Výsledky vyhledávání - "Emmi Jokinen"

Akademický článek

Evolution and modulation of antigen-specific T cell responses in melanoma patients

Autor: Jani Huuhtanen, Liang Chen, Emmi Jokinen, Henna Kasanen, Tapio Lönnberg, Anna Kreutzman, Katriina Peltola, Micaela Hernberg, Chunlin Wang, Cassian Yee, Harri Lähdesmäki, Mark M. Davis, Satu Mustjoki

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-14 (2022)

Previous studies have characterized the diversity and dynamics of the T cell receptor (TCR) repertoire in patients with solid cancer. Here, by analyzing TCR repertoire data from multiple datasets, the authors report that melanoma-associated antigen-s

Externí odkaz: https://doaj.org/article/768266209ecd42159605fd10e39aeab5

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Akademický článek

S176: FUNCTIONAL AND ANTIGEN-SPECIFIC CHARACTERIZATION OF IMMUNE CELLS AT THE SINGLE-CELL LEVEL REVEALS CONVERGENCE OF ADAPTIVE AND INNATE IMMUNITY IN IMMUNE APLASTIC ANEMIA

Publikováno v: HemaSphere, Vol 7, p e2285644 (2023)

Externí odkaz: https://doaj.org/article/e86b35d4b8084784b622157a832f1600

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Akademický článek

Single-cell characterization of anti–LAG-3 and anti–PD-1 combination treatment in patients with melanoma

Publikováno v: The Journal of Clinical Investigation, Vol 133, Iss 6 (2023)

Background Relatlimab plus nivolumab (anti–lymphocyte-activation gene 3 plus anti–programmed death 1 [anti–LAG-3+anti–PD-1]) has been approved by the FDA as a first-line therapy for stage III/IV melanoma, but its detailed effect on the immune

Externí odkaz: https://doaj.org/article/45e8a21ae8814471ba60e41684de20f1

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Akademický článek

Predicting recognition between T cell receptors and epitopes with TCRGP.

Autor: Emmi Jokinen, Jani Huuhtanen, Satu Mustjoki, Markus Heinonen, Harri Lähdesmäki

Publikováno v: PLoS Computational Biology, Vol 17, Iss 3, p e1008814 (2021)

Adaptive immune system uses T cell receptors (TCRs) to recognize pathogens and to consequently initiate immune responses. TCRs can be sequenced from individuals and methods analyzing the specificity of the TCRs can help us better understand individua

Externí odkaz: https://doaj.org/article/af10899f9cdf4d0d960986d9bf8992f8

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TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs

Autor: Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Vladimir Gligorijević, Satu Mustjoki, Richard Bonneau, Markus Heinonen, Harri Lähdesmäki

Motivation T cells use T cell receptors (TCRs) to recognize small parts of antigens, called epitopes, presented by major histocompatibility complexes. Once an epitope is recognized, an immune response is initiated and T cell activation and proliferat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0c9606ad564477c95a6bc6ab0cb219df
https://aaltodoc.aalto.fi/handle/123456789/119173

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TSignal: A transformer model for signal peptide prediction

Autor: Alexandru Dumitrescu, Emmi Jokinen, Juho Kellosalo, Ville Paavilainen, Harri Lähdesmäki

Signal peptides are short amino acid segments present at the N-terminus of newly synthesized proteins that facilitate protein translocation into the lumen of the endoplasmic reticulum, after which they are cleaved off. Specific regions of signal pept

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::c7ce3e48816a8c45f6477f186cc17e8a
https://doi.org/10.1101/2022.06.02.493958

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Predicting recognition between T cell receptors and epitopes using contextualized motifs

Autor: Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Vladimir Gligorijević, Satu Mustjoki, Richard Bonneau, Markus Heinonen, Harri Lähdesmäki

We introduce TCRconv, a deep learning model for predicting recognition between T-cell receptors and epitopes. TCRconv uses a deep protein language model and convolutions to extract contextualized motifs and provides state-of-the-art TCR-epitope predi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::3517d560a5c76793217e7125df3ae794
https://doi.org/10.1101/2022.05.23.493034

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Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods

Autor: Emmi Jokinen, Sanni Voutilainen, Markus Heinonen, Hannu Maaheimo, Anu Koivula, Martina Andberg, Juho Rousu, Juha Rouvinen, Merja Penttilä, Harri Lähdesmäki, Samuel Kaski, Johan Pääkkönen, Nina Hakulinen

Publikováno v: Applied Microbiology and Biotechnology
Voutilainen, S, Heinonen, M, Andberg, M, Jokinen, E, Maaheimo, H, Pääkkönen, J, Hakulinen, N, Rouvinen, J, Lähdesmäki, H, Kaski, S, Rousu, J, Penttilä, M & Koivula, A 2020, ' Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods ', Applied Microbiology and Biotechnology, vol. 104, no. 24, pp. 10515-10529 . https://doi.org/10.1007/s00253-020-10960-x
'Applied Microbiology and Biotechnology ', vol: 104, pages: 10515-10529 (2020)

Abstract In this work, deoxyribose-5-phosphate aldolase (Ec DERA, EC 4.1.2.4) from Escherichia coli was chosen as the protein engineering target for improving the substrate preference towards smaller, non-phosphorylated aldehyde donor substrates, in

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1df04bea6ee5917b68fa5f071bc2b647
https://doi.org/10.1007/s00253-020-10960-x

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mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion

Autor: Harri Lähdesmäki, Emmi Jokinen, Markus Heinonen

Publikováno v: Bioinformatics

Motivation Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins’ properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stabilit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::33761bcf72eb9848b2e31486e4cd41b0
https://doi.org/10.1093/bioinformatics/bty238

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Determining epitope specificity of T cell receptors with TCRGP

Autor: Jani Huuhtanen, Harri Lähdesmäki, Markus Heinonen, Emmi Jokinen, Satu Mustjoki

T cell receptors (TCRs) can recognize various pathogens and consequently start immune responses. TCRs can be sequenced from individuals and methods analyzing the specificity of the TCRs can help us better understand individuals’ immune status in di

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ecae14c45fe4ef15cec0b9ed81fe6cac
https://doi.org/10.1101/542332

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