Shradha Mukherjee

Nicknames: Shredder, a supervillain for villains and Goldy, a superhero for heroes.

"Dubito Ergo Cogito; Cogito Ergo Sum" (Latin)
"I doubt therefore I think; I think therefore I am" (English)
-quote by René Descartes.
ref: https://www.bbc.co.uk/programmes/p02pdc6n

About me

What is my profession? (who am I professionally?) At the microscopic level, 'I am an atom in the universe and an universe of atoms' to quote from Richard Feynman's poem. At the macroscopic level, I am a knowledge worker, that is a scientist and educator.

What is my philosophy? (who am I personally?) I am a minimalist, that is my philosophy is 'simple living high thinking' as described in poem 'The Character of a Happy Life' by Sir Henry Wotton and famous quote by Lao Tzu 'who knows that enough is enough, will always have enough'.

What are my accomplishments? (proven merit) My education includes graduate level degrees in chemistry, biochemistry and computation (health informatics). My research publications as first and/or corresponding author (2013-present) are in domains of neuroscience, neurological diseases, cancers, stem cells, neurotoxicity and heavy metal toxicity. These publications utilised techniques of molecular biology, biochemistry, bioinformatics, genomic/omics, statistics, machine learning, AI, natural language processing and network analysis. I have published papers (2013-present) in and reviewed papers (2020-present) for, @Nature https://www.nature.com/siteindex, @FrontiersIn https://www.frontiersin.org/journals and @ElsevierConnect https://www.elsevier.com/products/journals (Cell Press) tier 1 highly cited high impact family of journals in addition to others.

What are my soft skills? (work ethics) To put it simply, my soft skills are rooted in my passion for knowledge work. 'Give me problems, give me work, give me the most abstruse cryptogram or the most intricate analysis, and I am in my own proper atmosphere' quote from Sherlock Holmes, The Sign of Four by Sir Arthur Conan Doyle. My research experience has potentiated my ability to plan, problem-solve and perform intricate scientific experiments to unravel novel discoveries. My experience in scientific communication through presentations and publications, has honed my ability to convey complex ideas and technical information in a concise and accessible manner. Taken together, I am confident my proven merit and work ethics, make me an ideal candidate to contribute to your organization's success and create tangible value.

What position and salary do I want? (job, consultancy) I am unemployed and seeking consultancy or regular employment. I am interested in and a good fit for biology, chemistry and computational research or in other words research spanning multiple scientific disciplines. I am eager to pursue either conventional scientific research or AI/computation driven scientific research (https://news.cgtn.com/news/2025-03-10/Expert-China-s-AI-initiative-to-revolutionize-scientific-research-1BDn9n5xVSw/p.html). For regular job, I only request salary that financially covers for my food, lodging and ticket to travel to the destination of work. For consultancy position, I only request financial coverage for food, lodging and ticket cost, which is similar to academia conference/summer school per diem and ticket scholarships.

Where do I want the position? (preferred locations) In pursuit of knowledge I have traveled to countries spanning three continents (Asia, America, Europe), while adapting myself to their sense of place, in keeping with the gold standard set by my Gurus, namely great knowledge workers (explorers, artists and scientists), especially Captain James Cook, Rene Descartes and Friedrich Schiller. Ergo, I am especially keen to grow through knowledge work position in destinations that are gold standards for knowledge work, only in China (mainland preferred), EU (Spain, Italy most preferred, while Turkey is not preferred at all), UK, Switzerland, Australia, New Zealand, Canada, Japan, South Korea, Singapore, and US. The adaptation to their sense of place, has been especially labile for me because of the void created by the fact that I never felt any sense of place in India, the barbarian country where I was unfortunately born. My aptitude and values of honesty simplicity hardwork curiosity logic respect for mother nature, which resulted in my proven merit are antithetical to those of India et al (Indian subcontinent, South America, Africa, Middle-East) and its native overpopulating clingy needy useless unprofessional masses who could not be straightened up by the best efforts of civilized Europeans and North Americans (US, Canada not speaking of barbarian Mexico) because due to 'suicidal empathy' of Europeans they used more of the carrots than the sticks on these barbarian natives and did not take fellow civilized South-East Asian China/Japan et al's help (see references, ref1, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, ref10, ref11, ref12, ref13, ref14). Ergo, I have always longed for and worked hard to hone my talent so that my proven merit can get me to more civilized places (as listed under gold standards for knowledge work) so that the void within me can be filled by thier civilized sense of place, which is more in tune with what I am.

  • ref1: Sci-Fi Zobrist's exponential growth movie Inferno and Bartlett's beaker Inferno DanBrown https://youtu.be/6Z40g6Qsuk8
  • ref2: Causes and Effects of Climate Change NationalGeographic https://youtu.be/G4H1N_yXBiA
  • ref3: Overpopulation facts- the problem noone will discuss: Alexandra Paulat TEDxTopanga TedTalk https://youtu.be/fNxctzyNxC0
  • ref4: Sci-Fi Overpopulation Nightmare from 1960s- Star Trek's Mark of Gideon StarTrek https://youtu.be/KdsbuJfMpr0
  • ref5: China's World View Demystifying China to Prevent Global Conflict by David Daokui Li https://www.penguinrandomhouse.ca/books/748297/chinas-world-view-by-david-daokui-li/9780393292398
  • ref6: The War on the West by Douglas Murray https://www.harpercollins.com/products/the-war-on-the-west-douglas-murray?variant=39664581705762
  • ref7: The Great Philosophers: An Introduction To Western Philosophy by Bryan Magee The Great Philosophers: An Introduction To Western Philosophy by Bryan Magee
  • ref8: The European Miracle: Environments, Economics and Geopolitics in the History of Europe and Asia by Eric Jones https://www.cambridge.org/core/books/european-miracle/2937A1A02CC2A1F859AE2CD546B58EFD
  • ref9: The Brussels Effect: How the European Union Rules the World by Anu Bradford, Columbia Law School, Oxford University Press (also author of Digital Empires: The Global Battle to Regulate Technology)https://scholarship.law.columbia.edu/books/232/
  • ref10: Geopolitics and Identity in British Foreign Policy Discourse The Island Race by Nick Whittakerhttps://www.taylorfrancis.com/books/mono/10.4324/9781003374022/geopolitics-identity-british-foreign-policy-discourse-nick-whittaker
  • ref11: The Ascent of Money by Niall Ferguson (also author of Civilization The West and the Rest)https://www.penguinrandomhouse.com/books/302900/the-ascent-of-money-by-niall-ferguson/
  • ref12: Japan in an Era of Geopolitics: A New Foreign and Security Policy Direction is published by the Konrad-Adenauer-Stiftung Country Program Japan. (Available in English and Japanese)https://www.kas.de/en/web/japan/single-title/-/content/japan-in-an-era-of-geopolitics-2
  • ref13: New Economic Statecraft China, the United States and the European Union by Zhang Xiaotong https://www.routledge.com/New-Economic-Statecraft-China-the-United-States-and-the-European-Union/Xiaotong/p/book/9781032397931
  • ref14: The European Union and China's Belt and Road Impact, Engagement and Competition Edited by Vassilis Ntousas, Stephen Minashttps://www.taylorfrancis.com/books/edit/10.4324/9780367853235/european-union-china-belt-road-vassilis-ntousas-stephen-minas
  • What about work authorization? (visa) I need visa to work in the knowledge gold standard preferred locations, that is only in China (mainland preferred), EU (Spain, Italy most preferred, while Turkey is not preferred at all), UK, Switzerland, Australia, New Zealand, Canada, Japan, South Korea, Singapore, and US. I need visa eligible for work called work visa, so it cannot be a diplomatic or other non-work visa.

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    Education

    • MS IN COMPUTATION (HEALTH INFORMATICS), DR. ROBERT GREENES THESIS ADVISOR, ARIZONA STATE UNIVERSITY, TEMPE, U.S., CGPA 3.6 BEST POSSIBLE CGPA 4.0 — YEARS 2017-2019
    • MS IN CHEMISTRY, INDIAN INSTITUTE OF TECHNOLOGY, CHENNAI, INDIA, CGPA 7.63 BEST POSSIBLE CGPA 10.0 — YEARS 2003-2005
    • BS IN CHEMISTRY (3 YRS), BOTANY ZOOLOGY (2 YRS), PHYSICS (1 YR), FERGUSSON COLLEGE, PUNE, INDIA, TOTAL SCORE 2456 OUT OF 3100, REQUIRED PASSING SCORE 1240 OUT OF 3100 — YEARS 2000-2003
    • CERTIFICATE IN MANAGEMENT COURSE 'MANAGING THE COMPANY OF THE FUTURE', UNIVERSITY OF LONDON, LONDON BUSINESS SCHOOL — YEAR 2019
    • PHD IN BIOCHEMISTRY, UNIVERSITY OF HOUSTON, HOUSTON, U.S., CGPA 3.9 BEST POSSIBLE CGPA 4.0. — YEARS 2005-2011
      PHD first author thesis work (link to copy of my thesis on open science HAL archive: https://hal.science/hal-04084217).

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    Jobs

    • Full stack web developer, European Molecular Biology Laboratory- European Bioinformatics Institute, London, U.K. — 2022
      Database Management, Development of Python CLI, Web Development.
    • STAFF, UNIVERSITY OF CALIFORNIA LOS ANGELES, LOS ANGELES, U.S. — 2018-2021
      Molecular biology and bioinformatics experiments in field of neurological diseases. During Covid when labs were closed did patient screening at the hospital.
    • POSTDOCTORAL FELLOW, UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER, DALLAS, U.S. — 2011-2017
      Molecular biology and bioinformatics experiments in field of adult brain stem cells.

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    Teaching

    • UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER, DALLAS, U.S. — 2011-2017
      Mentored high school, undergraduate, graduate, postdoctoral researchers and medical students in molecular biology and bioinformatics skills in the postdoctoral research lab.
    • UNIVERSITY OF HOUSTON, HOUSTON, U.S. — 2005-2007
      Conducted “Introduction to Biology” and “Animal Anatomy and Physiology” lab course for undergraduate students

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    Standardised Examinations

    • TOEFL Score 280 out of 300, U.S. exam. 2004
    • GRE General Score 1450 out of 1600, U.S. exam. 2004
    • GATE Chemistry, Percentile Score 81.66 i.e. performance 81.66% BETTER than other candidates who appeared for the exam (top 18% of candidates), India exam. 2005

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    Publications And Codes


    Publications (Alt.Links): ORCiD | NCBI | EuroPMC | SemanticScholar
    Publications With Full Text (Alt.Links): HAL Open Science | Academia Edu
    Code Repositories (Alt.Links): Gitlab | Bitbucket | Github

    Publications in paid scientific journals. From complete list of publications, the major authorship (first author and corresponding author) papers are as follows:

    • Mukherjee S*†. Immune gene network of neurological diseases: Multiple Sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease (PD) and Huntington's disease (HD). Heliyon 2021; 7:12. https://doi.org/10.1016/j.heliyon.2021.e08518
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of this 'Publications And Codes' section. Codes for this project are in folder/repository named 'githubsubmittedadpdhdmsimmunesept2021' or 'GithubSubmittedADPDHDMSimmuneSept2021'.
    • Mukherjee S*†. Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples. Scientific Reports 2020; 10, 10937. https://doi.org/10.1038/s41598-020-67753-5
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of this 'Publications And Codes' section. Codes for this project are in folder/repository named 'githubscientificreportsglioblastomastemapril2020' or 'GithubScientificReportsGlioblastomaStemApril2020'.
    • Mukherjee S*†, Klaus C†, Pricop-Jeckstadt M, Miller JA and Struebing FL*†. A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks. Frontiers in Neuroscience 2019; 13:2. https://doi.org/10.3389/fnins.2019.00002
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of this 'Publications And Codes' section. Codes for this project are in folder/repository named 'githubfrontiersneuroscidec2018' or 'GithubFrontiersNeurosciDec2018'.
    • Mukherjee S*†. Genomics-Guided Immunotherapy for Precision Medicine in Cancer. Cancer Biotherapy and Radiopharmaceuticals 2019; 10.1089/cbr.2018.2758. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6802731 (write-up only as its review article)
    • Mukherjee S†, Brulet R, Zhang L and Hsieh J*. REST regulation of gene networks in adult neural stem cells. Nature Communications 2016; 7:13360. https://doi.org/10.1038/ncomms13360
      Code Availability: See book chapter, Mukherjee S†, Hsieh J*. Genome-Wide Identification of Transcription Factor-Binding Sites in Quiescent Adult Neural Stem Cells. In: Lacorazza H. (eds) Cellular Quiescence. Methods in Molecular Biology, vol 1686. Humana Press, New York, NY (Springer Nature) 2018. https://pubmed.ncbi.nlm.nih.gov/29030827.
    • Mukherjee S, Hsieh J. On your (methyl) mark, get TET1, go! Cell Stem Cell. 2013 Aug 1;13(2):133-4.PMID: 23910076.https://doi.org/10.1016/j.stem.2013.07.011 (write-up only as its review article)

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    Projects And Codes


    Code Repositories (Alt.Links): Gitlab | Bitbucket | Github

    Projects with codes and write-up are as follows:

