Partho Sen (PhD)

Data Scientist | Computational Biologist | Adjunct Professor | Precision Medicine

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About me

I've a 13-year background in computational biology and bioinformatics. My professional / research journey has been marked to unravel the intricacies of biochemical signatures and processes in humans and microbes.

Currently specializing in precision and systems medicine, my focus centers on multiple myeloma and other cancer types. By utilization of multiomics (genomics, transcriptomics, proteomics and metabolomics) and clinical datasets, I tend to delineate cellular signatures and pathways associated with cancer, contributing to the biomarker discovery, and thereby attributing towards the cancer treatment.

My prior research has delved into diverse health conditions, including Diabetes (Type 1 & 2), Non-Alcoholic Fatty Liver Disease (NAFLD), Obesity, and Cardiovascular disease (Atherosclerosis). The overarching objective of my work is to identify molecular markers that serve as key insights into disease mechanisms and underlying pathways. Thereby, aim to formulate innovative drugs, inhibitors, and therapeutic strategies.

In addition to my proficiency in mathematical, statistical modeling and data science, I am an accomplished computer programmer; well-versed in machine learning. My passion lies in harnessing large datasets to design tools and methods that address contemporary challenges in healthcare, as well as cell and tissue biology.

I am confident that with my expertise, we can achieve significant breakthroughs in understanding and treating diseases that have hitherto posed significant challenges.

Bio

Birthday
--
Email
partho.phd [@] gmail.com
Skype IM
--
Google Scholar
https://scholar.google.com
PubMed
https://pubmed.ncbi.nlm.nih.gov
Phone
--
Address
Mayo Clinic, 55902, Rochester, MINNESOTA (MN), USA

Programming Skills and Research Techniques

R
8 years
MATLAB
5 years
Python
2 years
HTML and PHP
1 year
MySQL and PostgreSQL
1 year
Bioinformatics: Next-Generation Sequencing (NGS)
Expert
Data science: Biological, Clinical and Multi-Omics data
Expert
Human disease marker/signature discovery & related pathways
Expert
Biostatistics and Mathematical modeling
Advance level
Machine Learning
Advance level

* Other soft and analytical skills are included in the CV *

Research and work experiences

Mayo Clinic, Rochester, Minnesota, USA
Department of Laboratory Medicine and Pathology
Aug, 2023 - pursuing
Data Science Analyst
German Heart Centre (Deutschen Herzzentrum München) - Technical University of Munich (TUM), Munich, Germany
Molecular Genetics of Atherosclerosis and Heart Attack
Sep, 2022 - Jul, 2023
Bioinformatics Scientist
University of Turku (Turun yliopisto), Turku, Finland
Department of Life Technologies, Faculty of Technology
Titled on June, 2022
Adjunct Professor/Docent in Computational Biology
Turku Bioscience - University of Turku, Turku, Finland
Systems Medicine
May, 2017 - Aug, 2022
Senior postdoctoral researcher
Örebro University, Örebro, Sweden
School of Medical Sciences, Systems Medicine
Oct, 2019 - Aug, 2022
Affiliated researcher
Chalmers University of Technology, Gothenburg, Sweden
Department of Biology and Biological Engineering
April, 2014 - 2017
Postdoctoral fellow
Jawaharlal Nehru University (JNU), New Delhi, India
School of Computational and Integrative Sciences (SCIS)
June, 2009 - June, 2010
Junior Research Fellow (JRF)

Education

Université of Montpellier 2, Montpellier, France
DIMNP-UMR 5235, Centre National de la recherche scientifique (CNRS)
Dec, 2010 - 2013
Doctor of Philosophy (PhD) in Biological Sciences (Systems Biology/Bioinformatics)
National Institute of Pharmaceutical Education and Research (N.I.P.E.R), Kolkata, India
June, 2007 - 2009
Master of Science in Pharmaceutical Sciences (M.S. Pharm) in Pharmacoinformatics
Roland Institute of Pharmaceutical Sciences (RIPS), Berhampur, Odisha, India
April, 2003 - 2007
Bachelor of Pharmacy (B.Pharm)

