PERSONAL INFORMATION

Family name, First name: Vähärautio (nee Saramäki), Anna

Researcher unique identifier(s): ResearcherID:  K-4279-2015, ORCID: orcid.org/0000-0003-4721-3954, Scopus Author ID: 54391753900

Date of birth: 1980-Feb-22

Nationality: Finnish

• EDUCATION

12/2008           PhD degree in Biochemistry from the Faculty of Natural and Environmental Sciences at the University of Kuopio (currently: University of Eastern Finland), Finland.

4/2004             MSc in biochemistry at the University of Kuopio, Finland (graded as excellent)

• CURRENTPOSITION

2015 – 2020    Academy of Finland Research Fellow (independent research position)

                        Medicum, Faculty of Medicine, University of Helsinki, Finland

• PREVIOUS POSITIONS

2012 – 2015    Senior Scientist, laboratory of Jussi Taipale

                        Genome-Scale Biology Program, University of Helsinki, Finland

2009 – 2012    Post-doctoral researcher, laboratory of Jussi Taipale

                        Department of Biosciences and Nutrition, Karolinska Institutet, Sweden

2009                Post-doctoral researcher, laboratory of Jussi Taipale

                        Genome-Scale Biology Program, University of Helsinki, Finland

2004 – 2008    PhD student, Faculty of Natural and Environmental Sciences

                        University of Kuopio, Finland.

• Main Grants

2015 – 2020   Academy Research Fellow (Academy of Finland, acceptance rate ~10%)

                      Medicum, Faculty of Medicine, University of Helsinki, Finland

2016 – 2020   H2020-PHC-2015

                      Medicum, Faculty of Medicine, University of Helsinki, Finland

2010 – 2012   Postdoctoral researcher’s grant (Academy of Finland, acceptance rate ~10%)

                      Department of Biosciences and Nutrition, Karolinska Institutet, Sweden / University of Helsinki, Finland

2009                Postdoctoral position in Sweden (Swedish Research Council, acceptance rate ~10%)

                        Granted funding terminated prematurely to start Academy of Finland grant. Department of Biosciences and Nutrition, Karolinska Institutet, Sweden

• SUPERVISION STUDENTS

2014-2015   Supervising MSc thesis of Matias Kinnunen in Faculty of Biological and Environmental Sciences, University of Helsinki, Finland, and thesis of specialisation studies in medicine of Tuomas Lohi, Faculty of Medicine, University of Helsinki, Finland.

• ORGANISATION OF SCIENTIFIC MEETINGS

2015                Single Cell Transcriptomics (Helsinki, Finland, May-27, 2015; Co-organiser with Dr. Päivi Saavalainen)

                        First international meeting on single-cell transcriptomics held in Finland. Speakers were international experts of the single-cell field, such as Mats Nilsson (SciLifeLab/Stockholm University, Sweden), Maria Kasper (Karolinska Institutet, Sweden), Dominic Grün (Hubrecht Institute, Netherlands) and Juha Kere, (Karolinska Institutet, Sweden/University of Helsinki, Finland) and the meeting attracted 140 participants.

• INVITED TALKS

                        Unique molecular identifiers for absolute quantitation in Genetic, epigenetic and functional aspects of complex diseases IV (GEF4): Special emphasis on epigenetics and bioinformatics, Kuopio, Finland, August 2014.

                        Counting absolute numbers of molecules using unique molecular identifiers in SRP Diabetes Mini- Symposium, Huddinge, Sweden, May 2012.

                        High throughput ChIP Sequencing in Sysdiet meeting 2/2010, Stockholm, Sweden, December 2010.

• MAJOR COLLABORATIONS

Sten Linnarsson, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden (Single-cell RNA-sequencing methodologies)

EU H2020 HERCULES network: Sampsa Hautaniemi from University of Helsinki, Finland (bioinformatics and sample co-ordination); Seija Grénman from Turku University Hospital, Department of Obstetrics and Gynaecology, Finland and Olli Carpén from University of Turku, Department of Pathology (clinical tumor material);  Tero Aittokallio and Krister Wennerberg from FIMM, Finland; Giorgio Stanta from University of Trieste, Italy; Jussi Taipale, Department of Biosciences and Nutrition, Karolinska Institutet, Sweden; Mauro Biffoni and Luca Pasquini from Istituto Superiore di Sanità, Italy; Benno Schwikowski from Institut Pasteur, France; Dino Paladin from AB ANALITICA S.R.L., Italy.

Kaisa Lehti, University of Helsinki, Finland and Karolinska Institutet, Sweden (Tumor derived cell cultures)

• CAREER BREAKS

Apr-4 - Dec-16, 2013, Jan-27 -Feb-14, 2014   Parental leave (9 months)

Oct-12, 2015 - Jul-31, 2016                            Parental leave (9 months planned).

• PUBLICATION SUMMARY

Published 10 peer-reviewed articles with 434 citations (Source: Web of Science), thus with on average ca. 40 citations per article. Highest journal impact factor (2014 edition) for first-authored paper: 32.072 (Nature Methods; Kivioja, Vähärautio et. al. 2012; 78 citations), also published a Report (Sur et. al. 2012; 2014; 61 citations) and wrote a Perspective (Vähärautio and Taipale, 2015) on Science (impact factor 33.611).

Complete list of publications 2006-2015:

A Peer-reviewed scientific articles: A1 Journal article (refereed), original research

Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander OP, Vogel H, McCoy RC, Qian K, Chong WS, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse‐Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. (2014) Nat Commun. 2014, 5:4737.

Turunen M, Spaeth JM, Keskitalo S, Park MJ, Kivioja T, Clark AD, Mäkinen N, Gao F, Palin K, Vähärautio A, Aavikko M, Kämpjärvi K, Nurkkala H, Vahteristo P, Kim CA, Aaltonen LA, Varjosalo M, Taipale J, Boyer TG. (2014) Uterine leiomyoma-linked MED12 mutations disrupt Mediator‐associated CDK activity. Cell Reports 7: 654-60. Cited 10 times.

Bonke M, Turunen M, Sokolova M, Vähärautio A, Kivioja T, Taipale M, Björklund M, Taipale J. (2013) Transcriptional networks controlling the cell cycle. G3 (Bethesda). 3:75-90.

Sur IK, Hallikas O, Vähärautio A, Yan J, Turunen M, Enge M, Taipale M, Karhu A, Aaltonen LA, Taipale J. (2012) Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors. Science. 338:1360-3. Cited 63 times.

Kivioja T*, Vähärautio A*, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J. (2012) Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 9, 72-74. * equal contribution. Cited 89 times.

Saramäki A, Diermeier S, Kellner R, Laitinen H, Väisänen S and Carlberg C. (2009) Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1α,25-dihydroxyvitamin D3, J Biol Chem. 284:8073-82.

Gravina S, Lescai F, Hurteau G, Brock GJ, Saramaki A, Salvioli S, Franceschi C, Roninson IB. (2009) Identification of single nucleotide polymorphisms in the p21 (CDKN1A) gene and correlations with longevity in the Italian population. Aging (Albany NY).1:470-80.

Malinen M*, Saramäki A*, Ropponen A, Degenhardt T, Väisänen S and Carlberg C. (2008) Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to trichostatin A and 1a,25-dihydroxyvitamin D3. Nucleic Acids Res. 36:121-32. *,  equal contribution

Degenhardt T, Saramäki A, Malinen M, Rieck M, Väisänen S, Huotari A, Herzig KH, Müller R, Carlberg C. (2007) Three members of the human pyruvate dehydrogenase kinase gene family are direct targets of the peroxisome proliferator-activated receptor beta/delta. J Mol Biol. 372: 341-55.

Carlberg C., Dunlop, TW, Saramäki A, Sinkkonen L, Matilainen M. and Väisanen S. (2007) Controlling the chromatin organization of vitamin D target genes by multiple vitamin D receptor binding sites. J Steroid Biochem Mol Biol. 103(3-5): 338-343.

Saramäki A, Banwell CM, Campbell MJ and Carlberg C. (2006) Regulation of the human p21(waf1/cip1) gene promoter via multiple binding sites for p53 and the vitamin D3 receptor. Nucleic Acids Res. 34:543-54. Cited 176 times.

B Non-refereed scientific articles

Vähärautio A, Taipale J. Perspective:Cancer by super-enhancer. (2014) Science 346:1291-2.

G Theses

G2 Master’s thesis

The synthesis and biological activity of N alkylated polyamine analogues. University of Kuopio, Finland. 04/2004.

G5 Doctoral dissertation

Regulation of the p21 (CDKN1A) Gene at the Chromatin level by 1α,25-dihydroxyvitamin D3. University of Kuopio, Finland. 12/2008; including articles:

Saramäki A, Diermeier S, Kellner R, Laitinen H, Väisänen S and Carlberg C. (2009) Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1α,25-dihydroxyvitamin D3, J Biol Chem. 284:8073-82.

Malinen M*, Saramäki A*, Ropponen A, Degenhardt T, Väisänen S and Carlberg C. (2008) Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to trichostatin A and 1a,25-dihydroxyvitamin D3. Nucleic Acids Res. 36:121-32. *,  equal contribution

Degenhardt T, Saramäki A, Malinen M, Rieck M, Väisänen S, Huotari A, Herzig KH, Müller R, Carlberg C. (2007) Three members of the human pyruvate dehydrogenase kinase gene family are direct targets of the peroxisome proliferator-activated receptor beta/delta. J Mol Biol. 372: 341-55.

Saramäki A, Banwell CM, Campbell MJ and Carlberg C. (2006) Regulation of the human p21(waf1/cip1) gene promoter via multiple binding sites for p53 and the vitamin D3 receptor. Nucleic Acids Res. 34:543-54.