Kivioja T*, Vähärautio A*, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J. (2012) Nat Methods. 9, 72- 74. (*equal contribution) 

This paper describes a universal method that can be applied to counting the absolute number of molecules in a given sample. This stems from the idea that if each molecule in a sample is made unique prior amplification - for example with addition of a random sequence tag - one can simply count the number of unique molecules from an amplified sample to obtain the original number of molecules. The method completely eliminates PCR bias, a common problem in accurately determining the number of RNA or DNA molecules in a cell. In this paper, the method was applied to RNA-seq and the authors showed that it can be can be used to improve accuracy of almost any next generation sequencing method, including ChIP- sequencing, genome assembly, diagnostic applications and manufacturing process control and monitoring. and has become a golden standard in quantitative single-cell RNA-sequencing. For this paper, Anna developed a custom RNA-seq library preparation method to include UMIs and performed the RNA-seq experiments (Cited 339 times; Source: Google Scholar).

Sur IK, Hallikas O, Vähärautio A, Yan J, Turunen M, Enge M, Taipale M, Karhu A, Aaltonen LA, Taipale J. (2012)  Science. 338:1360-3.

In this paper,  the authors generated mice lacking Myc- 335, a putative Myc regulatory element that contains rs6983267. rs6983267 is a colon-cancer associated SNP that accounts for more human cancer-related morbidity than any other genetic variant or mutation. In Myc-335 null mice, Myc transcripts were expressed at modestly reduced levels with a pattern similar to that of wild-type mice. The mutant mice displayed no overt phenotype but when crossed with APCmin mice, mutant mice were markedly resistant to intestinal tumourigenesis. These results highlight the fact that although a disease-associated polymorphism typically has a relatively modest effect size, the element that it affects can be critically important for the underlying pathological process. Thus, we may harbor switches that might not compromise the normal development but can be critical for disease pathogenesis. For this paper, Anna analyzed transcriptomics data from which the authors identified a modest decrease in Myc exon expression (Cited 151 times, Source: Google Scholar).

Bonke M, Turunen M, Sokolova M, Vähärautio A, Kivioja T, Taipale M, Björklund M, Taipale J. (2013) G3 (Bethesda). 3:75-90. 

In this paper, the authors studied transcriptional networks that regulate the cell cycle in Drosophila melanogaster, and found two interconnected feedback circuits, of which one controls overall protein homeostasis and connects mribosome and proteasome, and another that controls protein synthesis capacity and connects the ribosome and Myc/Max. For this study, Anna developed the basic library preparation methodology that she later adapted to molecule counting and applied this initial version to a large number of custom RNA-seq libraries for Drosophila RNAi samples (Cited 21 times; Source: Google Scholar).