May 2012

Curriculum vitae

Rasmus WernerssonCo-founder of Intomics A/S, Head of Informatics

intomicsDVD-kopi.indd 1 06/09/10 15:44:35

Personal information

Rasmus WernerssonMaglebjervej 73200 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

Aug 2009–Present: Head of Informatics at Intomics A/S and Co-founder ofthe company. Responsible for building and maintaining Intomics’ High PerformanceComputing system for integrative data analysis, and the development of Intomics’advanced text-mining facilities. Scientific project leader and advisor on multipleresearch projects with clients in the pharmaceutical industry.

Dec 2006–May 2011: Associate professor at the Center for Biological SequenceAnalysis at the Technical University of Denmark. My main focus was on teachingand the development of new courses, teaching materials and implementation of newforms of examination. This included both internal DTU courses, collaboration courseswith the University of Copenhagen, and providing continuing education to high-schoolscience teachers.

Jan 2002–Nov 2006: Assistant professor at the Center for Biological SequenceAnalysis at the Technical University of Denmark. Research: both lab-based researchon 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 (Windowsplatform) 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 atAssociate Professor level.

2001–2008: Diploma of Information Technology (IT-D) – with specialization inSoftware Development, Copenhagen University College of Engineering.

1993–1998: Master of Science (Candidatus scientiarium) in Biology, University ofCopenhagen. Thesis project: ”Direct cloning and expression of enzyme-genes fromnon-cultivatable organisms - experimental work performed at Novo Nordisk A/S (thesection later to become Novozymes A/S)”.

Experience and competences

Introduction

My education and work experience covers two main areas of expertise: 1) ExperimentalMolecular Biology and 2) Computer Science. A major theme in all of my working lifehas been to use my combined expertise on these subjects to facilitate the collaborationbetween ”wet-lab biologists” and ”computer people”. I strongly believe in the benefitsof not only developing new and interesting algorithms but also keeping the usefulnessand accessibility of the tools for the intended users (often biologists) in mind. Severalof my most cited publications (e.g. RevTrans1 and OligoWiz2), are on tools that werecreated to address a specific biology oriented problem.

A very important aspect of facilitating the optimal outcome of projects involvingboth experimentally generated data and advanced computational analysis is thatof communication. For example: in order to implement new algorithms to solvea particular research problem, it is vital that the bioinformatician understand thebiological context of the question and the limitation of the data. However, this goesboth ways and often the situation will be the reverse: - that the experimentalist is notaware 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 commu-nicator has been central to both my academic and industrial career. In my role asHead of Informatics at Intomics A/S I am often brought into scientific projects asan advisor on coordinating the experimental data generation with the data analysisstrategy. A major part of this is interviewing the experimental experts to get anin-depth understanding of the overall biological questions being asked, and based onthis making sure that the data analysis strategy will not only support this, but willbe further enhanced by bringing in even more advanced methods. A good exampleof this could be to add in a network biology point of view, where biological contextof known entities (e.g. biomarkers/drug targets) are investigated through analysis ofprotein-protein interaction networks or supported by pathway analysis.

1 R. Wernersson and A. G. Pedersen, Nucleic Acids Research, 20032 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 experimentalbiology and bioinformatics. In many cases my (experimental) work in one topic such aalternative splicing and cell cycle regulation in Yeast has uncovered an unmeet need forbioinformatics 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 criticalview on the data quality from a biologist point of view, and a pragmatic approach onhow 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 Yeastcell cycle. I was responsible for establishing and optimizing an experimental systemfor cell cycle research in Saccharomyces cerevisiae at our department at DTU. Theinstitute had a well establish fermentation platform with 2L bioreactors which allowedfine-grained control of growth conditions, including temperature. We therefore decidedto base our system on one of the thermo-sensitive cell cycle mutants previouslydescribed (CDC15-2)1, which allowed arrest-and-release synchronization experimentsto be conducted. To allow better control over growth conditions, and to allow forexperiments with labeled amino-acids to be performed, the fermentation protocolwas optimized for synthetic minimal medium. The verified and optimized protocol isdescribed in our main publication on weakly expressed cell cycle regulated genes2 andin the protocol collection for the DIAMONDS cell cycle project3.

