CURRICULUM VITAE

Arne Elofsson

Contents

• .  Degrees, positions and examinas
  • Grants
  • .  Research Group

.  Name

Nils Arne Elofsson

.  Date of Birth

Date of Birth: 10 Dec. 1966
Citizenship: Swedish.
Place of Birth: Stockholm, Sweden
Personal number: 661210-0096

.  Home Address

Folkungagatan 56 5 tr
116 22 Stockholm
+46-8-6413158

.  Address

Dep. of Biochemistry and Biophysics
Stockholm University
106 91 Stockholm
Phone: +46-8-5537 8568
Fax: +46-8-5537 8412
Email: arne@sbc.su.se

.  Degrees, positions and examinas

.  Scientific positions

0.25

• Jul 1989 - Aug 1993 PhD-position in Medical Biophysics at Dept. of Medical Biophysics, Karolinska Institutet. 7 May 1993 Thesis, ``Biophysical Aspects of Proteins'', Supervised by Rudolf Rigler and Lennart Nilsson.

• Sep 1993 - Aug 1995 Postdoctoral fellowship from Swedish Research Council for engineering Sciences, with David Eisenberg at Molecular Biology Institute, UCLA.

• Sep 1995 - Nov 1999 Forskarassistent at Dept. of Biochemistry, University of Stockholm
• Dec 1999 -Jan 2006 Lektor at Dept of Biochemistry and Stockholm Bioinformatics Center (SBC)
• Dec 1999 -June 2005 Vice director at SBC
• Feb 2006 - Professor in Bioinformatics at Department of Biochemistry and Biophysics, Stockholm University

.  Parental leave

0.25

• April - July 2005

.  Schools:

0.25

• Aug 1973 - Jun 1985 Studies at Smedslättens skola, Ålstens skola, Äppelvikens skola and Bromma Gymnasium Stockholm, Sweden
• Aug 1985 - Jun 1986 Studies in engineering physics (Teknisk fysik) at Uppsala University, Uppsala, Sweden.
• Aug 1986 - Jun 1988 Studies in the MD/PhD program (läkarlinjen med forskarinriktning) at Karolinska Institutet, Stockholm, Sweden.
• Aug 1988 - Jun 1989 Studies in engineering physics at Uppsala University and Royal Institute of Technology, Stockholm, Sweden.
• Jul 1989 - Aug 1993 PhD. Studies in Molecular Biophysics at Dept. of Medical Biophysics, Karolinska Institutet.

.  Exams and Degrees:

0.25

• Med Kand degree at Karolinska Institutet: June 13 1988
• PhD (dr Med. Vetenskap) at Karolinska Institutet: May 7 1993.
• Docentur at Department of Biochemistry and Biophysics, Stockholm University April 28 1999
• Full Professorship at Department of Biochemistry and Biophysics, Stockholm University Febr 1, 2006

.  Languages:

0.25

• Swedish - native
• English - fluent
• Spanish - basic
• French - basic

Summary

• 75 scientific publications including
  • 61 publication in peer reviewed journals
  • 5 review articles
  • 6 publication in books/proceedings
  • 3 submitted articles
• Cited more than 2100 times (From Citation Index)
• More than 200 (300) citations per year since 2003 (2005)
• Average citation per paper: 34
• H-index 25 (since 1990, i.e. 1.5/year)

Articles in peer reviewed journals

• 1990
  1. Arne Elofsson , Lennart Nilsson and Rudolf Rigler ``Studies on somatostatin with time-resolved spectroscopy and molecular dynamics simulations'', Int. J. Pept. Prot. Res. 1990:36, 297-301.
• 1991
  1. Arne Elofsson, Rudolf Rigler, Lennart Nilsson, Johnny Roslund, Günter Krause and Arne Holmgren, ``Motion of aromatic side chains, picosecond fluorescence, and internal energy transfer in Escherichia Coli Thioredoxin Studied by site directed mutagenesis, time-resolved fluorescence spectroscopy, and molecular dynamic simulations.'' Biochemistry, 1991:30 9648-9656.

