Profile Details

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Hire Dr. Shounak B.

Luxembourg

USD 60 /hr

Biomedical Data Mangement expert, Neurobiologist, Systems Biology knowledge mapping, Ontology developper

Profile Summary

I am a cell & molecular biologist with over 15 years of wet-lab and computational expertise. I specialized in clinical and non-clinical data harmonization, ontology delelopment, data curation, FAIR data implementation, knowledge management, literature-based knowledge extraction, and data management. I am experienced in systems biology markup language (SBML), Biological Expression Language (BEL), Cell designer, and other pathway curation tools. I am also expèerienced in contract research, team management, and project coordination. Currently, I have multicultural working experience, having work experience in the USA, Europe, and Asia, both in academia and industry.

Subject Matter Expertise

• ★ Cell Biology
• ★ Neurobiology
• ★ Data Management
• ☆ Molecular Biology
• ☆ Cell Signaling Pathways
• ☆ Neuroscience
• ☆ Bioinformatics

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Meta-Research, Fact Checking, Gap Analysis, Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Statistical Analysis, Data Visualization, Big Data Analytics, Data Cleaning

Work Experience

Senior Research Scientist -Ontology

Novo Nordisk

July 2022 - Present

Luxembourg Institute of Health

January 2021 - Present

Causality Biomodels

November 2018 - December 2020

Karolinska Institutet

August 2017 - September 2018

Case Western Reserve University

May 2015 - July 2017

Education

PhD (Biophysics Division)

Saha Institute of Nuclear Physics

August 2009 - February 2015

MSc (Biotechnology)

University of Calcutta

2006 - 2008

Certifications

• Data Mangement and Stewardship

  Elixir

  June 2021 - Present

• Data Mangement for Clinical Research

  coursera

  May 2021 - Present

• Good Clinical Practice in European Legislation

  European Forum of Good Clinical Practice

  March 2021 - Present

• Version Control with Git

  coursera

  July 2019 - Present

• Best Practices for Biomedical Research Data Mangement

  Harvard medical school

  January 2019 - Present

• Diploma in Cell and Molecular Biology

  Karolinska Institute

  August 2017 - Present

• Future Faculty Certification

  Case western Reserve University

  May 2017 - Present

Publications

JOURNAL ARTICLE

Baksi S, Pradhan A(2021). Thyroid hormone: sex-dependent role in nervous system regulation and disease . Biology of sex differences.

Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, Abeliovich H, Abildgaard MH, Abudu YP, Acevedo-Arozena A, et al.(2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) . Autophagy.

Sargsyan A, Kodamullil AT, Baksi S, Darms J, Madan S, Gebel S, Keminer O, Jose GM, Balabin H, DeLong LN, et al.(2020). The COVID-19 Ontology . Bioinformatics (Oxford, England).

Domingo-Fernández D, Baksi S, Schultz B, Gadiya Y, Karki R, Raschka T, Ebeling C, Hofmann-Apitius M, Kodamullil AT(2020). COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology . Bioinformatics (Oxford, England).

Baksi S, Singh N(2017). α-Synuclein impairs ferritinophagy in the retinal pigment epithelium: Implications for retinal iron dyshomeostasis in Parkinson's disease . Scientific reports.

Asthana A, Baksi S, Ashok A, Karmakar S, Mammadova N, Kokemuller R, Greenlee MH, Kong Q, Singh N(2017). Prion protein facilitates retinal iron uptake and is cleaved at the β-site: Implications for retinal iron homeostasis in prion disorders . Scientific reports.

Tripathi AK, Karmakar S, Asthana A, Ashok A, Desai V, Baksi S, Singh N(2017). Transport of Non-Transferrin Bound Iron to the Brain: Implications for Alzheimer's Disease . Journal of Alzheimer's disease : JAD.

Baksi S, Bagh S, Sarkar S, Mukhopadhyay D(2016). Systemic study of a natural feedback loop in Huntington's disease at the onset of neurodegeneration . Bio Systems.

Baksi S, Tripathi AK, Singh N(2016). Alpha-synuclein modulates retinal iron homeostasis by facilitating the uptake of transferrin-bound iron: Implications for visual manifestations of Parkinson's disease . Free radical biology & medicine.

Choudhury KR, Bucha S, Baksi S, Mukhopadhyay D, Bhattacharyya NP(2016). Chaperone-like protein HYPK and its interacting partners augment autophagy . European journal of cell biology.

Singh N, Asthana A, Baksi S, Desai V, Haldar S, Hari S, Tripathi AK(2015). The prion-ZIP connection: From cousins to partners in iron uptake . Prion.

Baksi S, Basu S, Mukhopadhyay D(2014). Mutant huntingtin replaces Gab1 and interacts with C-terminal SH3 domain of growth factor receptor binding protein 2 (Grb2) . Neuroscience research.

Kallol Bera and Shounak Baksi and Moupriya Nag and Subhas Chandra Bera and Debashis Mukhopadhyay and Soumen Basak(2014). A multicolor fluorescent peptide–nanoparticle scaffold: real time uptake and distribution in neuronal cells . New Journal of Chemistry. 38. (7). p. 2739. Royal Society of Chemistry ({RSC})

Baksi S, Jana NR, Bhattacharyya NP, Mukhopadhyay D(2013). Grb2 is regulated by foxd3 and has roles in preventing accumulation and aggregation of mutant huntingtin . PloS one.

OTHER

Schultz B, Zaliani A, Ebeling C, Reinshagen J, Bojkova D, Lage-Rupprecht V, Karki R, Lukassen S, Gadiya Y, Ravindra NG, et al.(2020). The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization .

Domingo-Fernández D, Baksi S, Schultz B, Gadiya Y, Karki R, Raschka T, Ebeling C, Hofmann-Apitius M, Kodamullil AT(2020). COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology .