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 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? (skills that have helped me achieve my proven merit) 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 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. The fair (giving credit where its due, not engage in plagiarism) and FAIR (findability, accessibility, interoperability, and reusability) science I practice, can be described by the line "whose armour is his honest thought, and simple truth his utmost skill" from poem 'The Character of a Happy Life' by Sir Henry Wotton. Its another way of saying, that in Science data driven truths have to be stated honestly, and cannot be diluted for sake of consensus, empathy or humility, science is not a majority vote. Sherlock Holmes sums this up nicely, in The Adventure of the Greek Interpreter by Arthur Conan Doyle "I cannot agree with those who rank modesty among the virtues. To the logician all things should be seen exactly as they are, and to underestimate one's self is as much a departure from truth as to exaggerate one's own powers."

What is my foundational work ethic? (FAIR basis of knowledge work) In the field of science, being FAIR and conducting fair/honest research is a crucial practical skill for any scientist to possess. I learned about this concept from my guru Captain Cook (one of three mentors, along with Rene Descartes and Friedrich Schiller), who emphasized the importance of revealing truths even if that meant going against pre-existing unproven dogma and majority opinion, as evidenced by Captain Cook's world map which even his rivals of the time the Dutch and French appreciated and used fairly after Royal National Geographic published it. This scientific process, was established by my other guru, Rene Descartes, during a time when speculation and subjectivity were becoming science. To combat this, Rene developed a logic and reason-based method for obtaining objective truths, as outlined in his work "Discourse on the Method" (French title: Discours de la méthode).
Examples of scientists defying majority consensus include the Wright brothers' flight of the plane and Galileo's discovery that the sun was at the center of the solar system. While the majority may choose to remain ignorant, science cannot be changed for them. History has shown that truth is more sustainable, as evidenced by the acceptance of these discoveries by the contemporary majority. Presently, there exist ignorant trends that challenge proven scientific truths, such as denial of climate change and impact of human activity on abiotic and biotic environment (what goes around comes around, so badly impacts humans too), the denial of genetic variation and adaptation between human races and populations, and the denial of non-interchangeable sexual dimorphism in humans. I believe that these ignorant trends will eventually fail, as truth is more sustainable and will ultimately prevail. Ignoring scientific evidence and truth can have dire consequences for any individual. Example ignoring the genetic and epigenetic differences between races, men and women, can greatly deter treatment outcomes and ignoring human induced climate change and pollution deters human health such as from microplastic pollution. It is important to recognize the importance of FAIR research practices because science uses pre-existing science, so if fake science is incorporated into knowledge space then research built on it will also be faulty. In summary, ‘Beauty is truth, truth beauty,—that is all Ye know on earth, and all ye need to know.’--quote John Keats. ref: FAIR (findability, accessibility, interoperability, and reusability) | Nature Journal https://www.nature.com/articles/sdata201618 ref: FAIR (findability, accessibility, interoperability, and reusability) Framework | EMBL-EBI https://www.ebi.ac.uk/about/news/perspectives/fairification-framework-making-your-data-findable-accessible-interoperable-and-reusable

What is my philosophy? (who am I personally?) What location do I want consistent with my philosophy? 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'. For me enough is using my proven merit to get to my preferred location, do my preferred knowledge work, live in a place with law and order i.e. security and lead a preferred lifestyle that is in harmony with nature and have a legal option if need be for preferred death (assisted suicide, assisted dying). Given the interdisciplinary nature of my education and research, I am best fit for work in sustainable innovation and environmental science (climate, flora and fauna). This is also consistent with my goal of living a life in harmony with nature, first inspired by my guru Friedrich Schiller's 'On The Aesthetic Education Of Man' (German title: 'Über die ästhetische Erziehung des Menschen') (one of my 3 gurus, the other two being Rene Descartes and Captain Cook) and also consistent with Buddhism, a religion I want to convert to which is basically about peaceful coexistance with nature. Ergo, UK, EU, Canada, Australia, New Zealand, US, Nepal, Singapore, South Korea and Japan that more or less meet all my above preferred conditions, rather philosophy, are also my preferred location -- work preference more met by UK, EU, Canada, Australia, New Zealand, US, slightly less met by Nepal, Singapore, South Korea and Japan, as evidenced by the historic sustained gold standard excellence in knowledge work by western civilization.

What position, work authorization and salary do I want? (job, consultancy, onsite, remote, temporary, full-time)

  • For work, I am eager to pursue either Traditional Work and Stationary Work or working as Digital Nomad and Working Traveler. I am unemployed and seeking consultancy or regular employment, either onsite or remote. 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, scientific writing assignments or teaching assignments for sustainable innovation in environmental science. Basically I want to be a environmental scientist, which requires interdisciplinary approach to science so can be simply called being a scientist -- this term scientists encompass knowledge workers who engage in hardwork both brainwork and legwork in pursuit of discovery and sustainable solutions, and should not be confused with unruly environmental activists/terrorists.
  • For payment, I only request financial coverage for food (to cover self-cooked food cost, not for restaurant food coverage) and lodging (to covert rent of apartment or cover rent of camper vans and designated camping site rent). My preferred currency is GBP as a small token of thanks to their mercy that made my life and work possible. The British hold a special place for me as indeed as we say in UK and as I believe to be true for me to the letter, "I have the honor [King Queen of UK and Commonwealth, Prince and Princess of Wales, currently serving UK Royals, real UK people (not the UK haters) and UK at large] to be your most humble and most obedient servant (of my generation)", it will be a dream come true if I have the honor to have that stated on my epitaph -- I plan to convert to Buddhism at some point in Nepal where Buddha was born, from current Hindu religion and avail burial upon death. One that serves is a servant so I am a servant of UK.
  • For authorization, ideally my preferred countries wouldn't need my merit but if they do (its a matter of freewill, just because I want them doesn't mean they have to want me), all they need to hire me is give me the minimally disruptive for local people and local culture legal authorization i.e. merit based work visa only which will be sufficient both to cover my work and life requirements -- for those fimiliar with population genetics, its called minimizing migration load and minimizing outbreeding depression to sustain the evolutionary adaptations especially for a population like that of humans, wild mice or cockroaches, which already has high genetic heterozygosity and is not endagered species. Now, I never was/am/will be interested in breeding so genetically I pose no threat, while culturally I am labile to adapt albeit because of being not only born but also being raised in non-western family it is practically impossible for me to be completely culturally integrated in the western culture, but I hope what I lack in genes and culture will be made up by my exceptional merit to get me a job in the west.
  • DEALBREAKER: It is absolutely critical for my self-respect rather for respect of the proven merit I have in knowledge work, that I be hired by virtue of merit alone, and not due to some quota like DEI, star PI lobby or some 'buddy system' lobby.
  • ref: Watch Prince William's speech in full as he called for the world to 'act together with urgency...save our world' | ITV News https://www.itv.com/news/2025-06-08/they-need-our-help-prince-william-issues-call-to-protect-worlds-oceans ref: 70% of species (flora, fauna) lost since 1970 | BBC https://youtu.be/-MK1Q2MCP8o ref: 1 million species (flora, fauna) currently at risk | DW News https://youtu.be/9XA7CmhMEt4 ref: Timelapse Our Forests showing loss of vegetation (flora, which is habitat of fauna) | BBC | https://youtu.be/ctlUvcKhsSg ref: Timelapse Our Oceans showing loss of ice | Google Earth | https://youtu.be/NHf-xSvpF-Y

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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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    Copyright © 2024 onwards Shradha Mukherjee