Publications

2017

Lietzen N, An LTT, Jaakkola MK, Kallionpää H, Oikarinen S, Mykkänen J, Knip M, Veijola R, Ilonen J, Toppari J, Hyöty H, Lahesmaa R, Elo LL. Enterovirus-Associated Changes in Blood Transcriptomic Profiles of Children with Genetic Susceptibility to Type 1 Diabetes. To appear in Diabetologia.

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*. A DREAM Challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer.  (*shared senior author) JCO Clinical Cancer Informatics, no. 1 (September 2017) 1-15. doi: 10.1200/CCI.17.00018

Rautakorpi LK, Seyednasrollah F, Mäkelä JM, Hirvonen OM, Laitinen T, Elo LL, Jyrkkiö SM. End-of-life chemotherapy use at a Finnish university hospital: a retrospective cohort study. Acta Oncol. 2017 May 31:1-5. doi: 10.1080/0284186X.2017.1332424. [Epub ahead of print]

Välikangas T, Suomi T, Elo LL. A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation. Brief Bioinform. 2017 May 31. doi: 10.1093/bib/bbx054. [Epub ahead of print]

Suomi T, Seyednasrollah F, Jaakkola MK, Faux T, Elo LL. ROTS: An R package for reproducibility-optimized statistical testing. PLOS Computational Biology 2017, 13(5): e1005562. https://doi.org/10.1371/journal.pcbi.1005562

Rautakorpi LK, Mäkelä JM, Seyednasrollah F, Hammais AM, Laitinen T, Hirvonen OM, Minn H, Elo LL, Jyrkkiö SM. Assessing the utilization of radiotherapy near end of life at a Finnish University Hospital: a retrospective cohort study. Acta Oncol. 2017 May 13:1-7. doi: 10.1080/0284186X.2017.1324638. [Epub ahead of print]

Suomi T, Elo LL. Enhanced differential expression statistics for data-independent acquisition proteomics. Sci Rep. 2017 Jul 19;7(1):5869. doi: 10.1038/s41598-017-05949-y.

Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM. HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma. Cancer Metab. 2017 Jul 4;5:5. doi: 10.1186/s40170-017-0167-y.

Seyednasrollah F, Mahmoudian M, Rautakorpi L, Hirvonen O, Laitinen T, Jyrkkiö S, Elo LL. Reply to Tuomas Mirtti and Tero Aittokallio’s Letter to the Editor re: Fatemeh Seyednasrollah, Mehrad Mahmoudian, Liisa Rautakorpi, et al. How Reliable are Trial-based Prognostic Models in Real-world Patients with Metastatic Castration-resistant Prostate Cancer? Eur Urol. 2017;71:838-40. pii: S0302-2838(17)30341-X. doi: 10.1016/j.eururo.2017.04.031. [Epub ahead of print]

Fatemeh Seyednasrollah, Mehrad Mahmoudian, Liisa Rautakorpi, Outi Hirvonen, Tarja Laitinen, Sirkku Jyrkkiö, Laura L. Elo. How Reliable are Trial-based Prognostic Models in Real-world Patients with Metastatic Castration-resistant Prostate Cancer? European Urology, Feb 8, 2017. doi: 10.1016/j.eururo.2017.01.043

Välikangas T, Suomi T, Elo LL. A systematic evaluation of normalization methods in quantitative label-free proteomics. Brief Bioinform. 2016 Oct 2. pii: bbw095. [Epub ahead of print]

Nuotio J, Pitkänen N, Magnussen CG, Buscot MJ, Venäläinen MS, Elo LL, Jokinen E, Laitinen T, Taittonen L, Hutri-Kähönen N, Lyytikäinen LP, Lehtimäki T, Viikari JS, Juonala M, Raitakari OT. Prediction of Adult Dyslipidemia Using Genetic and Childhood Clinical Risk Factors: The Cardiovascular Risk in Young Finns Study. Circ Cardiovasc Genet. 2017 Jun;10(3). doi: 10.1161/CIRCGENETICS.116.001604.

