-0-12-809633-8.20288-4
  6. Kaushik, Sandeep. "Protein Structure Visualization". Elsevier, 2018.
    https://doi.org/10.1016/B978-0-12-809633-8.20283-5
  7. Kaushik, Sandeep. "Translational and Disease Bioinformatics". Elsevier, 2018.
    https://doi.org/10.1016/B978-0-12-809633-8.20302-6
  8. Kaushik, Sandeep. "Bioinformatics Approaches for Studying Alternative Splicing". Elsevier, 2018.
    https://doi.org/10.1016/B978-0-12-809633-8.20228-8
  9. Kaushik, Sandeep. "Nucleic-Acid Structure Database". Elsevier, 2018.
    https://doi.org/10.1016/B978-0-12-809633-8.20285-9
  10. Kaushik, Sandeep. "Functional Genomics". Elsevier, 2018.
    https://doi.org/10.1016/B978-0-12-809633-8.20222-7
Conference poster
  1. Kaushik, Sandeep; Brancato, V; Oliveira, J M; Correlo, V.M.; Reis, R.L.; Kundu, S.C.. "An agent-based model for breast cancer research.". Paper presented in FoReCaST, 2017.
  2. Kaushik, Sandeep; Oliveira, J M; Correlo, V.M.; Reis, R.L.; Kundu, S.C.. "In silico models for breast cancer research.". Paper presented in Chem2Nature, 2017.
  3. Kaushik, Sandeep; Mahato, A; Chaudhary, C K; Yadav, I S ; Sharma, P; Gupta, O P; Gaikwad, K; et al. "Genome assembly and annotation of wheat chromosome arm 2AS.". Paper presented in Inernational Conference on Structural Genomics, 2015.
  4. Kaushik, Sandeep; Hossain, M S; Hussain, S S ; Muralidhar, K. "Molecular Docking Investigations on porcine L-Gulonate Dehydrogenase.". Paper presented in South Asian Biotechnology Conference, 2015.
  5. Kaushik, Sandeep; Dr Debasisa Mohanty; Surolia, Avadhesha. "Computational analysis of the structural stability and substrate specificity of legume lectins.". Paper presented in National Conference on Biology and Bioinformatics of Economically Important Plants and Microbes., 2012.
Journal article
  1. Kaushik, Sandeep. "Editorial: Multi-Omics Approaches to Study Signaling Pathways". Frontiers in Bioengineering and Biotechnology 8 (2020): http://dx.doi.org/10.3389/fbioe.2020.00829.
    10.3389/fbioe.2020.00829
  2. Anshumali Mittal; Tom C. Hobman; Kavyashree Manjunath; Rajesh Kumar Ranjan; Sandeep Kaushik; Sujeet Kumar; Vikash Verma. "COVID-19 pandemic: Insights into structure, function, and hACE2 receptor recognition by SARS-CoV-2". PLOS Pathogens (2020): https://doi.org/10.1371/journal.ppat.1008762.
    10.1371/journal.ppat.1008762
  3. Kaushik, Sandeep. "Big data in healthcare: management, analysis and future prospects". Journal of Big Data (2019): http://dx.doi.org/10.1186/s40537-019-0217-0.
    10.1186/s40537-019-0217-0
  4. Kaushik, Sandeep; Agrawal, Nikhil; Hossain, Md. Summon; Skelton, Adam A.; Muralidhar, Kambadur; Kaushik, Sandeep. "Unraveling the mechanism of l-gulonate-3-dehydrogenase inhibition by ascorbic acid: Insights from molecular modeling". Computational Biology and Chemistry 77 (2018): 146-153. http://www.sciencedirect.com/science/article/pii/S1476927118304018.
    Published • https://doi.org/10.1016/j.compbiolchem.2018.09.015
  5. Caballero, D.; Kaushik, S.; Correlo, V.M.; Oliveira, J.M.; Reis, R.L.; Kundu, S.C.. "Organ-on-chip models of cancer metastasis for future personalized medicine: From chip to the patient". Biomaterials 149 (2017): 98-115. http://dx.doi.org/10.1016/j.biomaterials.2017.10.005.
    Published • 10.1016/j.biomaterials.2017.10.005
  6. Anand, Amitesh; Verma, Priyanka; Singh, Anil Kumar; Kaushik, Sandeep; Pandey, Rajesh; Shi, Ce; Kaur, Harneet; et al. "Polyketide Quinones Are Alternate Intermediate Electron Carriers during Mycobacterial Respiration in Oxygen-Deficient Niches". Molecular Cell 60 4 (2015): 637-650. http://dx.doi.org/10.1016/j.molcel.2015.10.016.
    Published • 10.1016/j.molcel.2015.10.016
  7. Kaushik, Sandeep; Mohanty, Debasisa; Surolia, Avadhesha. "Molecular Dynamics Simulations onPars Intercerebralis MajorPeptide-C (PMP-C) Reveal the Role of Glycosylation and Disulfide Bonds in its Enhanced Structural Stability and Function". Journal of Biomolecular Structure and Dynamics 29 5 (2012): 905-920. http://dx.doi.org/10.1080/073911012010525026.
    Published • 10.1080/073911012010525026
  8. Kaushik, Sandeep; Krishnarjuna, Bankala; Raghothama, Srinivasarao; Aggarwal, Sangita; Raghunathan, Vidya; Ganjiwale, Anjali. "Theoretical and in vitro studies of a C-terminal peptide from PGKC of Leishmania mexicana mexicana". Molecular and Biochemical Parasitology 185 1 (2012): 27-35. http://dx.doi.org/10.1016/j.molbiopara.2012.06.004.
    Published • 10.1016/j.molbiopara.2012.06.004
  9. Kaushik, Sandeep; Mohanty, Debasisa; Surolia, Avadhesha. "Role of glycosylation in structure and stability of Erythrina corallodendron lectin (EcorL): A molecular dynamics study". Protein Science 20 3 (2011): 465-481. http://dx.doi.org/10.1002/pro.578.
    Published • 10.1002/pro.578
  10. Kaushik, Sandeep; Mohanty, Debasisa; Surolia, Avadhesha. "The Role of Metal Ions in Substrate Recognition and Stability of Concanavalin A: A Molecular Dynamics Study". Biophysical Journal 96 1 (2009): 21-34. http://dx.doi.org/10.1529/biophysj.108.134601.
    Published • 10.1529/biophysj.108.134601
Website
  1. Kaushik, Sandeep. FoReCaST. 2018. http://dev.forecast.3bs.pt.
Activities

