Photo of Timo Sipilä
  • PL 56 (Viikinkaari 9)

    00014

    Finland

20052018
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Personal profile

Curriculum vitae

Expertise:

  • Modern microbiology research from bench work to publications, data analysis and grant applications.
  • Wide knowledge of molecular techniques in biological research from qPCR to 454 pyrosequencing.
  • Good team work abilities with lots of experience in supervising lab work.
  • Excellent computer skills including bioinformatics and data analysis.

Business orientated with studies in Aalto University School of Economics (18 cr. marketing, 7 cr. Biobusiness modules I, II). 

Previous professional appointments:

2011 Instructor of Sanna Vesterinen lab training 10.01-08.04

2010 Instructor of Heidi Hulkko lab training 24.05-21.08.

2009 Instructor of Miriam Kellock lab training 01.06-31.08.

2009-2011 Post doctoral researcher, University of Helsinki, Department of Agricultural Sciences,”Sustainable cultivation methods for agriculture – increasing soil crop cover and optimizing ecosystem services of soil microorganisms(SUCCESS)”                                       

2008 Instructor of Master of Science thesis, Pave Väisänen: Expression of aromatic degradation genes in Sphingobium sp. HV3 agrestis. 

2006 Part time teacher, 18.09-29.09, University of Helsinki, Department of Bio- and environmental sciences, Lab course of Gene technology.

2006 Instructor of bachelor thesis, Anna-Kaisa Keskinen: Effec of PAH compounds on microbial community with extradiol dioxygenase gene in bulk soil and in rhizosphere of two different birch clones.          

2005 Instructor of bachelor thesis, Heini Harjunen: Analysis of polycyclic aromatic compounds and their metabolites using the GC-MS.

2004-201 Graduate student in University of Helsinki, Department of biosciences. Title of dissertation: Plasmids and aromatic degradation in Sphingomonas for bioremediation - Aromatic ring-cleavage genes in soil and rhizosphere

2004 ATK Support, 20.08-31.12, Simia Oy, Technical support person.     

2003 Researcher 10.3 - 31.10, North Savo Environment Centre, Research topic: Genetic diversity of yellow lady ´s lip (Cypripedium calceolus) in North Savo.  

2002 Trainee 1.6 - 31.8, North Savo Environment Centre, Research department. 

2002 Part time teacher 28.1 - 11.2, North Karelia Polytechnic, Practical course of molecular biology.

2001 Part time teacher 29.10 - 22.11, North Karelia Polytechnic, Lectures of molecular biology.

2001 Part time teacher 10.09 - 09.10, University of Joensuu, Biochemistry exercise “Isolation of acidic phosphatase”.          

2001 Research assistant 01.06 - 31.08, University of Joensuum, Molecular biology lab of Professor Tuomas Sopanen.

2000 Research assistant 01.06 - 31.08, University of Joensuu Molecular biology lab of Professor Tuomas Sopanen.

Education information

Doctor of Philosophy, General Microbiology, University of Helsinki, 11.08.2010.
Title of dissertation: Plasmids and aromatic degradation in Sphingomonas for bioremediation - Aromatic ring-cleavage genes in soil and rhizosphere.

Master of Science (MSc.), Biology, University of Joensuu, 30.04.2003
Title of pro gradu: Characterization of BpMADS5 gene promoter region

Keywords

  • 1183 Plant biology, microbiology, virology
  • Plant pathogen interactions
  • Microbial community fingerprinting
  • Cell Biology
  • Xenobiotic conversion
  • Genomics
  • Next generation sequencing

International and National Collaboration Publications and projects within past five years.

Publications 2005 2018

  • 13 Article
  • 8 Conference contribution
  • 1 Chapter
  • 1 Conference article

