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Employment (1)

University of Turku: Turku, FI

2015-07-01 to present (Medical Bioinformatics Centre, Turku Bioscience)
Employment
Source: Self-asserted source
Tomi Suomi

Education and qualifications (3)

University of Turku: Turku, FI

Master of Science (Department of Information Technology)
Education
Source: Self-asserted source
Tomi Suomi

University of Turku: Turku, FI

Bachelor of Science (Department of Information Technology)
Education
Source: Self-asserted source
Tomi Suomi

University of Turku: Turku, FI

Doctor of Philosophy
Education
Source: Self-asserted source
Tomi Suomi

Works (46)

Adaptive sequence alignment for metagenomic data analysis

Computers in Biology and Medicine
2025-03 | Journal article
Contributors: Sami Pietilä; Tomi Suomi; Niklas Paulin; Asta Laiho; Yannes S. Sclivagnotis; Laura L. Elo
Source: check_circle
Crossref

Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing

PROTEOMICS
2025-01-31 | Journal article
Contributors: Tim Van Den Bossche; Denis Beslic; Sam van Puyenbroeck; Tomi Suomi; Tanja Holstein; Lennart Martens; Laura L. Elo; Thilo Muth
Source: check_circle
Crossref

Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing

2025-01-10 | Preprint
Contributors: Tim Van Den Bossche; Denis Beslic; Sam van Puyenbroeck; Tomi Suomi; Tanja Holstein; Lennart Martens; Laura L. Elo; Thilo Muth
Source: check_circle
Crossref

Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing

2024-10-04 | Preprint
Contributors: Tim Van Den Bossche; Denis Beslic; Sam van Puyenbroeck; Tomi Suomi; Tanja Holstein; Lennart Martens; Laura L. Elo; Thilo Muth
Source: check_circle
Crossref

Disruption of HSD17B12 in mouse hepatocytes leads to reduced body weight and defect in the lipid droplet expansion associated with microvesicular steatosis

The FASEB Journal
2024-09 | Journal article
Contributors: Hanna Heikelä; Laura Mairinoja; Suvi T. Ruohonen; Kalle T. Rytkönen; Simone de Brot; Asta Laiho; Satu Koskinen; Tomi Suomi; Laura L. Elo; Leena Strauss et al.
Source: check_circle
Crossref

Maternal gluten, cereal, and dietary fiber intake during pregnancy and lactation and the risk of islet autoimmunity and type 1 diabetes in the child.

Clinical nutrition ESPEN
2024-05 | Journal article
Contributors: Hakola L; Lund-Blix NA; Takkinen HM; Tapanainen H; Niinistö S; Korhonen TE; Stene LC; Hyöty H; Toppari J; Ilonen J et al.
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk.

iScience
2024-05 | Journal article
Contributors: Bhosale SD; Moulder R; Suomi T; Ruohtula T; Honkanen J; Virtanen SM; Ilonen J; Elo LL; Knip M; Lahesmaa R
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

Distinct cellular immune responses in children en route to type 1 diabetes with different first-appearing autoantibodies

Nature Communications
2024-05-07 | Journal article
Contributors: Inna Starskaia; Milla Valta; Sami Pietilä; Tomi Suomi; Sirpa Pahkuri; Ubaid Ullah Kalim; Omid Rasool; Emilie Rydgren; Heikki Hyöty; Mikael Knip et al.
Source: check_circle
Crossref

Targeted serum proteomics of longitudinal samples from newly diagnosed youth with type 1 diabetes distinguishes markers of disease and C-peptide trajectory

Diabetologia
2023-11 | Journal article
Contributors: Robert Moulder; Tommi Välikangas; M. Karoliina Hirvonen; Tomi Suomi; Caroline A. Brorsson; Niina Lietzén; Sylvaine F. A. Bruggraber; Lut Overbergh; David B. Dunger; Mark Peakman et al.
Source: check_circle
Crossref

Gene expression signature predicts rate of type 1 diabetes progression

eBioMedicine
2023-06 | Journal article
Contributors: Tomi Suomi; Inna Starskaia; Ubaid Ullah Kalim; Omid Rasool; Maria K. Jaakkola; Toni Grönroos; Tommi Välikangas; Caroline Brorsson; Gianluca Mazzoni; Sylvaine Bruggraber et al.
Source: check_circle
Crossref

Multi-omics analysis reveals drivers of loss of β-cell function after newly diagnosed autoimmune type 1 diabetes: An INNODIA‡multicenter study

