| The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color JC Motamayor, K Mockaitis, J Schmutz, N Haiminen, DL Iii, O Cornejo, ... Genome biology 14, 1-25, 2013 | 312 | 2013 |
| Human skin, oral, and gut microbiomes predict chronological age S Huang, N Haiminen, AP Carrieri, R Hu, L Jiang, L Parida, B Russell, ... Msystems 5 (1), 10.1128/msystems. 00630-19, 2020 | 108 | 2020 |
| Challenges in benchmarking metagenomic profilers Z Sun, S Huang, M Zhang, Q Zhu, N Haiminen, AP Carrieri, ... Nature methods 18 (6), 618-626, 2021 | 107 | 2021 |
| Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity JP Shaffer, LF Nothias, LR Thompson, JG Sanders, RA Salido, ... Nature Microbiology 7 (12), 2128-2150, 2022 | 86 | 2022 |
| Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences AP Carrieri, N Haiminen, S Maudsley-Barton, LJ Gardiner, B Murphy, ... Scientific reports 11 (1), 4565, 2021 | 86 | 2021 |
| Phylogeny-aware analysis of metagenome community ecology based on matched reference genomes while bypassing taxonomy Q Zhu, S Huang, A Gonzalez, I McGrath, D McDonald, N Haiminen, ... Msystems 7 (2), e00167-22, 2022 | 61* | 2022 |
| Segmentation and dimensionality reduction E Bingham, A Gionis, N Haiminen, H Hiisilä, H Mannila, E Terzi Proceedings of the 2006 SIAM International Conference on Data Mining, 372-383, 2006 | 61 | 2006 |
| SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment C Marotz, P Belda-Ferre, F Ali, P Das, S Huang, K Cantrell, L Jiang, ... Microbiome 9 (1), 132, 2021 | 58* | 2021 |
| GenomicTools: a computational platform for developing high-throughput analytics in genomics A Tsirigos, N Haiminen, E Bilal, F Utro Bioinformatics 28 (2), 282-283, 2012 | 51 | 2012 |
| Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results N Haiminen, DN Kuhn, L Parida, I Rigoutsos PloS one 6 (9), e24182, 2011 | 46 | 2011 |
| Application of genome wide association and genomic prediction for improvement of cacao productivity and resistance to black and frosty pod diseases JA Romero Navarro, W Phillips-Mora, A Arciniegas-Leal, A Mata-Quirós, ... Frontiers in Plant Science 8, 1905, 2017 | 44 | 2017 |
| EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets K Cantrell, MW Fedarko, G Rahman, D McDonald, Y Yang, T Zaw, ... MSystems 6 (2), 10.1128/msystems. 01216-20, 2021 | 38 | 2021 |
| Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity C Martino, BP Kellman, DR Sandoval, TM Clausen, CA Marotz, SJ Song, ... BioRxiv, 2020.08. 17.238444, 2020 | 37 | 2020 |
| Food authentication from shotgun sequencing reads with an application on high protein powders N Haiminen, S Edlund, D Chambliss, M Kunitomi, BC Weimer, B Ganesan, ... NPJ science of food 3 (1), 24, 2019 | 36 | 2019 |
| Monitoring the microbiome for food safety and quality using deep shotgun sequencing KL Beck, N Haiminen, D Chambliss, S Edlund, M Kunitomi, BC Huang, ... npj Science of Food 5 (1), 3, 2021 | 34 | 2021 |
| Functional profiling of COVID-19 respiratory tract microbiomes N Haiminen, F Utro, E Seabolt, L Parida Scientific Reports 11 (1), 6433, 2021 | 31* | 2021 |
| Randomization methods for assessing data analysis results on real‐valued matrices M Ojala, N Vuokko, A Kallio, N Haiminen, H Mannila Statistical Analysis and Data Mining: The ASA Data Science Journal 2 (4 …, 2009 | 28 | 2009 |
| DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid E Ganda, KL Beck, N Haiminen, JD Silverman, B Kawas, BD Cronk, ... Msystems 6 (3), 10.1128/msystems. 00619-21, 2021 | 26 | 2021 |
| A topological data analysis approach on predicting phenotypes from gene expression data S Mandal, A Guzmán-Sáenz, N Haiminen, S Basu, L Parida International Conference on Algorithms for Computational Biology, 178-187, 2020 | 26 | 2020 |
| Comparing segmentations by applying randomization techniques N Haiminen, H Mannila, E Terzi BMC bioinformatics 8, 1-8, 2007 | 26 | 2007 |