Dr. Steffen Möller

Head of Bioinformatics Group

Proteome Center Rostock
Schillingallee 69
18057 Rostock

Email:
Phone:
+49 381 4 94 49 30
Fax:
+49 381 4 94 49 32
 

Research interests

In general, this is any computational tool that supports biological research. The work I personally liked most is

  • GPCR coupling prediction
  • Intergenomics on disease-associated chromosomal loci
  • many more on agents and transmembrane proteins

Current activities involve the computer aided interpretation of what we get from genome-wide SNP studies. And it was these thoughts that guided me into the field of grid computing. Something that albeit having published on is less of a science but more of a promotional nature is my involvement with the Debian Linux distribution. This is bunch of enthusiastic people who mutually help each other and (en passent the world) in maintaining their research infrastructure. This comprises both general IT and bioinformatics applications.

Active Projects

  • EU project "Know ARC" on grid computing. A single look on the Nordu Grid monitor says more than a 1 000 words. I am investigating how grid technologies can become more applicable for bioinformatics:
  • Dynamic Runtime Environments
  • Embedding grid jobs in bioinformatics workflow suite Taverna
  • Expression QTL analysis in a murine model of Multiple Sclerosis 

Others

  • Apical-basolateral distribution of epithelial membrane proteins
  • sugaR - R package for plotting a diabetes diary

Rewards

For my first degree in the early nineties of the last century I was joining some fun competitions that I like to think back about:

  • National Programming Contest, U Texas, Austin, TX, USA
  • 1995 Shocc - Shortest C Contest, Kaiserslautern, Germany

and I had helped with the 1994 MICE (Most Intelligent Corn Eater) competition in Hildesheim, Germany. Since then I contributed to two projects that were rewarded: 

  • 2005 - Intergenomics on QTL (German QUECKENSTEDT Award for research in multiple sclerosis)
  • 2006 - prediction of a pical-basolateral sorting in kidney epithelia (Jugend forscht)

Publikationen

2011

  • Krishna Kumar Kandaswamy and Kuo-Chen Chou and Thomas Martinetz and Steffen Möller and P. N. Suganthan and S. Sridharan and Ganesan Pugalenthi: AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties. Journal of Theoretical Biology, no. 270, pp. 56-62, 2011
    BibTeX
    @article{KaChMaMoSuSrGa11,
    author = {Krishna Kumar Kandaswamy and Kuo-Chen Chou and Thomas Martinetz and Steffen M{\"o}ller and P. N. Suganthan and S. Sridharan and Ganesan Pugalenthi},
    title = {{AFP}-{P}red: {A} random forest approach for predicting antifreeze proteins from sequence-derived properties},
    journal = {Journal of Theoretical Biology},
    volume = {270},
    number = {1},
    pages = {56--62},
    year = {2011},
    }
    
    

2010

  • Krishna Kumar Kandaswamy and Ganesan Pugalenthi and Steffen Möller and Enno Hartmann and Kai-Uwe Kalies and P.N.Suganthan and Thomas Martinetz: Prediction of apoptosis protein locations with Genetic Algorithms and Support Vector Machines through a new mode of pseudo amino acid composition. Protein Peptide Letters, no. 17, pp. 1473-1479, 2010
    BibTeX
    @article{KaPuMoHaKaSuMa10,
    author = {Krishna Kumar Kandaswamy and Ganesan Pugalenthi and Steffen M{\"o}ller and Enno Hartmann and Kai-Uwe Kalies and P.N.Suganthan and Thomas Martinetz},
    title = {Prediction of apoptosis protein locations with {G}enetic {A}lgorithms and {S}upport {V}ector {M}achines through a new mode of pseudo amino acid composition},
    journal = {Protein Peptide Letters},
    pages = {1473--1479},
    volume = {17},
    year = {2010},
    }
    