• 1992
  1. Chris Sander, Gerrit Vriend, Fernando Bazan, Amnon Horovitz, Haruki Nakamura, Luis Ribas, Alexei V. Finkelstein, Andrew Lockhart, Rainer Merkl, L. Jeanne Perry, Stephen C. Emery, Christine Gaboriaud, Cara Marks, John Moult, Christophe Verlinde, Marc Eberhard, Arne Elofsson, Tim J. P. Hubbard, Lynne Regan, Jay Banks, Roberto Jappelli, Arthur M. Lesk and Anna Tramontano, ``Protein Design on Computers. Five New Proteins: Shpilka, Grendel, Fingerclasp, Leather and Aida'' Proteins, Structure Function and Genetics; 1992:12, 105-110

• 1993
  1. Arne Elofsson and Lennart Nilsson, ``How consistent are Molecular Dynamics simulations ? A comparison between the structure and Dynamics of Reduced and Oxidised Escherichia Coli Thioredoxin.'' J. Mol. Biol. 1993:233, 766-780.

  2. Arne Elofsson and Lennart Nilsson, ``Free Energy Perturbations in Ribonuclease T1 Substrate Binding. Study of the Influence of Simulation Length, Internal Freedom and structure in Free Energy Perturbations'' Molecular Simulations 1993:10(2-6), 255-276.

  3. Arne Elofsson, Tadeusz Kolinski, Rudolf Rigler and Lennart Nilsson ``Site Specific Point Mutations Changes Specificity. A Molecular Modelling Study by Free Energy Simulations of the Thermodynamics in Ribonuclease T1 Substrate Interactions'' Proteins, Structure Function and Genetics 1993 17:161-175

• 1995
  1. Arne Elofsson, Scott LeGrand and David Eisenberg ``Local moves, an efficient method for protein folding simulations'' Proteins, Structure Function and Genetics 1995 23:73-82

• 1996
  1. Arne Elofsson and Lennart Nilsson, ``A 1.2 ns Molecular Dynamic Simulation of Ribonuclease T1-3'-Guanosine monophosphate complex'' J. Phys. Chem, 1996 100:2480-2488

  2. Arne Elofsson, Daniel Fischer, Danny W. Rice, Scott M. LeGrand and David Eisenberg ``A study of combined structure-sequence profiles'' 1996 Folding & Design 1:451-461

• 1997
  1. Miklos Cserzö, Erik Wallin, Istvan Simon, Gunnar von Heijne and Arne Elofsson, ``Prediction of transmembrane -helices: Application of the Dense Alignment Surface method'' Protein Engineering, 1997, 10(6):673-676

  2. Erik Wallin, Tomotake Tsukihara, Shinya Yoshikawa, Gunnar von Heijne and Arne Elofsson ``Architecture of helix bundle membrane proteins. An analysis of cytochrome c oxidase from bovine mitochondria.'', Protein Science 1997 6:808-815

  3. Ismael Mingarro, Arne Elofsson, Gunnar von Heijne ``Helix-helix packing in a membrane-like environment.'' , J. Mol. Biol. 1997 272(4):633-541

• 1998
  1. K. Seshadri, Robert Garemyr, Erik Wallin, Gunnar von Heijne and Arne Elofsson ``Architecture of -barrel membrane proteins: Analysis of trimeric porins'' Protein Science 1998 7(9):2026-2032

• 1999
  1. Jeanette Hargbo and Arne Elofsson ``Hidden Markov models that use predicted secondary structure for fold recognition'' , Proteins: Struct. Funct. Genet. 1999 36(1):68-76.

  2. Xiao-Ping Zhang, Arne Elofsson, David Andreu and Elzbieta Glaser ``Interaction of Mitochondrial presequences with DnaK and Mitochondrial hsp70'' , J. Mol. Biol. 1999 23;288(1):177-190.

  3. Arne Elofsson and Erik L.L. Sonnhammer ``A comparison of sequence and structure protein domain families as a basis for structural genomics.'' Bioinformatics 1999 15(6):480-500

  4. Lawrence A. Kelley, Robert M. MacCallum, Michael Sternberg, Kevin Karplus, Daniel Fischer, Arne Elofsson, Adam Godzik, Leszek Rychlewski, Krysztof Pawlowski, David Jones and Kevin Bryson ``CAFASP-1: Critical assessment of fully automated structure prediction.'' Proteins Struct. Funct. Genet. 1999; Suppl 3:209-217.

  5. Robert Garemyr and Arne Elofsson ``A study of the electrostatic treatment in molecular dynamics simulations'' Proteins, Struct. Funct. Genet. 1999 37(3):417-428

  6. Magnus Monné, IngMarie Nilsson, Arne Elofsson and Gunnar von Heijne ``Turns in transmembrane helices. Derivation of the minimal length of a ``helical hairpin'' and derivation of a fine-grained turn propensity scale. , J. Mol. Biol. 1999 293(4):807-814.

