Virus infections and immunity

Publications

Research output per year 2000 2001 2004 2006 2007 2008 2010 2011 2012 2013 2014 2015 2016 2017 2019 2020 2021 2023 2024 2025

• 184 Article
• 12 Chapter
• 11 Review Article
• 8 Conference contribution
• 5 More
  • 2 Letter
  • 1 Entry for encyclopedia / dictionary
  • 1 Comment/debate
  • 1 Doctoral Thesis

Research output per year

Research output per year

Search results

• 2025

  A customizable multiplex protein microarray for antibody testing and its application for tick-borne and other infectious diseases

  Krishnamurthy, H. K., Jayaraman, V., Krishna, K., Wang, T., Bei, K., Changalath, C., Matilda, S., Rai, A. J., Welc-Falęciak, R., Pawełczyk, A., Blanton, L. S., Chrdle, A., Fořtová, A., Růžek, D., Nasrallah, G. K., Abu-Raddadi, L. J., Al-Sadeq, D. W., Abdallah, M. A. A., Lilleri, D. & Fornara, C. & 10 others, D’Angelo, P., Furione, M., Söderlund-Venermo, M., Hedman, K., Chochlakis, D., Makridaki, E., Ntoula, A., Psaroulaki, A., Escárcega-Ávila, A. & Rajasekaran, J. J., 20 Jan 2025, In: Scientific Reports. 15, 1, 12 p., 2527.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Altered immune landscape of cervical lymph nodes reveals Epstein-Barr virus signature in multiple sclerosis

  Sarkkinen, J., Yohannes, D. A., Kreivi, N., Dürnsteiner, P., Elsakova, A., Huuhtanen, J., Nowlan, K., Kurdo, G., Linden, R., Saarela, M., Tienari, P. J., Kekäläinen, E., Perdomo, M. & Laakso, S. M., 21 Feb 2025, In: Science immunology. 10, 104, 15 p., eadl3604.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Individual patient and donor seroprofiles in convalescent plasma treatment of COVID-19 in REMAP-CAP clinical trial

  Nurmi, V., Mayne, R., Knight, C., Almonacid-Mendoza, H. L., Secret, S., Estcourt, L., Hepojoki, J., Šuštić, T., Lamikanra, A. A., Tsang, H. P., Menon, D. K., Shankar-Hari, M., van der Schoot, C. E., Vidarsson, G., Roberts, D. J., Simmonds, P., Hedman, K. & Harvala, H., Feb 2025, In: Journal of Infection. 90, 2, 10 p., 106412.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Multiple DNA Viruses and HPV Integration in Inverted Papilloma and Associated Sinonasal Carcinoma

  Jauhiainen, M. K., Pyöriä, L., Viitasalo, S., Aaltonen, L.-M., Söderlund-Venermo, M., Hagström, J., Mäkitie, A. A., Perdomo, M. F. & Sinkkonen, S. T., Feb 2025, In: Laryngoscope. 135, 2, p. 677-686 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Reactivation of a Transplant Recipient's Inherited Human Herpesvirus 6 and Implications to the Graft

  Hannolainen, L., Pyöriä, L., Pratas, D., Lohi, J., Skuja, S., Rasa-Dzelzkaleja, S., Murovska, M., Hedman, K., Jahnukainen, T. & Perdomo, M. F., 15 Feb 2025, In: Journal of Infectious Diseases. 231, 2, p. e267-e276 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2024

  An experimental sorting method for improving metagenomic data encoding

  Pratas, D. & Pinho, A. J., 2024, 2024 Data Compression Conference (DCC). Bilgin, A., Fowler, J. E., Serra-Sagrista, J., Ye, Y. & Storer, J. A. (eds.). IEEE, p. 578-578 1 p. (IEEE Data Compression Conference).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• A sensitive compression-based method for filtering targeted FASTQ sequencing reads

  Sousa, M. J. P., Pinho, A. J. & Pratas, D., 2024, 32nd European Signal Processing Conference, EUSIPCO 2024. IEEE, p. 1561-1565 5 p. (European Signal Processing Conference).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• A sorting tool for improving FASTA data compression tools

  Fonseca, T., Sousa, M. J. P., Pinho, A. J. & Pratas, D., 2024, 32nd European Signal Processing Conference, EUSIPCO 2024. IEEE, p. 1566-1570 5 p. (European Signal Processing Conference).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• B cell immune response to human bocaviruses

  Karaaslan, C., Wirz, O., Tan, G., Globinska, A., Boonpiyathad, T., Hedman, K., Vaselek, S., Söderlund-Venermo, M., Jartti, T., Akdis, M. & Akdis, C. A., 2024, In: Clinical and Experimental Allergy. 54, 6, p. 388-401 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Biochemical rationale for transfusion of high titre COVID-19 convalescent plasma

