Curriculum vitae - CBS

February 2014
Curriculum vitae
Rasmus Wernersson
Co-founder of Intomics A/S, Head of Informatics
Personal information
Rasmus Wernersson
Maglebjervej 7
3200 Helsinge
Born in August 1974 in Copenhagen.
Married to Jette Lundsbøl Wernersson.
Father of Carl (born October 2000) and Sven (born January 2004).
Danish citizen.
Work experience
Feb 2013–Present: External Associate Professor at the Institute for Systems Biology,
Technical University of Denmark. My main task has been to develop a new course on Systems
Biology aimed at Bachelor level students. This includes both designing the course structure,
writing most the the teaching materials as well as being the main teacher and course responsible.
Aug 2009–Present: Head of Informatics at Intomics A/S and co-founder of the company.
Responsible for building and maintaining Intomics’ High Performance Computing system for
integrative data analysis, and the development of Intomics’ advanced text-mining facilities.
Scientific project leader and advisor on multiple research projects with clients in the pharmaceutical industry.
Dec 2006–May 2011: Associate professor at the Center for Biological Sequence Analysis
at the Technical University of Denmark. My main focus was on teaching and the development
of new courses, teaching materials and implementation of new forms of examination. This
included both internal DTU courses, collaboration courses with the University of Copenhagen,
and providing continuing education to high-school science teachers.
Jan 2002–Nov 2006: Assistant professor at the Center for Biological Sequence Analysis
at the Technical University of Denmark. Research: both lab-based research on cell-cycle and
bioinformatics research.
Dec 1998–Dec 2001: Application and server Programmer at the software house ”Dansk
PC Programmering”. Software development in Borland Delphi (Windows platform) and Java
(Windows and Linux platforms).
1991–1992: Freelance programmer for the computer game company ”KingSoft” (Aarchen,
Germany). 8-bit assembly programming.
Education
2005–2006: Education in University Teaching at DTU (”UDtU”).
11/2 year Science of Education program – provides qualifications for teaching at Associate
Professor level.
2001–2008: Diploma of Information Technology (IT-D) – with specialization in Software
Development, Copenhagen University College of Engineering.
1993–1998: Master of Science (Candidatus scientiarium) in Biology, University of Copenhagen. Thesis project: ”Direct cloning and expression of enzyme-genes from non-cultivatable
organisms - experimental work performed at Novo Nordisk A/S (the section later to become
Novozymes A/S)”.
Experience and competences
Introduction
My education and work experience covers two main areas of expertise: 1) Experimental
Molecular Biology and 2) Computer Science. A major theme in all of my working life has been
to use my combined expertise on these subjects to facilitate the collaboration between ”wet-lab
biologists” and ”computer people”. I strongly believe in the benefits of not only developing
new and interesting algorithms but also keeping the usefulness and accessibility of the tools
for the intended users (often biologists) in mind. Several of my most cited publications (e.g.
RevTrans1 and OligoWiz2 ), are on tools that were created to address a specific biology oriented
problem.
A very important aspect of facilitating the optimal outcome of projects involving both
experimentally generated data and advanced computational analysis is that of communication.
For example: in order to implement new algorithms to solve a particular research problem, it
is vital that the bioinformatician understand the biological context of the question and the
limitation of the data. However, this goes both ways and often the situation will be the reverse:
- that the experimentalist is not aware of the full possibilities and strengths of the data analysis.
I see communication as being one of my core competences, and the role as a communicator
has been central to both my academic and industrial career. In my role as Head of Informatics
at Intomics A/S I am often brought into scientific projects as an advisor on coordinating
the experimental data generation with the data analysis strategy. A major part of this is
interviewing the experimental experts to get an in-depth understanding of the overall biological
questions being asked, and based on this making sure that the data analysis strategy will not
only support this, but will be further enhanced by bringing in even more advanced methods.
