Harri Lähdesmäki

Professor (Associate Professor)

Research outputs

  1. 2019
  2. Published

    Early detection of peripheral blood cell signature in children developing β-cell autoimmunity at a young age

    Kallionpää, H., Somani, J., Tuomela, S., Ullah, U., De Albuquerque, R., Lönnberg, T., Komsi, E., Siljander, H., Honkanen, J., Härkönen, T. & 11 others, Peet, A., Tillmann, V., Chandra, V., Anagandula, M. K., Frisk, G., Otonkoski, T., Rasool, O., Lund, R., Lähdesmäki, H., Knip, M. & Lahesmaa, R., 1 Oct 2019, In : DIABETES. 68, 10, p. 2024-2034 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Published

    Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease

    Konki, M., Malonzo, M., Karlsson, I. K., Lindgren, N., Ghimire, B., Smolander, J., Scheinin, N. M., Ollikainen, M., Laiho, A., Elo, L. L. & 7 others, Lonnberg, T., Roytta, M., Pedersen, N. L., Kaprio, J., Lahdesmaki, H., Rinne, J. O. & Lund, R. J., 2 Sep 2019, In : Clinical epigenetics. 11, 1, 12 p., 130.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Published

    Bayesian metabolic flux analysis reveals intracellular flux couplings

    Heinonen, M., Osmala, M., Mannerström, H., Wallenius, J., Kaski, S., Rousu, J. & Lähdesmäki, H., 15 Jul 2019, In : Bioinformatics. 35, 14, p. i548-i557 btz315.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Published

    An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data

    Cheng, L., Ramchandran, S., Vatanen, T., Lietzén, N., Lahesmaa, R., Vehtari, A. & Lähdesmäki, H., 17 Apr 2019, In : Nature Communications. 10, 1, p. 1-11 11 p., 1798.

    Research output: Contribution to journalArticleScientificpeer-review

  6. Published

    Deep learning with differential Gaussian process flows

    Hegde, P., Heinonen, M., Lähdesmäki, H. & Kaski, S., Apr 2019, The 22nd International Conference on Artificial Intelligence and Statistic. Vol. 89. p. 1-15 16 p. (Proceedings of Machine Learning Research; vol. 89).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  7. Published

    A Mathematical Model for Enhancer Activation Kinetics During Cell Differentiation

    Nousiainen, K., Intosalmi, J. & Lähdesmäki, H., 1 Jan 2019, Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings. Vega-Rodríguez, M. A., Holmes, I. & Martín-Vide, C. (eds.). Springer Verlag, p. 191-202 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11488 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  8. Accepted/In press

    ODE2VAE: Deep generative second order ODEs with Bayesian neural networks

    Yildiz, C., Heinonen, M. & Lähdesmäki, H., 2019, (Accepted/In press) NeurIPS.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  9. 2018
  10. Published

    Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

    Vatanen, T., Plichta, D. R., Somani, J., Münch, P. C., Arthur, T. D., Hall, A. B., Rudolf, S., Oakeley, E. J., Ke, X., Young, R. A. & 18 others, Haiser, H. J., Kolde, R., Yassour, M., Luopajärvi, K., Siljander, H., Virtanen, S. M., Ilonen, J., Uibo, R., Tillmann, V., Mokurov, S., Dorshakova, N., Porter, J. A., McHardy, A. C., Lähdesmäki, H., Vlamakis, H., Huttenhower, C., Knip, M. & Xavier, R. J., 17 Dec 2018, In : Nature Microbiology.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Published

    Characterization and non-parametric modeling of the developing serum proteome during infancy and early childhood

    Lietzén, N., Cheng, L., Moulder, R., Siljander, H., Laajala, E., Härkönen, T., Peet, A., Vehtari, A., Tillmann, V., Knip, M. & 2 others, Lähdesmäki, H. & Lahesmaa, R., 1 Dec 2018, In : Scientific Reports. 8, 1, p. 1-13 5883.

    Research output: Contribution to journalArticleScientificpeer-review

  12. Published

    snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions

    Nousiainen, K., Kanduri, K., Ricaño-Ponce, I., Wijmenga, C., Lahesmaa, R., Kumar, V. & Lähdesmäki, H., 1 Dec 2018, In : Bioinformatics (Oxford, England). 34, 23, p. 4112-4114 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Published

    The human gut microbiome in early-onset type 1 diabetes from the TEDDY study

    Vatanen, T., Franzosa, E. A., Schwager, R., Tripathi, S., Arthur, T. D., Vehik, K., Lernmark, Å., Hagopian, W. A., Rewers, M. J., She, J. X. & 12 others, Toppari, J., Ziegler, A. G., Akolkar, B., Krischer, J. P., Stewart, C. J., Ajami, N. J., Petrosino, J. F., Gevers, D., Lähdesmäki, H., Vlamakis, H., Huttenhower, C. & Xavier, R. J., 25 Oct 2018, In : Nature. 562, 7728, p. 589-594 6 p.

    Research output: Contribution to journalLetterScientificpeer-review

  14. Published

    MGPfusion: Predicting protein stability changes with Gaussian process kernel learning and data fusion

    Jokinen, E., Heinonen, M. & Lähdesmäki, H., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i274-i283

    Research output: Contribution to journalArticleScientificpeer-review

  15. Published

    Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells

    Mohammad, I., Nousiainen, K., Bhosale, S. D., Starskaia, I., Moulder, R., Rokka, A., Cheng, F., Mohanasundaram, P., Eriksson, J. E., Goodlett, D. R. & 2 others, Lähdesmäki, H. & Chen, Z., 31 May 2018, In : PLoS Biology. 16, 5, e2004194.

    Research output: Contribution to journalArticleScientificpeer-review

  16. Published

    Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

    Schmidt, A., Marabita, F., Kiani, N. A., Gross, C. C., Johansson, H. J., Éliás, S., Rautio, S., Eriksson, M., Fernandes, S. J., Silberberg, G. & 8 others, Ullah, U., Bhatia, U., Lähdesmäki, H., Lehtiö, J., Gomez-Cabrero, D., Wiendl, H., Lahesmaa, R. & Tegnér, J., 7 May 2018, In : BMC Biology. 16, 1, p. 1-35 47.

    Research output: Contribution to journalArticleScientificpeer-review

  17. Published

    Atopic asthma after rhinovirus-induced wheezing is associated with DNA methylation change in the SMAD3 gene promoter

    Lund, R. J., Osmala, M., Malonzo, M., Lukkarinen, M., Leino, A., Salmi, J., Vuorikoski, S., Turunen, R., Vuorinen, T., Akdis, C. & 3 others, Lähdesmäki, H., Lahesmaa, R. & Jartti, T., 5 May 2018, In : Allergy. 73, 8, p. 1735-1740 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  18. E-pub ahead of print
  19. Published

    Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells

    Ubaid Ullah, U., Andrabi, S. B. A., Tripathi, S. K., Dirasantha, O., Kanduri, K., Rautio, S., Gross, C. C., Lehtimäki, S., Bala, K., Tuomisto, J. & 7 others, Bhatia, U., Chakroborty, D., Elo, L. L., Lähdesmäki, H., Wiendl, H., Rasool, O. & Lahesmaa, R., 20 Feb 2018, In : Cell Reports. 22, 8, p. 2094-2106 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    Generative models for quantification of DNA modifications

    Äijö, T., Bonneau, R. & Lähdesmäki, H., 1 Jan 2018, Methods in Molecular Biology. p. 37-50 14 p. (Methods in Molecular Biology; vol. 1807).

    Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  21. Published

    A Nonparametric Spatio-temporal SDE Model

    Yildiz, C., Heinonen, M. & Lähdesmäki, H., 2018, NIPS 2018 Spatiotemporal Workshop: 32nd Conference on Neural Information Processing Systems (NIPS 2018), Montréal, Canada. Neural Information Processing Systems Foundation, p. 1-5

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

  22. Published

    Learning Stochastic Differential Equations With Gaussian Processes Without Gradient Matching

    Yildiz, C., Heinonen, M., Intosalmi, J., Mannerström, H. & Lähdesmäki, H., 2018, IEEE International Workshop on Machine Learning for Signal Processing. IEEE, 6 p. 8516991

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  23. Published

    Learning unknown ODE models with Gaussian processes

    Heinonen, M., Yildiz, C., Mannerström, H., Intosalmi, J. & Lähdesmäki, H., 2018, Proceedings of the 35th International Conference on Machine Learning, ICML 2018. Vol. 5. p. 3120-3132 13 p. (Proceedings of Machine Learning Research; vol. 80).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  24. 2017
  25. Published

    Efficient statistical methods for detecting differential methylation

    Halla-aho, V. & Lähdesmäki, H., 22 Jul 2017.

    Research output: Contribution to conferencePaperScientific

  26. Published

    Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation

    Tripathi, S. K., Chen, Z., Larjo, A., Kanduri, K., Nousiainen, K., Äijo, T., Ricaño-Ponce, I., Hrdlickova, B., Tuomela, S., Laajala, E. & 5 others, Salo, V., Kumar, V., Wijmenga, C., Lähdesmäki, H. & Lahesmaa, R., 30 May 2017, In : Cell Reports. 19, 9, p. 1888-1901 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

    RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells

    Lund, R. J., Rahkonen, N., Malonzo, M., Kauko, L., Emani, M. R., Kivinen, V., Närvä, E., Kemppainen, E., Laiho, A., Skottman, H. & 5 others, Hovatta, O., Rasool, O., Nykter, M., Lähdesmäki, H. & Lahesmaa, R., 9 May 2017, In : Stem Cell Reports. 8, 5, p. 1442-1454 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    Acquired Somatic Mutations in T Cells in Patients with Aplastic Anemia and Hypoplastic Myelodysplastic Syndromes

    Lundgren, S., Keränen, M., Nousiainen, K., Eldfors, S., Hannula, S., Hannunen, T., Ellonen, P., Walldin, G., Clemente, M., Ebeling, F. & 5 others, Rajala, H., Maciejewski, J. P., Lähdesmäki, H., Hellstrom-Lindberg, E. & Mustjoki, S., 2017, In : BLOOD. 130, Suppl 1, p. 1169-1169 1 p.

    Research output: Contribution to journalArticleScientificpeer-review

  29. Published

    TET2 and 3 proteins control iNKT cell lineage specification and TCR mediated expansion

    Tsagaratou, A., Avalos, E. G., Rautio, S., Browne, J. S., Togher, S., Pastor, W., Rothenberg, E. V., Lahdesmaki, H. & Rao, A., 2017, In : JOURNAL OF IMMUNOLOGY. 198, 1, Supplement, p. 215.11

    Research output: Contribution to journalArticleScientificpeer-review

  30. Published

    TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells

    Tsagaratou, A., González-Avalos, E., Rautio, S., Scott-Browne, J. P., Togher, S., Pastor, W. A., Rothenberg, E. V., Chavez, L., Lähdesmäki, H. & Rao, A., 2017, In : NATURE IMMUNOLOGY. 18, 1, p. 45-53

    Research output: Contribution to journalArticleScientificpeer-review

  31. 2016
  32. Published

    Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

    van Dijk, A. D. J., Lähdesmäki, H., de Ridder, D. & Rousu, J., 13 Dec 2016, In : BMC Bioinformatics. 17, Supplement 16, 2 p.