• 2000
  1. Erik Lindahl and Arne Elofsson ``Identification of related proteins, on family, superfamily and fold level.'' J. Mol. Biol. 2000 295:613-625

  2. Naomi Siew, Arne Elofsson, Leszek Rychlewski and Daniel Fischer ``MaxSub: An automated measure to assess the quality of protein structure predictions.'' Bioinformatics 2000 16(9):776-785

  3. Daniel Fischer, Arne Elofsson and Leszek Rychlewski ``The 2000 Olympic Games of Protein Structure Prediction'' Protein Engineering 2000 13(10):667-670

• 2001
  1. Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer and Leszek Rychlewski ``LiveBench-1: Continuous Benchmarking of Protein Structure Prediction Servers'' Protein Science 2001 10(2):352-361.

  2. Janusz M Bujnicki, Arne Elofsson, Daniel Fischer and Leszek Rychlewski ``Structure Prediction Meta Server'', Bioinformatics 2001 17: 750-751

  3. Olivia Eriksson, Yishao Zhou and Arne Elofsson ``Side chain-positioning as an integer programming problem.'' ``WABI 2001 1st Workshop on Algorithms in BioInformatics'' 2001

  4. Susana Cristobal, Adam Zemla, Daniel Fischer, Leszek Rychlewski and Arne Elofsson ``A study of quality measures for protein threading models.'', BMC Bioinformatics 2001 2:5.

  5. Jesper Lundström, Leszek Rychlewski,Janusz Bujnicki and Arne Elofsson ``Pcons: A neural network based consensus predictor that improves fold recognition.'' Protein Science 2001 10(11):2354-2362

  6. Daniel Fischer, Arne Elofsson, Leszek Rychlewski, Florencio Pazos, Alfonso Valencia, Burkhard Rost, Angel R. Ortiz, Roland L. Dunbrack ``CAFASP2: The second critical assessment of fully automated structure prediction methods'', Proteins Struct. Funct. Genet. 200145(Suppl 5):171-183

  7. Janusz M Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski ``LiveBench-2: large-scale automated evaluation of protein structure prediction servers.'' 2001 Proteins Struct. Funct. Genet. 45(Suppl 5):184-191

• 2002
  1. Arne Elofsson ``A study on protein sequence alignment quality.'' Proteins Struct. Funct. Genet. 2002 46(3):330-339

  2. David A. Liberles, Anna Thoren, Gunnar von Heijne and Arne Elofsson. ``The use of Phylogenetic profils for Gene Predictions'', Current Genomics 2002 3:131-137

  3. Maria Hedman, Hans De Loof, Gunnar von Heijne and Arne Elofsson ``Improved detection of homologous membrane proteins by inclusion of information from topology predictions,'' Protein Science 2002 11(3):652-658

  4. Pierre Dönnes and Arne Elofsson Prediction of MHC Class I Binding Peptides, using SVMHC, BMC: bioinformatics 2002 3(1):25
     This paper was rated ``highly accessed'' by BMC bioinformatics.

• 2003
  1. Krzysztof Ginalski, Arne Elofsson, Daniel Fischer and Leszek Rychlewski, ``3D-Jury: a simple approach to improve protein structure predictions'' Bioinformatics 2003 19(8):1015-1018.

  2. * Björn Wallner and Arne Elofsson ``Can correct protein models be identified ?'' , Protein Science 2003 12(5):1073-1086

  3. Olof Emanuelsson, Arne Elofsson, Gunnar von Heijne and Susana Cristobal ``In silico prediction of the peroxisomal proteome in fungi, plants and animals.'' , J. Mol. Biol 2003 330:443-456

  4. Björn Wallner, Huishang Fang and Arne Elofsson, ``Automatic consensus based fold recognition using Pcons, ProQ and Pmodeller.'' Proteins Struct. Funct. Genet. 2003 53(S6):534-541

  5. Leszek Rychlewski, Daniel Fischer and Arne Elofsson ``LiveBench-6: large-scale automated evaluation of protein structure prediction servers.'' Proteins Struct. Funct. Genet. 2003 53(S6):542-547

  6. Daniel Fischer, Leszek Rychlewski, Roland L. Dunbrack, Angel R. Ortiz and Arne Elofsson, ``CAFASP3: The third critical assessment of Fully Automated protein structure prediction methods.'' Proteins Struct. Funct. Genet. 2003 53(S6):503-516

• 2004
  1. Björn Wallner, Huisheng Fang, Tomas Ohlson, Johannes Frey-Skött and Arne Elofsson ``Using evolutionary information for the query and target improves fold recognition.'' , 2004 Proteins Struct. Funct. Genet. 54(2):342-350

  2. * Håkan Viklund and Arne Elofsson ``Best $\alpha$-helical transmembrane protein topology prediction are achieved using hidden Markov models and evolutionary information.'', Protein Science 2004 13(7):1908-1917.