Publications

2024
  • Andrabi, SBA., Kalim, UU., Palani, S., Khan, MM., Khan, MH., Fagersund, J., Orpana, J., Paulin, N., Batkulwar, K., Junttila, S., Buchacher, T., Grönroos, T., Toikka, L., Ammunet, T., Sen, P. , Orešič, M., Kumpulainen, V., Tuomisto, JEE., Sinha, R., Marson, A., Rasool, O., Elo, LL., Lahesmaa, R. Long Noncoding RNA LIRIL2R Modulates FOXP3 Levels and Suppressive Function of Human CD4+ Regulatory T Cells by Regulating IL2RA. PNAS , 121(23), e2315363121. [html] [pdf]
  • Sen, P. , Fan, Y., Schlezinger, J., Ehrlich, S., Webster, T., Hyötyläinen, T., Pedersen, O., Orešič, M. Exposure to environmental toxicants is associated with gut microbiome dysbiosis, insulin resistance and obesity. Environ. Int. , 186, 108569. [html] [pdf]
  • Sen, P.* , Emese, P.*, Honkanen, J.K., Chen, O., Yolken, R., Jaana, S. Dysregulation of microbiota in first episode psychosis patients were associated with symptom severity and treatment response. Biol. Psychiatry. , 95(4):370-379. [html] [pdf]
2023
  • Scheidt, Wv., Reichart, B., Meiser, B., Scheidt, Mv., Sen, P. , Schwarz, F., Harmel, E., Bengel, FM., Dick, A., Ueberfuhr, P., Reichenspurner, H., Jaeckel, E., Schwinzer, R., Hagl, C. Unique 40-year survival after heart transplantation with normal graft function and spontaneous operational tolerance. Clin. Res. Cardiol. , 1-11. [html] [pdf]
  • Sabatini, S., Sen, P. , Carli, F., Samantha Pezzica, S., Rosso, C., Lembo, E., Verrastro, O., Daly, A., Govaere, O., Cockel, S., Hyötyläinen, T., Mingrone, G., Bugianesi, E., Orešič, M., Gastaldelli, A. Higher Hepatic Glucose Production and Gluconeogenesis are Features of Severe Metabolic Dysfunction-Associated Steatohepatitis Even in Absence of T2D. Sneak Peek. [preprint]
  • Lamichhane, S., Sen, P. , Dickens, AM., Kråkström, Jorma, M., Johanna Lempainen, J., Hyoty, H., Lahesmaa, R., Veijola, K., Toppari, J., Hyötyläinen, T., Knip, M., Orešič, M. Circulating metabolic signatures of rapid and slow progression to type 1 diabetes in islet autoantibody-positive children. Front Endocrinol. , 14, 1211015. [html] [pdf]
  • Sen, P. , Orešič, M. Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine. Metabolites. , 13,7,855. [html] [pdf]
  • Aatsinki, A.-K., Lamichhane, S. Isokääntä, H., Sen, P. , Kråkström, M., Alves, M. A., Keskitalo, A., Munukka, E., Karlsson, H., Perasto, L., Lukkarinen, M., Oresic, M., Kailanto, H.-M.; Karlsson, L., Lahti, L., Dickens, A. M. Dynamics of Gut Metabolome and Microbiome Maturation during Early Life. medRxiv. , 2023.05.29.23290441. [preprint]
  • Krefting, J., Sen, P. , David-Rus, D., Güldener, U., Hawe, J.S., Scheidt M.V., 2, Cassese, S., and Schunkert, H. Use of big data from health insurance for assessment of cardiovascular outcomes. Front. Artif. Intell. , 6. [html] [pdf]
  • Mathema, V., Sen, P. , Lamichhane, S., Khoomrung, S., Orešič, M. Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine. Computational and Structural Biotechnology Journal (CSBJ) , 21, 1372-1382. [html] [pdf]
2022
  • Lamichhane, S.*, Sen, P.* , Dickens, AM., Alves, MA., Härkönen, T., Honkanen, J., Vatanen, T., Xavier, RJ., Hyötyläinen, T., Knip, M., Orešič, M. Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes. Cell Rep Med. , 100762. [html] [pdf]
  • Sen, P. , Govaere, O., Sinioja, T., McGlinchey, A., Geng, D., Ratziu, V., Bugianesi, E., Schattenberg, JM., Vidal-Puig, A., Allison, M., Cockell, S., Daly, AK., Hyötyläinen, T., Anstee, QM., Oresic, M. Quantitative modelling of human liver reveals dysregulation of glycosphingolipid pathways in nonalcoholic fatty liver disease. iScience , 104949. [html] [pdf]
  • Ribeiro, HC., Sen, P. , P, Dickens, AM., Cruz, ECS., Oresic, M., Sussulini, A. Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis. Metabolomics , 18(8), 1-13. [html] [pdf]
