Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

Rasmus Wernersson

External Associate Professor at DTU - Head of Informatics at Intomics A/S

Rasmus Wernersson - at Rørvig Mølle, 2006 IMPORTANT NOTICE:
My current affiliation with DTU is as External Associate Professor (part time) and my main job is Head of Informatics at Intomics A/S.

DTU e-mail address: raz@cbs.dtu.dk
Intomics e-mail address: raz@intomics.com

Postal address:
Department of Systems Biology, Technical University of Denmark,
Building 208, DK-2800 Lyngby, Denmark

Curriculum vitae
(updated Feb 2014)
PDF - formatted for duplex printing.

View Rasmus Wernersson's profile on LinkedIn
Nature Network


Publications

Note: For the few publications currently not available under Open Access - just drop me an email if you need a PDF reprint.

2012-2013

(None): Working full time in the industry.

2011

The strength of intron donor splice sites in human genes displays a bell-shaped pattern
Kai Wang, Rasmus Wernersson, and Søren Brunak
Bioinformatics (2011) 27 (22): 3079-3084
PubMedID: 21994226

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design
Lars Rønn Olsen, Niels Bjørn Hansen, Mads Tvillinggaard Bonde, Hans Jasper Genee, Dorte Koefoed Holm, Simon Carlsen, Bjarne Gram Hansen, Kiran Raosaheb Patil, Uffe Hasbro Mortensen, and Rasmus Wernersson
Nucleic Acids Research (2011) 39 (suppl. 2): W61-W67
PubMedID: 21622660

2010

Optimization of the BLASTN substitution matrix for prediction of nonspecific DNA microarray hybridization
Aron Eklund, Pia Friis, Rasmus Wernersson, Zoltan Szallasi
Nucleic Acids Research (2010) 38 (4): e27. (Epub 2009 Dec 6.)
PubMedID: 19969549

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
Nicholas Gauthier, Lars Juhl Jensen, Rasmus Wernersson, Søren Brunak, Thomas Skøt Jensen
Nucleic Acids Research (2010) 38 (suppl 1): D699-D702. (the 2010 Database issue)
PubMedID: 19934261
Web: http://www.cyclebase.org

2009

InterMap3D: predicting and visualizing co-evolving protein residues
Rodrigo Gouveia-Oliveira, Francisco S. Roque, Rasmus Wernersson, Thomas Sicheritz-Ponten, Peter W. Sackett, Anne Mølgaard and Anders G. Pedersen
Bioinformatics 2009 25(15):1963-1965
PubMedID: 19528088
Web: http://www.cbs.dtu.dk/services/InterMap3D/

Book chapter: Probe design for expression arrays using OligoWiz
Rasmus Wernersson
In DNA Arrays for Biomedical Research: Methods and Protocols, Vol 529
Martin Dufva (Editor), Springer Protocols / Humana Press, 2009
ISBN: 978-1-934115-69-5

2008

Cyclebase.org - a comprehensive multi-organism online database of cell cycle experiments
Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, and Thomas Skøt Jensen
Nucleic Acids Research, 2008, Vol. 36, Database issue D854-D859
PubMedID: 17940094
Web: http://www.cyclebase.org

2007

Forsøg med ny online eksamensform i "Introduktion til Bioinformatik"
Rasmus Wernersson
DTU Avisen, November 2007. Lang udgave baseret på den original text: PDF
English summary: short article to the internal DTU newspaper detailing my experience with the new online exam, I have introducted to the "Introduction to Bioinformatics" course.

Dice & DNA
Rasmus Wernersson
BioScience Education e-journal 10-5 (2007). Download provisional PDF: DiceAndDNA_provisional_HQ.pdf (1.1 mb)
DOI:10.3108/beej.10.5
Web: BLAST exercise

Probe Selection for DNA Microarrays using OligoWiz
Rasmus Wernersson, Agnieszka S. Juncker and Henrik Bjørn Nielsen
Nature Protocols 2, 2677 - 2691 (2007)
PubMedID: 18007603
Web: http://www.cbs.dtu.dk/services/OligoWiz/

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob H. Havgaard, Søren Brunak, Merete Fredholm and Christian Bendixen
Bioinformatics 2007 23(13):i387-i391
PubMedID: 17646321
Web: http://snp.agrsci.dk/maviant/