2023-03-28 | Preprint
Contributors: Jose Juan Almagro Armenteros; Caroline Brorsson; Christian Holm Johansen; Karina Banasik; Gianluca Mazzoni; Robert Moulder; Karoliina Hirvonen; Tomi Suomi; Omid Rasool; Sylvaine FA Bruggraber et al.
Source: check_circle
Crossref

Profiling of peripheral blood B-cell transcriptome in children who developed coeliac disease in a prospective study

Heliyon
2023-02 | Journal article
Contributors: Astrid Oras; Henna Kallionpää; Tomi Suomi; Satu Koskinen; Asta Laiho; Laura L. Elo; Mikael Knip; Riitta Lahesmaa; Alar Aints; Raivo Uibo
Source: check_circle
Crossref

Computational solutions for spatial transcriptomics

Computational and Structural Biotechnology Journal
2022 | Journal article
Part of ISSN: 2001-0370
Contributors: Iivari Kleino; Paulina Frolovaitė; Tomi Suomi; Laura L. Elo
Source: Self-asserted source
Tomi Suomi via Crossref Metadata Search

Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach

Nature Communications
2022-12-22 | Journal article
Contributors: Tommi Välikangas; Tomi Suomi; Courtney E. Chandler; Alison J. Scott; Bao Q. Tran; Robert K. Ernst; David R. Goodlett; Laura L. Elo
Source: check_circle
Crossref

Introducing untargeted data-independent acquisition for metaproteomics of complex microbial samples

ISME Communications
2022-12-01 | Journal article
Contributors: Sami Pietilä; Tomi Suomi; Laura L Elo
Source: check_circle
Crossref

A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis.

JAMA network open
2022-08 | Journal article
Contributors: Sun D; Nguyen TM; Allaway RJ; Wang J; Chung V; Yu TV; Mason M; Dimitrovsky I; Ericson L; Li H et al.
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

COVID-19-specific transcriptomic signature detectable in blood across multiple cohorts

Frontiers in Genetics
2022-08-05 | Journal article
Part of ISSN: 1664-8021
Contributors: Tomi Suomi
Source: Self-asserted source
Tomi Suomi

Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes

2022-06 | Preprint
Contributors: Jaakkola MK; Kukkonen-Macchi A; Suomi T; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

Statistical and machine learning methods to study human CD4+ T cell proteome profiles

Immunology Letters
2022-05 | Journal article
Part of ISSN: 0165-2478
Source: Self-asserted source
Tomi Suomi
grade
Preferred source (of 2)‎

Correction to: PhosPiR: an automated phosphoproteomic pipeline in R

Briefings in Bioinformatics
2022-05-13 | Journal article
Contributors: Ye Hong; Dani Flinkman; Tomi Suomi; Sami Pietilä; Peter James; Eleanor Coffey; Laura L Elo
Source: check_circle
Crossref

Type 1 Diabetes in Children With Genetic Risk May Be Predicted Very Early With a Blood miRNA.

Diabetes care
2022-04-01 | Journal article
Source: Self-asserted source
Tomi Suomi

PhosPiR: an automated phosphoproteomic pipeline in R

Briefings in Bioinformatics
2022-01-17 | Journal article
Contributors: Ye Hong; Dani Flinkman; Tomi Suomi; Sami Pietilä; Peter James; Eleanor Coffey; Laura L Elo
Source: check_circle
Crossref

Improved risk prediction of chemotherapy-induced neutropenia-model development and validation with real-world data.

Cancer medicine
2021-12-03 | Journal article
Source: Self-asserted source
Tomi Suomi

Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer.

Nature communications
2021-11-29 | Journal article
Source: Self-asserted source
Tomi Suomi

PhosPiR: An automated phospho-proteomic pipeline in R

2021-09 | Preprint
Contributors: Hong Y; Flinkman D; Suomi T; Pietilä S; James P; Coffey E; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

Enhanced longitudinal differential expression detection in proteomics with robust reproducibility optimization regression

2021-04 | Preprint
Contributors: Välikangas T; Suomi T; Chandler CE; Scott AJ; Tran BQ; Ernst RK; Goodlett DR; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

Metaproteomics boosted up by untargeted data-independent acquisition data analysis framework

2020-12 | Preprint
Contributors: Pietilä S; Suomi T; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics

Cell Systems
2020-07 | Journal article
Part of ISSN: 2405-4712
Source: Self-asserted source
Tomi Suomi

Data-independent acquisition mass spectrometry in metaproteomics of gut microbiota - implementation and computational analysis.

