Research output per year
Research output per year
Personal profile
Artistic and research interests
I work on computational biology and probabilistic machine learning with applications in biomedicine.
Keywords
- Computational biology
- Machine learning
- Deep generative models
- Bioinformatics
- Artificial intelligence
- Probabilistic modelling
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Recent external collaboration on country level. Dive into details by clicking on the dots or
Research output
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Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis
Plichta, D. R., Somani, J., Pichaud, M., Wallace, Z. S., Fernandes, A. D., Perugino, C. A., Lähdesmäki, H., Stone, J. H., Vlamakis, H., Chung, D. C., Khanna, D., Pillai, S. & Xavier, R. J., Dec 2021, In: GENOME MEDICINE. 13, 1, 14 p., 35.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
lgpr: an interpretable non-parametric method for inferring covariate effects from longitudinal data
Timonen, J., Mannerström, H., Vehtari, A. & Lähdesmäki, H., 21 Jan 2021, (E-pub ahead of print) In: Bioinformatics.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access -
Predicting recognition between T cell receptors and epitopes with TCRGP
Jokinen, E., Huuhtanen, J., Mustjoki, S., Heinonen, M. & Lähdesmäki, H., 1 Mar 2021, In: PLoS computational biology. 17, 3, p. 1-27 27 p., e1008814.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia
Lundgren, S., Keränen, M. A. I., Kankainen, M., Huuhtanen, J., Walldin, G., Kerr, C. M., Clemente, M., Ebeling, F., Rajala, H., Brück, O., Lähdesmäki, H., Hannula, S., Hannunen, T., Ellonen, P., Young, N. S., Ogawa, S., Maciejewski, J. P., Hellström-Lindberg, E. & Mustjoki, S., 2021, (E-pub ahead of print) In: Leukemia.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access -
Adult-Onset Anti-Citrullinated Peptide Antibody-Negative Destructive Rheumatoid Arthritis Is Characterized by a Disease-Specific CD8+ T Lymphocyte Signature
Kelkka, T., Savola, P., Bhattacharya, D., Huuhtanen, J., Lönnberg, T., Kankainen, M., Paalanen, K., Tyster, M., Lepistö, M., Ellonen, P., Smolander, J., Eldfors, S., Yadav, B., Khan, S., Koivuniemi, R., Sjöwall, C., Elo, L. L., Lähdesmäki, H., Maeda, Y., Nishikawa, H. & 3 others, , 19 Nov 2020, In: FRONTIERS IN IMMUNOLOGY. 11, 12 p., 578848.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile
Projects
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Immunoregulation and Therapeutic Precision in Rheumatoid Arthritis
01/01/2021 → 31/12/2022
Project: Academy of Finland: Other research funding
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Bridging the Reality Gap in Autonomous Learning
Lähdesmäki, H. & Iakovlev, V.
01/01/2020 → 31/12/2022
Project: Academy of Finland: Other research funding
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FCAI: Finnish Center for Artificial Intelligence (FCAI)
01/01/2019 → 31/12/2022
Project: Academy of Finland: Other research funding
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Quantifying molecular networks at single-cell level
Lähdesmäki, H., Intosalmi, J., Somani, J., Gadd, C., Lankinen, A., Osmala, M., Iakovlev, V., Dumitrescu, A., Laajala, E. & Halla-aho, V.