    
  • Krishna Kumar Kandaswamy and Ganesan Pugalenthi and Enno Hartmann and Kai-Uwe Kalies and Steffen Möller and P.N. Suganthan and Thomas Martinetz: SPRED: A machine learning approach for the identification of classical and non-classical secretory proteins in mammalian genomes. Biochemical and biophysical research communications, no. 391, pp. 1306-1311, 2010
    BibTeX
    @article{KaPuHaKaMoSuMa10,
    author = {Krishna Kumar Kandaswamy and Ganesan Pugalenthi and Enno Hartmann and Kai-Uwe Kalies and Steffen M{\"o}ller and P.N. Suganthan and Thomas Martinetz},
    title = {{SPRED}: {A} machine learning approach for the identification of classical and non-classical secretory proteins in mammalian genomes},
    journal = {Biochemical and biophysical research communications},
    volume = {391},
    number = {3},
    pages = {1306--1311},
    year = {2010},
    pdf = {http://www.inb.uni-luebeck.de/publications/pdfs/KaPuHaKaMoSuMa09.pdf},
    }
    
    

2009

  • X. Zhou and H. Krabbenhöft and M. Niinimäki and A. Depeuringe and S. Möller and H. Müller: An Easy Setup for Parallel Medical Image Processing: Using Taverna and ARC. Stud Health Technol Inform., no. 147, pp. 41-50, 2009
    BibTeX
    @article{ZhKrNiDeMoMu09,
    author = {X. Zhou and H. Krabbenh{\"o}ft and M. Niinim{\"a}ki and A. Depeuringe and S. M{\"o}ller and H. M{\"u}ller},
    title = {An {E}asy {S}etup for {P}arallel {M}edical {I}mage {P}rocessing: {U}sing {T}averna and {ARC}},
    journal = {Stud Health Technol Inform.},
    year = {2009},
    volume = {147},
    pages = {41--50},
    }
    
    

2008

  • Hajo N. Krabbenhöft and Steffen Möller and Daniel Bayer: Integrating ARC Grid Middleware with Taverna Workflows. Bioinformatics, no. 24, pp. 1221-1222, 2008
    BibTeX
    @article{KrMoBa08,
    author = {Hajo N. Krabbenh{\"o}ft and Steffen M{\"o}ller and Daniel Bayer},
    title = {Integrating {ARC} {G}rid {M}iddleware with {T}averna {W}orkflows},
    journal = {Bioinformatics},
    volume = {24},
    number = {9},
    pages = {1221--1222},
    year = {2008},
    opt_pmid = 18353787,
    }
    
    
  • Daniel F. Schwarz and Oliver Hädicke and Jeanette Erdmann and Andreas Ziegler and Daniel Bayer and Steffen Möller: SNPtoGO: characterizing SNPs by enriched GO terms. Bioinformatics, no. 24, pp. 146-148, 2008
    BibTeX Link
    @article{ScHaErZiBaMo08,
    author = {Daniel F. Schwarz and Oliver H{\"a}dicke and Jeanette Erdmann and Andreas Ziegler and Daniel Bayer and Steffen M{\"o}ller},
    title = {{SNPtoGO}: characterizing {SNPs} by enriched {GO} terms},
    journal = {Bioinformatics},
    year = {2008},
    volume = {24},
    number = {1},
    pages = {146--148},
    url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm551v1},
    }
    
    

2007

  • Emanuela Merelli and Giuliano Armano and Nicola Cannata and Flavio Corradini and Mark d`Inverno and Andreas Doms and Phillip Lord and Andrew Martin and Luciano Milanesi and Steffen Möller and Michael Schroeder and Michael Luck: Agents in bioinformatics, computational and systems biology.. Briefings in Bioinformatics, no. 8, pp. 45-59, 2007
    BibTeX
    @article{MeArCaCoInDoLoMaMiMoScLu07,
    author = {Emanuela Merelli and Giuliano Armano and Nicola Cannata and Flavio Corradini and Mark d'Inverno and Andreas Doms and Phillip Lord and Andrew Martin and Luciano Milanesi and Steffen M{\"o}ller and Michael Schroeder and Michael Luck},
    title = {Agents in bioinformatics, computational and systems biology.},
    journal = {Briefings in Bioinformatics},
    volume = {8},
    number = {1},
    year = {2007},
    pages = {45--59},
    ee = {http://dx.doi.org/10.1093/bib/bbl014},
    bibsource = {DBLP, http://dblp.uni-trier.de},
    }
    