    Research output: Contribution to journalEditorialScientific

  33. Published

    Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

    van Dijk, A. D. J., Lähdesmäki, H., de Ridder, D. & Rousu, J., Dec 2016, In : BMC Bioinformatics. 17

    Research output: Contribution to journalSpecial issueScientificpeer-review

  34. Published

    A subpopulation model to analyze heterogeneous cell differentiation dynamics

    Chan, Y. H., Intosalmi, J., Rautio, S. & Lähdesmäki, H., 1 Nov 2016, In : Bioinformatics. 32, 21, p. 3306-3313 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

    Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells

    Rahkonen, N., Stubb, A., Malonzo, M., Edelman, S., Emani, M. R., Närvä, E., Lähdesmäki, H., Ruohola-Baker, H., Lahesmaa, R. & Lund, R., 1 Nov 2016, In : STEM CELL RESEARCH. 17, 3, p. 498-503 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  36. Published

    LuxGLM: A probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs

    Äijö, T., Yue, X., Rao, A. & Lähdesmäki, H., 1 Sep 2016, In : Bioinformatics. 32, 17, p. i511-i519

    Research output: Contribution to journalArticleScientificpeer-review

  37. Published

    Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks

    Intosalmi, J., Nousiainen, K., Ahlfors, H. & Lähdesmäki, H., 15 Jun 2016, In : Bioinformatics. 32, 12, p. 288-296

    Research output: Contribution to journalArticleScientificpeer-review

  38. Published

    Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

    Vatanen, T., Kostic, A. D., D'Hennezel, E., Siljander, H., Franzosa, E. A., Yassour, M., Kolde, R., Vlamakis, H., Arthur, T. D., Hämäläinen, A. M. & 15 others, Peet, A., Tillmann, V., Uibo, R., Mokurov, S., Dorshakova, N., Ilonen, J., Virtanen, S. M., Szabo, S. J., Porter, J. A., Lähdesmäki, H., Huttenhower, C., Gevers, D., Cullen, T. W., Knip, M. & Xavier, R. J., 5 May 2016, In : CELL. 165, 4, p. 842-853 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  39. Published

    Comparative analysis of human and mouse transcriptomes of Th17 cell priming

    Tuomela, S., Rautio, S., Ahlfors, H., Oling, V., Salo, V., Ullah, U., Chen, Z., Hämälistö, S., Tripathi, S., Äijö, T. & 6 others, Rasool, O., Soueidan, H., Wessels, L., Stockinger, B., Lähdesmäki, H. & Lahesmaa, R., May 2016, In : SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 83, 5, p. 380-380 1 p.

    Research output: Contribution to journalMeeting AbstractScientific

  40. Published

    Enterovirus-associated changes in plasma proteome of children with genetic susceptibility to type 1 diabetes

    Lietzen, N., Cheng, L., Oikarinen, S., Goo, Y. A., Goodlett, D., Toppari, J., Ilonen, J., Veijola, R., Knip, M., Lähdesmäki, H. & 2 others, Hyöty, H. & Lahesmaa, R., May 2016, In : SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 83, 5, p. 381-381 1 p.

    Research output: Contribution to journalMeeting AbstractScientificpeer-review

  41. Published

    Identification of global regulators of T-helper cell lineage specification

    Kanduri, K., Tripathi, S., Larjo, A., Mannerström, H., Ullah, U., Lund, R., Hawkins, R. D., Ren, B., Lähdesmäki, H. & Lahesmaa, R., May 2016, In : SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 83, 5, p. 379-379 1 p.

    Research output: Contribution to journalMeeting AbstractScientificpeer-review

  42. Published

    Comparative analysis of human and mouse transcriptomes of Th17 cell priming

    Tuomela, S., Rautio, S., Ahlfors, H., Öling, V., Salo, V., Ullah, U., Chen, Z., Hämälistö, S., Tripathi, S. K., Äijö, T. & 6 others, Rasool, O., Soueidan, H., Wessels, L., Stockinger, B., Lähdesmäki, H. & Lahesmaa, R., 22 Mar 2016, In : ONCOTARGET. 7, 12, p. 13416-13428 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways

    Äijö, T., Huang, Y., Mannerström, H., Chavez, L., Tsagaratou, A., Rao, A. & Lähdesmäki, H., 14 Mar 2016, In : GENOME BIOLOGY. 17, 1, p. 1-22 49.