    • Mukherjee S*†. Machine Learning classifier built with heavy metal signature biomarker genes as features to distinguish between heavy metal exposure from non-heavy metal exposure gene expression samples. 2023 https://hal.science/hal-04084188
      Please note, this is pre-print of the manuscript, which is under review for publication in a scientific journal.
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of this 'Projects And Codes' section. Codes for this project are in folder/repository named 'pbothers_rnaseq_ml_feb2023' or 'PbOthers_RNAseq_ML_Feb2023'.
    • COPY OF MY MASTERS (MS) THESIS AS AVAILABLE IN LIBRARY OF ARIZONA STATE UNIVERSITY, U.S.: Mukherjee S*†. Targeted BEL network representation and characterization of commonly mutated genes in Non-Small Cell Lung Carcinoma (NSCLC). 2019 https://hal.science/hal-04084202
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of 'Projects And Codes' section. Codes for this project are in folder/repository named 'bmi593_appliedproject_nsclc', 'BMI593_AppliedProject_NSCLC', 'nsclc_drugtargetsmutations_nov2019' or 'NSCLC_DrugTargetsMutations_Nov2019'.
    • COPY OF MY PHD THESIS AS AVAILABLE IN LIBRARY OF UNIVERSITY OF HOUSTON, U.S.: Mukherjee S*† et. al. Gestational lead exposure shortens cell cycle length and activates developmental molecular network of neurogenesis in postnatal retina. 2011 https://hal.science/hal-04084217
      Code Availability: Wet lab research so no codes.

    Projects with codes related to papers (write-up) published in paid scientific journals are as follows:

    • Glioblastome_Drug_Gene_Disease_Database_SQL.
      #Citation: Mukherjee S*†. Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples. Scientific Reports 2020; 10, 10937. https://doi.org/10.1038/s41598-020-67753-5
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of 'Projects And Codes' section. Codes for this project are in folder/repository named 'glioblastoma_drug_gene_disease_database_sql' or 'Glioblastome_Drug_Gene_Disease_Database_SQL'.
    • Glioblastoma_Grade_Stem_Cell_Genes_Deconvolution_to_Regression.
      #Citation: Mukherjee S*†. Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples. Scientific Reports 2020; 10, 10937. https://doi.org/10.1038/s41598-020-67753-5
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of 'Projects And Codes' section. Codes for this project are in folder/repository named 'glioblastoma_grade_stem_cell_genes_deconvolution_to_regression' or 'Glioblastoma_Grade_Stem_Cell_Genes_Deconvolution_to_Regression'.
    • Neurons_RNAseq_Expression_DESeq2_visualization_GO.
      #Citation 1: Mukherjee S*†. Immune gene network of neurological diseases: Multiple Sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease (PD) and Huntington's disease (HD). Heliyon 2021; 7:12. https://doi.org/10.1016/j.heliyon.2021.e08518
      #Citation 2: Mukherjee S*†. Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples. Scientific Reports 2020; 10, 10937. https://doi.org/10.1038/s41598-020-67753-5
      #Citation 3: Mukherjee S*†, Klaus C†, Pricop-Jeckstadt M, Miller JA and Struebing FL*†. A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks. Frontiers in Neuroscience 2019; 13:2. https://doi.org/10.3389/fnins.2019.00002
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of 'Projects And Codes' section. Codes for this project are in folder/repository named 'neurons_rnaseq_expression_deseq2_visualization_go' or 'Neurons_RNAseq_Expression_DESeq2_visualization_GO'.
    • StemCells_RNAseq_Expression_edgeR_visualization_GO.
      #Citation 1: Mukherjee S*†. Immune gene network of neurological diseases: Multiple Sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease (PD) and Huntington's disease (HD). Heliyon 2021; 7:12. https://doi.org/10.1016/j.heliyon.2021.e08518
      #Citation 2: Mukherjee S*†. Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples. Scientific Reports 2020; 10, 10937. https://doi.org/10.1038/s41598-020-67753-5
      #Citation 3: Mukherjee S*†, Klaus C†, Pricop-Jeckstadt M, Miller JA and Struebing FL*†. A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks. Frontiers in Neuroscience 2019; 13:2. https://doi.org/10.3389/fnins.2019.00002
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of 'Projects And Codes' section. Codes for this project are in folder/repository named 'stemcells_rnaseq_expression_edger_visualization_go' or 'StemCells_RNAseq_Expression_edgeR_visualization_GO'.

    Projects with codes and write-up that are copyrighted are as follows:

    • EMBL_EBI_Exams_2022. #Warning: This project is protected by copyright. Copyright © 2022 Shradha Mukherjee for solutions. All rights reserved. Acknowledgement and/or Copyright © 2022 EMBL-EBI for questions.
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of 'Projects And Codes' section. Codes for this project are in folder/repository named 'embl_ebi_exams_2022' or 'EMBL_EBI_Exams_2022'.
    • Glioblastoma_Comorbidities_NLP_May2019 Class Project. #Warning: This project is protected by copyright. Copyright © 2019 Mohamed Mohamed (researcher/communication), Victoria Oladoye (researcher/documentation), Sierra Murray (evaluator/appraisal), Shradha Mukherjee (researcher/scheduling) and Arizona State University for question. All rights reserved.
      Code Availability: Yes, please see Code Repositories (5 Alt.Links)' provided at start of 'Projects And Codes' section. Codes for this project are in folder/repository named 'gbothers_nlp_may2019' or 'GBothers_NLP_May2019'.

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