% Publications of Tuomas Borman (ORCID 0000-0002-8563-8884)
% Generated automatically by scripts/update-publications.R. Do not edit.

@article{Vargas2026Joint, title={Joint-RPCA: domain-aware multi-omics integration for systems microbiology}, ISSN={1744-4292}, url={http://dx.doi.org/10.1038/s44320-026-00236-3}, DOI={10.1038/s44320-026-00236-3}, journal={Molecular Systems Biology}, publisher={Springer Science and Business Media LLC}, author={Cordazzo Vargas, Bianca and Martino, Cameron and Dilmore, Amanda Hazel and Metcalf, Jessica L and Burcham, Zachary M and Lahti, Leo and Bektanov, Aituar and Borman, Tuomas and Salomaa, Veikko and Niiranen, Teemu and Havulinna, Aki S and Gregor, Rachel and Eyal, Stav and Meijler, Michael M and Mizrahi, Itzhak and Song, Se Jin and Bartko, Andrew and Dorrestein, Pieter C and Morton, James T and McDonald, Daniel and Knight, Rob and Shenhav, Liat}, year={2026}, month=Aug }

@article{Han2026Uncomplicated, title={Uncomplicated and Complicated Acute Appendicitis Induce Different Cytokine Patterns}, volume={134}, ISSN={1600-0463}, url={http://dx.doi.org/10.1111/apm.70168}, DOI={10.1111/apm.70168}, number={2}, journal={APMIS}, publisher={Wiley}, author={Han, Tatu and Borman, Tuomas and Vanhatalo, Sanja and Lahti, Leo and Löyttyniemi, Eliisa and Hurme, Saija and Munukka, Eveliina and Kallonen, Teemu and Hakanen, Antti and Hollmén, Maija and Salminen, Paulina}, year={2026}, month=Feb }

@article{Borman2025HoloFoodR, title={HoloFoodR: a statistical programming framework for holo-omics data integration workflows}, volume={41}, ISSN={1367-4811}, url={http://dx.doi.org/10.1093/bioinformatics/btaf605}, DOI={10.1093/bioinformatics/btaf605}, number={11}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Borman, Tuomas and Sannikov, Artur and Finn, Robert D and Limborg, Morten Tønsberg and Rogers, Alexander B and Kale, Varsha and Hanhineva, Kati and Lahti, Leo}, editor={Kendziorski, Christina}, year={2025}, month=Nov }

@article{Borman2025Orchestrating, title={Orchestrating Microbiome Analysis with Bioconductor}, url={http://dx.doi.org/10.1101/2025.10.29.685036}, DOI={10.1101/2025.10.29.685036}, publisher={openRxiv}, author={Borman, Tuomas and Benedetti, Giulio and Muluh, Geraldson and Raulo, Aura and Valderrama, Benjamin and Sannikov, Artur and Peschel, Stefanie and Liu, Yihan and Hindström, Rasmus and Pärnänen, Katariina and Müller, Christian L. and Havulinna, Aki S. and Shetty, Sudarshan and Ramos, Marcel and Braccia, Domenick J. and Bravo, Héctor Corrada and Ernst, Felix M. and Waldron, Levi and Bastiaanssen, Thomaz F. S. and Mallick, Himel and Lahti, Leo}, year={2025}, month=Oct }

@article{Sherwani2025Multi, title={Multi-omics time-series analysis in microbiome research: a systematic review}, volume={26}, ISSN={1477-4054}, url={http://dx.doi.org/10.1093/bib/bbaf502}, DOI={10.1093/bib/bbaf502}, number={5}, journal={Briefings in Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Sherwani, Moiz Khan and Ruuskanen, Matti O and Feldner-Busztin, Dylan and Nisantzis Firbas, Panos and Boza, Gergely and Móréh, Ágnes and Borman, Tuomas and Putu Erawijantari, Pande and Scheuring, István and Gopalakrishnan, Shyam and Lahti, Leo}, year={2025}, month=Aug }

@article{Benedetti2024iSEEtree, title={iSEEtree: interactive explorer for hierarchical data}, volume={5}, ISSN={2635-0041}, url={http://dx.doi.org/10.1093/bioadv/vbaf107}, DOI={10.1093/bioadv/vbaf107}, number={1}, journal={Bioinformatics Advances}, publisher={Oxford University Press (OUP)}, author={Benedetti, Giulio and Seraidarian, Ely and Pralas, Theotime and Jeba, Akewak and Borman, Tuomas and Lahti, Leo}, editor={Zhu, Shanfeng}, year={2024}, month=Dec }

@article{Konig2024Fecal, title={Fecal microbiota profiles of growing pigs and their relation to growth performance}, volume={19}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0302724}, DOI={10.1371/journal.pone.0302724}, number={5}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={König, Emilia and Beasley, Shea and Heponiemi, Paulina and Kivinen, Sanni and Räkköläinen, Jaakko and Salminen, Seppo and Collado, Maria Carmen and Borman, Tuomas and Lahti, Leo and Piirainen, Virpi and Valros, Anna and Heinonen, Mari}, editor={Carbonero, Franck}, year={2024}, month=May, pages={e0302724} }

@article{Konig2024Fewer, title={Fewer culturable Lactobacillaceae species identified in faecal samples of pigs performing manipulative behaviour}, volume={14}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-023-50791-0}, DOI={10.1038/s41598-023-50791-0}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={König, Emilia and Heponiemi, Paulina and Kivinen, Sanni and Räkköläinen, Jaakko and Beasley, Shea and Borman, Tuomas and Collado, Maria Carmen and Hukkinen, Vilja and Junnila, Jouni and Lahti, Leo and Norring, Marianna and Piirainen, Virpi and Salminen, Seppo and Heinonen, Mari and Valros, Anna}, year={2024}, month=Jan }

@article{Gao2023miaSim, title={miaSim: an R/Bioconductor package to easily simulate microbial community dynamics}, volume={14}, ISSN={2041-210X}, url={http://dx.doi.org/10.1111/2041-210x.14129}, DOI={10.1111/2041-210x.14129}, number={8}, journal={Methods in Ecology and Evolution}, publisher={Wiley}, author={Gao, Yu and Şimşek, Yağmur and Gheysen, Emma and Borman, Tuomas and Li, Yi and Lahti, Leo and Faust, Karoline and Garza, Daniel Rios}, year={2023}, month=May, pages={1967–1980} }