A good example of this could be to add in a network biology point of view, where biological
context of known entities (e.g. biomarkers/drug targets) are investigated through analysis of
protein-protein interaction networks or supported by pathway analysis.
1
2
R. Wernersson and A. G. Pedersen, Nucleic Acids Research, 2003
R. Wernersson, A. S. Junker, and H. B. Nielsen, Nature Protocols, 2007
Figure 1: Cyclebase.org. Providing easy access to integrative cell cycle analysis.
Academic research
The driving force behind my research has been the interface between experimental biology and
bioinformatics. In many cases my (experimental) work in one topic such a alternative splicing
and cell cycle regulation in Yeast has uncovered an unmeet need for bioinformatics tools, which
has then been implemented as side-projects. Furthermore, I have in several cases come into
on-going projects, as a problem-solver with a critical view on the data quality from a biologist
point of view, and a pragmatic approach on how to address the data analysis issues from a
programmers point of view.
Experimental work
One of the topics I would like to highlight here is my experimental work on the Yeast cell
cycle. I was responsible for establishing and optimizing an experimental system for cell
cycle research in Saccharomyces cerevisiae at our department at DTU. The institute had a
well establish fermentation platform with 2L bioreactors which allowed fine-grained control
of growth conditions, including temperature. We therefore decided to base our system
on one of the thermo-sensitive cell cycle mutants previously described (CDC15-2)1 , which
allowed arrest-and-release synchronization experiments to be conducted. To allow better
control over growth conditions, and to allow for experiments with labeled amino-acids to
be performed, the fermentation protocol was optimized for synthetic minimal medium. The
verified and optimized protocol is described in our main publication on weakly expressed
cell cycle regulated genes2 and in the protocol collection for the DIAMONDS cell cycle project3 .
During the project it became evident that the different cell cycle experiments described in the
literature (our own and others) were difficult to access and analyze for people not experts in
bioinformatics, and that a lot could be gained from analyzing all the available data together.
To address this need we created the Cyclebase.org4,5 online database, which I think of as a
prime example of combining very high quality bioinformatics analyses with a very intuitive and
easy to use interface aimed at biologists (Figure 1).
Applied Bioinformatics
Another topic common to my research is the field of Applied Bioinformatics – the building
of high quality bioinformatics tools. The OligoWiz package for design of probes for DNA
microarrays6,7 was initially created to make it easy to design special purpose arrays for our
own use (e.g. splice-detecting arrays), but quickly turned out to be quite popular to a much
wider audience (see Figure 2). This has led to the continued development of the software for
1
2
3
4
5
6
7
The CDC15-2 strain in a W303 background was kindly donated by Dr. Bruce Futcher, one of the leading
experts in the field
U de Licthenberg, R Wernersson et al, Yeast, 2005
http://www.sbcellcycle.org/Deliverables/synchronization scer2.pdf
N G Gauthier, M E Larsen, R Wernersson et al. Nucleic Acids Research, 2006
N G Gauthier, L J Jensen, R Wernersson et al. Nucleic Acids Research, 2008
H B Nielsen, R Wernersson, S Knudsen. Nucleic Acids Research, 2003
R Wernersson, H B Nielsen. Nucleic Acids Research, 2005
almost a decade, improved algorithms for probe design1 , probe normalization2 and a number
of review publications including a book chapter3 and a paper in Nature Protocols4 .
Figure 2: OligoWiz 2.0. Screenshot from the OligoWiz 2.0 graphical user interface.
Genomics
Several of my publications have a large genomics component, ranging from software for extraction of genetic annotation5 over genome-wide studies of RNA splicing6,7 to my involvement in
the Danish-Chinese pig genome sequencing project. In the pig genome sequencing project, I
coordinated and performed a large part of the evolution-based analysis together with Mikkel
Heide Schierup from the University of Århus8 .