During the project it became evident that the different cell cycle experiments describedin the literature (our own and others) were difficult to access and analyze for people notexperts in bioinformatics, and that a lot could be gained from analyzing all the availabledata 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 bioinformaticsanalyses 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 – thebuilding of high quality bioinformatics tools. The OligoWiz package for design ofprobes for DNA microarrays6,7 was initially created to make it easy to design specialpurpose arrays for our own use (e.g. splice-detecting arrays), but quickly turned outto be quite popular to a much wider audience (see Figure 2). This has led to the

1 The CDC15-2 strain in a W303 background was kindly donated by Dr. Bruce Futcher, one of theleading experts in the field

2 U de Licthenberg, R Wernersson et al, Yeast, 20053 http://www.sbcellcycle.org/Deliverables/synchronization_scer2.pdf4 N G Gauthier, M E Larsen, R Wernersson et al. Nucleic Acids Research, 20065 N G Gauthier, L J Jensen, R Wernersson et al. Nucleic Acids Research, 20086 H B Nielsen, R Wernersson, S Knudsen. Nucleic Acids Research, 20037 R Wernersson, H B Nielsen. Nucleic Acids Research, 2005

continued development of the software for almost a decade, improved algorithms forprobe design1, probe normalization2 and a number of review publications including abook 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 forextraction of genetic annotation5 over genome-wide studies of RNA splicing6,7 to myinvolvement in the Danish-Chinese pig genome sequencing project. In the pig genomesequencing project, I coordinated and performed a large part of the evolution-basedanalysis together with Mikkel Heide Schierup from the University of Arhus and I’mthe shared first author of the main publication8.

1 A Eklund, P Friis, R Wernersson et al. Nucleic Acids Research, 20102 G M Bruun, R Wernersson et al. Nucleic Acids Research, 20073 R Wernersson Springer Protocols / Humana Press, 20094 R Wernersson et al. Nature Protocols, 20075 R Wernersson, Nuclecic Acids Research, 20056 H Nielsen and R Wernersson, BMC Genomics, 20067 K Wang, R Wernersson, S Brunak, Bioinformatics, 20118 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 Uni-versity of Denmark, by a group of researchers, myself included, within the fields ofBioinformatics and Systems Biology.

Establishing a High Performance Computing facility

As the Head of Informatics at Intomics is has been my responsibility to manage allthe aspects of building up and maintaining a High Performance Computing (HPC)infrastructure. This includes decisions on configuration and scaling of the system andnetwork, installation and monitoring of hardware in a rack-based environment, main-tainance of a large local installation of bioinformatics relevant databases (e.g. UniProt,PubMed, Ensembl), writing and porting bioinformatics software and coordinating theefforts 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:

• Programming languages: Assembly (expert), C, Basic, Java (expert), ML, Pascal,Python (expert), Perl, R, Shell scripting

• Programming paradigms: Object oriented programming and design, Agile soft-ware development, Model-View-Controller, Client-Server

• User interface design and implementation - e.g. Java GUIs and web UI.• Databases: MySQL, Oracle• Algorithm development and optimization• Linux system administration• Network administration

Project leader and scientific advisor

As mentioned earlier, my other line of responsibilities at Intomics is as a scientificadvisor and project leader. I have experience in managing all parts of the projectwork-flow:

• Pre-project negotiations with the client (identify the core biological questions,suggest a data analysis plan and negotiate the contract details)

• Project leading though-out the project (including the continued evaluationof progress and data quality and based on this to suggest adjustments to thestrategy)

• Post-project evaluation and followup (including communication of the resultsto a larger audience, for example through internal seminars, or in cases wheremore publicity is wanted, through conference presentations1,2)

from data to biology

Data analysis in drug discovery

Discovery Phase II Phase I Phase III Market Preclinical development

Target discovery

Biomarker discovery and optimisation

Knowledge discovery

Data mining projects

Figure 3: Scope of projects

I have been involved in contract research projects for a number of large scandinavianpharmaceutical companies including Leo Pharma, AstraZenica and H. Lundbeck. Mostof this work has been related to the pre-clinical part of drug development. Notice, how-ever, that Intomics also do knowledge management projects that spans most aspectsof clinical research (Figure 3), and from this I have a solid understanding of the entiredrug development process.