Nordic Exome Variant Catalogue a Web Resource for Genomic Data Browsing

Sipilä, T. P., Metspalu, A., Häppölä, P., Palta, P., Kals, M. & Palotie, A., 2018, 2018 IEEE 14th International Conference on e-Science (e-Science). IEEE, p. 393 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi, J., Smolander, O-P., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., Lamminmäki, A., Immanen, J., Lan, T., Tanskanen, J., Rastas, P., Amiryousefi, A., Jayaprakash, B., Kammonen, J. I., Hagqvist, R., Eswaran, G., Ahonen, V. H., Serra, J. A., Asiegbu, F. O., Barajas-Lopez, J. D. D. & 65 othersBlande, D., Blokhina, O., Blomster, T., Broholm, S., Brosche, M., Cui, F., Dardick, C., Ehonen, S. E., Elomaa, P., Escamez, S., Fagerstedt, K. V., Fujii, H., Gauthier, A., Gollan, P. J., Halimaa, P., Heino, P. I., Himanen, K., Hollender, C., Kangasjarvi, S., Kauppinen, L., Kelleher, C. T., Kontunen-Soppela, S., Koskinen, J. P., Kovalchuk, A., Karenlampi, S. O., Kärkönen, A. K., Lim, K-J., Leppälä, J., Macpherson, L., Mikola, J., Mouhu, K., Mähönen, A. P., Niinemets, U., Oksanen, E., Overmyer, K., Palva, E. T., Pazouki, L., Pennanen, V., Puhakainen, T., Poczai, P., Possen, B. J. H. M., Punkkinen, M., Rahikainen, M. M., Rousi, M., Ruonala, R., van der Schoot, C., Shapiguzov, A., Sierla, M., Sipilä, T. P., Sutela, S., Teeri, T. H., Tervahauta, A. I., Vaattovaara, A., Vahala, J., Vetchinnikova, L., Welling, A., Wrzaczek, M., Xu, E., Paulin, L. G., Schulman, A. H., Lascoux, M., Albert, V. A., Auvinen, P., Helariutta, Y. & Kangasjarvi, J., 8 May 2017, In : Nature Genetics. 49, 6, p. 904-912 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Rhizoremediation in Cold Climates

Yrjälä, K., Sipilä, T. P. & Mukherjee, S., 2017, Psychrophiles: From Biodiversity to Biotechnology. Margesin, R. (ed.). Cham: Springer , p. 661-685 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapterScientific

Isolation and characterization of resident yeasts from the phylloplane of Arabidopsis thaliana

Wang, K., Sipilä, T. P. & Overmyer, K. L., Dec 2016, In : Scientific Reports. 6, 13 p., 39403.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Increased transcriptome sequencing efficiency with modified Mint-2 digestion-ligation protocol

Kammonen, J. I., Smolander, O-P., Sipilä, T., Overmyer, K., Auvinen, P. & Paulin, L., 15 May 2015, In : Analytical Biochemistry. 477, p. 38-40 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Projects 2006 2011

Peatland Ecology Group in the University of Helsinki (PEATLANDERS)

Badorek, T., Jauhiainen, J., Juottonen, H., Juutinen, S., Kaila, A., Kojola, S., Koskinen, M., Kotiaho, M., Laiho, R., Laine, A., Lampela, M., Larmola, T., Leppälä, M., Maanavilja, L., Minkkinen, K., Mäkiranta, P., Ojanen, P., Pearson, M., Peltoniemi, K., Putkinen, A., Riutta, T. E., Sarkkola, S., Seppä, H., Sipilä, T., Straková , P., Tuittila, E., Ťupek, B., Vasander, H., Väliranta, M., Yli-Petäys, M. & Yrjälä, K.

23/02/2011 → …

Project: Research Evaluation 2011

Öljyllä saastuneen maan metagenomiikka

Mukherjee, S., Sipilä, T. & Yrjälä, K.

01/01/2010 → …

Project: Research project

Burkholderia bacteria for bioremediation of PAHs

Yrjälä, K., Andreolli, M., Mukherjee, S. & Sipilä, T.

01/01/2009 → …

Project: Research project

Haavan kehittäminen ympäristöbioteknillisiä sovelluksia varten

Yrjälä, K., Mukherjee, S., Sipilä, T. & Pulkkinen, P.

01/01/2006 → …

Project: Research project

Activities 2005 2017

  • 7 Peer review of manuscripts
  • 1 Organisation and participation in conferences, workshops, courses, seminars
  • 1 Supervisor or co-supervisor of doctoral thesis

Journal of Basic Microbiology (Journal)

Timo Sipilä (Reviewer)
13 Oct 2017

Activity: Publication peer-review and editorial work typesPeer review of manuscripts

Applied Soil Ecology (Journal)

Timo Sipilä (Reviewer)
1 Aug 2017

Activity: Publication peer-review and editorial work typesPeer review of manuscripts

Canadian Journal of Plant Pathology (Journal)

Timo Sipilä (Reviewer)
24 Jul 2017

Activity: Publication peer-review and editorial work typesPeer review of manuscripts

Pedosphere (Journal)

Timo Sipilä (Reviewer)
16 Mar 2016

Activity: Publication peer-review and editorial work typesPeer review of manuscripts

Soil Science Society of America Journal (Journal)

Timo Sipilä (Reviewer)
24 Mar 2016

Activity: Publication peer-review and editorial work typesPeer review of manuscripts