  3. Tomas Ohlson, Björn Wallner and Arne Elofsson ``Profile-profile methods provide improved fold-recognition. A study of different profile-profile alignment methods.'', Proteins Struct. Funct. Genet. 2004 57(1):188-197.

• 2005
  1. * Ann-Charlotte Berglund, Björn Wallner, Arne Elofsson, and David A. Liberles. ``Tertiary Windowing to Detect Positive Selection'' J. Mol. Evol. 2005 60(4), 499-504

  2. * Erik Granseth, Gunnar von Heijne, Arne Elofsson ``A Study of the Membrane-Water Interface Region of Membrane Proteins'' J. Mol. Biol 2005 346(1):377-385.
     This paper was the 9'th hottest paper from JMB published between Jan and Mar of 2005.

  3. * Diana Ekman, Åsa K. Björklund, Sara Light, Johannes Frey-Skött and Arne Elofsson "Multi-domain proteins in the three kingdoms of life - Orphan domains and other unassigned regions." J. Mol. Biol 2005 348(1):231-243

  4. Björn Wallner and Arne Elofsson ``All are not equal. A benchmark of different homology modeling programs.'' Protein Science 2005 14(5), 1315-1327

  5. * Åsa K. Björklund, Diana Ekman, Sara Light, Johannes Frey-Skött and Arne Elofsson ``Domain rearrangements in protein evolution'' J. Mol. Biol 2005 353(4):911-923
     This paper was the 7'th hottest paper from J. Mol. Biol. published between Oct and Dec of 2005.

  6. Björn Wallner and Arne Elofsson ``Pcons5: combining consensus, structural evaluation and fold recognition scores,'' 2005Bioinformatics 21(23):4248-4254.

  7. Tomas Ohlson and Arne Elofsson ``Profnet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins.'', BMC Bioinformatics 2005 6:253

  8. Sara Light, Per Kraulis and Arne Elofsson ``Preferential attachment in the evolution of metabolic networks'', BMC Genomics, 2005 6:159
     This paper was rated ``highly accessed'' by BMC genomics.

• 2006
  1. Björn Wallner and Arne Elofsson ``Identification of correct regions in protein models using structural, alignment and consensus information'', Protein Science 2006 15(4):900-913.

  2. * Diana Ekman, Sara Light, Åsa K. Björklund and Arne Elofsson ``What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?'', Genome Biology 7(6):R45 2006.
     This paper was featured on the cover picture and ranked as 10:th most downloaded article in July 2006 and ranked as ``highly accessed'' by Genome Biology

  3. * Erik Granseth, Håkan Viklund and Arne Elofsson ``ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins'', Bioinformatics 2006 22(14):e191-196

  4. Mauro Amico, Michele Finelli, Ivan Rossi Andrea Zauli, Arne Elofsson, Håkan Viklund, Gunnar von Heijne, David Jones, Anders Krogh, Piero Fariselli, Pier Luigi Martelli, Rita Casadio ``PONGO: a web server for multiple predictions of all-alpha transmembrane proteins'' Nucleic Acids Research 2006 1;34(Web Server issue):W169-72.

  5. * Håkan Viklund, Erik Granseth and Arne Elofsson ``Reentrant regions in $\alpha$-helical transmembrane proteins are divided in 3 structural classes and abundant in small residues'', J. Mol. Biol. 2006 361(3):591-603

  6. * Åsa K. Björklund, Diana Ekman and Arne Elofsson ``Expansion of protein domain repeats'' PLOS Comp. Biol. 2006 2(8): e114

  7. Tomas Ohlson, Varun Aggerwal, Arne Elofsson and Robert M MacCallum ``Improved alignment quality by combining information, predicted secondary structure and self-organising maps.'' BMC Bioinformatics 2006 7(1):357

• 2007
  1. Björn Wallner, Per Larsson and Arne Elofsson ``Pcons.net: Protein Structure Prediction Meta Server'' Nucleic Acids Research 2007 35:W369-74

  2. Diana Ekman, Åsa K. Björklund and Arne Elofsson ``Quantification of the elevated rate of domain rearrangements in metazoan.'' J. Mol. Biol. 2007 372(5):1337-48.