Seyednasrollah F, Mäkelä J, Pitkänen N, Juonala M, Hutri-Kähönen N, Lehtimäki T, Viikari J, Kelly T, Li C, Bazzano L, Elo LL*, Raitakari OT*. Prediction of adulthood obesity using genetic and childhood clinical risk factors in the Cardiovascular Risk in Young Finns Study. To appear in Circ Cardiovasc Genet. (*equal contribution) [IF 3.808]

Jaakkola MK, Seyednasrollah F, Koivu L, Hirvonen O, Jyrkkiö S, Elo LL. Comparison of methods to detect differentially expressed genes between single-cell populations. To appear in Brief Bioinform.

Guinney J, Wang T, Laajala TD, Prostate Cancer Challenge DREAM Community, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC. A prognostic model to predict overall survival for patients with metastatic castration-resistant prostate cancer: results from a crowdsourced challenge using retrospective, open clinical trial data. Lancet Oncol. 2017 Jan;18(1):132-142. doi: 10.1016/S1470-2045(16)30560-5. [IF 26.509]

Suomi T, Elo LL. Accurate Detection of Differential Expression and Splicing Using Low-Level Features. Methods Mol Biol. 2017;1507:141-151. doi:10.1007/978-1-4939-6518-2_11

2016

Laajala TD, Seikkula H, Seyednasrollah F, Mirtti T, Boström PJ, Elo LL. Longitudinal modeling of ultrasensitive and traditional prostate-specific antigen and prediction of biochemical recurrence after radical prostatectomy. Sci Rep. 2016 Nov 2;6:36161. doi: 10.1038/srep36161.

Mehrad Mahmoudian*, Fatemeh Seyednasrollah*, Liisa Koivu, Outi Hirvonen, Sirkku Jyrkkiö, Laura L. Elo. A predictive model of overall survival in patients with metastatic castration-resistant prostate cancer. F1000Research. f1000research.com/articles/5-2674/v1 (*equal contribution)

Välikangas T, Suomi T and Elo LL. A systematic evaluation of normalisation methods in quantitative label-free proteomics. Briefings in Bioinformatics, 2016 Oct 2. doi: 10.1093/bib/bbw095

Kaukonen R, Mai A, Georgiadou M, Saari M, De Franceschi N, Betz T, Sihto H, Ventelä S, Elo LL, Jokitalo E, Westermarck J, Kellokumpu-Lehtinen PL, Joensuu H, Grenman R, Ivaska J. Normal stroma suppresses cancer cell proliferation via mechanosensitive regulation of JMJD1a-mediated transcription. Nat Commun. 7:12237, 2016. [IF 11.329]

Kohtala S, Theilmann W, Suomi T, Wigren HK, Stenberg T, Elo LL, Rokka A, Rantamäki T. Brief isoflurane anesthesia produces prominent phosphoproteomic changes in the adult mouse hippocampus. ACS Chem Neurosci. 7(6):749-56, 2016. [IF 4.348]

Jaakkola MK, Elo LL. Empirical comparison of structure-based pathway methods. Brief Bioinform. 17(2):336-45, 2016. [IF 8.399]

Jaakkola MK, Seyednasrollah F, Mehmood A and Elo LL. Comparison of methods to detect differentially expressed genes between single-cell populations. Briefings in Bioinformatics. 2016 Jul 3. doi: 10.1093/bib/bbw057.

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016 Jan 26;17(1):13. doi: 10.1186/s13059-016-0881-8.

Vehmas AP, Adam M, Laajala TD, Kastenmüller G, Prehn C, Rozman J, Ohlsson C, Fuchs H, Hrabě de Angelis M, Gailus-Durner V, Elo LL, Aittokallio T, Adamski J, Corthals G, Poutanen M, Strauss L. Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse. J Proteomics. 2016 Feb 5;133: 66-75. doi: 10.1016/j.jprot.2015.12.009.

Seyednasrollah F, Rantanen K, Jaakkola PM, Elo LL. ROTS: reproducible RNA-seq biomarker detector–prognostic markers for clear cell renal cell cancer. Nucleic Acids Res. 2016 Jan 8;44(1):e1. doi: 10.1093/nar/gkv806

Salomäki-Myftari H, Vähätalo LH, Ailanen L, Pietilä S, Laiho A, Hänninen A, Pursiheimo JP, Munukka E, Rintala A, Savontaus E, Pesonen U, Koulu MNeuropeptide Y Overexpressing Female and Male Mice Show Divergent Metabolic but Not Gut Microbial Responses to Prenatal Metformin Exposure. PLoS One. 2016 Sep 28;11(9):e0163805. doi: 10.1371/journal.pone.0163805.