1
2
3
4
5
6
7
8
A Eklund, P Friis, R Wernersson et al. Nucleic Acids Research, 2010
G M Bruun, R Wernersson et al. Nucleic Acids Research, 2007
R Wernersson Springer Protocols / Humana Press, 2009
R Wernersson et al. Nature Protocols, 2007
R Wernersson, Nuclecic Acids Research, 2005
H Nielsen and R Wernersson, BMC Genomics, 2006
K Wang, R Wernersson, S Brunak, Bioinformatics, 2011
R Wernersson, M H Schierup et al. BMC Genomics, 2005
Industry experience
In 2009 Intomics A/S was founded as a spin-off company from the Technical University of
Denmark, by a group of researchers, myself included, within the fields of Bioinformatics and
Systems Biology.
Establishing a High Performance Computing facility
As the Head of Informatics at Intomics is has been my responsibility to manage all the
aspects of building up and maintaining a High Performance Computing (HPC) infrastructure.
This includes decisions on configuration and scaling of the system and network, installation
and monitoring of hardware in a rack-based environment, maintainance of a large local
installation of bioinformatics relevant databases (e.g. UniProt, PubMed, Ensembl), writing
and porting bioinformatics software and coordinating the efforts of our entire development
team to construct a well organized Systems Biology / Bioinformatics platform. I have played
a major role in the development of Intomics’ advanced text mining pipeline, which is a key
component in many of our projects.
Summary of core IT competences:
ˆ Programming languages: Assembly (expert), C, Basic, Java (expert), ML, Pascal, Python
(expert), Perl, R, Shell scripting
ˆ Programming paradigms: Object oriented programming and design, Agile software development, Model-View-Controller, Client-Server
ˆ User interface design and implementation - e.g. Java GUIs and web UI.
ˆ Databases: MySQL, Oracle
ˆ Algorithm development and optimization
ˆ Linux system administration
ˆ Network administration
Project leader and scientific advisor
As mentioned earlier, my other line of responsibilities at Intomics is as a scientific advisor and
project leader. I have experience in managing all parts of the project work-flow:
ˆ Pre-project negotiations with the client (identify the core biological questions, suggest
a data analysis plan and negotiate the contract details)
ˆ Project leading though-out the project (including the continued evaluation of progress
and data quality and based on this to suggest adjustments to the strategy)
ˆ Post-project evaluation and followup (including communication of the results to a larger
audience, for example through internal seminars, or in cases where more publicity is
wanted, through conference presentations1,2 )
1
2
R. Wernersson (Intomics A/S) and J. Larsen (H. Lundbeck A/S), The Brain Atlas project - large scale data
analysis on depression., 2nd Intomics Symposium on ”Data mining in drug discovery”, Scion-DTU,
November 2011.
R. Wernersson (Intomics A/S) and J. Larsen (H. Lundbeck A/S), Biomarkers and Data Integration - Building blocks for understanding disease biology., 13th Annual Drug Discovery & Development Leaders
Summit, Zurich, June 2012.
Data analysis in drug discovery
Discovery
Preclinical
development
Phase I
Phase II
Phase III
Market
Target
discovery
Biomarker discovery
and optimisation
Knowledge discovery
Data mining projects
Figure 3: Scope of projects
from data to biology
I have been involved in contract research projects for a number of pharmaceutical companies
including Merck Serono, Shire, Leo Pharma, AstraZeneca and H. Lundbeck. Most of this work
has been related to the pre-clinical part of drug development. Notice, however, that Intomics
also do knowledge management projects that spans most aspects of clinical research (Figure 3),
and from this I have a solid understanding of the entire drug development process.
Teaching at DTU
Teaching Bioinformatics to a wider audience is a subject that is near and dear to me, and is
in many aspect a natural continuation of my commitment as a communicator. Throughout my
academic career I have spend a very large amount of time and effort to pursue this goal, and
even after co-founding Intomics A/S and shifting to a job in the industry, I have continued
to teach at the University in my spare time (first as a guest lecturer and later as a formally
affiliated External Associate Professor). See Table 1 for a condensed overview of my main
teaching activities.