    
  • Dirk Eddelbuettel and David Vernazobres and Albrecht Gebhardt and Steffen Möller: apt-get install cran bioc: On automated builds of 1700 R packages for Debian. in useR conference, Ames, Iowa, 2007
    BibTeX Link
    @inproceedings{EdVeGeMo07,
    author = {Dirk Eddelbuettel and David Vernazobres and Albrecht Gebhardt and Steffen M{\"o}ller},
    title = {apt-get install cran bioc: {O}n automated builds of 1700 {R} packages for {D}ebian},
    booktitle = {use{R} conference},
    address= {Ames, Iowa},
    year = {2007},
    url = {http://user2007.org/},
    }
    
    
  • D. Bayer and T. Bhimdi and G. Oechsler and F. Orellana and A. Wäänänen and B. Kónya and S. Möller: Dynamic Runtime Environments for Grid Computing. in Cracow`07 Grid Workshop, pp. 155-162, Cracow, Poland, 2007
    BibTeX
    @inproceedings{BaBhOeOrWaKoMo07,
    title={Dynamic Runtime Environments for Grid Computing},
    author={D. Bayer and T. Bhimdi and G. Oechsler and F. Orellana and A. W{\"a}{\"a}n{\"a}nen and B. K{\'o}nya and S. M{\"o}ller},
    address={Cracow, Poland},
    booktitle={Cracow'07 Grid Workshop},
    pages={155--162},
    year={2007},
    }
    
    
  • Steffen Möller and Daniel Bayer and David Vernazobres and Albrecht Gebhardt and Dirk Eddelbuettel: Scientific Grid Computing via Community-Controlled Autobuilding of Software Packages Across Architectures. in NETTAB, Pisa, Italy, 2007
    BibTeX Link
    @inproceedings{MoBaVeGeEd07,
    author = {Steffen M{\"o}ller and Daniel Bayer and David Vernazobres and Albrecht Gebhardt and Dirk Eddelbuettel},
    title = {Scientific Grid Computing via Community-Controlled Autobuilding of Software Packages Across Architectures},
    booktitle = {NETTAB},
    address = {Pisa, Italy},
    year = {2007},
    url = {http://nettab.org/2007/},
    }
    
    

2006

  • Steffen Möller and Uwe K. Zettl and Robert Goertsches and Pablo Serrano-Fernández: Comparative Genomics for the Investigation of Autoimmune Diseases. Curr. Pharm. Des., no. 12, pp. 3707-3722, 2006
    BibTeX Link
    @article{MoeZeGoeSe06,
    author = {Steffen M{\"o}ller and Uwe K. Zettl and Robert Goertsches and Pablo Serrano-Fern{\'a}ndez},
    title = {Comparative Genomics for the Investigation of Autoimmune Diseases},
    journal = {Curr. Pharm. Des.},
    year = {2006},
    volume = {12},
    number = {29},
    pages = {3707--3722},
    url = {http://www.ingentaconnect.com/content/ben/cpd/2006/00000012/00000029/art00003},
    }
    
    
  • Johan Öckinger and Pablo Serrano-Fernández and Steffen Möller and Saleh M. Ibrahim and Tomas Olsson and Maja Jagodic: Definition of a 1.06 Mb region linked to neuroinflammation in humans, rats and mice. Genetics, no. 173, pp. 1539-1545, 2006
    BibTeX Link
    @article{OecFeMoeIbOlJa06,
    author = {Johan {\"O}ckinger and Pablo Serrano-Fern{\'a}ndez and Steffen M{\"o}ller and Saleh M. Ibrahim and Tomas Olsson and Maja Jagodic},
    title = {Definition of a 1.06 Mb region linked to neuroinflammation in humans, rats and mice},
    year = {2006},
    journal = {Genetics},
    volume = {173},
    number = {3},
    pages = {1539--1545},
    url={http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16624898},
    }
    