  • Johnson, Katherine., Leary J, Peter., Govaere, Olivier., Barter J, Matthew., Charlton H, Sarah., Cockell, Simon., Tiniakos, Dina., et al. Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: diagnostic and mechanistic relevance. JHEP Reports. , 4(2), 100409. [html] [pdf]
  • Sen, P. , Qadri, S., Luukkonen, P.K., Ragnarsdottir, O., McGlinchey, A., Jantti, S., Juuti, A., Arola, J., Schlezinger, J.J., Webster, T.F., et al. Exposure to environmental contaminants is associated with altered hepatic lipid metabolism in non-alcoholic fatty liver disease. J Hepatol. , 76(2), 283-293. [html] [pdf]
2021
  • Sen, P. , Andrabi, S.B.A., Buchacher, T., Khan, M.M., Kalim, U.U., Lindeman, T.M., Alves, M.A., Hinkkanen, V., Kemppainen, E., Dickens, A.M., et al. Quantitative genome-scale metabolic modeling of human CD4+ T cell differentiation reveals subset-specific regulation of glycosphingolipid pathways. Cell Rep. , 37, 109973. [html] [pdf]
  • Petersen, A.O., Julienne, H., Hyotylainen, T., Sen, P. , Fan, Y., Pedersen, H.K., Jantti, S., Hansen, T.H., Nielsen, T., Jorgensen, T., et al. Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species. Sci Rep., 11, 13252. [html] [pdf]
  • Sen, P. , Hyotylainen, T., and Oresic, M. 1-deoxyceramides - key players in lipotoxicity and progression to type 2 diabetes? Acta Physiol., e13635. [html] [pdf]
  • Sen, P. , Lamichhane, S., Mathema, V.B., McGlinchey, A., Dickens, A.M., Khoomrung, S., and Oresic, M. Deep learning meets metabolomics: a methodological perspective. Brief Bioinform. 22, 1531-1542. [html] [pdf]
  • Alves, M.A., Lamichhane, S., Dickens, A., McGlinchey, A., Ribeiro, H.C., Sen, P. , Wei, F., Hyotylainen, T., and Oresic, M. Systems biology approaches to study lipidomes in health and disease. Biochim Biophys Acta Mol Cell Biol Lipids. , 1866, 158857. [html] [pdf]
  • Dickens, A.M.*, Sen, P. *, Kempton, M.J., Barrantes-Vidal, N., Iyegbe, C., Nordentoft, M., Pollak, T., Riecher-Rössler, A., Ruhrmann, S., Sachs, G., et al. Dysregulated Lipid Metabolism Precedes Onset of Psychosis. Biol Psychiatry. , 89, 288-297. [html] [pdf]
  • Lamichhane, S., Sen, P. , Alves, M.A., Ribeiro, H.C., Raunioniemi, P., Hyotylainen, T., and Oresic, M. Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations. Metabolites. , 11. [html] [pdf]
  • Lamichhane, S. ,* Sen, P. ,* Dickens, A.M., Amaral Alves, M., Karkonen, T., Honkanen, J., Vatanen, T., Xavier, R.J., Hyotylainen, T., Knip, M., et al. Dynamics of gut microbiome - mediated bile acid metabolism in progression to islet autoimmunity. medRxiv. , 2021.2008.2020.21262371. [preprint]
  • Sen, P. , Govaere, O., Sinioja, T., McGlinchey, A., Geng, D., Ratziu, V., Bugianesi, E., Schattenberg, J.M., Vidal-Puig, A., Allison, M., et al. Quantitative genome-scale analysis of human liver reveals dysregulation of glycosphingolipid pathways in progressive nonalcoholic fatty liver disease. medRxiv. , 2021.2002.2009.21251354. [preprint]
  • Lamichhane, S., Dickens, A.M., Sen, P. , Laurikainen, H., Borgan, F., Suvisaari, J., Hyötyläinen, T., Howes, O., Hietala, J., and Orešič, M. Association Between Circulating Lipids and Future Weight Gain in Individuals With an At-Risk Mental State and in First-Episode Psychosis. Schizophr Bull. , (47) 160–169 [html] [pdf]
2020
  • Sinisalu, L., Sen, P. , Salihović, S., Virtanen, S.M., Hyöty, H., Ilonen, J., Toppari, J., Veijola, R., Orešič, M., Knip, M., et al. (2020). Early-life exposure to perfluorinated alkyl substances modulates lipid metabolism in progression to celiac disease. Environ Res. , 188, 109864. [html] [pdf]