    Research output: Contribution to journalArticleScientificpeer-review

  44. Published

    Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells

    Konki, M., Pasumarthy, K., Malonzo, M., Sainio, A., Valensisi, C., Söderström, M., Emani, M. R., Stubb, A., Närvä, E., Ghimire, B. & 6 others, Laiho, A., Järveläinen, H., Lahesmaa, R., Lähdesmäki, H., Hawkins, R. D. & Lund, R. J., 25 Feb 2016, In : Scientific Reports. 6, 22190.

    Research output: Contribution to journalArticleScientificpeer-review

  45. Published

    Synthetic transcription amplifier system for orthogonal control of gene expression in saccharomyces cerevisiae

    Rantasalo, A., Czeizler, E., Virtanen, R., Rousu, J., Lähdesmäki, H., Penttilä, M., Jäntti, J. & Mojzita, D., 1 Feb 2016, In : PloS one. 11, 2, p. 1-19 e0148320.

    Research output: Contribution to journalArticleScientificpeer-review

  46. Published

    The landscape of copy number variations in Finnish families with autism spectrum disorders

    Kanduri, C., Kantojärvi, K., Salo, P. M., Vanhala, R., Buck, G., Blancher, C., Lähdesmäki, H. & Järvelä, I., 1 Jan 2016, In : AUTISM RESEARCH. 9, 1, p. 9-16 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    Control of Foxp3 stability through modulation of TET activity

    Yue, X., Trifari, S., Äijö, T., Tsagaratou, A., Pastor, W. A., Zepeda-Martínez, J. A., Lio, C. W. J., Li, X., Huang, Y., Vijayanand, P. & 2 others, Lähdesmäki, H. & Rao, A., 2016, In : JOURNAL OF EXPERIMENTAL MEDICINE. 213, 3, p. 377-397 21 p.

    Research output: Contribution to journalArticleScientificpeer-review

  48. Published

    Generating data to improve protein stability prediction

    Heinonen, M., Jokinen, E., Kaski, S., Rousu, J. & Lähdesmäki, H., 2016, Patent No. Provisional US 62/361511

    Research output: Patent

  49. Published

    Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo

    Heinonen, M., Mannerström, H., Rousu, J., Kaski, S. & Lähdesmäki, H., 2016, Proceedings of the 19th International Conference on Artificial Intelligence and Statistics: JMLR: W&CP. JMLR, p. 732-740 9 p. ( JMLR: Workshop and Conference Proceedings; vol. 51).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  50. 2015
  51. Published

    MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis

    Rautio, S. & Lähdesmäki, H., 24 Dec 2015, In : BMC Bioinformatics.

    Research output: Contribution to journalArticleScientificpeer-review

  52. Published

    Self-organization and missing values in SOM and GTM

    Vatanen, T., Osmala, M., Raiko, T., Lagus, K., Sysi-Aho, M., Orešič, M., Honkela, T. & Lähdesmäki, H., 5 Jan 2015, In : Neurocomputing. 147, 1, p. 60-70 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  53. Published

    Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data

    Intosalmi, J., Ahlfors, H., Rautio, S., Mannerström, H., Chen, Z., Lahesmaa, R., Stockinger, B. & Lähdesmäki, H., 2015, In : BMC SYSTEMS BIOLOGY. 9, 81, 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  54. Published

    A probabilistic method for quantifying chromatin interactions

    Halla-Aho, V., Mannerström, H. & Lähdesmäki, H., 2015, Machine Learning in Computational Biology: A workshop at the Annual Conference on Neural Information Processing Systems (NIPS 2015) .

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

  55. Published

    BinDNase: A discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

    Kähärä, J. & Lähdesmäki, H., 2015, In : Bioinformatics. 31, 17, p. 2852-2859

    Research output: Contribution to journalArticleScientificpeer-review

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