Journal of proteome research
2019-11-22 | Journal article
Source: Self-asserted source
Tomi Suomi
grade
Preferred source (of 2)‎

A Data Analysis Protocol for Quantitative Data-Independent Acquisition Proteomics.

Methods in molecular biology (Clifton, N.J.)
2019-01 | Journal article
Contributors: Pietilä S; Suomi T; Aakko J; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 3)‎

A systematic evaluation of normalization methods in quantitative label-free proteomics

Briefings in Bioinformatics
2018 | Journal article
EID:

2-s2.0-85041216726

Contributors: Välikangas, T.; Suomi, T.; Elo, L.L.
Source: Self-asserted source
Tomi Suomi via Scopus - Elsevier

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection

Nature Communications
2018-10-24 | Journal article
Source: Self-asserted source
Tomi Suomi
grade
Preferred source (of 2)‎

Data-independent acquisition mass spectrometry enables reproducible characterization of microbiota function

2018-09 | Other
OTHER-ID:

PPR55554

Contributors: Aakko J; Pietila S; Suomi T; Mahmoudian M; Toivonen R; Kouvonen P; Rokka A; Hanninen A; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

SimPhospho: a software tool enabling confident phosphosite assignment.

Bioinformatics (Oxford, England)
2018-08 | Journal article
Contributors: Suni V; Suomi T; Tsubosaka T; Imanishi SY; Elo LL; Corthals GL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

Accurate Detection of Differential Expression and Splicing Using Low-Level Features.

Methods in molecular biology (Clifton, N.J.)
2017 | Journal article
Contributors: Suomi T; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma.

Cancer & metabolism
2017 | Journal article
Contributors: Miikkulainen P; Högel H; Rantanen K; Suomi T; Kouvonen P; Elo LL; Jaakkola PM
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics.

Bioinformatics (Oxford, England)
2017-09 | Journal article
Contributors: Saraei S; Suomi T; Kauko O; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

Enhanced differential expression statistics for data-independent acquisition proteomics.

Scientific reports
2017-07 | Journal article
Contributors: Suomi T; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation.

Briefings in bioinformatics
2017-05 | Journal article
Contributors: Välikangas T; Suomi T; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

ROTS: An R package for reproducibility-optimized statistical testing

PLOS Computational Biology
2017-05-25 | Journal article
Contributors: Tomi Suomi; Timothée Poisot; Fatemeh Seyednasrollah; Maria K. Jaakkola; Thomas Faux; Laura L. Elo
Source: check_circle
Crossref
grade
Preferred source (of 3)‎

A systematic evaluation of normalization methods in quantitative label-free proteomics.

Briefings in bioinformatics
2016-10 | Journal article
Contributors: Välikangas T; Suomi T; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central

Brief Isoflurane Anesthesia Produces Prominent Phosphoproteomic Changes in the Adult Mouse Hippocampus.

ACS chemical neuroscience
2016-06 | Journal article
Contributors: Kohtala S; Theilmann W; Suomi T; Wigren HK; Porkka-Heiskanen T; Elo LL; Rokka A; Rantamäki T
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

Using Peptide-Level Proteomics Data for Detecting Differentially Expressed Proteins.

Journal of proteome research
2015-11 | Journal article
Contributors: Suomi T; Corthals GL; Nevalainen OS; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

Optimization of Statistical Methods Impact on Quantitative Proteomics Data.

Journal of proteome research
2015-10 | Journal article
Contributors: Pursiheimo A; Vehmas AP; Afzal S; Suomi T; Chand T; Strauss L; Poutanen M; Rokka A; Corthals GL; Elo LL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

Cross-correlation of spectral count ranking to validate quantitative proteome measurements.

Journal of proteome research
2014-04 | Journal article
Contributors: Kannaste O; Suomi T; Salmi J; Uusipaikka E; Nevalainen O; Corthals GL
Source: Self-asserted source
Tomi Suomi via Europe PubMed Central
grade
Preferred source (of 2)‎

Organizing the nozzle magazine of a gantry-type PCB assembly machine

The International Journal of Advanced Manufacturing Technology
2013-04 | Journal article
Part of ISSN: 0268-3768
Contributors: Timo Knuutila; Tomi Suomi; Stefan Emet; Mika Johnsson; Olli S. Nevalainen
Source: Self-asserted source
Tomi Suomi via Crossref Metadata Search
grade
Preferred source (of 2)‎

Peer review (1 review for 1 publication/grant)

Review activity for Nature communications (1)