Kemppainen K, Wentus N, Lassila T, Laiho A, Törnquist K. Sphingosylphosphorylcholine regulates the Hippo signaling pathway in a dual manner. Cell Signal. 2016 Dec;28(12):1894-1903. doi: 10.1016/j.cellsig.2016.09.004.

Mokkala K, Röytiö H, Munukka E, Pietilä S, Ekblad U, Rönnemaa T, Eerola E, Laiho A, Laitinen K. Gut Microbiota Richness and Composition and Dietary Intake of Overweight Pregnant Women Are Related to Serum Zonulin Concentration, a Marker for Intestinal Permeability. J Nutr. 2016

Konki M, Pasumarthy K, Malonzo M, Sainio A, Valensisi C, Söderström M, Emani MR, Stubb A, Närvä E, Ghimire B, Laiho A, Järveläinen H, Lahesmaa R, Lähdesmäki H, Hawkins RD, Lund RJ. Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells. Sci Rep. 2016 Feb 25;6:22190. doi: 10.1038/srep22190.

Vehniäinen ER, Bremer K, Scott JA, Junttila S, Laiho A, Gyenesei A, Hodson PV, Oikari AO. Retene causes multifunctional transcriptomic changes in the heart of rainbow trout (Oncorhynchus mykiss) embryos. Environ Toxicol Pharmacol. 2016 Jan;41:95-102. doi: 10.1016/j.etap.2015.11.015.

Klén R, Noponen T, Koikkalainen J, Lötjönen J, Thielemans K, Hoppela E, Sipilä H, Teräs M, Knuuti J. Evaluation of motion-correction methods for dual-gated cardiac positron emission tomography/computed tomography imaging. Nucl Med Commun. 2016 Sep;37(9):956-

Venäläinen MS, Mononen ME, Salo J, Räsänen LP, Jurvelin JS, Töyräs J, Virén T, Korhonen RK. Quantitative Evaluation of the Mechanical Risks Caused by Focal Cartilage Defects in the KneeSci Rep. 2016 Nov 29;6:37538. doi: 10.1038/srep37538.

Räsänen LP, Tanska P, Mononen ME, Lammentausta E, Zbýň Š, Venäläinen MS, Szomolanyi P, van Donkelaar CC, Jurvelin JS, Trattnig S, Nieminen MT, Korhonen RK. Spatial variation of fixed charge density in knee joint cartilage from sodium MRI – Implication on knee joint mechanics under static loading. J Biomech. 2016 Oct 3;49(14):3387-3396. doi: 10.1016/j.jbiomech.2016.09.011.

Marin-Riera M, Brun-Usan M, Zimm R, Välikangas T, Salazar-Ciudad I. Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model. Bioinformatics. 2016 Jan 15;32(2):219-25. doi: 10.1093/bioinformatics/btv527.

Older

Suomi T, Corthals GL, Nevalainen OS, Elo LL. Using Peptide-Level Proteomics Data for Detecting Differentially Expressed Proteins. J Proteome Res. 2015 Nov 6; 14(11): 4564-70. doi: 10.1021/acs.jproteome.5b00363

Pursiheimo A, Vehmas AP, Afzal S, Suomi T, Chand T, Strauss L, Poutanen M, Rokka A, Corthals GL, Elo LL. Optimization of Statistical Methods Impact on Quantitative Proteomics Data. J Proteome Res. 2015 14(10): 4118-4126. doi:10.1021/acs.jproteome.5b00183

Emani MR, Närvä E, Stubb A, Chakroborty D, Viitala M, Rokka A, Rahkonen N, Moulder R, Denessiouk K, Trokovic R, Lund R, Elo LL, Lahesmaa R. The L1TD1 Protein Interactome Reveals the Importance of Post-transcriptional Regulation in Human Pluripotency. Stem Cell Reports 4(3):519-528, 2015.

Seyednasrollah F, Laiho A, Elo LL. Comparison of methods for detecting differential expression in RNA-seq studies. Brief Bioinform. 2015 Jan 16(1):59-70.

