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From longitudinal proteomics to dynamic individualized diagnostics

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Publications

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

Author(s): Fourati S*, Talla A*, Mahmoudian M*, Burkhart JG*, Klén R*, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R, The Respiratory Viral DREAM Challenge Consortium, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK
Published in: Nature Communications, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-06735-8

Stable Iterative Variable Selection.

Author(s): Mehrad Mahmoudian; Mehrad Mahmoudian; Mikko S. Venäläinen; Riku Klén; Laura L. Elo; Laura L. Elo
Published in: Bioinformatics, 15, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab501

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

Author(s): Venäläinen MS, Heervä E, Hirvonen O, Saraei S, Suomi T, Mikkola T, Bärlund M, Jyrkkiö S, Laitinen T, Elo LL
Published in: Cancer Medicine, 2022, ISSN 2045-7634
Publisher: John Wiley & Sons
DOI: 10.1002/cam4.4465

Persistent coxsackievirus B1 inciencefection results in extensive changes in the transcriptome of a pancreatic cell line

Author(s): Buchacher T, Honkimaa A, Välikangas T, Lietzén N, Hirvonen K, Laiho JE, Sioofy-Khojine AB, Eskelinen EL, Hyöty H, Elo LL, Lahesmaa R
Published in: iScience, 2021, ISSN 2589-0042
Publisher: Cell Press Elsevier Inc.
DOI: 10.1016/j.isci.2021.103653

Integrative omics approaches provide biological and clinical insights: examples from mitochondrial diseases

Author(s): Sofia Khan, Gulayse Ince-Dunn, Anu Suomalainen, Laura L Elo
Published in: The Journal of Clinical Investigation, 2020, ISSN 0021-9738
Publisher: American Society for Clinical Investigation
DOI: 10.1172/jci129202

Computational deconvolution to estimate cell type-specific gene expression from bulk data

Author(s): Jaakkola MK, Elo LL.
Published in: NAR Genomics and Bioinformatics, 2021, ISSN 2631-9268
Publisher: Oxford University Press
DOI: 10.1093/nargab/lqaa110

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

Author(s): Mi Yang , Francesca Petralia , Zhi Li, Hongyang Li, Weiping Ma, Xiaoyu Song, Sunkyu Kim, Heewon Lee, Han Yu, Bora Lee , Seohui Bae , Eunji Heo, Jan Kaczmarczyk, Piotr Stępniak, Michał Warchoł, Thomas Yu, Anna P Calinawan, Paul C Boutros, Samuel H Payne, Boris Reva, NCI-CPTAC-DREAM Consortium; Emily Boja, Henry Rodriguez, Gustavo Stolovitzky, Yuanfang Guan, Jaewoo Kang, Pei Wang, David Fenyö, J
Published in: Cell Systems, 2020, ISSN 2405-4720
Publisher: Cell Press
DOI: 10.1016/j.cels.2020.06.013

A DREAM Challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer

Author(s): Seyednasrollah F*, Koestler DC*, Wang T*, Piccolo SR, Vega R, Greiner R, Fuchs C, Gofer E, Kumar L, Wolfinger RD, Winner KK, Bare C, Neto EC, Yu T, Shen L, Abdallah K, Norman T, Stolovitzky G, PCC-DREAM Community, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Elo LL*, Zhou FL*, Guinney J*, Costello JC*
Published in: JCO Clinical Cancer Informatics, 2017, ISSN 2473-4276
Publisher: American Society of Clinical Oncology
DOI: 10.1200/cci.17.00018

CIP2A Constrains Th17 Differentiation by Modulating STAT3 Signaling

Author(s): Mohd Moin Khan, Ubaid Ullah, Meraj H. Khan, Lingjia Kong, Robert Moulder, Tommi Välikangas, Santosh Dilip Bhosale, Elina Komsi, Omid Rasool, Zhi Chen, Laura L. Elo, Jukka Westermarck, Riitta Lahesmaa
Published in: iScience, 23/3, 2020, Page(s) 100947, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2020.100947

Deep learning tools are top performers in long non-coding RNA prediction

Author(s): Tea Ammunét; Ning Wang; Sofia Khan; Laura L Elo
Published in: Briefings in Functional Genomics, 1, 2022, ISSN 2041-2649
Publisher: Oxford University Press
DOI: 10.1093/bfgp/elab045

Longitudinal modeling of ultrasensitive and traditional prostate-specific antigen and prediction of biochemical recurrence after radical prostatectomy

Author(s): Laajala TD*, Seikkula H*, Seyednasrollah F, Mirtti T, Boström PJ, Elo LL.
Published in: Scientific Reports, 2016, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep36161

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

Author(s): Pietilä S*, Suomi T*, Elo LL
Published in: ISME Communications, 2022, ISSN 2730-6151
Publisher: Springer Nature
DOI: 10.1101/2020.12.21.423800

Estimating cell type-specific differential expression using deconvolution.

