u Kimmo Palin
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Kimmo Palin

CV

Kimmo Palin
Ph.D.
Genome-Scale Biology Program & 
Finnish Center of Excellence in Cancer Genetics Research
Biomedicum Helsinki
P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

Tel. +358- nine - one nine one 25681
Mob. +358- five zero - three three nine 2372
E-mail: kpalin-3cf4baa69a676819f20181019-@cs.helsinki.fi


Research

I got my PhD. in Computer Science on 20.12.2007 at University Of Helsinki. Up to July 2012, I was PostDoc at the Wellcome Trust Sanger Institute near Cambridge, UK

My research intrests are bioinformatics and computational biology. My training in Uni. Helsinki is based on algorithmics so I prefer "nice and neat" combinatorial problems with clear answers. Of course biology is not usually nice and neat.

ORCID 0000-0002-4621-6128, Google scholar citations.

Software

Teaching

Publications

Peer reviewed

  1. Identity-by-descent-based phasing and imputation in founder populations using graphical models By Palin, K., Campbell, H., Wright, A. F., Wilson, J. F. and Durbin, R. (2011), Genetic Epidemiology. doi: 10.1002/gepi.20635 pdf SLRP software
  2. Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo By Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J. EMBO J. 2010 Jun 1. [Epub ahead of print]
  3. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities By Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J. Genome Res. 2010 Jun;20(6):861-73. Epub 2010 Apr 8.
  4. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. By Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, ... Kimmo Palin, ... Donnelly P Nature Nature. 2010 Apr 1;464(7289):713-20.
  5. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. By Sari Tuupanen, Mikko Turunen, Rainer Lehtonen, Outi Hallikas, Sakari Vanharanta, Teemu Kivioja, Mikael Björklund, Gonghong Wei, Jian Yan, Iina Niittymäki, Jukka-Pekka Mecklin, Heikki Järvinen, Ari Ristimäki, Mariachiara Di-Bernardo, Phil East, Luis Carvajal-Carmona, Richard S Houlston, Ian Tomlinson, Kimmo Palin,, Esko Ukkonen, Auli Karhu, Jussi Taipale & Lauri A Aaltonen. Nature Genetics 41, 885 - 890 (2009)
  6. Integrating sequence, evolution and functional genomics in regulatory genomics. By Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E. Genome Biol. 2009 Jan 30;10(1):202.
  7. Locating potential enhancer elements by comparative genomics using the EEL software By Kimmo Palin, Jussi Taipale and Esko Ukkonen. Nature Protocols 1(1), 27. June 2006, Pages 368-374.
  8. Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen and Jussi Taipale. CELL 124(1), 13 January 2006, Pages 47-59. The EEL software is available.. Article pdf. Algorithmic supplement.
  9. From Gene Networks to Gene Function by Schlitt, T., Palin, K., Rung, J., Dietmann, S., Lappe, M., Ukkonen, E., Brazma, A. Genome Res. 2003 13: p. 2568-2576
  10. Correlating Gene Promoters and Expression in Gene Disruption Experiments by Kimmo Palin, Esko Ukkonen, Alvis Brazma and Jaak Vilo, in European Conference on Computational Biology 2002. Bioinformatics 2002 Oct;18 Suppl 2:S172-80.
    Supplemental Data

Theses

Other

Photography

I've started a new hobby on Black and White photography. Joined the Ylioppilaskamerat, took the Black and White course and started shooting. Some of the results can be seen here.

Old School work and Sofware

I have completed my studies and a lot of things have been done during that time. I have done some exercises such as

During the academic year 2000-2001 I was in ISEP exchange in University Of South Carolina in Columbia South-Carolina, USA. From there I have a lot of pictures.

Last but not the least, my TKK91 simulator (available also in RPM for RedHat users. Version RH 7.3 and RH 9.0 Courtesy Jonas Franz) got a whole lot more popular when our department blocked all MS-Windows logins due to security concerns just when Computer Organization I course need the old KOKSI simulator.


Kimmo Palin
Last modified: Mon Apr 28 13:47:22 EEST 2008