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs
Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J Gilchrist, Frank Panitz, Claus B Jorgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J Nielsen, Jakob H Havgaard, Carina Rosenkilde, Jun Wang, Heng Li, Ruiqiang Li, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Jun Yu, Jiang Wang, Hans-Henrik Staerfeldt, Rasmus Wernersson, Lone B Madsen, Bo Thomsen, Henrik Hornshoj, Zhan Bujie, Xuegang Wang, Xuefei Wang, Lars Bolund, Soren Brunak, Huanming Yang, Christian Bendixen and Merete Fredholm
Genome Biology 2007, 8:R45 (2 april 2007)
PubMedID: 17407547
Web: http://www.piggenome.dk

Thermodynamic probe intensity correction for oligonucleotide microarrays
Georg M. Bruun, Rasmus Wernersson, Agnieszka S. Juncker, Hanni Willenbrock and Henrik Bjørn Nielsen
Nucleic Acids Research, 2007, Vol. 35, No. 7 e48 (Accepted for publication December 2006)
PubMedID: 17337437
Web: http://www.cbs.dtu.dk/suppl/probes/

2006

An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes
Henrik Nielsen and Rasmus Wernersson
BMC Genomics 2006, 7:256
PubMedID: 17034638
Web: http://www.cbs.dtu.dk/suppl/introns/

Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation
Rasmus Wernersson.
Nucl. Acids Res. 2006 34: W385-W388
PubMedID: 16845033
Web: http://www.cbs.dtu.dk/services/VirtualRibosome/

FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB
Rasmus Wernersson, Kristoffer Rapacki, Hans-Henrik Stærfeldt, Peter Wad Sackett, and Anne Mølgaard
Nucl. Acids Res. 2006 34: W84-W88
PubMedID: 16845115
Web: http://www.cbs.dtu.dk/services/FeatureMap3D/

2005

Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
Rasmus Wernersson*, Mikkel H Schierup*, Frank G Jorgensen, Jan Gorodkin, Frank Panitz, Hans-Henrik Staerfeldt, Ole F Christensen, Thomas Mailund, Henrik Hornshoj, Ami Klein, Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane K-S Wong, Jun Yu, Jian Wang, Christian Bendixen, Merete Fredholm, Soren Brunak, Huanming Yang, Lars Bolund
BMC Genomics 2005, 6:70 (10 May 2005)
PubMedID: 15885146
Data download: www.piggenome.dk (moved from www.piggenome.org in 2006) [Mirror]
[* = equal contributors]

New weakly expressed cell cycle regulated genes in yeast
Ulrik de Lichtenberg*, Rasmus Wernersson*, Thomas Skøt Jensen*, Henrik Bjørn Nielsen, Anders Fausbøll, Peer Schmidt, Flemming Bryde Hansen, Steen Knudsen and Søren Brunak
Yeast, 2005, Volume 22, Issue 15 , Pages 1191 - 1201.
PubMedID: 16278933
Web: http://www.cbs.dtu.dk/cellcycle/ (PDF + data is located here)
[* = equal contributors]

OligoWiz 2.0 - integrating sequence feature annotation into design of microarray probes
Rasmus Wernersson and Henrik Bjørn Nielsen.
Nucleic Acids Research, 2005, Vol. 33, Web Server issue W611-W615
PubMedID: 15980547
Web: http://www.cbs.dtu.dk/services/OligoWiz2/

FeatureExtract - extraction of sequence annotation made easy.
Rasmus Wernersson.
Nucleic Acids Research, 2005, Vol. 33, Web Server issue W567-W569
PubMedID: 15980537
Web: http://www.cbs.dtu.dk/services/FeatureExtract/

2003

RevTrans - Constructing alignments of coding DNA from aligned amino acid sequences.
Rasmus Wernersson and Anders Gorm Pedersen.
Nucl. Acids Res., 2003, 31(13), 3537-3539.
PubMedID: 12824361
Web: http://www.cbs.dtu.dk/services/RevTrans/

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.
Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen.
Nucleic Acids Research, 2003, Vol. 31, No. 13 3491-3496
PubMedID: 12824351
Web: http://www.cbs.dtu.dk/services/OligoWiz/

Presentations

Seminar: Assessment and exams in education (Held at the IT University Oct 21st, 2010)
Invited talk:Presenting our experiences from implementing an online exam with open internet access for the "Introduction to Bioinformatics" course at DTU. Links: Seminar programme | Abstract to my talk

ISMB 2005
Advanced Micro-array Probe Design Using OligoWiz 2.0 (Software demo)
Links: Short abstract | Detailed abstract (pdf)

Pig Genome Sequencing Consortium Yearly Meeting, May 2005
Developments in the Pig Genome Datawarehouse, Aspects of the BMC paper, and (pig) oligo design.

