プロフィール詳細

プロジェクトを作成

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Dr. Tania T.に依頼

India

Computational biologist: scRNA-seq, ATAC-seq, RNA-seq analysis. Building pipelines to drive therapeutic discoveries.

プロフィール概要

I'm a translational scientist with 10+ years of expertise bridging computational genomics and wet lab immunology, specializing in single-cell RNA-seq (scRNA-seq), ATAC-seq, and advanced bioinformatics analysis using R and Python. My research focuses on designing mechanistic in vitro studies—including organoid models and multicolor flow cytometry—to characterize immune cell populations and validate therapeutic compounds for drug discovery. I've led end-to-end genomics projects at Columbia University, secured independent €78,000 in grant funding, and collaborated with industry partners to inform therapeutic development decisions. With a Ph.D. in Respiratory Genetics and expertise spanning pathway analysis, regulatory network inference, and functional immunology assays, I translate complex biological data into actionable insights that drive innovation. I'm currently available for bioinformatics consulting, data analysis projects, and collaborative research ventures in biotech, pharma, and academic settings

専門分野

• ☆ Computational Biology
• ☆ Molecular Biology
• ☆ Biomarkers
• ☆ Genetics
• ☆ Omics
• ☆ Transcriptomics
• ☆ Comparative Genomics
• ☆ Genomics
• ☆ PCR
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ DNA Sequencing
• ☆ Gene Expression Analysis
• ☆ Genome Sequencing
• ☆ RNA Sequencing
• ☆ Cell Biology
• ☆ Cell-Based Assays
• ☆ Gene Regulation
• ☆ Stem Cell Research
• ☆ Biotechnology & Bioengineering
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Cell Culture
• ☆ Primary Cells
• ☆ 3D Cell Culture
• ☆ Tissue Engineering
• ☆ R

サービス

• Research
• Consulting
• Data & AI

Research Scientific and Technical Research

Consulting Scientific and Technical Consulting

Data & AI Data Visualization

職務経験

Genomics data analysis

Freelancer/Independent

1月 2024 - 現在

Postdoctoral research scientist

Columbia University

12月 2019 - 現在

ERS- long term research fellow/postdoc

Karolinska Institutet

12月 2017 - 12月 2019

学歴

Ph.D (research institute- biotechnology)

SRM University

3月 2013 - 12月 2018

M.Tech (Genetic Engineering )

SRM University

7月 2010 - 5月 2012

B.Tech (Biotechnology)

Karunya University

6月 2006 - 5月 2010

認定資格

• Foundations of Data Science

  coursera

  1月 2024 - 現在

出版物

JOURNAL ARTICLE

Matkovic Leko, I., Schneider, R.T., Thimraj, T.A., Schrode, N., Beitler, D., Liu, H.-Y., Beaumont, K., Chen, Y.-W., Snoeck, H.-W.(2023). A distal lung organoid model to study interstitial lung disease, viral infection and human lung development . Nature Protocols.

Matkovic Leko, I., Schneider, R.T., Thimraj, T.A., Schrode, N., Beitler, D., Liu, H.-Y., Beaumont, K., Chen, Y.-W., Snoeck, H.-W.(2023). A distal lung organoid model to study interstitial lung disease, viral infection and human lung development . Nature Protocols.

Upadhyay, S., Chakraborty, A., Thimraj, T.A., Baldi, M., Steneholm, A., Ganguly, K., Gerde, P., Ernstgård, L., Palmberg, L.(2022). Establishment of Repeated In Vitro Exposure System for Evaluating Pulmonary Toxicity of Representative Criteria Air Pollutants Using Advanced Bronchial Mucosa Models . Toxics. 10. (6).

Upadhyay, S., Chakraborty, A., Thimraj, T.A., Baldi, M., Steneholm, A., Ganguly, K., Gerde, P., Ernstgård, L., Palmberg, L.(2022). Establishment of Repeated In Vitro Exposure System for Evaluating Pulmonary Toxicity of Representative Criteria Air Pollutants Using Advanced Bronchial Mucosa Models . Toxics. 10. (6).

(2021). Circulating Secretoglobin Family 1A Member 1 (SCGB1A1) Levels as a Marker of Biomass Smoke Induced Chronic Obstructive Pulmonary Disease . Toxics.

