Olof Emanuelsson - Royal Institute of Technology (KTH)

http://www.biotech.kth.se/~olof.emanuelsson/
[A picture of me]

News

Since May 2010, we're located at the new Science for Life Laboratory on the Karolinska Institutet campus.

Introduction

In May 2009 I started my current position as assistant professor ("forskarassistent" in Swedish) at the School of Biotechnology at the Royal Institute of Technology (KTH). I'm also associated with the Science for Life Laboratory. My position is funded by the Swedish Research Council (VR).

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 relationship between histone modification, gene regulation, and gene expression; 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.

Teaching

During the 2010-2011 academic year I will organize or co-organize the following classes:
[BB2440]: Bioinformatics and biostatistics, 7.0 hp. Aug 2010-Oct 2010.
[BB2490]: Analysis of Data fram High-throughput Molecular Biology Experiments, 7.5 hp. Jan 2011-Mar 2011.

Short bio

2009-         Assistant professor, Biotechnology, KTH
2008-2010         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

visiting address:
Office A3651 (3rd floor, which is one floor up from main entrance)
Tomtebodavägen 23A (α-house)
Science for Life Laboratory
SE-17165 Solna, SWEDEN
map [eniro.se]
map [hitta.se]

postal address:
KTH - Royal Institute of Technology
SciLifeLab
Box 1031
SE-17121 Solna, SWEDEN

email: olof.emanuelssonNo_Spam@biotech.kth.se (remove "No_Spam" and any characters you deem superfluous)
phone: +46-8-5248 1458
fax: +46-8-5248-1425

Publications (21 in total)

PubMed entries of all published articles.

[21] Klevebring D, Fagerberg L, Lundberg E, Emanuelsson O, Uhlén M, Lundeberg J (2010): Analysis of transcript and protein overlap in a human osteosarcoma cell line. BMC Genomics 11: e684 (BMC Genomics) (PubMed)

[20] Klevebring D, Bjursell M, Emanuelsson O, Lundeberg J (2010): In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines. PLoS ONE 5: e9762 (PLoS ONE) (PubMed)

[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


My old web site.

2010-12-08