  3. Björn Wallner and Arne Elofsson ``Assessment of global and local model quality in CASP7 using Pcons and ProQ'' Proteins 2007Sep 25;69(S8):184-193

  4. Andreas Bernsel, Håkan Viklund and Arne Elofsson ``Remote homology detection of integral membrane proteins using conserved sequence features'' Proteins 2007 Dec 12

• 2008
  1. Costas Papaloukas, Erik Granseth, Håkan Viklund and Arne Elofsson ``Estimating the Length of Transmembrane Helices Using Z-coordinate Predictions'', Protein Science 2008 17: 271-278;

  2. Andreas Bernsel, Håkan Viklund, Jenny Falk, Erik Lindahl, Gunnar von Heijne, Arne Elofsson ``Prediction of membrane-protein topology from first principles Proc. Natl. Acad. Sci 2008, in press

Review articles

1. Lena EF Milchert, David A Liberles and Arne Elofsson ``The salmon genome (and other issues in bioinformatics)'' Genome Biology 2002 3(7):reports4022.1-4022.4

2. David A. Liberles, Anna Thoren, Gunnar von Heijne and Arne Elofsson. ``The use of Phylogenetic profils for Gene Predictions'', Current Genomics 2002 3:131-137

3. Åsa Björklund, Anna Thoren, Gunnar von Heijne and ``The use of Phylogenetic profils for Gene Predictions Revisited'', Current Genomics 2006 7(2):79-86

4. Arne Elofsson and Gunnar von Heijne ``Membrane Protein Structure: Prediction vs Reality'', Annu Rev. Biochem 2007 Jan 17

5. Timothy Hughes, Diana Ekman, Himanshu Ardawatia, Arne Elofsson, and David A. Liberles ``Gene duplication, whole genome duplication, and Paramecium tetraurelia'' Genome Biology 2007 8(5):213

Chapters in books

1. Rigler, R., Wennerberg, A. B. A., Cooke, R. M., Arne Elofsson, Nilsson, L., Vogel, H., Holley, L. H., Carlquist, M., Langel, U., Bartfai, T., and Campbell, I. ``On the solution structure of Galanin.''. In Galanin ed. T. Hökfelt and T. Bartfai, McMillan, (1991)

2. Arne Elofsson, ``Recent advances in how to test knowledge based energy functions for protein folding studies.'' in ``Recent Research Developments in Physical Chemistry'' 1997

3. Xiao-Ping Zhang, Arne Elofsson and Elzbieta Glaser ``Interaction of mt-HSP70 with mitochondrial presequences'' Plant Mitochondria: From gene to Function (Moller, I.M., Gardeström, P., Glimelius, K. and Glaser, E., eds), Bacjuys Publ, pp. 101-105 1998

4. Huisheng Fang, Björn Wallner, Jesper Lundström, Christer von Wowern and Arne Elofsson ``Improved fold recognition by using the Pcons consensus approach'' Chapter in ``Protein structure prediction:Bioinformatic approach'' IUL biotechnology Series, La Jolla, pp. 397-416 2001

5. Björn Wallner and Arne Elofsson ``Prediction of global and local model qualities using MQAPs'' Chapter in In press 2007

Articles in conference proceedings

1. Scott LeGrand, Arne Elofsson and David Eisenberg, ``The Effect of a Distance Cutoff on the Performance of the Distance Matrix Error when Used as a Potential Function to Drive Conformational Search'', In: Distance-based Approaches to Protein Structure Determination II. Edited by Henrik Bohr 1994

2. Daniel Fischer, Arne Elofsson, Danny W Rice, Scott LeGrand. and David Eisenberg ``Assessing the Performance of Fold Recognition Methods By Means of a Comprehensive Benchmark.'' in Proc. Pacific Symposium on Biocomputing, Hawaii, 300-318 January 1996.

Submitted articles

1. Håkan Viklund and Arne Elofsson ``OCTOPUS: A topology predictor for transmembrane proteins that includes reentrant regions in the topological grammar.'', submitted

2. Per Larsson, Björn Wallner, Erik Lindahl and Arne Elofsson ``On the use of multiple templates to improve quality of homology model'', submitted

Freely available GPL licensed computer programs

All programs are available from http://bioinfo.se/ and are licensed under the GPL license.