Veerapaneni, V.V., Upadhyay, S., Thimraj, T.A., Siddaiah, J.B., Krishnarao, C.S., Lokesh, K.S., Thimmulappa, R., Palmberg, L., Ganguly, K., Anand, M.P.(2021). Circulating secretoglobin family 1a member 1 (Scgb1a1) levels as a marker of biomass smoke induced chronic obstructive pulmonary disease . Toxics. 9. (9).

Veerapaneni, V.V., Upadhyay, S., Thimraj, T.A., Siddaiah, J.B., Krishnarao, C.S., Lokesh, K.S., Thimmulappa, R., Palmberg, L., Ganguly, K., Anand, M.P.(2021). Circulating secretoglobin family 1a member 1 (Scgb1a1) levels as a marker of biomass smoke induced chronic obstructive pulmonary disease . Toxics. 9. (9).

(2020). Addressing the challenges of E-cigarette safety profiling by assessment of pulmonary toxicological response in bronchial and alveolar mucosa models . Scientific reports.

Ganguly, K., Nordström, A., Thimraj, T.A., Rahman, M., Ramström, M., Sompa, S.I., Lin, E.Z., O’Brien, F., Koelmel, J., Ernstgård, L., et al.(2020). Addressing the challenges of E-cigarette safety profiling by assessment of pulmonary toxicological response in bronchial and alveolar mucosa models . Scientific Reports. 10. (1).

Ganguly, K., Nordström, A., Thimraj, T.A., Rahman, M., Ramström, M., Sompa, S.I., Lin, E.Z., O’Brien, F., Koelmel, J., Ernstgård, L., et al.(2020). Addressing the challenges of E-cigarette safety profiling by assessment of pulmonary toxicological response in bronchial and alveolar mucosa models . Scientific Reports. 10. (1).

(2019). Evaluation of diacetyl mediated pulmonary effects in physiologically relevant air-liquid interface models of human primary bronchial epithelial cells . Toxicology in vitro : an international journal published in association with BIBRA.

Thimraj, T.A., Sompa, S.I., Ganguly, K., Ernstgård, L., Johanson, G., Palmberg, L., Upadhyay, S.(2019). Evaluation of diacetyl mediated pulmonary effects in physiologically relevant air-liquid interface models of human primary bronchial epithelial cells . Toxicology in Vitro. 61.

Thimraj, T.A., Sompa, S.I., Ganguly, K., Ernstgård, L., Johanson, G., Palmberg, L., Upadhyay, S.(2019). Evaluation of diacetyl mediated pulmonary effects in physiologically relevant air-liquid interface models of human primary bronchial epithelial cells . Toxicology in Vitro. 61.

(2018). Putative Systemic Biomarkers of Biomass Smoke-Induced Chronic Obstructive Pulmonary Disease among Women in a Rural South Indian Population . Disease markers.

(2018). Association of Elevated Serum GM-CSF, IFN-<i>γ</i>, IL-4, and TNF-<i>α</i> Concentration with Tobacco Smoke Induced Chronic Obstructive Pulmonary Disease in a South Indian Population . International journal of inflammation.

Mitra, A., Vishweswaraiah, S., Thimraj, T.A., Maheswarappa, M., Krishnarao, C.S., Sundararaja Lokesh, K., Biligere Siddaiah, J., Ganguly, K., Anand, M.P.(2018). Association of Elevated Serum GM-CSF, IFN- γ, IL-4, and TNF- α Concentration with Tobacco Smoke Induced Chronic Obstructive Pulmonary Disease in a South Indian Population . International Journal of Inflammation. 2018.

Mitra, A., Vishweswaraiah, S., Thimraj, T.A., Maheswarappa, M., Krishnarao, C.S., Sundararaja Lokesh, K., Biligere Siddaiah, J., Ganguly, K., Anand, M.P.(2018). Association of Elevated Serum GM-CSF, IFN- γ, IL-4, and TNF- α Concentration with Tobacco Smoke Induced Chronic Obstructive Pulmonary Disease in a South Indian Population . International Journal of Inflammation. 2018.

Vishweswaraiah, S., Thimraj, T.A., George, L., Krishnarao, C.S., Lokesh, K.S., Siddaiah, J.B., Larsson, K., Upadhyay, S., Palmberg, L., Anand, M.P., et al.(2018). Putative systemic biomarkers of biomass smoke-induced chronic obstructive pulmonary disease among women in a rural South Indian population . Disease Markers. 2018.