Teaching and course development
One of my main efforts has been that as the organizer and main teacher of the ”flagship”
course: 27611: Introduction to Bioinformatics. This is a bachelor-level course, for which I
was responsible for a major reconstruction that helped turn it into one of the institute’s most
popular courses with more than 80 students each year.
One of the main thoughts that went into the transformation of the course, was to realize that
for most students bioinformatics would be a tool subject rather than a research topic, much
in the same vein as mathematics and statistics are for most students. We therefore decided
to postpone the more advanced subjects to later courses. Since the intended audience was
”bio” oriented students, we also decided to re-write all parts of the course that had previously
required UNIX command-line tools. This also had the added benefit that we could redesign
the course to rely only on public available databases (e.g. GenBank and UniProt), and tools
(E.g. BLAST and PyMol) that the students could later use for all kinds of ”everyday use” (for
example finding a DNA sequence for primer-design). As part of this initiative practically ALL
of the computer exercises was rewritten from scratch and put up as an online resource. During
this process we also came up with a novel way to teach the statistics behind the ”BLAST”
algorithm - this is summarized in the peer-reviewed pedagogical publication ”Dice & DNA”1
(Figure 4).
Online teaching materials and differential teaching
Having all teaching material online at our own website allowed for easy experimenting with
new types of materials. Since the course had been retooled for a broader audience of students,
there was a need to give the ”top 10% students” access to more advanced topics, in order to
keep up the interest. We solved this by recording small video lectures that high-lighted some
of the inner details of the tools (e.g. the dynamic programming algorithm for pairwise alignments of DNA/protein), and linking them into the online course plan - clearly marking them
as ”Advanced topics”. Likewise, we also experimented with linking in background materials
on topics that the students were expected to know beforehand, but where some may need a
reminder. This also had the added benefit to reduce the amount of ”reminder” slides in our
presentations.
1
R Wernersson, BioScience Education e-journal, 2007
d
c
b
a
2002 & 2003
Assisting teacher
Initiator and main teacher
Teacher and course-responsible
Assisting teacher (entire course)
Main teacher and course-responsibled
Assisting teacher (entire course)
Teacher
Teacher
Main teacher and course-responsible
Main teacher and course-responsiblea
Main teacher and course-responsibleb
Together with A. G. Pedersenc
Guest lecturer
Guest lecturer
Main teacher and course-responsible
Guest lecturer
Table 1: Teaching at the Technical University of Denmark (DTU) 2002-2013
Introduction to Bioinformatics
Internal seminars on technical subjects within Bioinformatics
Introduction to Bioinformatik
Molecular Evolution
2004
Introduction to Bioinformatics
Molecular Evolution
DNA Microarray Analysis
Biological Sequence Analysis (PhD course)
2005, 2006, 2007 & 2008
Introduction to Bioinformatics
Introduction to Bioinformatics - Turbo Version
Bioinformatics for Human Biologists
Continued education course for high-school science teachers
2009, 2010 & 2011
Introduction to Bioinformatics
Introduction to Bioinformatics - Turbo Version
2012
Introduction to Systems Biology (held twice in 2013)
Introduction to Bioinformatics
A special condensed version of the 27611 course taught in English. The course was establish, designed and implemented by me in order to address a need
to offer a course similar to the 26711 course aimed at Master level students.
In cooperation with the University of Copenhagen - course designed, organized and implemented by me.
Course established, designed, implemented and taught by Anders Gorm Pedersen and me in collaboration.
I organized and implemented a major reconstruction of the course in 2006-2007
27011
”TechTalks”
27611
27615
27611
27615
27612
27803
27611
27622
27655
”GymLærer”
27611
27622
27040
27611
2013
Figure 4: Dice & DNA: rethinking the way to teach a difficult subject
The ”Systems Biology Teaching Wiki”
Since the use of online materials had been so successful in the 27611 course, Anders Gorm
Pedersen1 and I took the initiative to set up a Wiki2 for teaching materials at the department –
this is the system that later morphed into the institute-wide ”Systems Biology Teaching Wiki”3
that is now used to a great extend across multiple courses.