1. Palign - a flexible and powerful sequence alignment and search program. http://bioinfo.se/palign/
2. modHMM - A modular HMM program that can use profile-profile comparisons. http://www.modhmm.org/
3. ProQ - A set of programs to predict the quality of a protein model. http://bioinfo.se/ProQ/
4. LGscore - A program to measure the quality of a protein model. http://bioinfo.se/lgscore/
5. Pfrag - a fast and free homology modelling program

Freely available web-applications

These services are freely available

• For globular protein structure predictions. All tools are now available through http://pcons.net/ - a meta-server using pcons and Pfrag to predict structures.
  • Pcons - A consensus fold recogniton server receiving than ten thousend requests per year.
  • Pmodeller - A consensus homology modelling server.
  • Pfrag - A fast an accurate homolgy modelling method.
  • ProQ - A quality predictor for protein models.
  • Pmembr - A fold recognition server for membrane proteins.
• For membrane proteins. All servers are now available through http://topcons.net/
  • octopus - Combined predictor of topology and reentrant regions
  • SCAMPI - A scale based membrane protein predictor
  • pro/prodiv-TMHMM - The state of the art predictor of transmembrane regions.
  • DAS - A predictor of transmembrane regions.
  • Zpred - a predictor of the distance to the membrane center.

The 10 most important articles (that also are the most important for this project) are marked with a *

Grants

• Since 1995 received individual research grants for 32 286 KSEK (3.5 MEuro)
  • Research councils 8 265 kSEK
  •  European Union 1 195 kEuro
  • Strategic foundation 8 835 kSEK
  • Other foundations 4 192 KSEK
• Equipment (computing clusters) 10 200 KSEK
• Co-applicant in center grants 98 000 KSEK (10.5 MEuro)

Grants received per year in kSEK

Year	VR	SSF	EU	other	Equipment	Centers
2007	1575	1855	8740	-	2700
2006	1500	430	-	-
2005						58 000
2004	1200	1800	1850	1044
2003			4300	163
2002	970
2001				2375
2000		4750		400	7500	40 000

Research councils

• 1995 TFR ``Computing resources'' 300 kSEK
• 1995-1997 TFR ``Protein bioinformatics in the post genomic era. Interactions, multi domain, membrane proteins and other challenges.''1 300 kSEK
• 1997-1999 NFR ``Protein structure prediction''300 kSEK
• 1999-2000 TFR ``Protein structure prediction''620 kSEK
• 2000-2002 NFR ``Protein structure prediction'' 500 kSEK
• 2003 VR (NT) ``Development of improved methods to predict the function and structure of proteins'' 160 kSEK
• 2003-2005 VR (NT) ``Development of improved methods to predict the function and structure of proteins.''810 kSEK
• 2005-2006 VR (M) ``Classification, identification and prediction of GPCRs and other membrane protein families''1 200 kSEK
• 2007-2009 VR (NT)''Structure based classification, identification and prediction of GPCRs and other membrane protein families''1 500 kSEK
• 2007 Cluster for computational chemistry (Co-app)2 700 kSEK
• 2008-2010 VR (M) ``The evolution of protein domain repeats and their implication for signalling and disease''1 575 kSEK

Strategic Foundation

• 2000-2004 Stockholm Bioinformatics Center (Co Applicant)40 000 kSEK
  My grant1 500 kSEK
  My salary3 250 kSEK
• 2005-2008 Bio-X: Studies of membrane protein interactions5 000 kSEK
  My part 1 800 kSEK
• Center for Biomembrane Research (Co-applicant)58 000 kSEK
  2006 CBR grant to me 430 kSEK 2007 CBR grant to me 1 855 kSEK

European Union

• FP6
  • 2004-2006 STREP: ``GeneFun - Gene Function Predictions'' LSHG-CT-2004-503567 240 kEuro
  • 2004-2009 NoE: ``Biosapiens A European Virtual Institute for Genome Annotation'' (Co-applicant)200 kEuro
  • 2005-2010 NoE: ``EMBRACE A European Model for Bioinformatics Research and Community Education'' LSHG-CT-2004-512092205 kEuro
• FP7
  • 2008-2012 IRP: ``POCEMON Personal health systems for monitoring and point of care'' 233 kEuro
  • 2008-2012 IRP: ``EDICT European Drug Initiative on Channels and Transporters'' 517 kEuro
  • 2008-2010 ITN: ``Transys - A systems approach to defining membrane protein networks and applications'', 200 kEuro