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2017/11/15 - 2017/11/17 FoReCaST 2017 Conference (Organization & participation).
Conference
 FoReCaST Conference
Biomaterials Biodegradables and Biomimetics, Portugal
2017/06/05 - 2017/06/09 CHEM2NATURE
Workshop
 CHEM2NATURE
Biomaterials Biodegradables and Biomimetics, Portugal
2015/06/07 - 2015/06/11 International Conference on Structural Genomics 2015 (Poster)
Conference
 International Conference on Structural Genomics 2015
Weizmann Institute of Science, Israel
2015/02/12 - 2015/02/14 International South Asian Biotechnology Conference (Poster)
Conference
 International South Asian Biotechnology Conference
South Asian University, India
2013/08/24 - 2013/08/27 Bioinformatics for Human Genome Analysis
Workshop
 Workshop on Bioinformatics for Human Genome Analysis
Institute of Bioinformatics, India
2012/12/30 - 2013/01/01 Genomeet
Conference
 Genomeet 2012
Institute of Genomics and Integrative Biology CSIR, India
2012/02/17 - 2012/02/19 Biology and Bioinformatics of Economically Important Plant and Microbes (Poster Presentation)
Conference
 Biology and Bioinformatics of Economically Important Plant and Microbes 2012
University of North Bengal, India
2010/10/26 - 2010/10/27 Indo-Swiss Bioinformatics Symposium
Symposium
 Indo-Swiss Bioinformatics Symposium
Indian Institute of Technology Delhi, India
2006/12/18 - 2006/12/20 5th International Conference on Bioinformatics (InCoB) 2006
Conference
 International Conference on Bioinformatics
Indian Institute of Technology Delhi, India

Jawaharlal Nehru University, India

Department of Biotechnology Ministry of Science and Technology, India
2005/01/12 - 2005/01/15 International Workshop on Biomedical MR
Workshop
 International Workshop on Biomedical MR
All India Institute of Medical Sciences, India
Distinctions

Other distinction

2015 Travel Award (International Conference on Structural Genomics )
Weizmann Institute of Science, Israel
2005 CSIR-UGC National Eligibility Test (NET)
Council of Scientific and Industrial Research, India

University Grants Commission, India
2005 CSIR-Junior/Senior Research Fellowship
Council of Scientific and Industrial Research, India
2002 Post-Graduate Scholarship (All India 4th rank)
Department of Biotechnology Ministry of Science and Technology, India
1998 Merit Certificate (National Mathematics Olympiad)
1996 Merit Certificate (for 1st rank in IXth standard)
Guru Nanak Yuvak Sindhi Seva Mandal, India
1996 Merit Certificate (Quiz Competition)
Navodaya Vidyalaya Samiti, India
1995 Merit Certificate (National Mathematics Olympiad)