1 R. Wernersson (Intomics A/S) and J. Larsen (H. Lundbeck A/S), The Brain Atlas project - large scaledata analysis on depression., 2nd Intomics Symposium on ”Data mining in drug discovery”,Scion-DTU, November 2011.

2 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 & DevelopmentLeaders Summit, Zurich, June 2012.

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 topursue this topic, and even after co-founding Intomics A/S and shifting to a job in theindustry, I have continued giving guest lectures at selected courses at DTU – see Table 1for a condensed overview of my main teaching activities. Besides my involvement incoursework I have also co-supervised 4 Master thesis students and 3 PhD students.

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 turnit 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 realizethat for most students bioinformatics would be a tool subject rather than a researchtopic, much in the same vain as mathematics and statistics are for most students. Wetherefore decided to postpone the more advanced subjects to later courses. Since theintended audience was ”bio” oriented students, we also decided to re-write all partsof the course that had previously required UNIX command-line tools. This also hadthe added benefit that we could redesign the course to rely only on public availabledatabases (e.g. GenBank and UniProt), and tools (E.g. BLAST and PyMol) that thestudents could later use for all kinds of ”everyday use” (for example finding a DNAsequence for primer-design). As part of this initiative practically ALL of the computerexercises was rewritten from scratch and put up as an online resource1. During thisprocess 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”2 (Figure 4).

Online teaching materials and differential teaching

Having all teaching material online at our own website allowed for easy experimentingwith new types of materials. Since the course had been retooled for a broader audienceof students, there was a need to give the ”top 10% students” access to more advancedtopics, in order to keep up the interest. We solved this by recording small videolectures that high-lighted some of the inner details of the tools (e.g. the dynamicprogramming algorithm for pairwise alignments of DNA/protein), and linking theminto the online course plan - clearly marking them as ”Advanced topics”. Likewise,we also experimented with linking in background materials on topics that the studentswere expected to know beforehand, but where some may need a reminder. This alsohad the added benefit to reduce the amount of ”reminder” slides in our presentations.

1 I personally wrote more than 60% of the new exercise manuals.2 R Wernersson, BioScience Education e-journal, 2007

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The ”Systems Biology Teaching Wiki”

Since the use of online materials had been so successful in the 27611 course, AndersGorm Pedersen1 and I took the initiative to set up a Wiki2 for teaching materials at thedepartment – this is the system that later morphed into the institute-wide ”SystemsBiology 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 thata traditional 4-hour pen-and-paper exam would feel oddly out of place. I wanted tointroduce a type of exam where the students could actually use the online tools anddatabases they had learned about during the course, to solve real biological questionsfor the exam. In collaboration with the Exam Office we got the permission to be thevery first course at DTU to experiment with the implementation of a 100% onlineexam 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 thesuccessful implementation in 20074 the experiences from 27611 have been used in thedesign of online exams for other courses. The interest for online exams turned out to

1 Professor (Docent) at the Center for Biological Sequence Analysis at DTU2 I was the original system administrator for the Wiki and 27611 was ”ported” to the wiki system as

the very first course.3 http://wiki.bio.dtu.dk/teaching4 R. Wernersson, Forsøg med ny online eksamensform i ”Introduktion til Bioinformatik”, DTUAvisen, 2007.

go beyond DTU and our experiences was presented at the Seminar on Assessment andExams 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). This includes all steps from putting together the curriculum, negotiatingthe establishment of the course with the Study Board, organizing everything fromteaching, practical details and exams, to coordinating the efforts between internal andexternal resources (e.g. the ”Bioinformatics for Human Biologists” course which wasa 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 educationbetween University of Copenhagen and DTU: ”IT and Health”, where my responsibilitywas 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 scienceto a broader audience. As part of this I have had a lecture on Molecular Evolu-tion (”DNA in Time and Space”) which I have taught to high-school pupils for anumber of years when they came to visit DTU as part of the ”DTU Explore” initiative.

