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.
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
Keywords
- Computational biology
- Machine learning
- Deep generative models
- Bioinformatics
- Artificial intelligence
- Probabilistic modelling
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Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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LuxHMM : DNA methylation analysis with genome segmentation via hidden Markov model
Malonzo, M. H. & Lähdesmäki, H., Dec 2023, In: BMC Bioinformatics. 24, 1, 58.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile4 Downloads (Pure) -
Single-cell characterization of anti-LAG-3 and anti-PD-1 combination treatment in patients with melanoma
Huuhtanen, J., Kasanen, H., Peltola, K., Lönnberg, T., Glumoff, V., Brück, O., Dufva, O., Peltonen, K., Vikkula, J., Jokinen, E., Ilander, M., Lee, M. H., Mäkelä, S., Nyakas, M., Li, B., Hernberg, M., Bono, P., Lähdesmäki, H., Kreutzman, A. & Mustjoki, S., 15 Mar 2023, In: JOURNAL OF CLINICAL INVESTIGATION. 133, 6, e164809.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile4 Downloads (Pure) -
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs
Jokinen, E., Dumitrescu, A., Huuhtanen, J., Gligorijevic, V., Mustjoki, S., Bonneau, R., Heinonen, M. & Lähdesmäki, H., 1 Jan 2023, In: Bioinformatics. 39, 1, 8 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile19 Downloads (Pure) -
A Variational Autoencoder for Heterogeneous Temporal and Longitudinal Data
Öǧretir, M., Ramchandran, S., Papatheodorou, D. & Lähdesmäki, H., 2022, Proceedings - 21st IEEE International Conference on Machine Learning and Applications, ICMLA 2022. Wani, M. A., Kantardzic, M., Palade, V., Neagu, D., Yang, L. & Chan, K-Y. (eds.). IEEE, p. 1522-1529 8 p.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review
Open AccessFile6 Downloads (Pure) -
ChromDMM: a Dirichlet-multinomial mixture model for clustering heterogeneous epigenetic data
Osmala, M., Eraslan, G. & Lähdesmäki, H., 15 Aug 2022, In: Bioinformatics. 38, 16, p. 3863-3870 8 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile11 Downloads (Pure)
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Heal-Art jatko/Lähdesmäki
Lähdesmäki, H., Halla-aho, V., Jokinen, E., Dumitrescu, A., Lankinen, A. & Osmala, M.
01/01/2021 → 31/12/2022
Project: Academy of Finland: Other research funding
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B-REAL/Lähdesmäki
Lähdesmäki, H., Jokinen, E., Korpela, D., Iakovlev, V., Laajala, E., Ögretir, M. & Timonen, J.
01/01/2020 → 31/12/2022
Project: Academy of Finland: Other research funding
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Heal-Art/Lähdesmäki
Lähdesmäki, H., Jokinen, E., Dumitrescu, A., Somani, J. & Osmala, M.
01/01/2018 → 31/12/2020
Project: Academy of Finland: Other research funding
Datasets
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Modeling binding specificities of transcription factor pairs with random forests
Antikainen, A. A. (Creator), Heinonen, M. (Creator) & Lähdesmäki, H. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.c.6031779.v1, https://springernature.figshare.com/collections/Modeling_binding_specificities_of_transcription_factor_pairs_with_random_forests/6031779/1 and 2 more links, https://doi.org/10.6084/m9.figshare.20003418.v1, https://doi.org/10.6084/m9.figshare.20003421.v1 (show fewer)
Dataset
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Probabilistic modeling methods for cell-free DNA methylation based cancer classification
Halla-aho, V. (Creator) & Lähdesmäki, H. (Contributor), figshare, 1 Jan 2022
DOI: 10.6084/m9.figshare.c.5931075.v1, https://springernature.figshare.com/collections/Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/5931075/1 and 4 more links, https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518510/1, https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518513/1, https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518516/1, https://springernature.figshare.com/articles/journal_contribution/Additional_file_1_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518507/1 (show fewer)
Dataset
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LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model
Malonzo, M. (Creator) & Lähdesmäki, H. (Creator), figshare, 13 Apr 2023
DOI: 10.6084/m9.figshare.c.6584741, https://springernature.figshare.com/collections/LuxHMM_DNA_methylation_analysis_with_genome_segmentation_via_hidden_Markov_model/6584741
Dataset
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Additional file 2 of LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model
Malonzo, M. (Creator) & Lähdesmäki, H. (Creator), figshare, 13 Apr 2023
DOI: 10.6084/m9.figshare.22610645.v1, https://springernature.figshare.com/articles/dataset/Additional_file_2_of_LuxHMM_DNA_methylation_analysis_with_genome_segmentation_via_hidden_Markov_model/22610645/1
Dataset
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Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples
Laajala, E. (Creator), Halla-aho, V. (Creator), Grönroos, T. (Creator), Kalim, U. U. (Creator), Vähä-Mäkilä, M. (Creator), Nurmio, M. (Creator), Kallionpää, H. (Creator), Lietzén, N. (Creator), Mykkänen, J. (Creator), Rasool, O. (Creator), Toppari, J. (Creator), University, M. (Creator), Knip, M. (Creator), Lund, R. (Creator), Lahesmaa, R. (Creator) & Lähdesmäki, H. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.19311109.v2, https://tandf.figshare.com/articles/dataset/Permutation-based_significance_analysis_reduces_the_type_1_error_rate_in_bisulfite_sequencing_data_analysis_of_human_umbilical_cord_blood_samples/19311109/1
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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Evaluator of a docent application, at University of Helsinki
Harri Lähdesmäki (Examiner)
2016Activity: Academic assessments › Statement of assessment of docentship
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Foreign Organisation
Harri Lähdesmäki (Visiting researcher)
17 May 2016Activity: Visiting an external institution types › Visiting an external academic institution
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School of Science (Organisational unit)
Harri Lähdesmäki (Member)
Mar 2016 → Jan 2017Activity: Memberships (typically long-term positions of trust) › Position of trust in an academic community
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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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Scientists unravel the effects of new medication for advanced melanoma with the help of AI
02/03/2023
2 items of Media coverage
Press/Media: Media appearance
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Levinneen melanooman hoitoon uusi lääke
Jani Huuhtanen & Harri Lähdesmäki
20/02/2023
1 item of Media coverage
Press/Media: Media appearance
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New medication for the treatment of advanced melanoma
Jani Huuhtanen & Harri Lähdesmäki
17/02/2023
1 item of Media coverage
Press/Media: Media appearance
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New medication for the treatment of advanced melanoma
17/02/2023
1 item of Media coverage
Press/Media: Media appearance
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Finnish firms seek better therapies
Jani Huuhtanen & Harri Lähdesmäki
03/11/2022
1 item of Media coverage
Press/Media: Media appearance