Others grants

• 1996 Magnus Bergvall60 kSEK
• 1999 Sven och Ebba-Christina Högbergs prize150 kSEK
• 2000-2004 K.A.Wallenberg Computer cluster (Co-applicant)
  7.500 kSEK
• 2000-2005 K.A.Wallenberg SweLL Teaching grant (Co-applicant)
  (my part) 400 kSEK
• 2001-2005 PhD position ``Research shool in genomics and bioinformaics'' 2.075 kSEK
• 2001-2004 Lawski PhD scholarship to Olivia Eriksson300 kSEK
• 2002-2003 Carl Trygger163 kSEK
• 2004-2005 Research position from Walleberg Consortium North1.044 kSEK

Invited talks and lectures

0.25

• Invited to talk at International society for molecular modelings conference on Structural Genomics in Cambridge, UK 2000
• Invited to workshop Algorithmique et Biologie at Pasteur, Paris 2000
• Invited talk at Bioinformatics'2001 (2001)
• Invited talk at CASP5 (Dec, 2002)
• Invited talk at TERAPROT workshop in Paris (Jan, 2003)
• Invited talk at University of Saarbrucken (Jun, 2003)
• Invited talk at University of Bergen (Nov, 2003)
• Invited talk at UCLA (Mar, 2004)
• Invited talk at the Biotech Forum in Copenhagen (Oct 2004)
• Invited talk at the Computational Biology Workshop in Stockholm in Stockholm (Oct 2004)
• Invited talk at the COST meeting in Toulouse (Oct 2004)
• vited talk to ``Sequence-structure-function: Theoretical and experimental approaches'' in Warsaw (Apr 2005)
• Invited short talk at CASP6 (Dec, 2007) Delivered by Björ Wallner
• Invited talk to ``Public CASP meeting'', New York (May 2006)
• Selected talk at ISMB'06 (Aug, 2006) Delivered by Erik Granseth
• Invited talk to ``III International Symposium on Biochemistry and Molecular Biology''m Havanna October, 2006
• Invited talk at CASP7 (Dec, 2006) Delivered by Björn Wallner
• Invited talk to ``Biosapiens workshop'', Israel (Jan 2007)
• Selected talk at highlight track at ISMB'07 (Aug, 2007) Delivered by Åsa K. Björklund
• Invited talk at ``EMBN workshop'', Groningen Jan 2008
• Invited talk at ``EBI membrane workshop'', Hinxton, Feb 2008
• Invited talk at ``Bioinformatics winter school'', Bologna Feb 2008
• Invited talk to ``CASP 7.5 meeting'', Madrid (April 2008)

Organizing international conferences

0.25

• Organized workshop ``Biophysical aspects of protein folding'' (60 participants) 1997
• Organized the conference Bioinformatics'99 (app. 250 participants/conference)
• Member of organization committee for Bioinformatics'2000, '2001, '2002 and '2007
• Co-founder of the ABC-meeting in computational chemistry. A bi-annual meeting of computational chemistry scientists in the Stockholm-Uppsala area.
• Co-founder of the meetings in bioinformatics. An annual meeting of bioinformaticians in the Stockholm-Uppsala area.

Awards

0.25

• Sven och Ebba-Christina Högbergs pris 1999

Memberships

0.25

• 1998-2000 Secretary in the Swedish Biophysical society.
• 2004-2010 President of the Society for Bioinformatics in the Nordic countries

Editorial boards

0.25

• 1997 Editor of ``Internet journal of science''
• 2007 Member of editorial board for hihglight track for ISMB'07
• 2008 Member of editorial board for hihglight track for ISMB'08
• 2008-11 Associate editor for Protein science

Program committes

0.25

• 2001-2008 member of program committee at the Annual Conference on Intelligent Systems for Molecular Biology (ISMB)
• 1999-2008 Member of program committee for Bioinformatics'XX (chair 1999 and 2004)
• 2004 Member of program committee Data Mining in Functional Genomics and Proteomics:Current Trends and Future Directions, ECAI-2004 workshop
• 2006 Member of program committee for The European Symposium of the Protein Society, 2007
• 2006 Member of the CASP7 consultancy group
• 2006 Member of program committee for GCB'06
• 2008 Member of program committe for ECCB'08

Reviewing

0.25

• Member of the National Research Council review group for biotechnology, 2006, 2007
• Reviewing >20 articles annually from J. Mol. Biol., Proteins, Bioinformatics, Nucleic Acids Research, BMC Bioinformatics, Nat Biotech. Plos. Comp Biol. and other journals.

