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

I am a scientist. I am interested in and a good fit for computational research spanning multiple scientific disciplines. 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.

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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 (5 Alt.Links): ORCiD | NCBI | EuroPMC | SemanticScholar
Publications With Full Text (5 Alt.Links): HAL Open Science | Academia Edu | MEGAnzPubs | pCloudPubs | Sync.comPubs
Code Repositories (5 Alt.Links): Gitlab | Bitbucket | MEGAnzCodes | FilenCodes | kDriveCodes

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 (5 Alt.Links): Gitlab | Bitbucket | MEGAnzCodes | FilenCodes | kDriveCodes

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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