27611 as a pioneer in online exams
Having completed the transformation of the course in 2007, it became evident that a traditional
4-hour pen-and-paper exam would feel oddly out of place. I wanted to introduce a type of exam
where the students could actually use the online tools and databases they had learned about
during the course, to solve real biological questions for the exam. In collaboration with the
Exam Office we got the permission to be the very first course at DTU to experiment with
the implementation of a 100% online exam with full internet access, provided that we handled
all technical issues ourselves. Great care was taken into preparing exam questions that would
challenge the students, make full use of the internet access and minimize the risk of cheating.
Following the successful implementation in 20074 the experiences from 27611 have been used
1
2
3
4
Professor (Docent) at the Center for Biological Sequence Analysis at DTU
I was the original system administrator for the Wiki and 27611 was ”ported” to the wiki system as the very
first course.
http://wiki.bio.dtu.dk/teaching
R. Wernersson, Forsøg med ny online eksamensform i ”Introduktion til Bioinformatik”, DTU Avisen,
2007.
in the design of online exams for other courses. The interest for online exams turned out to go
beyond DTU and our experiences was presented at the Seminar on Assessment and Exams in
Education at ITU in 20101 .
Establishing new courses
During my time a DTU I have been involved in establishing a number of new courses (see
Table 1) – most recently course 27040: ”Introduction to Systems Biology” in 2013. This
includes all steps from putting together the curriculum, negotiating the establishment of the
course with the Study Board, organizing everything from teaching, practical details and exams,
to coordinating the efforts between internal and external resources (e.g. the ”Bioinformatics
for Human Biologists” course which was a joint effort between DTU and the Faculty of Health
at the University of Copenhagen).
I was also involved in the process of the establishment of the new joint education between University of Copenhagen and DTU: ”IT and Health”, where my responsibility was to coordinate
the Bioinformatics course2 .
Teaching Bioinformatics to high-school teachers and pupils
At DTU there has been a number of initiatives to reach out and teach science to a broader
audience. As part of this I have had a lecture on Molecular Evolution (”DNA in Time and
Space”) which I have taught to high-school pupils for a number of years when they came to
visit DTU as part of the ”DTU Explore” initiative.
Furthermore, together with Anders Gorm Pedersen, I designed, implemented and taught DTU’s
contribution to the continuing education of high-school science teachers (”Efteruddannelseskursus: Bioinformatik Til Gymnasiet”). For this effort both Anders and I were awarded a bonus
from the institute for commitment beyond expectation. The course is still on-going and more
than 150 teachers has been through this up-qualification course.
1
2
R Wernersson and A G Pedersen, Presenting our experiences from implementing an online exam with open
internet access for the ”Introduction to Bioinformatics” course at DTU., Seminar on Assessment and
Exams in Education, IT-University of Denmark, October 2010.
The actual implementation of the course was performed by Thomas Nordahl Petersen, as I was at that point
(co)-responsible for 3 other courses.
Scientific achievements
Invited and contributed talks
13th Annual Drug Discovery & Development Leaders Summit, Zurich, June 2012.
Biomarkers and Data Integration - Building blocks for understanding disease biology.
Presenters: Rasmus Wernersson (Intomics) and Jennifer Larsen (H. Lundbeck).
2nd Intomics Symposium on ”Data mining in drug discovery”, Scion-DTU, November
2011.
The Brain Atlas project - large scale data analysis on depression.
Presenters: Rasmus Wernersson (Intomics) and Jennifer Larsen (H. Lundbeck).
Seminar on Assessment and Exams in Education, IT-University of Denmark, October
2010.
Presenting our experiences from implementing an online exam with open internet access for
the ”Introduction to Bioinformatics” course at DTU.
