Partho Sen - UTU Research Portal - UTU Research Portal

Partho Sen

Docent, Biokemia (Bioteknologian laitos)

Systems Medicine

partho.sen@utu.fi

ORCID identifier: https://orcid.org/0000-0003-0475-2763

ResearchGate

My personal website

Google Scholar profile

Areas of expertise

Machine Learning, Biomarker Discovery, R (Programming Language), Python (Programming Language), MATLAB, Snakemake, High Performance Computing (HPC), Computational Biology, Bioinformatics, Mathematical Modeling,
Statistical Modeling, Statistical Data Analysis, Metabolomics, Single Cell Sequencing, Functional Genomics, Transcriptomics, Metagenomics, NGS, Proteomics, Human Genetics.

Biography

Hi, I'M Partho Sen, and I'M a data scientist with 12 years of experience in computational biology and bioinformatics. I have expertise in analyzing complex datasets to understand how biochemical processes work in humans and microbes. My focus is on precision and systems medicine, where I research various health conditions like Diabetes, Non-Alcoholic Fatty Liver Disease (NAFLD), Obesity, and Cardiovascular disorders. My objective is to discover molecular markers that can help us comprehend the disease mechanism and underlying pathways. By understanding these mechanisms, we can create novel drugs or inhibitors and design new therapeutic strategies.

In addition to my mathematical modelling and data science skills, I am a proficient programmer with vast experience in machine learning, systems biology, and biomarker discovery in healthcare. I'm passionate about utilizing large datasets to create innovative tools and methods that can address modern challenges in healthcare and cell/tissue biology.

With my expertise, I'm confident we can make significant breakthroughs in understanding and treating diseases that have yet to be solved.Hi, I'M Partho Sen, and I'M a data scientist with 12 years of experience in computational biology and bioinformatics. I have expertise in analyzing complex datasets to understand how biochemical processes work in humans and microbes. My focus is on precision and systems medicine, where I research various health conditions like Diabetes, Non-Alcoholic Fatty Liver Disease (NAFLD), Obesity, and Cardiovascular disorders. My objective is to discover molecular markers that can help us comprehend the disease mechanism and underlying pathways. By understanding these mechanisms, we can create novel drugs or inhibitors and design new therapeutic strategies. In addition to my mathematical modelling and data science skills, I am a proficient programmer with vast experience in machine learning, systems biology, and biomarker discovery in healthcare. I'm passionate about utilizing large datasets to create innovative tools and methods that can address modern challenges in healthcare and cell/tissue biology. With my expertise, I'm confident we can make significant breakthroughs in understanding and treating diseases that have yet to be solved.

Publications

1 of 2

Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine (2023)
- Computational and Structural Biotechnology Journal
Mathema Vivek Bhakta, Sen Partho, Lamichhane Santosh, Orešič Matej, Khoomrung Sakda
(Refereed review article in scientific journal (A2))
Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes (2022)
- Cell Reports Medicine
Lamichhane Santosh, Sen Partho, Dickens Alex M., Alves Marina Amaral, Härkönen Taina, Honkanen Jarno, Vatanen Tommi, Xavier Ramnik J., Hyötyläinen Tuulia, Knip Mikael, Oresic Matej
(Refereed journal article or data article (A1))
Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance (2022)
- JHEP Reports
Katherine Johnson, Peter J Leary, Olivier Govaere, Matthew J Barter, Sarah H Charlton, Simon J Cockell, Dina Tiniakos, Michalina Zatorska, Pierre Bedossa, M Julia Brosnan, Jeremy F Cobbold, Mattias Ekstedt, Guruprasad P Aithal, Karine Clément, Jörn M Schattenberg, Jerome Boursier, Vlad Ratziu, Elisabetta Bugianesi, Quentin M Anstee, Ann K Daly, on behalf of the
LITMUS Consortium Investigators,