An LTT, Pursiheimo A, Moulder R, Elo LL. Statistical Analysis of Protein Microarray Data: A Case Study in Type 1 Diabetes Research. Journal of Proteomics and Bioinformatics, vol. S12: 003, 2014. doi: 10.4172/jpb.S12-003

Laiho A, Elo LL. A Note on an Exon-based Strategy to Identify Differentially Expressed Genes in RNA-seq Experiments. PLoS ONE. 2014 Dec 26;9(12):e115964. doi: 10.1371/journal.pone.0115964.

Kallionpää H*, Elo LL*, Laajala E*, Mykkänen J, Ricaño-Ponce I, Vaarma M, Laajala TD, Hyöty H, Ilonen J, Veijola R, Simell T, Wijmenga C, Knip M, Lähdesmäki H, Simell O, Lahesmaa R. Innate immune activity is detected prior to seroconversion in children with HLA-conferred type 1 diabetes susceptibility. Diabetes. 2014 Jul;63(7): 2402-2414. doi: 10.2337/db13-1775. (*equal contribution)

Elo LL and Schwikowski B. Analysis of Time-Resolved Gene Expression Measurements Across Individuals. PLoS ONE. 2013; 8(12): e82340.

Kallio A, Elo LL. Optimizing Detection of Transcription Factor-Binding Sites in ChIP-seq Experiments. Methods Mol Biol. 2013; 1038: 181-91. doi: 10.1007/978-1-62703-514-9_11.

Lahti L, Torrente A, Elo LL, Brazma A, Rung J. A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. Nucleic Acids Res. 2013 May 41(10): e110. doi: 10.1093/nar/gtk229.

Elo LL, Schwikowski B. Mining proteomic data for biomedical research. Invited review. WIREs Data Mining Knowl Discov. 2012 2(1): 1-13.

Nylund C, Rappu P, Pakula E, Heino A, Laato L, Elo LL, Vihinen P, Pyrhönen S, Owen GR, Larjava H, Kallajoki M, Heino J. Melanoma-associated cancer-testis antigen 16 (CT16) regulates the expression of apoptotic and antiapoptotic genes and promotes cell survival. PLoS One. 2012; 7(9): e45382. doi: 10.1371/journal.pone.0045382.

Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T. Optimized detection of transcription factor binding sites in ChIP-seq experiments. Nucleic Acids Res. 2012 Jan 40(1): e1, 2012. doi: 10.1093/nar/gkr839.

Lahti L, Elo LL, Aittokallio T, Kaski S. Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays. IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar 8(1): 217-225. doi: 10.1109/TCBB.2009.38.

Elo LL*, Järvenpää H*, Tuomela S*, Raghav S*, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R. Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity. 2010 Jun 25;32(6): 852-862. doi: 10.1016/j.immuni.2010.06.011.  (*equal contribution)

Elo LL*, Mykkänen J*, Nikula T, Järvenpää H, Simell S, Aittokallio T, Hyöty H, Ilonen J, Veijola R, Simell T, Knip M, Simell O, Lahesmaa R. Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling. J Autoimmun. 2010 Aug 35(1): 70-76. doi: 10.1016/j.jaut.2010.03.001. (*equal contribution)

Ahlfors H, Limaye A, Elo LL, Tuomela S, Burute M, Gottimukkala KV, Notani D, Rasool O, Galande S, Lahesmaa R. SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. Blood. 2010 Sep 2;116(9): 1443-1453. doi: 10.1182/blood-2009-11-252205.

Moulder R*, Lönnberg T*, Elo LL, Filén JJ, Rainio E, Corthals G, Oresic M, Nyman TA, Aittokallio T, Lahesmaa R. Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation. Mol Cell Proteomics. 2010 Sep 9(9): 1937-1953. doi: 10.1074/mcp.M900483-MCP200. (*equal contribution)

Laajala TD, Raghav S, Tuomela S, Lahesmaa R*, Aittokallio T*, Elo LL. A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics. 2009 10:618. doi: 10.1186/1471-2164-10-618. (*equal contribution)

Laajala E, Aittokallio T, Lahesmaa R, Elo LL. Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biol. 2009 10: R77. doi: 10.1186/gb-2009-10-7-r77.