  • Sen, P. , Dickens, A.M., López-Bascón, M.A., Lindeman, T., Kemppainen, E., Lamichhane, S., Rönkkö, T., Ilonen, J., Toppari, J., Veijola, R., Hyöty, H., Hyötyläinen, T., Knip, M., Orešič, M. (2020). Metabolic alterations in immune cells associate with progression to type 1 diabetes. Diabetologia. 63, 1017-1031. [html] [pdf]
  • McGlinchey, A., Sinioja, T., Lamichhane, S., Sen, P. , Bodin, J., Siljander, H., Dickens, A.M., Geng, D., Carlsson, C., Duberg, D., et al. (2020). Prenatal exposure to perfluoroalkyl substances modulates neonatal serum phospholipids, increasing risk of type 1 diabetes. Environ Int. , 143, 105935. [html] [pdf]
  • Khoomrung, S., Nookaew, I., Sen, P. , Olafsdottir, T.A., Persson, J., Moritz, T., Andersen, P., Harandi, A.M., and Nielsen, J. (2020). Metabolic Profiling and Compound-Class Identification Reveal Alterations in Serum Triglyceride Levels in Mice Immunized with Human Vaccine Adjuvant Alum. J Proteome Res. , 19, 269-278. [html] [pdf]
2019
  • Sen, P. , and Orešič, M. (2019). Metabolic Modelling of Human Gut Microbiota on a Genome Scale: An Overview. Metabolites. , 9 [html] [pdf]
  • Sen, P. , Carlsson, C., Virtanen, S.M., Simell, S., Hyöty, H., Ilonen, J., Toppari, J., Veijola, R., Hyötyläinen, T., Knip, M., et al. (2019). Persistent Alterations in Plasma Lipid Profiles Before Introduction of Gluten in the Diet Associated With Progression to Celiac Disease. Clin Transl Gastroenterol. , 10, 1-10. [html] [pdf]
  • Sen, P. , Lamichhane, S., Dickens, A., and Oresic, M. (2019). The Role of Omic Technologies in the Study of the Human Gut Microbiome. Reference Module in Food Science. [html]
2018 - 2013
  • Lamichhane, S., Sen, P. , Dickens, A.M., Oresic, M., and Bertram, H.C. (2018). Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe. Methods. , 149, 3-12. [html] [pdf]
  • Sen, P. Kemppainen, E., and Orešič, M. (2017). Perspectives on Systems Modelling of Human Peripheral Blood Mononuclear Cells. Front Mol Biosci. 4, 96. [html] [pdf]
  • Sen, P. , Mardinogulu, A., and Nielsen, J. (2017). Selection of complementary foods based on optimal nutritional values. Sci Rep. , 7, 5413. [html] [pdf]
  • Thankaswamy-Kosalai, S.*, Sen, P. *, and Nookaew, I. (2017). Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics. Genomics. , 109, 186-191. [html] [pdf]
  • Vincent, A., Savolainen, O.I., Sen, P. , Carlsson, N.G., Almgren, A., Lindqvist, H., Lind, M.V., Undeland, I., Sandberg, A.S., and Ross, A.B. (2017). Herring and chicken/pork meals lead to differences in plasma levels of TCA intermediates and arginine metabolites in overweight and obese men and women. Mol Nutr Food Res. , 61. [html] [pdf]
  • Olafsdottir, T.A., Lindqvist, M., Nookaew, I., Andersen, P., Maertzdorf, J., Persson, J., Christensen, D., Zhang, Y., Anderson, J., Khoomrung, S., Sen, P. , et al. (2016). Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants. Sci Rep. , 6, 39097. [html] [pdf]
  • Sen, P. , Vial, H.J., and Radulescu, O. (2016). Mathematical modelling and omic data integration to understand dynamic adaptation of Apicomplexan parasites and identify pharmaceutical targets. Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery , 7, 457. [html] [pdf]
  • Shoaie, S., Ghaffari, P., Kovatcheva-Datchary, P., Mardinoglu, A., Sen, P. , Pujos-Guillot, E., de Wouters, T., Juste, C., Rizkalla, S., Chilloux, J., et al. (2015). Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. Cell Metab. , 22, 320-331. [html] [pdf]
  • Sen, P. , Vial, H.J., and Radulescu, O. (2013). Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways. BMC Syst Biol. , 7, 123. [html] [pdf]
PhD thesis
  • Sen, P. (2013). Integrated modelling of lipid metabolism in Plasmodium, the causative parasite of malaria (Université Montpellier II-Sciences et Techniques du Languedoc). [html] [pdf]