James Clark, Heather J Cordell, Rebecca Darlay, Christopher P Day, Tim Hardy, Yang-Lin Liu, Fiona Oakley, Jeremy Palmer, Rachel Queen, Kristy Wonders, Patrick M Bossuyt, Adriaan G Holleboom, Hadi Zafarmand, Yasaman Vali, Jenny Lee, Karine Clement, Raluca Pais, Detlef Schuppan, Michael Allison, Sergio Rodriguez Cuenca, Vanessa Pellegrinelli, Michele Vacca, Antonio Vidal-Puig, Tuulia Hyötyläinen, Aidan McGlinchey, Matej Orešič, Partho Sen, Jose Mato, Óscar Millet, Jean-Francois Dufour, Stephen Harrison, Stefan Neubauer, Michael Pavlides, Ferenc Mozes, Salma Akhtar, Rajarshi Banerjee, Matt Kelly, Elizabeth Shumbayawonda, Andrea Dennis, Charlotte Erpicum, Manuel Romero-Gomez, Rocío Gallego-Durán, Isabel Fernández, Morten Karsdal, Diana Leeming, Mette Juul Fisker, Elisabeth Erhardtsen, Daniel Rasmussen, Per Qvist, Antonia Sinisi, Estelle Sandt, Maria Manuela Tonini, Maurizio Parola, Chiara Rosso, Fabio Marra, Amalia Gastaldelli, Sven Francque, Stergios Kechagias, Hannele Yki-Järvinen, Kimmo Porthan, Saskia van Mil, George Papatheodoridis, Helena Cortez-Pinto, Luca Valenti, Salvatore Petta, Luca Miele, Andreas Geier, Christian Trautwein, Paul Hockings, Phil Newsome, David Wenn, Cecília Maria Pereira Rodrigues, Rémy Hanf, Pierre Chaumat, Christian Rosenquist, Aldo Trylesinski, Pablo Ortiz, Kevin Duffin, Carla Yunis, Melissa Miller, Theresa Tuthill, Judith Ertle, Ramy Younes, Leigh Alexander, Rachel Ostroff, Mette Skalshøi Kjær, Lars Friis Mikkelsen, Clifford Brass, Lori Jennings, Maria-Magdalena Balp, Miljen Martic, Guido Hanauer, Sudha Shankar, Richard Torstenson, Céline Fournier, Richard Ehman, Michael Kalutkiewicz, Kay Pepin, Joel Myers, Diane Shevell, Gideon Ho, Henrik Landgren, Rob Myers, Lynda Doward, Diane Whalley, James Twiss
(Refereed journal article or data article (A1))
Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis (2022)
- Metabolomics
Caracho Ribeiro Henrique, Sen Partho, Dickens Alex, Santa Cruz Elisa Castañeda, Orešič Matej, Sussulini Alessandra
(Refereed journal article or data article (A1))
Quantitative modelling of human liver reveals dysregulation of glycosphingolipid pathways in nonalcoholic fatty liver disease (2022)
- iScience
Sen Partho, Govaere Olivier, Sinioja Tim, McGlinchey Aidan, Geng Dawei, Ratziu Vlad, Bugianesi Elisabetta, Schattenberg Jörn M, Vidal-Puig Antonio, Allison Michael, Cockell Simon, Daly Ann K, Hyötyläinen Tuulia, Anstee Quentin M, Orešič Matej
(Refereed journal article or data article (A1))
1‐deoxyceramides – key players in lipotoxicity and progression to type 2 diabetes? (2021)
- Acta Physiologica
Sen Partho, Hyötyläinen Tuulia, Orešič Matej
(Article or data-article in scientific journal (B1))
Association Between Circulating Lipids and Future Weight Gain in Individuals With an At-Risk Mental State and in First-Episode Psychosis (2021)
- Schizophrenia Bulletin
Lamichhane Santosh, Dickens Alex M, Sen Partho, Laurikainen Heikki, Borgan Faith, Suvisaari Jaana, Hyötyläinen Tuulia, Howes Oliver, Hietala Jarmo, Orešič Matej
(Refereed journal article or data article (A1))
Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species (2021)
- Scientific Reports
Petersen Anders Ø, Julienne Hanna, Hyötyläinen Tuulia, Sen Partho, Fan Yong, Krogh Pedersen Helle, Jäntti Sirkku, Hansen Tue H., Nielsen Trine, Jørgensen Torben, Hansen Torben, Myers Pernille Neve, Nielsen H. Bjørn, Ehrlich S. Dusko, Orešič Matej, Pedersen Oluf
(Refereed journal article or data article (A1))
Exposure to environmental contaminants is associated with altered hepatic lipid metabolism in non-alcoholic fatty liver disease (2021)
- Journal of Hepatology
Sen Partho, Qadri Sami, Luukkonen Panu K, Ragnarsdottir Oddny, McGlincheyAidan , Jäntti Sirkku, Juuti Anne, Arola Johanna, Schlezinger Jennifer J, Webster Thomas F, Orešič Matej, Yki-Järvinen Hannele, Hyötyläinen Tuulia
(Refereed journal article or data article (A1))
Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations (2021)
- Metabolites
Lamichhane Santosh, Sen Partho, Amaral Alves Marina, Ribeiro Henrique C, Raunioniemi Peppi, Hyötyläinen Tuulia, Orešič Matej
(Refereed review article in scientific journal (A2))
Quantitative genome-scale metabolic modeling of human CD4+ T cell differentiation reveals subset-specific regulation of glycosphingolipid pathways (2021)
- Cell Reports
Partho Sen, Syed Bilal Ahmad Andrabi, Tanja Buchacher, Mohd Moin Khan, Ubaid Ullah Kalim, Tuomas Mikael Lindeman, Marina Amaral Alves, Victoria Hinkkanen, Esko Kemppainen, Alex M Dickens, Omid Rasool, Tuulia Hyötyläinen, Riitta Lahesmaa, Matej Orešič
(Refereed journal article or data article (A1))
Deep learning meets metabolomics: a methodological perspective (2020)
- Briefings in Bioinformatics
Partho Sen, Santosh Lamichhane, Vivek B Mathema, Aidan McGlinchey, Alex M Dickens, Sakda Khoomrung, Matej Orešič
(Refereed review article in scientific journal (A2))
Dysregulated lipid metabolism precedes onset of psychosis (2020)
- Biological Psychiatry
Alex M Dickens, Partho Sen, Matthew J Kempton, Neus Barrantes-Vidal, Conrad Iyegbe, Merete Nordentoft, Thomas Pollak, Anita Riecher-Rössler, Stephan Ruhrmann, Gabriele Sachs, Rodrigo Bressan, Marie-Odile Krebs, G Paul Amminger, Lieuwe de Haan, Mark van der Gaag, Lucia Valmaggia, Tuulia Hyötyläinen, Matej Orešič, Philip McGuire
(Refereed journal article or data article (A1))
Early-life exposure to perfluorinated alkyl substances modulates lipid metabolism in progression to celiac disease (2020)
- Environmental Research
Lisanna Sinisalu, Partho Sen, Samira Salihovic, Suvi Virtanen, Heikki Hyoty, Jorma Ilonen, Jorma Toppari, Riitta Veijola, Matej Oresic, Mikael Knip, Tuulia Hyotylainen
(Refereed journal article or data article (A1))
Metabolic alterations in immune cells associate with progression to type 1 diabetes (2020)
- Diabetologia
Partho Sen, Alex M. Dickens, María Asunción López-Bascón, Tuomas Lindeman, Esko Kemppainen, Santosh Lamichhane, Tuukka Rönkkö, Jorma Ilonen, Jorma Toppari, Riitta Veijola, Heikki Hyöty, Tuulia Hyötyläinen, Mikael Knip, Matej Orešič
(Refereed journal article or data article (A1))
Prenatal exposure to perfluoroalkyl substances modulates neonatal serum phospholipids, increasing risk of type 1 diabetes (2020)
- Environment International
Aidan McGlinchey, Tim Sinioja, Santosh Lamichhane, Partho Sen, Johanna Bodin, Heli Siljander, Alex M Dickens, Dawei Geng, Cecilia Carlsson, Daniel Duberg, Jorma Ilonen, Suvi M Virtanen, Hubert Dirven, Hanne F Bentsen, Karin Zimmer, Unni C Nygaard, Matej Oresic, Mikael Knip, Tuulia Hyotylainen
(Refereed journal article or data article (A1))
Systems biology approaches to study lipidomes in health and disease (2020)
- Biochimica et Biophysica Acta Molecular and Cell Biology of Lipids
Marina Amaral Alves, Santosh Lamichhane, Alex Dickens, Aidan McGlinchey, Henrique C Ribeiro, Partho Sen, Fang Wei, Tuulia Hyötyläinen, Matej Orešič
(Refereed review article in scientific journal (A2))
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview (2019)
- Metabolites
Partho Sen, Matej Orešič
(Refereed review article in scientific journal (A2))
Metabolic profiling and compound-class identification reveal alterations in serum triglyceride levels in mice immunized with human vaccine adjuvant Alum (2019) Sakda Khoomrung, Intawat Nookaew, Partho Sen, Thorunn A Olafsdottir, Josefine Persson, Thomas Moritz, Peter Andersen, Ali M Harandi, Jens Nielsen
(Refereed journal article or data article (A1))
Persistent Alterations in Plasma Lipid Profiles Before Introduction of Gluten in the Diet Associated With Progression to Celiac Disease (2019)
- Clinical and Translational Gastroenterology
Sen P, Carlsson C, Virtanen SM, Simell S, Hyöty H, Ilonen J, Toppari J, Veijola R, Hyötyläinen T, Knip M, Orešič M
(Refereed journal article or data article (A1))