  Verbrugghe, C., Wouters, E., Devloo, R., Nurmi, V., Seghers, S., De Bleser, D., Harvala, H., Compernolle, V. & Feys, H. B., 9 Oct 2024, In: Scientific Reports. 14, 1, 12 p., 23579.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Blood donation screening for hepatitis B virus core antibodies: The importance of confirmatory testing and initial implication for rare blood donor groups

  Fu, M. X., Ingram, J., Roberts, C., Nurmi, V., Watkins, E., Dempsey, N., Golubchik, T., Breuer, J., Brailsford, S., Irving, W. L., Andersson, M., Simmonds, P. & Harvala, H., 2024, In: Vox Sanguinis. 119, 5, p. 447-459 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Copy models for protein sequence compression

  Pinho, A. J. & Pratas, D., 2024, 2024 Data Compression Conference (DCC). Bilgin, A., Fowler, J. E., Serra-Sagrista, J., Ye, Y. & Storer, J. A. (eds.). IEEE, p. 342-351 10 p. (IEEE Data Compression Conference).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• Fetal cord plasma herpesviruses and preeclampsia: an observational cohort study

  Häkkinen, I. M. K., Yazgeldi Gunaydin, G., Pyöriä, L., Kojima, S., Parrish, N., Perdomo , M. F., Wedenoja, J., Hedman, K., Heinonen, S., Kajantie, E., Laivuori, H., Kere, J., Katayama, S. & Wedenoja, S., 25 Jun 2024, In: Scientific Reports. 14, 1, 7 p., 14605.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Improving the generation of viral consensus sequences using adaptive models

  Sousa, M. J. P., Pinho, A. J. & Pratas, D., 2024, 32nd European Signal Processing Conference, EUSIPCO 2024. IEEE, p. 1691-1695 5 p. (European Signal Processing Conference).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome

  Pyöriä, L., Pratas, D., Toppinen, M., Simmonds, P., Hedman, K., Sajantila, A. & Perdomo, M. F., 22 Oct 2024, In: Nucleic Acids Research. 52, 21, p. 13073-13093 21 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation

  Soares, R., Azevedo, L., Vasconcelos, V., Pratas, D., Sousa, S. F. & Carneiro, J., 27 Nov 2024, In: Journal of Chemical Information and Modeling. 64, 24, p. 9576-9593 18 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Parvovirus B19 and Human Herpes Virus 6B and 7 Are Frequently Found DNA Viruses in the Human Thymus But Show No Definitive Link With Myasthenia Gravis

  Nowlan, K., Hannolainen, L., Assimakopoulou, I. M., Dürnsteiner, P., Sarkkinen, J., Suokas, S., Hedman, L., Tienari, P. J., Hedman, K., Niku, M., Aaltonen, L.-M., Huuskonen, A., Räsänen, J. V., Ilonen, I. K., Mäyränpää, M. I., Dunkel, J., Laakso, S. M., Söderlund-Venermo, M., Perdomo, M. F. & Kekäläinen, E., 2024, In: Journal of Infectious Diseases. 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Perinnöllinen herpesvirus elinsiirron kiusana

  Translated title of the contribution: Reactivation of a transplant recipient's inherited human herpesvirus 6 and implictions to the graftHannolainen, L., Pyöriä, L., Pratas, D., Lohi, J., Skuja, S., Rasa-Dzelzkaleja, S., Murovska, M., Hedman, K., Jahnukainen, T. & Perdomo, M. F., 2024, In: Duodecim. 140, 13-14, 1 p.

  Research output: Contribution to journal › Comment/debate › Professional

• Presence of herpesviruses, parvoviruses, and polyomaviruses in sinonasal lymphoma

  Jauhiainen, M. K., Mohanraj, U., Perdomo , M. F., Hagström, J., Haglund, C., Mäkitie, A. A., Söderlund-Venermo, M. & Sinkkonen, S. T., 17 May 2024, In: European Archives of Oto-Rhino-Laryngology. 281, p. 4201–4211 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2023

  AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data

  Silva, J. M., Qi, W., Pinho, A. J. & Pratas, D., 2023, In: GigaScience. 12, giad101.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Elimistömme on lukuisten terveyteemme vaikuttavien virusten koti

  Pyöriä, L., Pratas, D. R. M., Toppinen, M., Hedman, K., Sajantila, A. & Perdomo , M., 1 Apr 2023, In: Duodecim. 139, 8, 1 p.