Danish Center for Scientific Computing - User Conference, DTU, April 2008.
Future Trends and Challenges within the Bioinformatics use of Scientific Computing.
ISMB 2005, Detroit, June 2005.
Advanced Micro-array Probe Design Using OligoWiz 2.0
Pig Genome Sequencing Consortium Yearly Meeting, Copenhagen, May 2005
Developments in the Pig Genome Data-warehouse, 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
Pig Genome Sequencing Consortium Yearly Meeting, Copenhagen, March 2004
The CBS data-warehouse and preliminary scientific results
ISMB 2003, Brisbane, June 2003
OligoWiz: A powerful, flexible yet easy-to-use tool for designing oligonucleotides for DNA
microarrays (Software demo)
Publications, February 2014
Three most cited papers
ˆ 2441 citations: ”Title: RevTrans: multiple alignment of coding DNA from aligned amino
acid sequences ”. R. Wernersson and A. G. Pedersen. 2003
ˆ 184 citations: ”Pigs in sequence space: A 0.66 X coverage pig genome survey based on
shotgun sequencing ”. R. Wernersson, M. H. Schierup et al. 2005
ˆ 131 citations: ”Design of oligonucleotides for microarrays and perspectives for design
of multi-transcriptome arrays”. H. Nielsen, R. Wernersson and S. Knudsen. 2003
2011
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 - Web Server issue, W61-W67
The strength of intron donor splice sites in human genes displays a bell-shaped
pattern
Kai Wang, Rasmus Wernersson, and Søren Brunak
Bioinformatics, 2011, Bioinformatics vol. 27(22), 3079-3084
2010
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, and Thomas Skøt
Jensen
Nucleic Acids Research, 2010, Vol. 38, Database issue, D699-D702
Optimization of the BLASTN substitution matrix for prediction of nonspecific
DNA microarray hybridization
Aron Eklund, Pia Friis, Rasmus Wernersson, and Zoltan Szallasi
Nucleic Acids Research, 2010, Vol. 38, issue 4, e27
1
Google Scholar statistics.
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, Bioinformatics vol. 25(15), 1963-1965
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.
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
2007
Forsøg med ny online eksamensform i ”Introduktion til Bioinformatik”1
Rasmus Wernersson
DTU Avisen, November 2007. (An extended version of this article can be downloaded from
my personal website: www.cbs.dtu.dk/∼raz).
Probe Selection for DNA Microarrays using OligoWiz
Rasmus Wernersson, Agnieszka S. Juncker and Henrik Bjørn Nielsen
Nature Protocols, 2 , 2677 - 2691 (2007)
Dice & DNA
Rasmus Wernersson
BioScience Education e-journal, 10-5, 2007
Thermodynamic probe intensity correction for oligonucleotide microarrays
Georg M. Bruun, Rasmus Wernersson, Agnieszka S. Juncker, Hanni Willenbrock and Henrik
Bjørn Nielsen
Nucleic Acids Research, Vol. 35, No. 7 e48, 2007
1
English summary: short article to the internal DTU newspaper detailing my experience with the new online
exam, I have introduced to the ”Introduction to Bioinformatics” course.
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 Stærfeldt, Rasmus Wernersson, Lone B Madsen, Bo Thomsen,
Henrik Hornshoj, Zhan Bujie, Xuegang Wang, Xuefei Wang, Lars Bolund, Søren Brunak,
Huanming Yang, Christian Bendixen and Merete Fredholm
Genome Biology, 8:R45, 2007
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, 23(13), i387-i391, 2007
2006
An overabundance of phase 0 introns immediately after the start codon in
eukaryotic genes
Henrik Nielsen and Rasmus Wernersson
BMC Genomics, 7, 256, 2006
Virtual Ribosome — a comprehensive DNA translation tool with support for
integration of sequence feature annotation
Rasmus Wernersson
Nucleic Acids Research, 34 - Web Server issue, p. W385–W388, 2006
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
Nucleic Acids Research, 34 - Web Server issue, p. W84–W88, 2006
State-of-the-art in Saccharomyces cerevisiae synchronization protocols
Søren Brunak, Rasmus Wernersson, Thomas Skøt Jensen & Ulrik de Lichtenberg
DIAMONDS (EU project: LSHG-CT-2004-512143), Deliverable 1-D1.1, 2006.