Author(s): Maria K. Jaakkola; Laura L. Elo; Laura L. Elo
Published in: Briefings in Bioinformatics, 15, 2022, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab433

SimPhospho: a software tool enabling confident phosphosite assignment

Author(s): Suni V, Suomi T, Tsubosaka T, Imanishi SY, Elo LL, Corthals GL
Published in: Bioinformatics, 2018, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty151

Complex Interplay Between MAZR and Runx3 Regulates the Generation of Cytotoxic T Lymphocyte and Memory T Cells.

Author(s): Alexandra Franziska Gülich; Ramona Rica; Caroline Tizian; C. Viczenczova; Kseniya Khamina; Thomas Faux; Daniela Hainberger; Thomas Penz; Rémy Bosselut; Christoph Bock; Christoph Bock; Asta Laiho; Laura L. Elo; Andreas Bergthaler; Wilfried Ellmeier; Shinya Sakaguchi
Published in: Frontiers in Immunology, 1, 2021, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2021.535039

Development of Preoperative Risk Prediction Models for Short-Term Revision and Death Following Total Hip Arthroplasty Using data from the Finnish Arthroplasty Register

Author(s): Venäläinen MS, Panula VJ, Klén R, Haapakoski JJ, Eskelinen AP, Manninen MJ, Kettunen JS, Puhto AP, Vasara AI, Mäkelä KT, Elo LL
Published in: JB JS Open Access, 2021, ISSN 2472-7245
Publisher: The Journal of Bone and Joint Surgery Inc.
DOI: 10.2106/jbjs.oa.20.00091

Umbilical Cord Blood DNA Methylation in Children Who Later Develop Type 1 Diabetes

Author(s): Laajala E, Ullah U, Grönroos T, Rasool O, Halla-aho V, Konki M, Kattelus R, Mykkänen J, Nurmio M, Vähä-Mäkilä M, Kallionpää H, Lietzén N, Ghimire BR, Laiho A, Hyöty H, Elo LL, Ilonen J, Knip M, Lund RJ, Orešič M, Veijola R, Lähdesmäki H, Toppari J, Lahesmaa R
Published in: Diabetologia, 2022, ISSN 1432-0428
Publisher: Springer
DOI: 10.1007/s00125-022-05726-1

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

Author(s): Tommi Välikangas, Tomi Suomi, Laura L. Elo
Published in: Briefings in Bioinformatics, 2017, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbx054

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

Author(s): Tommi Välikangas, Tomi Suomi, Laura L. Elo
Published in: Briefings in Bioinformatics, 2018, Page(s) bbw095, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbw095

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

Author(s): Sohrab Saraei, Tomi Suomi, Otto Kauko, Laura L Elo
Published in: Bioinformatics, 2017, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btx573

Enterovirus-associated changes in blood transcriptomic profiles of children with genetic susceptibility to type 1 diabetes

Author(s): Niina Lietzen, Le T. T. An, Maria K. Jaakkola, Henna Kallionpää, Sami Oikarinen, Juha Mykkänen, Mikael Knip, Riitta Veijola, Jorma Ilonen, Jorma Toppari, Heikki Hyöty, Riitta Lahesmaa, Laura L. Elo
Published in: Diabetologia, 61/2, 2018, Page(s) 381-388, ISSN 0012-186X
Publisher: Springer Verlag
DOI: 10.1007/s00125-017-4460-7

Prediction of Adulthood Obesity Using Genetic and Childhood Clinical Risk Factors in the Cardiovascular Risk in Young Finns StudyCLINICAL PERSPECTIVE

Author(s): Fatemeh Seyednasrollah, Johanna Mäkelä, Niina Pitkänen, Markus Juonala, Nina Hutri-Kähönen, Terho Lehtimäki, Jorma Viikari, Tanika Kelly, Changwei Li, Lydia Bazzano, Laura L. Elo, Olli T. Raitakari
Published in: Circulation: Cardiovascular Genetics, 10/3, 2017, Page(s) e001554, ISSN 1942-3268
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/CIRCGENETICS.116.001554