• external reviewer for ESF grant, 2008
• external reviewer for grant submitted to Wellcome Trust, 2006
• external reviewer for grant submitted to Norwegian Research Council, 2005
• external reviewer for grant submitted to Cancer UK, 2005
• external reviewer for grant submitted to Science Foundation Ireland, 2003
• external reviewer for grant submitted to Israel Science Foundation , 2002
• external reviewer for grant submitted to Netherlands Genomics Initiative, 2001
• external reviewer for grant submitted to Singapore Science program , 2001

PhD-reviews/committees

0.25

• 2000 Helsinki University Jarmo Alander
• 2002 Karolinska Institutet Pekka Mark
• 2003 Karolinska Institutet Nina Stålberg
• 2004 Karolinska Institutet Christian Storm
• 2006 Karolinska Institutet (Chair) Markus Wistrand
• 2006 Karolinska Institutet ???
• 2006 Stockholm University ??
• 2007 University of Sydney (opponent) ??

.  Research Group

.  Graduate Students:

• PhD students 0.25
  1. Olivia Eriksson, Jun-2001-currentMathematical Bioinformatics
  2. Åsa Björklund, May-2004-currentProtein domain networks
  3. Diana Ekman, May-2004-currentProtein domain networks
  4. Andreas Bernsel Sep-2004-currentMembrane proteins
  5. Kristoffer Illergård, Mar-2005-currentDomain evolution
  6. Per Larsson , Mar-2005-currentHomology Modelling
  7. Linnea Hedin, Sep-2005-currentBio-X, proteomics
  8. Aron Hennerdahl, Sep-2006-currentMembrane proteins
  9. Jenny Falk, Sep-2006-currentMembrane proteins

.  Postdoctoral visitors:

0.25

1. Anni Kauko Feb 2007 - Current ``Membrane protein structure analysis''
2. Håkan Viklund, Nov-2007-currentHidden Markov Models

.  Most important Collaborators

0.25

• Dr. Erik Lindahl, Protein and membrane simulations
• Doc. Susana Cristobal, Stockholm UniversityBiochemistry
• Prof. Gunnar von Heijne, Stockholm UniversityMembrane proteins

.  International collaborations

0.25

• Biosapiens - EU NoE
• GeneFun - EU Strep program LSHG-CT-2004-503567
• EMBRACE - EU NoE LHSG-CT-2004-512092
• EDICT -
• Pocemon -
• Transys -

.  Alumni

0.25

• Guest professors at sabbatical in my group 0.25
  1. Dr. Costas Papaloukas, Jul 2006 - Jan 2007Zpred2

• Post-docs 0.25
  1. Dr. Miklos Cserzö, Jan 1996 - Jun 1996DAS
  2. Dr. K. Seshadri, Jun 1997 - Feb 1998Analysis of Membrane proteins
  3. Dr. Mats Eriksson, Sep 1998 -Apr 2000Drug design
  4. Dr. Huisheng Fang, Dec 2000-Dec 2002Fold Recognition
  5. Dr. Meftun Ahmed, Jan 2002-Aug 2002Peroxisomes
  6. Dr. Nick Braun, Nov 2002-Apr 2003Evolution of protein thermodynamics
  7. Erik Sandelin, Mar 2003-Sep 2006Protein structure predictions

• Supervised doctoral thesis 0.25
  1. Håkan Viklund, Nov 23, 2007 ``Membrane proteins''
  2. Erik Granseth, Sep 24, 2007 ``Membrane protein structures''
  3. Sara Light May 19, 2006 ``Investigations into the evolution of biological networks''
  4. Tomas Ohlson Feb 24, 2006 ``The use of evolutionary information in protein alignments and homology identification''
  5. Björn Wallner Sept 30, 2005 ``Protein structure prediction: Model Building and Quality Assessment''

• Supervised licentiate thesis 0.25
  1. Robert Garemyr ``A study of the electrostatic treatment in molecular dynamics simulations.'', Sept 1999
  2. Jakob Halaska `` BioScript3D - A Biomolecular Visualization & Animation Tool''

• Supervised more than 30 ``Master'' thesis (Examensarbeten)

About this document ...

CURRICULUM VITAE

This document was generated using the LaTeX2HTML translator Version 2002-2-1 (1.71)

Copyright © 1993, 1994, 1995, 1996, Nikos Drakos, Computer Based Learning Unit, University of Leeds.
Copyright © 1997, 1998, 1999, Ross Moore, Mathematics Department, Macquarie University, Sydney.

The command line arguments were:
latex2html -split 0 cv

The translation was initiated by Arne Elofsson on 2008-03-30