Furthermore, together with Anders Gorm Pedersen, I designed, implemented andtaught DTU’s contribution to the continuing education of high-school science teach-ers (”Efteruddannelseskursus: Bioinformatik Til Gymnasiet”). For this effort bothAnders and I were awarded a bonus from the institute for commitment beyond expec-tation. The course is still on-going and more than 150 teachers has been through thisup-qualification course.

1 R Wernersson and A G Pedersen, Presenting our experiences from implementing an online examwith open internet access for the ”Introduction to Bioinformatics” course at DTU., Seminar onAssessment and Exams in Education, IT-University of Denmark, October 2010.

2 The actual implementation of the course was performed by Thomas Nordahl Petersen, as I was atthat point (co)-responsible for 3 other courses.

Scientific achievements

Invited and contributed talks

13th Annual Drug Discovery & Development Leaders Summit, Zurich, June2012.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 internetaccess 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 2005Developments in the Pig Genome Data-warehouse, Aspects of the BMC paper, and(pig) oligo design

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

Pig Genome Sequencing Consortium Yearly Meeting, Copenhagen, March2004The CBS data-warehouse and preliminary scientific results

ISMB 2003, Brisbane, June 2003OligoWiz: A powerful, flexible yet easy-to-use tool for designing oligonucleotides forDNA microarrays (Software demo)

Publications, May 2012

Three most cited papers

• 1791 citations: ”Title: RevTrans: multiple alignment of coding DNA fromaligned amino acid sequences ”. R. Wernersson and A. G. Pedersen. 2003

• 144 citations: ”Pigs in sequence space: A 0.66 X coverage pig genome surveybased on shotgun sequencing ”. R. Wernersson, M. H. Schierup et al. 2005

• 110 citations: ”Design of oligonucleotides for microarrays and perspectives fordesign of multi-transcriptome arrays”. H. Nielsen, R. Wernersson and S. Knud-sen. 2003

2011

PHUSER (Primer Help for USER): a novel tool for USER fusion primerdesignLars 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 WernerssonNucleic Acids Research, 2011, 39 - Web Server issue, W61-W67

The strength of intron donor splice sites in human genes displays a bell-shaped patternKai Wang, Rasmus Wernersson, and Søren BrunakBioinformatics, 2011, Bioinformatics vol. 27(22), 3079-3084

2010

Cyclebase.org: version 2.0, an updated comprehensive, multi-speciesrepository of cell cycle experiments and derived analysis resultsNicholas Gauthier, Lars Juhl Jensen, Rasmus Wernersson, Søren Brunak, and ThomasSkøt JensenNucleic Acids Research, 2010, Vol. 38, Database issue, D699-D702

Optimization of the BLASTN substitution matrix for prediction of nonspe-cific DNA microarray hybridizationAron Eklund, Pia Friis, Rasmus Wernersson, and Zoltan SzallasiNucleic Acids Research, 2010, Vol. 38, issue 4, e27

1 Google Scholar statistics.

2009

InterMap3D: predicting and visualizing co-evolving protein residuesRodrigo Gouveia-Oliveira, Francisco S. Roque, Rasmus Wernersson, Thomas Sicheritz-Ponten, Peter W. Sackett, Anne Mølgaard and Anders G. PedersenBioinformatics, 2009, Bioinformatics vol. 25(15), 1963-1965

Book chapter: ”Probe design for expression arrays using OligoWiz”Rasmus WernerssonIn DNA Arrays for Biomedical Research: Methods and Protocols, Vol 529; MartinDufva (Editor), Springer Protocols / Humana Press, 2009.

2008

Cyclebase.org — a comprehensive multi-organism online database of cellcycle experimentsNicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichten-berg, Lars Juhl Jensen, Søren Brunak, and Thomas Skøt JensenNucleic Acids Research, 2008, Vol. 36, Database issue, D854-D859

2007

Forsøg med ny online eksamensform i ”Introduktion til Bioinformatik”1

Rasmus WernerssonDTU Avisen, November 2007. (An extended version of this article can be downloadedfrom my personal website: www.cbs.dtu.dk/~raz).