2nd YSBN workshop, Copenhagen May 14-16, 2004
Presenting the Systems Biology work at the Center for Biological Sequence Analysis
Links: YSBN website

Pig Genome Sequencing Consortium Yearly Meeting, March 2004
The CBS data warehouse and preliminary scientific results

ISMB 2003
OligoWiz: A powerful, flexible yet easy-to-use tool for designing oligonucleotides for DNA microarrays (Software demo)
Links: Abstract | Slides (pdf)

Bioinformatics 2003
OligoWiz - A Flexible Design Tool for Microarray Probes


Teaching

2010

Course 27611: Introduction to Bioinformatics - Lektionsplan 2010
Role: Course organizer, main teacher.

Course 27622: Introduction to Bioinformatics - Turbo version - Course programme 2010
Role: Course organizer, main teacher.

Inter-University Course: Bioinformatics for Human Biologists - Course programme 2010
Role: Course organizer, main teacher.
(Run together with University of Copenhagen - Master-level course for students at the Human Biology study line).

Inter-University Course: Bioinformatik - IT og Sundhed - Course programme 2010
Role: Teacher.
(Run together with University of Copenhagen - Bachelor-level course for students at the "IT og Sundhed" study line).

Course for high-school teachers: Efteruddannelseskursus i Bioinformatik til gymnasiet - Lektionsplan - Hold 1
Role: Course co-organizer and main teacher (both together with Anders Gorm Pedersen)
This couse is a new type of outreach for teaching bioinformatics to high-school (gymnasium) teachers. The aim is to integrate aspects of bioinformatics in the BioTech/Biology etc. classes taught at the high-schools.

2009

Course 27611: Introduction to Bioinformatics - Lektionsplan 2009
Role: Course organizer, main teacher.

Course 27622: Introduction to Bioinformatics - Turbo version - Course programme 2009
Role: Course organizer, main teacher.
(This course was established by me and ran for the first time in 2009).

Inter-University Course: Bioinformatics for Human Biologists - Course programme 2009
Role: Course organizer, main teacher.
(Run together with University of Copenhagen - Master-level course for students at the Human Biology study line).

Inter-University Course: Bioinformatik - IT og Sundhed - Course programme 2009
Role: Teacher.
(Run together with University of Copenhagen - Bachelor-level course for students at the "IT og Sundhed" study line).

2008

Course 27612: DNA Microarray Analysis
Teacher: Lecture and exercise on probe design for DNA microarrays.

Course 27611: Introduction to Bioinformatics - Lektionsplan 2008
Course organizer, main teacher.

Course 27615: Molecular Evolution
Teacher. Author of exercises.

Course 27803: Biological Sequence Analysis (PhD course)
Teacher: Lecture and exercise on probe design for DNA microarrays.

2007

Course 27612: DNA Microarray Analysis
Teacher: Lecture and exercise on probe design for DNA microarrays.

Course 27611: Introduction to Bioinformatics - Lektionsplan 2007
Course organizer, main teacher.

Course 27615: Molecular Evolution
Teacher. Author of exercises.

Course 27803: Biological Sequence Analysis (PhD course)
Teacher: Lecture and exercise on probe design for DNA microarrays.

2006

Course 27612: DNA Microarray Analysis
Teacher: Lecture and exercise on probe design for DNA microarrays.

Course 27611: Introduction to Bioinformatics
Course organizer, main teacher.

Course 27615: Molecular Evolution
Teacher. Author of exercises.

Course 27803: Biological Sequence Analysis (PhD course)
Teacher: Lecture and exercise on probe design for DNA microarrays.

2005

Course 27611: Introduction to Bioinformatics
Course organizer, teacher.

Course 27615: Molecular Evolution
Teacher. Author of exercises.

Course 27614: Advanced Bioinformatics
Teacher.

Course 27803: Biological Sequence Analysis (PhD course)
Teacher. Session on probe design for DNA microarrays.

2004

Course 27011: Introduction to Bioinformatics
Course organizer, teacher.

Course 27015: Molecular Evolution
Teacher. Author of exercises.

2003

TechTalks: A series of seminars on programming techniques and Unix tools
Organizer and main teacher

Course 27011: Introduction to Bioinformatics
Instructor.

Course 27803: Biological Sequence Analysis (PhD course)
Instructor

2002

TechTalks: A series of seminars on programming techniques and Unix tools
Organizer and main teacher

Course 27011: Introduction to Bioinformatics
Instructor.

Course 27803: Biological Sequence Analysis (PhD course)
Instructor


Doing lab work on the Yeast cell cycle

Lab work
Flemming Bryde Hansen, Thomas Skøt Jensen, Ulrik de Lichtenberg, Anders Fausbøll and Rasmus Wernersson, 2003
[Stats...]