http://www.sbcellcycle.org/Deliverables/synchronization scer2.pdf
2005
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, 22, p. 1191–1201, 2005
‡ = Equal contributors
OligoWiz 2.0 — integrating sequence feature annotation into the design of
microarray probes
Rasmus Wernersson and Henrik Bjørn Nielsen
Nucleic Acids Research, 33 - Webserver Issue, p. W611–W615, 2005
FeatureExtract — extraction of sequence annotation made easy
Rasmus Wernersson
Nucleic Acids Research, 33 - Webserver Issue, p. W567–W569, 2005
Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun
sequencing
Rasmus Wernersson‡, Mikkel H Schierup‡, Frank G Jørgensen, Jan Gorodkin, Frank Panitz,
Hans-Henrik Stærfeldt, Ole F Christensen, Thomas Mailund, Henrik Hornshøj, Ami Klein,
Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane K-S Wong, Jun Yu, Jian Wang,
Christian Bendixen, Merete Fredholm, Søren Brunak, Huanming Yang and Lars Bolund
BMC Genomics, 6, 70, 2005
‡ = Equal contributors
2003
RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences
Rasmus Wernersson and Anders Gorm Pedersen
Nucleic Acids Research, 31 - Webserver Issue, p. 3537–3539, 2003
Design of oligonucleotides for microarrays and perspectives for design of multitranscriptome arrays
Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen
Nucleic Acids Research, 31 - Webserver Issue, p. 3491–3496, 2003
Scientific web-servers
CycleBase.org
(team work)
URL: http://www.cyclebase.org
Abstract: ”Cyclebase is centralized, standardized resource for researchers to inspect and download cell-cycle datasets. Results of our state-of-the-art analyses of individual experiments as
well as combined datasets are also included.”
FeatureExtract
(solo work)
URL: http://www.cbs.dtu.dk/services/FeatureExtract/
Abstract: ”The FeatureExtract server extracts sequence and feature annotation, such as intron/exon structure, from GenBank entries and other GenBank format files.”
FeatureMap3D
(with Anne Mølgaard)
URL: http://www.cbs.dtu.dk/services/FeatureMap3D/
Abstract: ”FeatureMap3D combines protein sequence-based information with structural data
from the Protein Data Bank (PDB).”
InterMap3D
(team work)
URL: http://www.cbs.dtu.dk/services/InterMap3D/
Abstract: ”InterMap3D predicts interacting protein residues by identifying co-evolving pairs of
aminoacids from an alignment of protein sequences.”
OligoWiz 2.0
(with Henrik Bjørn Nielsen)
URL: http://www.cbs.dtu.dk/services/OligoWiz2/
Abstract: ”OligoWiz 2.0 is a powerful tool for microarray probe design that allows for integration of sequence annotation such as exon/intron structure, UTR regions, TSS, etc.”
PHUSER
(team work)
URL: http://www.cbs.dtu.dk/services/PHUSER/
Abstract: ”PHUSER offers quick and easy design of PCR optimized primers for USER fusion
of custom DNA fragments.”
RevTrans
(with Anders Gorm Pedersen)
URL: http://www.cbs.dtu.dk/services/RevTrans/
Abstract: ”RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple
alignment.”
Virtual Ribosome
(solo work)
URL: http://www.cbs.dtu.dk/services/VirtualRibosome/
Abstract: ”The Virtual Ribosome is a comprehensive tool for translating DNA sequences to the
corresponding peptide sequences.”