Note: As of June 2009, this web site is no longer maintained. Please visit my new home page.

Olof Emanuelsson - Royal Institute of Technology

http://www.sbc.su.se/~olofe/
[A picture of me]

News

As of May 2009 I've started a position as assistant professor ("forskarassistent" in Swedish) at the School of Biotechnology at the Royal Institute of Technology (KTH). The position is funded by the Swedish Research Council (VR).

I'm currently looking for students interested in doing a degree project (30hp), "exjobb", in my group. Suitable background is [a] knowledge of molecular biology and [b] programming experience.

All projects are purely theoretical/computational, no wet lab work. Therefore, programming experience of some kind is necessary but you don't have to be a pro. We are mostly using perl or other script languages.

Project descriptions will be submitted to exjobbspoolen, but interested students are encouraged to get in touch with me as soon as possible (see below for contact info).

Research interests

My current research interests include the bioinformatics aspects of next-generation sequencing based methods for transcription mapping ("RNA-seq") and regulatory sequence detection ("ChIP-seq"); physical gene clustering and chromatin-structure mediated gene regulation; the statistics and biochemistry of microarray experiments with particular focus on high-density tiling oligonucleotide microarrays; prediction of subcellular localization of proteins based on sequence signals; analysis of subcellular localization signals.

I participated in the development of web-accessible tools for (i) tiling array design, OligoTiler, and (ii) prediction of protein subcellular localization, ChloroP, TargetP, and PeroxiP. Locally running copies of the predictors ChloroP and TargetP are available, please contact software@cbs.dtu.dk for details.

Short bio

2009-         Assistant professor, Biotechnology, KTH
2008-         Guest Researcher, VBSG, Swedish University of Agricultural Sciences (SLU)
2005-2009 Research Associate, SBC, SU
2005-2006 Research Affiliate, MB&B, Yale
2003-2005 Post-doctoral fellow, Gerstein lab, Yale
1999-2003 Ph. D. DBB, Stockholm University
1998         Master of Science, Molecular Biotechnology Engineering (in English, in Swedish), Uppsala University

Contact info

postal address:
KTH - Royal Institute of Technology
School of Biotechnology
Albanova University Center
SE-10691 Stockholm, SWEDEN

visiting address:
Office B3:1001 (3rd floor, which is actually 2 floors down from main entrance)
Roslagstullsbacken 21
Albanova University Center
Stockholm, SWEDEN
map [hitta.se]

email: olof.emanuelssonNo_Spam@biotech.kth.se (remove "No_Spam")
phone: +46-8-5537-8317

Publications (19 in total)

PubMed entries of all published articles.

[19] Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk K J (2008): Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS ONE 23: e1994 (PubMed)

[18] Gerstein M B, Bruce C, Rozowsky J, Zheng D, Du J, Korbel J O, Emanuelsson O, Zhang Z D, Weissman S, Snyder M (2007): What is a gene, post-ENCODE? History and an updated definition Genome Res. 17: 669-681 (PubMed) [review]

[17] The ENCODE Project Consortium (2007): Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816 (PubMed)
> ENCODE main web site

[16] Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nature Protocols 2: 953-971 (PubMed) [review]

[15] Euskirchen G, Rozowsky J S, Wei C-L, Lee W H, Zhang Z D, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein M, Ruan Y, Snyder M (2007): Mapping of Transcription Factor Binding Regions in Mammalian Cells by ChIP: Comparison of Array and Sequencing Based Technologies. Genome Res. 17: 898-909 (PubMed)

[14] Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky J S, Urban A E, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein M (2007): Assessing the Performance of Different High-density Tiling Microarray Strategies for Mapping Transcribed Regions of the Human Genome. Genome Res. 17: 886-897 [Epub ahead of print 21 Nov 2006] (PubMed)
> Accompanying web site at Yale

[13] Royce T E, Rozowsky J S, Luscombe N M, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein M B (2006): Extrapolating traditional DNA microarray statistics to the tiling and protein microarray technologies Methods Enzymol. 411:282-311 (PubMed) [review]

[12] Bertone P, Trifonov V, Rozowsky J S, Schubert F, Emanuelsson O, Karro J, Kao M-Y, Snyder M, Gerstein M (2006): Design Optimization Methods for Genomic DNA Tiling Arrays. Genome Res. 16:271-281 (PubMed)

[11] White E J, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley E J, Weissman S, Gerstein M, Groudine M, Snyder M, Schübeler D (2004): DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc. Natl. Acad. Sci U S A 101:17771-17776 (PubMed)
> Replication timing web site at Yale

[10] The ENCODE Project Consortium (2004): The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306:636-640 (PubMed) [This is the ENCODE marker paper]
> ENCODE main web site

[9] Sun Q, Emanuelsson O, van Wijk K J (2004): Analysis of curated and predicted plastid subproteomes of Arabidopsis thaliana; Subcellular compartmentalization leads to distinctive proteome properties. Plant Physiology 135:723-734 (PubMed)
> Plastid proteome database

[8] Westerlund I, von Heijne G, Emanuelsson O (2003): LumenP --- A neural network predictor for protein localization in the thylakoid lumen. Protein Science 12:2360-2366 (PubMed)

[7] Emanuelsson O, Elofsson A, von Heijne G, Cristobal S (2003): In silico prediction of the peroxisomal proteome in fungi, plants and animals. J.Mol.Biol. 330:443-456 (PubMed)
> Supplemental material
> PeroxiP predictor of PTS1 peroxisomal proteins

[6] Emanuelsson O (2002): Predicting protein subcellular localisation from amino acid sequence information. Briefings in Bioinformatics 3:361-376 (PubMed) [review]

[5] Peltier J-B, Emanuelsson O, Kalume D E, Ytterberg J, Friso G, Rudella A, Liberles D A, Söderberg L, Roepstorff P, von Heijne G, van Wijk K J (2002): Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell 14:211-236 (PubMed)

[4] Emanuelsson O, von Heijne G (2001): Prediction of organellar targeting signals. Biochem. Biophys. Acta, 1541:114-119. (PubMed) [review]

[3] Emanuelsson O, von Heijne G, Schneider G (2001): Analysis and prediction of mitochondrial targeting peptides. Methods Cell Biol. 65:175-187 (PubMed) [review]

[2] Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000): Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J.Mol.Biol. 300:1005-1016 (PubMed)
> TargetP subcellular localization predictor

[1] Emanuelsson O, Nielsen H, von Heijne G (1999): ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Science 8:978-984. (PubMed)
> ChloroP predictor of chloroplast proteins


2009-06-04