20082020

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

2020

A personalised approach for identifying disease-relevant pathways in heterogeneous diseases

Somani, J., Ramchandran, S. & Lähdesmäki, H., 1 Dec 2020, In : npj Systems Biology and Applications. 6, 1, 17.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
1 Downloads (Pure)
2019

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.). 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

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

Open Access
File
3 Citations (Scopus)
138 Downloads (Pure)

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

Open Access
File
83 Downloads (Pure)

Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies

Intosalmi, J., Scott, A. C., Hays, M., Flann, N., Yli-Harja, O., Lähdesmäki, H., Dudley, A. M. & Skupin, A., 19 Dec 2019, In : BMC Molecular and Cell Biology. 20, 1, 59.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
24 Downloads (Pure)

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

Open Access
File
27 Downloads (Pure)

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., Peet, A., Tillmann, V., Chandra, V., Anagandula, M. K., Frisk, G., Otonkoski, T., Rasool, O., Lund, R., Lähdesmäki, H., Knip, M. & 1 others, Lahesmaa, R., 1 Oct 2019, In : DIABETES. 68, 10, p. 2024-2034 11 p.

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)

Enhancer prediction in the human genome by probabilistic modeling of the chromatin feature patterns

Osmala, M. & Lähdesmäki, H., 17 Oct 2019, (Submitted) In : Springer.

Research output: Contribution to journalArticleScientificpeer-review

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., Haiser, H. J., Kolde, R., Yassour, M., Luopajärvi, K., Siljander, H., Virtanen, S. M., Ilonen, J., Uibo, R., Tillmann, V., Mokurov, S. & 8 others, Dorshakova, N., Porter, J. A., McHardy, A. C., Lähdesmäki, H., Vlamakis, H., Huttenhower, C., Knip, M. & Xavier, R. J., 1 Mar 2019, In : Nature Microbiology. 4, 3, p. 470-479

Research output: Contribution to journalArticleScientificpeer-review

19 Citations (Scopus)

ODE2VAE: Deep generative second order ODEs with Bayesian neural networks

Yildiz, C., Heinonen, M. & Lähdesmäki, H., 2019, 33rd Conference on Neural Information Processing Systems: NeurIPS 2019 . Neural Information Processing Systems Foundation, (Advances in Neural Information Processing Systems).

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

Open Access

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., 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

Open Access
File
35 Downloads (Pure)
2018

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

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., Lähdesmäki, H., Lahesmaa, R. & Jartti, T., 5 May 2018, In : Allergy. 73, 8, p. 1735-1740 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
12 Citations (Scopus)
128 Downloads (Pure)

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., Lähdesmäki, H. & Lahesmaa, R., 1 Dec 2018, In : Scientific Reports. 8, 1, p. 1-13 5883.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
3 Citations (Scopus)
133 Downloads (Pure)

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

1 Citation (Scopus)

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

3 Citations (Scopus)

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

Open Access
File
1 Citation (Scopus)
18 Downloads (Pure)

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

Open Access
File
6 Citations (Scopus)
67 Downloads (Pure)

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., Lähdesmäki, H. & Chen, Z., 31 May 2018, In : PLoS Biology. 16, 5, e2004194.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
3 Citations (Scopus)
127 Downloads (Pure)

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

Open Access
File
60 Downloads (Pure)

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., 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. & 2 others, Huttenhower, C. & Xavier, R. J., 25 Oct 2018, In : Nature. 562, 7728, p. 589-594 6 p.

Research output: Contribution to journalLetterScientificpeer-review

Open Access
File
104 Citations (Scopus)
415 Downloads (Pure)

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., 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

Open Access
File
6 Citations (Scopus)
172 Downloads (Pure)

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., 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

Open Access
File
12 Citations (Scopus)
128 Downloads (Pure)
2017

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., 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

Efficient statistical methods for detecting differential methylation

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

Research output: Contribution to conferencePaperScientific

File
17 Downloads (Pure)

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., 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

Open Access
File
18 Citations (Scopus)
143 Downloads (Pure)

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., 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

Open Access
File
2 Citations (Scopus)
94 Downloads (Pure)

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

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

43 Citations (Scopus)
2016

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

Open Access
File
11 Citations (Scopus)
170 Downloads (Pure)

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

2 Citations (Scopus)

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., 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

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., 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

11 Citations (Scopus)

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., Lähdesmäki, H. & Rao, A., 2016, In : JOURNAL OF EXPERIMENTAL MEDICINE. 213, 3, p. 377-397 21 p.

Research output: Contribution to journalArticleScientificpeer-review

115 Citations (Scopus)

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

4 Citations (Scopus)

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., 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

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., 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

Open Access
File
11 Citations (Scopus)
120 Downloads (Pure)

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

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

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

6 Citations (Scopus)

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

Open Access
File
9 Citations (Scopus)
321 Downloads (Pure)

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

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

Open Access
File
3 Citations (Scopus)
50 Downloads (Pure)

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

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

Open Access
File
15 Citations (Scopus)
144 Downloads (Pure)

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

15 Citations (Scopus)

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., Peet, A., Tillmann, V., Uibo, R., Mokurov, S., Dorshakova, N., Ilonen, J., Virtanen, S. M., Szabo, S. J., Porter, J. A., Lähdesmäki, H. & 5 others, 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

364 Citations (Scopus)
2015

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

5 Citations (Scopus)

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