PASI: A novel pathway method to identify delicate group effects

Author(s): Maria K. Jaakkola, Aidan J. McGlinchey, Riku Klén, Laura L. Elo
Published in: PLOS ONE, 13/7, 2018, Page(s) e0199991, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0199991

Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells

Author(s): Ubaid Ullah, Syed Bilal Ahmad Andrabi, Subhash Kumar Tripathi, Obaiah Dirasantha, Kartiek Kanduri, Sini Rautio, Catharina C. Gross, Sari Lehtimäki, Kanchan Bala, Johanna Tuomisto, Urvashi Bhatia, Deepankar Chakroborty, Laura L. Elo, Harri Lähdesmäki, Heinz Wiendl, Omid Rasool, Riitta Lahesmaa
Published in: Cell Reports, 22/8, 2018, Page(s) 2094-2106, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2018.01.070

Enhanced differential expression statistics for data-independent acquisition proteomics

Author(s): Tomi Suomi, Laura L. Elo
Published in: Scientific Reports, 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-05949-y

ROTS: An R package for reproducibility-optimized statistical testing

Author(s): Tomi Suomi, Fatemeh Seyednasrollah, Maria K. Jaakkola, Thomas Faux, Laura L. Elo
Published in: PLOS Computational Biology, 13/5, 2017, Page(s) e1005562, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1005562

Quantitative Proteomics Reveals the Dynamic Protein Landscape during Initiation of Human Th17 Cell Polarization

Author(s): Subhash K. Tripathi, Tommi Välikangas, Ankitha Shetty, Mohd Moin Khan, Robert Moulder, Santosh D. Bhosale, Elina Komsi, Verna Salo, Rafael Sales De Albuquerque, Omid Rasool, Sanjeev Galande, Laura L. Elo, Riitta Lahesmaa
Published in: iScience, 11, 2019, Page(s) 334-355, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2018.12.020

A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation

Author(s): Shetty A*, Tripathi SK*, Junttila S*, Buchacher T*, Biradar R, Bhosale SD, Envall T, Laiho A, Moulder R, Rasool O, Galande S, Elo LL*, Lahesmaa R*
Published in: Nucleic Acids Research, 2022, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac256

Likelihood contrasts: a machine learning algorithm for binary classification of longitudinal data

Author(s): Riku Klén, Markku Karhunen, Laura L. Elo
Published in: Scientific Reports, 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-57924-9

Weight loss trajectories in the Healthy Weight Coaching - a real-life web-based obesity management program

Author(s): Kupila S, Venäläinen MS, Suojanen LL, Rosengård-Bärlund M, Ahola AJ, Elo LL, Pietiläinen KH
Published in: JMIR Formative Research, 2022, ISSN 2561-326X
Publisher: JMIR Publications
DOI: 10.2196/26374

How reliable are trial-based prognostic models in real-world patients with metastatic castration resistant prostate cancer?

Author(s): Seyednasrollah F, Mahmoudian M, Rautakorpi L, Hirvonen O, Laitinen T, Jyrkkiö S, Elo LL
Published in: Euporean Urology, 2017, ISSN 0302-2838
Publisher: Elsevier BV
DOI: 10.1016/j.eururo.2017.01.043

Predicting Skeletal Muscle and Whole-Body Insulin Sensitivity Using NMR-Metabolomic Profiling

Author(s): Riku Klén, Miikka-Juhani Honka, Jarna C Hannukainen, Ville Huovinen, Marco Bucci, Aino Latva-Rasku, Mikko S Venäläinen, Kari K Kalliokoski, Kirsi A Virtanen, Riikka Lautamäki, Patricia Iozzo, Laura L Elo, Pirjo Nuutila
Published in: Journal of the Endocrine Society, 4/4, 2020, ISSN 2472-1972
Publisher: Oxford Academic Journals
DOI: 10.1210/jendso/bvaa026

Differential ATAC-seq and ChIP-seq peak detection using ROTS.