  Research output: Contribution to journal › Letter › Professional

  Open Access

  File

• Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications

  Silva, J. M., Pratas, D. & Matos, S., 25 Jun 2023, Technological Innovation for Connected Cyber Physical Spaces. DoCEIS 2023. IFIP Advances in Information and Communication Technology. Camarinha-Matos, L. M. & Ferrada, F. (eds.). Cham: Springer, p. 161-174 14 p. (IFIP Advances in Information and Communication Technology; vol. 678).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

  Open Access

  File

• Herpesviruses, polyomaviruses, parvoviruses, papillomaviruses, and anelloviruses in vestibular schwannoma

  Jauhiainen, M. K., Mohanraj, U., Lehecka, M., Niemelä, M., Hirvonen, T. P., Pratas, D., Perdomo, M. F., Söderlund-Venermo, M., Mäkitie, A. A. & Sinkkonen, S. T., Apr 2023, In: Journal of NeuroVirology. 29, 2, p. 226-231 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• JARVIS2: a data compressor for large genome sequences

  Pratas, D. & Pinho, A. J., Mar 2023, Proceedings - DCC 2023: 2023 Data Compression Conference. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 288-297 10 p. (Data Compression Conference Proceedings).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• Mapping human pathogens in wastewater using a metatranscriptomic approach

  Carneiro, J., Pascoal, F., Semedo, M., Pratas, D., Tomasino, M. P., Rego, A., Carvalho, M. D. F., Mucha, A. P. & Magalhaes, C., 15 Aug 2023, In: Environmental Research. 231, 11 p., 116040.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• TargIDe: a machine -learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa

  Carneiro, J., Magalhaes, R. P., Roque, V. D. L. O. M., Simoes, M., Pratas, D. & Sousa, S. F., Jun 2023, In: Journal of Computer - Aided Molecular Design. 37, 5-6, p. 265–278 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• The Relationship Between SARS-CoV-2 Neutralizing Antibody Titers and Avidity in Plasma Collected From Convalescent nonvaccinated and Vaccinated Blood Donors

  Nurmi, V., Knight, C., Estcourt, L., Hepojoki, J., Lamikanra, A. A., Tsang, H. P., Roberts, D. J., Polack, F. P., Simmonds, P., Hedman, K., Alvarez-Paggi, D. & Harvala, H., 11 Aug 2023, In: Journal of Infectious Diseases. 228, 3, p. 245-250 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Unmasking the Tissue-Resident Eukaryotic DNA Virome in Humans

  Pyöriä, L., Pratas, D. R. M., Toppinen, M., Hedman, K., Sajantila, A. & Perdomo , M., 24 Apr 2023, In: Nucleic Acids Research. 51, 7, p. 3223-3239 17 p., gkad199.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2022

  Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation

  Mielonen, O. I., Pratas, D., Hedman, K., Sajantila, A. & Perdomo , M., 12 Jan 2022, In: Viruses (Basel). 14, 1, 12 p., 133.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods

  Silva, J. M., Pratas, D., Caetano, T. & Matos, S., 2022, Pattern Recognition and Image Analysis. IbPRIA 2022. Pinho, A. J., Georgieva, P., Teixeira, L. F. & Sánchez, J. A. (eds.). Cham: Springer, p. 309-320 12 p. (Lecture Notes in Computer Science; vol. 13256).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• Raskaudenaikaiset virusinfektiot ja vastasyntynyt

  Puhakka, L., Lappalainen, M. & Hedman, K., 2022, In: Duodecim. 138, 11, p. 987-993 7 p.

  Research output: Contribution to journal › Review Article › peer-review

  Open Access

  File

• The complexity landscape of viral genomes

  Silva, J. M., Pratas, D., Caetano, T. & Matos, S., 2022, In: GigaScience. 11, 16 p., 079.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

  Qi, W., Lim, Y.-W., Patrignani, A., Schlaepfer, P., Bratus-Neuenschwander, A., Gruter, S., Chanez, C., Rodde, N., Prat, E., Vautrin, S., Fustier, M.-A., Pratas, D., Schlapbach, R. & Gruissem, W., 24 Mar 2022, In: GigaScience. 11, 21 p., 028.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Torque Teno Virus Primary Infection Kinetics in Early Childhood

  Väisänen, E., Kuisma, I., Mäkinen, M., Ilonen, J., Veijola, R., Toppari, J., Hedman, K. & Söderlund-Venermo, M., Jun 2022, In: Viruses (Basel). 14, 6, 10 p., 1277.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2021