    *Signifies equal contributions

Conferences and meetings

  • 2023: EASL Congress 2023, Vienna, Austria (oral presentation)
  • 2023: DigiMed Bayern Retreat: Team Meeting 12, Munich, Germany
  • 2022: AISF monothematic conference - "Artificial Intelligence and liver diseases", Rome, Italy (oral presentation)
  • 2022: The 2nd Nordic Metabolomics Conference 2022, Copenhagen, Denmark (oral presentation)
  • 2022: 18th International Conference of the Metabolomics Society 2022, Valencia, Spain (oral presentation)
  • 2021: The International Liver Congress 2021, EASL, online (oral presentation)
  • 2021: 17th International Conference of the Metabolomics Society 2021 (online) (poster presentation)
  • 2020: EASD EGIR-NAFLD abstract meeting 2020 (oral presentation)
  • 2020: 16th International Conference of the Metabolomics Society 2020 (online) (oral presentation)
  • 2019: 15th International Conference of the Metabolomics Society 2019, The Hague, Netherlands (oral and poster presentation)
  • 2019: Metabolomics and Human Health, Gordon Research Conference, Ventura, CA, US (oral presentation)
  • 2019: Nordic Metabolomics Society meeting, Oslo, Norway (poster presentation)
  • 2018: Nordic Metabolomics Society meeting, Orebro, Sweden (oral and poster presentation)
  • 2016: BioVacSafe EU meeting, Lyon, France (poster presentation)
  • 2015: 4th Conference on Constraint-Based Reconstruction and Analysis (COBRA), Germany (poster)
  • 2015: Workshop on metabolic phenotyping in personalized health care, Imperial College London (poster)
  • 2015: Informatics Alignment Workshop, eTRICKS, Imperial College London
  • 2015: BioVacSafe EU meeting, Ghent, Belgium (poster presentation)
  • 2013: The Evimalar cluster 1-4 meeting, Créte, Greece (oral and poster presentation)
  • 2013: 9th Annual BioMalPar, EVIMalar conference, EMBL, Heidelberg, Germany (poster)
  • 2013: IT workshop on RNA-Seq, PlasmoDB, GeneDB, VectorBase, EMBL ATC, Heidelberg, Germany
  • 2012: Metabolomics workshop, University of Glasgow, UK
  • 2011: EVIMALAR cluster 4 meeting, Delft, Netherlands (poster presentation)

Editorial activities

  • 2022 - 2023: Guest editor at Life (ISSN 2075-1729), a MDPI journal: Co-edited a special issue entitled "Interactions between Microorganisms, Their Environment and Host". [weblink]

Academic achievements

  • 2019: Travel award from University of Turku for Gordon Research Conference, Ventura, CA, US
  • 2018: Travel award from Nordic Metabolomics society, Örebro, Sweden
  • 2016: Travel grants (3 times) from Kunt and Alice Wallenberg foundation, Gothenburg, Sweden.
  • 2012: Travel grant form University of Montpellier 2, France, to attend metabolomics workshop at University of Glasgow, UK.
  • 2010: Korean Government Fellowship Program (KGSP 2010), South Korea via Ministry of HRD, New-Delhi, India.
  • 2007: Fellowship from National Institute of Pharmaceutical Education and Research (NIPER) to pursue MS Pharm study. MS Pharm second best student (Parmacoinformatics, batch 2009).
  • 2007: Graduate aptitude test in engineering (GATE), Indian Institutes of Technology (IIT).

News

Open for submission!

Special Issue: Interactions between Microorganisms, Their Environment and Host

Happy to edit a Special Issue: "Interactions between Microorganisms, Their Environment and Host" for Life (ISSN 2075-1729), a MDPI journal, alongside Dr. Manish Kumar at USCD, California. For more info

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