Vishweswaraiah, S., Thimraj, T.A., George, L., Krishnarao, C.S., Lokesh, K.S., Siddaiah, J.B., Larsson, K., Upadhyay, S., Palmberg, L., Anand, M.P., et al.(2018). Putative systemic biomarkers of biomass smoke-induced chronic obstructive pulmonary disease among women in a rural South Indian population . Disease Markers. 2018.

(2017). Transcriptomic analysis comparing mouse strains with extreme total lung capacities identifies novel candidate genes for pulmonary function . Respiratory research.

(2017). Homeobox, Wnt, and Fibroblast Growth Factor Signaling is Augmented During Alveogenesis in Mice Lacking Superoxide Dismutase 3, Extracellular . Lung.

Thimraj, T.A., Birru, R.L., Mitra, A., Schulz, H., Leikauf, G.D., Ganguly, K.(2017). Homeobox, Wnt, and Fibroblast Growth Factor Signaling is Augmented During Alveogenesis in Mice Lacking Superoxide Dismutase 3, Extracellular . Lung. 195. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 263-270.

Thimraj, T.A., Birru, R.L., Mitra, A., Schulz, H., Leikauf, G.D., Ganguly, K.(2017). Homeobox, Wnt, and Fibroblast Growth Factor Signaling is Augmented During Alveogenesis in Mice Lacking Superoxide Dismutase 3, Extracellular . Lung. 195. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 263-270.

George, L., Mitra, A., Thimraj, T.A., Irmler, M., Vishweswaraiah, S., Lunding, L., H&#252;hn, D., Madurga, A., Beckers, J., Fehrenbach, H., et al.(2017). Transcriptomic analysis comparing mouse strains with extreme total lung capacities identifies novel candidate genes for pulmonary function . Respiratory Research. 18. (1).

George, L., Mitra, A., Thimraj, T.A., Irmler, M., Vishweswaraiah, S., Lunding, L., H&#252;hn, D., Madurga, A., Beckers, J., Fehrenbach, H., et al.(2017). Transcriptomic analysis comparing mouse strains with extreme total lung capacities identifies novel candidate genes for pulmonary function . Respiratory Research. 18. (1).

(2014). Secreted phosphoprotein 1 is a determinant of lung function development in mice . American journal of respiratory cell and molecular biology.

Ganguly, K., Martin, T.M., Concel, V.J., Upadhyay, S., Bein, K., Brant, K.A., George, L., Mitra, A., Thimraj, T.A., Fabisiak, J.P., et al.(2014). Secreted phosphoprotein 1 is a determinant of lung function development in mice . American Journal of Respiratory Cell and Molecular Biology. 51. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 637-651.

Ganguly, K., Martin, T.M., Concel, V.J., Upadhyay, S., Bein, K., Brant, K.A., George, L., Mitra, A., Thimraj, T.A., Fabisiak, J.P., et al.(2014). Secreted phosphoprotein 1 is a determinant of lung function development in mice . American Journal of Respiratory Cell and Molecular Biology. 51. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 637-651.

OTHER

Leko, I.M., Schrode, N., Torres, J., Pezet, M., Thimraj, T.A., Beaumont, K.G., Snoeck, H.-W.(2023). Generation and expansion of transitional lung organoids from human pluripotent stem cells . bioRxiv.

Leko, I.M., Schrode, N., Torres, J., Pezet, M., Thimraj, T.A., Beaumont, K.G., Snoeck, H.-W.(2023). Generation and expansion of transitional lung organoids from human pluripotent stem cells . bioRxiv.

BOOK CHAPTER

Thimraj, T.A., George, L., Asrafuzzaman, S., Upadhyay, S., Ganguly, K.(2017). Oxidative signaling in chronic obstructive airway diseases . Immunity and Inflammation in Health and Disease: Emerging Roles of Nutraceuticals and Functional Foods in Immune Support. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 79-98.

Thimraj, T.A., George, L., Asrafuzzaman, S., Upadhyay, S., Ganguly, K.(2017). Oxidative signaling in chronic obstructive airway diseases . Immunity and Inflammation in Health and Disease: Emerging Roles of Nutraceuticals and Functional Foods in Immune Support. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 79-98.