01/09/2017 → 31/08/2021
Project: Academy of Finland: Other research funding
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FGCI: Finnish Grid and Cloud Infrastructure Stage 2 : enabling data sciences
01/01/2018 → 31/12/2019
Project: Academy of Finland: Other research funding
Datasets
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Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data
Intosalmi, J. (Contributor), Ahlfors, H. (Contributor), Rautio, S. (Contributor), Mannerström, H. (Creator), Chen, Z. (Contributor), Lahesmaa, R. (Contributor), Stockinger, B. (Contributor) & Lähdesmäki, H. (Contributor), 1 Jan 2015
DOI: 10.6084/m9.figshare.c.3612158.v1, https://figshare.com/collections/Analyzing_Th17_cell_differentiation_dynamics_using_a_novel_integrative_modeling_framework_for_time-course_RNA_sequencing_data/3612158/1
Dataset
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A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways
Äijö, T. (Contributor), Huang, Y. (Contributor), Mannerström, H. (Contributor), Chavez, L. (Contributor), Tsagaratou, A. (Contributor), Rao, A. (Contributor) & Lähdesmäki, H. (Contributor), 1 Jan 2016
DOI: 10.6084/m9.figshare.c.3604346.v1, https://figshare.com/collections/A_probabilistic_generative_model_for_quantification_of_DNA_modifications_enables_analysis_of_demethylation_pathways/3604346/1
Dataset
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Identification of global regulators of T-helper cell lineage specification
Kanduri, K. (Contributor), Tripathi, S. (Contributor), Larjo, A. (Contributor), Mannerström, H. (Contributor), Ullah, U. (Contributor), Lund, R. (Contributor), Hawkins, D. (Contributor), Ren, B. (Contributor), Lähdesmäki, H. (Contributor) & Lahesmaa, R. (Contributor), 1 Jan 2015
DOI: 10.6084/m9.figshare.c.3642353.v1, https://figshare.com/collections/Identification_of_global_regulators_of_T-helper_cell_lineage_specification/3642353/1
Dataset
Prizes
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Elias Tillandz prize 2012 for article
Lähdesmäki, Harri (Recipient), 2012
Prize: Award or honor granted for a specific work
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Elias Tillandz prize 2013 for article
Lähdesmäki, Harri (Recipient), 2013
Prize: Award or honor granted for a specific work
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IARIA Best Paper Award for our paper
Lähdesmäki, Harri (Recipient), 2008
Prize: Award or honor granted for a specific work
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Tampere Science Foundation award for the best doctoral thesis
Lähdesmäki, Harri (Recipient), 2005
Prize: Award or honor granted for a specific work
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The first position in the 5th Dialogue for Reverse Engineering Assessments and Methods (DREAM)
Lähdesmäki, Harri (Recipient), 16 Nov 2010
Prize: Award or honor granted for a specific work
Activities
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Faster Bayesian inference in Joint Species Distribution Models
Gleb Tikhonov (Speaker), Jarno Vanhatalo (Contributor), Otso Ovaskainen (Contributor) & Harri Lähdesmäki (Contributor)
22 Jun 2020 → 26 Jun 2020Activity: Talk or presentation types › Conference presentation
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Foreign Organisation
Harri Lähdesmäki (Visiting researcher)
17 May 2016Activity: Visiting an external institution types › Visit abroad
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Foreign Organisation
Harri Lähdesmäki (Visiting researcher)
18 May 2016Activity: Visiting an external institution types › Visit abroad
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Evaluator of a docent application, at University of Helsinki
Harri Lähdesmäki (Examiner)
2016Activity: Examination types › Statement of assessment of docentship
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International Workshop on Machine Learning in Systems Biology
Harri Lähdesmäki (Member)
3 Sep 2016 → 4 Sep 2016Activity: Participating in or organising an event types › Membership of an organizing committee or other positions of trust of a conference or a seminar
Press / Media
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Suomalaistutkijoiden kehittämä tekoäly ennustaa, mikä puolustusjärjestelmän avain sopii koronaviruksen lukkoihin
Emmi Jokinen & Harri Lähdesmäki
22/04/2021
1 item of Media coverage
Press/Media: Media appearance
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Suomalaistutkijat kehittivät tekoälyn auttamaan koronataistelussa – ”Malli on sovellettavissa periaatteessa kaikkia kohtaamiamme taudinaiheuttajia vastaan”
Emmi Jokinen & Harri Lähdesmäki
22/04/2021
1 item of Media coverage
Press/Media: Media appearance
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Biologisten mekanismien alkulähteillä
16/05/2019
1 item of Media coverage
Press/Media: Media appearance