Author(s): Thomas Faux; Kalle T Rytkönen; Mehrad Mahmoudian; Niklas Paulin; Sini Junttila; Asta Laiho; Laura L. Elo
Published in: NAR Genomics and Bioinformatics, 1, 2021, ISSN 2631-9268
Publisher: Oxford University Press
DOI: 10.1093/nargab/lqab059

PhosPiR: An automated phosphoproteomic pipeline in R

Author(s): Hong Y, Flinkman D, Suomi T, Pietilä S, James P, Coffey E, Elo LL
Published in: Briefings in Bioinformatics, 2022, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab510

Serum Proteomic Profiling to Identify Biomarkers of Premature Carotid Atherosclerosis

Author(s): Bhosale SD, Moulder R, Venäläinen MS, Koskinen JS, Pitkänen N, Juonala MT, Kähönen MAP, Lehtimäki TJ, Viikari JSA, Elo LL, Goodlett RD, Lahesmaa R, Raitakari OT.
Published in: Sci Rep, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-27265-9

Pancreas whole tissue transcriptomics highlights the role of the exocrine pancreas in patients with recently diagnosed type 1 diabetes

Author(s): Välikangas T*, Lietzén N*, Jaakkola MK, Krogvold L, Eike MC, Kallionpää H, Tuomela S, Mathews C, Gerling IC, Oikarinen S, Hyöty H, Dahl-Jorgensen K, Elo LL*, Lahesmaa R*
Published in: Frontiers in Endocrinology, 2022, ISSN 1664-2392
Publisher: Frontiers Media
DOI: 10.3389/fendo.2022.861985

Easy-to-use tool for evaluating the elevated acute kidney injury risk against reduced cardiovascular disease risk during intensive blood pressure control

Author(s): Mikko S. Venäläinen, Riku Klén, Mehrad Mahmoudian, Olli T. Raitakari, Laura L. Elo
Published in: Journal of Hypertension, 38/3, 2020, Page(s) 511-518, ISSN 0263-6352
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1097/hjh.0000000000002282

Early DNA methylation changes in children developing beta cell autoimmunity at a young age

Author(s): Starskaia I, Laajala E, Grönroos T, Härkönen T, Junttila S, Kattelus R, Kallionpää H, Laiho A, Suni V, Tilmann V, Lund R, Elo LL, Lähdesmäki H, Knip M, Ullah U, Lahesmaa R
Published in: Diabetologia, 2022, ISSN 1432-0428
Publisher: Springer
DOI: 10.1007/s00125-022-05657-x

Protein interactome of the Cancerous Inhibitor of protein phosphatase 2A (CIP2A) in Th17 cells

Author(s): Mohd Moin Khan, Tommi Välikangas, Meraj Hasan Khan, Robert Moulder, Ubaid Ullah, Santosh Dilip Bhosale, Elina Komsi, Umar Butt, Xi Qiao, Jukka Westermarck, Laura L. Elo, Riitta Lahesmaa
Published in: Current Research in Immunology, 1, 2020, Page(s) 10-22, ISSN 2590-2555
Publisher: Cell Press
DOI: 10.1016/j.crimmu.2020.02.001

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

Author(s): Suomi T*, Kalim UU*, Rasool O, Laiho A, Kallionpää H, Vähä-Mäkilä M, Nurmio M, Mykkänen J, Härkönen T, Hyöty H, Ilonen J, Veijola R, Toppari J, Knip M, Elo LL*, Lahesmaa R*
Published in: Diabetes Care, 2022, ISSN 0149-5992
Publisher: American Diabetes Association
DOI: 10.2337/dc21-2120

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

Author(s): Suomi T, Elo LL
Published in: Immunology Letters, 2022, ISSN 0165-2478
Publisher: Elsevier BV
DOI: 10.1016/j.imlet.2022.03.006

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

Author(s): Pietilä S, Suomi T, Aakko J, Elo LL
Published in: Functional Proteomics: Methods in Molecular Biology, 2019, ISBN 978-1-4939-8813-6
Publisher: Humana New York, NY
DOI: 10.1007/978-1-4939-8814-3_27

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

Author(s): Jaakkola MK, Suomi T, Kukkonen-Macchi A, Elo LL.
Published in: bioRxiv, 2022
Publisher: bioRxiv
DOI: 10.1101/2022.06.21.497110

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

Author(s): Välikangas T, Suomi T, Chandler CE, Scott AJ, Tran BQ, Ernst RK, Goodlett DR, Elo LL
Published in: bioRxiv, 2022
Publisher: bioRxiv
DOI: 10.1101/2021.04.19.440388