  A 10-Minute "Mix and Read" Antibody Assay for SARS-CoV-2

  Rusanen, J., Kareinen, L., Levanov, L., Mero, S. M., Pakkanen, S. H., Kantele, A., Amanat, F., Krammer, F., Hedman, K., Vapalahti, O. & Hepojoki, J., Feb 2021, In: Viruses (Basel). 13, 2, 12 p., 143.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models

  Silva, M., Pratas, D. & Pinho, A., May 2021, In: Entropy. 23, 5, 17 p., 530.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• A semi-automatic methodology for analysing distributed and private biobanks

  Almeida, J. R., Pratas, D. & Oliveira, J. L., Mar 2021, In: Computers in Biology and Medicine. 130, 8 p., 104180.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Automatic analysis of artistic paintings using information-based measures

  Silva, J. M., Pratas, D., Antunes, R., Matos, S. & Pinho, A. J., Jun 2021, In: Pattern Recognition. 114, 13 p., 107864.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Comparison of approaches for IgG avidity calculation and a new highly sensitive and specific method with broad dynamic range

  Nurmi, V., Hedman, L., Perdomo, M. F., Weseslindtner, L. & Hedman, K., Sept 2021, In: International Journal of Infectious Diseases. 110, p. 479-487 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Kinetics of neutralizing antibodies of covid-19 patients tested using clinical d614g, b.1.1.7, and b 1.351 isolates in microneutralization assays

  Virtanen, J., Uusitalo, R., Korhonen, E. M., Aaltonen, K., Smura, T., Kuivanen, S., Pakkanen, S. H., Mero, S., Patjas, A., Riekkinen, M., Kantele, A., Nurmi, V., Hedman, K., Hepojoki, J., Sironen, T., Huhtamo, E. & Vapalahti, O., Jun 2021, In: Viruses (Basel). 13, 6, 9 p., 996.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Parvoviral genomes in human soft tissues and bones over decades

  Toppinen, M., 2021, Helsinki. 92 p.

  Research output: Thesis › Doctoral Thesis › Collection of Articles

  Open Access

• Persistence of human bocavirus 1 in tonsillar germinal centers and antibody-dependent enhancement of infection

  Xu, M., Perdomo , M., Mattola, S., Pyöriä, L., Toppinen, M., Qiu, J., Vihinen-Ranta, M., Hedman, K., Nokso-Koivisto, J., Aaltonen, L.-M. & Söderlund-Venermo, M., 2 Feb 2021, In: mBio. 12, 1, 15 p., ARTN e03132-20.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Revisiting the Neurospora crassa mitochondrial genome

  Monteiro, J., Pratas, D., Videira, A. & Pereira, F., Oct 2021, In: Letters in Applied Microbiology. 73, 4, p. 495-505 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Serological approaches for viral diagnosis

  Hedman, K. & Nurmi, V., 2021, Encyclopedia of Virology. 4th ed. ed. Oxford: Academic Press

  Research output: Chapter in Book/Report/Conference proceeding › Entry for encyclopedia / dictionary › Professional

• Survey of Viral Reactivations in Elite Athletes: A Case-Control Study

  Pyöriä, L., Valtonen, M., Luoto, R., Gröönroos, W., Waris, M., Heinonen, O. J., Ruuskanen, O. & Perdomo , M., Jun 2021, In: Pathogens. 10, 6, 8 p., 666.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• The Human Bone Marrow Is Host to the DNAs of Several Viruses

  Toppinen, M., Sajantila, A., Pratas, D., Hedman, K. & Perdomo, M. F., 22 Apr 2021, In: Frontiers in Cellular and Infection Microbiology. 11, 7 p., 657245.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• The presence of herpesviruses in malignant but not in benign or recurrent pleomorphic adenomas

  Jauhiainen, M. K., Xu, M., Pyöriä, L., Atula, T., Aro, K., Markkanen, A., Haglund, C., Hagström, J., Mäkitie, A. A. & Söderlund-Venermo, M., 2021, In: Tumor Biology. 43, 1, p. 249-259 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2020

  A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level

  Pratas, D., Toppinen, M., Pyöriä, L., Hedman, K., Sajantila, A. & Perdomo, M. F., Aug 2020, In: GigaScience. 9, 8, 11 p., 086.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Efficient DNA sequence compression with neural networks

  Silva, M., Pratas, D. & Pinho, A. J., Nov 2020, In: GigaScience. 9, 11, 15 p., 119.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• GTO: A toolkit to unify pipelines in genomic and proteomic research

  Almeida, J. R., Pinho, A. J., Oliveira, J. L., Fajarda, O. & Pratas, D., 2020, In: SoftwareX. 12, 6 p., 100535.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File