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From longitudinal proteomics to dynamic individualized diagnostics

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Publications

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
DOI: 10.1172/jci129202

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
DOI: 10.1016/j.cels.2020.06.013

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, Issue 23/3, 2020, Page(s) 100947, ISSN 2589-0042
DOI: 10.1016/j.isci.2020.100947

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
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
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
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, Issue 61/2, 2018, Page(s) 381-388, ISSN 0012-186X
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, Issue 10/3, 2017, Page(s) e001554, ISSN 1942-3268
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, Issue 13/7, 2018, Page(s) e0199991, ISSN 1932-6203
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, Issue 22/8, 2018, Page(s) 2094-2106, ISSN 2211-1247
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, Issue 7/1, 2017, ISSN 2045-2322
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, Issue 13/5, 2017, Page(s) e1005562, ISSN 1553-7358
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, Issue 11, 2019, Page(s) 334-355, ISSN 2589-0042
DOI: 10.1016/j.isci.2018.12.020

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, Issue 10/1, 2020, ISSN 2045-2322
DOI: 10.1038/s41598-020-57924-9

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, Issue 4/4, 2020, ISSN 2472-1972
DOI: 10.1210/jendso/bvaa026

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, Issue 38/3, 2020, Page(s) 511-518, ISSN 0263-6352
DOI: 10.1097/hjh.0000000000002282

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, Issue 1, 2020, Page(s) 10-22, ISSN 2590-2555
DOI: 10.1016/j.crimmu.2020.02.001