| A survey of best practices for RNA-seq data analysis A Conesa, P Madrigal, S Tarazona, D Gomez-Cabrero, A Cervera, ... Genome biology 17, 1-19, 2016 | 3012 | 2016 |
| Comparison of software packages for detecting differential expression in RNA-seq studies F Seyednasrollah, A Laiho, LL Elo Briefings in bioinformatics 16 (1), 59-70, 2015 | 517 | 2015 |
| A systematic evaluation of normalization methods in quantitative label-free proteomics T Välikangas, T Suomi, LL Elo Briefings in bioinformatics 19 (1), 1-11, 2018 | 299 | 2018 |
| Six-week endurance exercise alters gut metagenome that is not reflected in systemic metabolism in over-weight women E Munukka, JP Ahtiainen, P Puigbó, S Jalkanen, K Pahkala, A Keskitalo, ... Frontiers in microbiology 9, 2323, 2018 | 197 | 2018 |
| Innate immune activity is detected prior to seroconversion in children with HLA-conferred type 1 diabetes susceptibility H Kallionpää, LL Elo, E Laajala, J Mykkänen, I Ricano-Ponce, M Vaarma, ... Diabetes 63 (7), 2402-2414, 2014 | 190 | 2014 |
| Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming LL Elo, H Järvenpää, S Tuomela, S Raghav, H Ahlfors, K Laurila, B Gupta, ... Immunity 32 (6), 852-862, 2010 | 172 | 2010 |
| A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments TD Laajala, S Raghav, S Tuomela, R Lahesmaa, T Aittokallio, LL Elo BMC genomics 10, 1-15, 2009 | 162 | 2009 |
| Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open … J Guinney, T Wang, TD Laajala, KK Winner, JC Bare, EC Neto, SA Khan, ... The Lancet Oncology 18 (1), 132-142, 2017 | 161 | 2017 |
| Systematic evaluation of differential splicing tools for RNA-seq studies A Mehmood, A Laiho, MS Venäläinen, AJ McGlinchey, N Wang, LL Elo Briefings in bioinformatics 21 (6), 2052-2065, 2020 | 149 | 2020 |
| Improving missing value estimation in microarray data with gene ontology J Tuikkala, L Elo, OS Nevalainen, T Aittokallio Bioinformatics 22 (5), 566-572, 2006 | 141 | 2006 |
| A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation T Välikangas, T Suomi, LL Elo Briefings in bioinformatics 19 (6), 1344-1355, 2018 | 138 | 2018 |
| Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process LL Elo, H Järvenpää, M Orešič, R Lahesmaa, T Aittokallio Bioinformatics 23 (16), 2096-2103, 2007 | 130 | 2007 |
| Normal stroma suppresses cancer cell proliferation via mechanosensitive regulation of JMJD1a-mediated transcription R Kaukonen, A Mai, M Georgiadou, M Saari, N De Franceschi, T Betz, ... Nature communications 7 (1), 12237, 2016 | 123 | 2016 |
| Gut microbiota composition is associated with temperament traits in infants AK Aatsinki, L Lahti, HM Uusitupa, E Munukka, A Keskitalo, S Nolvi, ... Brain, behavior, and immunity 80, 849-858, 2019 | 121 | 2019 |
| ROTS: An R package for reproducibility-optimized statistical testing T Suomi, F Seyednasrollah, MK Jaakkola, T Faux, LL Elo PLoS computational biology 13 (5), e1005562, 2017 | 117 | 2017 |
| Comparison of methods to detect differentially expressed genes between single-cell populations MK Jaakkola, F Seyednasrollah, A Mehmood, LL Elo Briefings in bioinformatics 18 (5), 735-743, 2017 | 111 | 2017 |
| Missing value imputation improves clustering and interpretation of gene expression microarray data J Tuikkala, LL Elo, OS Nevalainen, T Aittokallio BMC bioinformatics 9, 1-14, 2008 | 90 | 2008 |
| Reproducibility-optimized test statistic for ranking genes in microarray studies LL Elo, S Filén, R Lahesmaa, T Aittokallio IEEE/ACM transactions on computational biology and bioinformatics 5 (3), 423-431, 2008 | 83 | 2008 |
| SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation H Ahlfors, A Limaye, LL Elo, S Tuomela, M Burute, KVP Gottimukkala, ... Blood, The Journal of the American Society of Hematology 116 (9), 1443-1453, 2010 | 82 | 2010 |
| Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma S Hahtola, S Tuomela, L Elo, T Häkkinen, L Karenko, B Nedoszytko, ... Clinical Cancer Research 12 (16), 4812-4821, 2006 | 80 | 2006 |