Probe Selection for DNA Microarrays using OligoWizRasmus Wernersson, Agnieszka S. Juncker and Henrik Bjørn NielsenNature Protocols, 2 , 2677 - 2691 (2007)

Dice & DNARasmus WernerssonBioScience Education e-journal, 10-5, 2007

Thermodynamic probe intensity correction for oligonucleotide microarraysGeorg M. Bruun, Rasmus Wernersson, Agnieszka S. Juncker, Hanni Willenbrock andHenrik Bjørn NielsenNucleic Acids Research, Vol. 35, No. 7 e48, 2007

1 English summary: short article to the internal DTU newspaper detailing my experience with thenew online exam, I have introduced to the ”Introduction to Bioinformatics” course.

Porcine transcriptome analysis based on 97 non-normalized cDNA librariesand 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 HHavgaard, 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, XuefeiWang, Lars Bolund, Søren Brunak, Huanming Yang, Christian Bendixen and MereteFredholmGenome Biology, 8:R45, 2007

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluationand annotationFrank 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, TrineGreen, Bente J. Nielsen, Jakob H. Havgaard, Søren Brunak, Merete Fredholm andChristian BendixenBioinformatics, 23(13), i387-i391, 2007

2006

An overabundance of phase 0 introns immediately after the start codon ineukaryotic genesHenrik Nielsen and Rasmus WernerssonBMC Genomics, 7, 256, 2006

Virtual Ribosome — a comprehensive DNA translation tool with supportfor integration of sequence feature annotationRasmus WernerssonNucleic Acids Research, 34 - Web Server issue, p. W385–W388, 2006

FeatureMap3D: a tool to map protein features and sequence conservationonto homologous structures in the PDBRasmus Wernersson, Kristoffer Rapacki, Hans-Henrik Stærfeldt, Peter Wad Sackettand Anne MølgaardNucleic Acids Research, 34 - Web Server issue, p. W84–W88, 2006

State-of-the-art in Saccharomyces cerevisiae synchronization protocolsSøren Brunak, Rasmus Wernersson, Thomas Skøt Jensen & Ulrik de LichtenbergDIAMONDS (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 yeastUlrik de Lichtenberg‡, Rasmus Wernersson‡, Thomas Skøt Jensen‡, Henrik BjørnNielsen, Anders Fausbøll, Peer Schmidt, Flemming Bryde Hansen, Steen Knudsen andSøren BrunakYeast, 22, p. 1191–1201, 2005‡ = Equal contributors

OligoWiz 2.0 — integrating sequence feature annotation into the design ofmicroarray probesRasmus Wernersson and Henrik Bjørn NielsenNucleic Acids Research, 33 - Webserver Issue, p. W611–W615, 2005

FeatureExtract — extraction of sequence annotation made easyRasmus WernerssonNucleic Acids Research, 33 - Webserver Issue, p. W567–W569, 2005

Pigs in sequence space: A 0.66X coverage pig genome survey based onshotgun sequencingRasmus Wernersson‡, Mikkel H Schierup‡, Frank G Jørgensen, Jan Gorodkin, FrankPanitz, 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, HuanmingYang and Lars BolundBMC Genomics, 6, 70, 2005‡ = Equal contributors

2003

RevTrans: Multiple alignment of coding DNA from aligned amino acidsequencesRasmus Wernersson and Anders Gorm PedersenNucleic Acids Research, 31 - Webserver Issue, p. 3537–3539, 2003

Design of oligonucleotides for microarrays and perspectives for design ofmulti-transcriptome arraysHenrik Bjørn Nielsen, Rasmus Wernersson and Steen KnudsenNucleic Acids Research, 31 - Webserver Issue, p. 3491–3496, 2003

Scientific web-servers

CycleBase.org

(team work)URL: http://www.cyclebase.orgAbstract: ”Cyclebase is centralized, standardized resource for researchers to inspectand download cell-cycle datasets. Results of our state-of-the-art analyses of individualexperiments 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, suchas 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 structuraldata 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-evolvingpairs 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 forintegration 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 USERfusion 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, alignsthe peptide sequences, and uses this as a scaffold for constructing the correspondingDNA 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 se-quences to the corresponding peptide sequences.”