    
  • X. Yu and K. Bauer P. Wernhoff and D. Koczan and S. Möller and H.-J. Thiesen and S.M. Ibrahim: Fine mapping of collagen-induced arthritis quantitative trait loci in an advanced intercross line. J. Immunol., no. 177, pp. 7042-7049, 2006
    BibTeX
    @article{YuBaWeKoMoThIb06,
    author = {X. Yu and K. Bauer P. Wernhoff and D. Koczan and S. M{\"o}ller and H.-J. Thiesen and S.M. Ibrahim},
    title = {Fine mapping of collagen-induced arthritis quantitative trait loci in an advanced intercross line},
    journal = {J. Immunol.},
    year = {2006},
    volume = {177},
    number = {10},
    pages = {7042--7049},
    }
    
    
  • Robert Goertsches and Pablo Serrano-Fernández and Steffen Möller and Dirk Koczan and Uwe K. Zettl: Multiple Sclerosis Therapy Monitoring Based on Gene Expression. Curr. Pharm. Des., no. 12, pp. 3761-3779, 2006
    BibTeX Link
    @article{GoeSeMoeKoZe06,
    author = {Robert Goertsches and Pablo Serrano-Fern{\'a}ndez and Steffen M{\"o}ller and Dirk Koczan and Uwe K. Zettl},
    title = {Multiple {S}clerosis {T}herapy {M}onitoring {B}ased on {G}ene {E}xpression},
    journal = {Curr. Pharm. Des.},
    year = {2006},
    volume = {12},
    number = {29},
    pages = {3761--3779},
    url = {http://www.ingentaconnect.com/content/ben/cpd/2006/00000012/00000029/art00008},
    }
    
    

2005

  • Steffen Möller and Pablo Serrano-Fernández and Michael Watson and Dirk Koczan and Vassilis Kotsikoris and Manfred Kunz and Martin Blüggel and Jens Pahnke and Harald Illges and Stefan Mikkat and Hans-Jürgen Thiesen and Michael O. Glocker and Uwe K. Zettl and Saleh M. Ibrahim: Collection of soluble variants of membrane proteins for transcriptomics and proteomics.. In Silico Biol., no. 5, pp. 295-311, 2005
    BibTeX Link
    @article{MoSeWaKoKoKu05,
    author = {Steffen M{\"o}ller and Pablo Serrano-Fern{\'a}ndez and Michael Watson and Dirk Koczan and Vassilis Kotsikoris and Manfred Kunz and Martin Bl{\"u}ggel and Jens Pahnke and Harald Illges and Stefan Mikkat and Hans-J{\"u}rgen Thiesen and Michael O. Glocker and Uwe K. Zettl and Saleh M. Ibrahim},
    title = {Collection of soluble variants of membrane proteins for transcriptomics and proteomics.},
    journal = {In Silico Biol.},
    volume = {5},
    number = {3},
    pages = {295--311},
    year = {2005},
    url= {http://www.bioinfo.de/isb/2005/05/0028/},
    }
    
    
  • V. Aidinis and P. Carninci and M. Armaka and W. Witke and V. Harokopos and N. Pavelka and D. Koczan and C. Argyropoulos and M.M. Thwin and S. Möller and W. Kazunori and P. Gopalakrishnakone and P. Ricciardi-Castagnoli and H.-J. Thiesen and Y. Hayashizaki and G. Kollias: Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.. PLoS Genet., no. 1, pp. e48, 2005
    BibTeX Link
    @article{AiCaArWiHaPaKoArThMoeKaGoRiThHaKo05,
    author = {V. Aidinis and P. Carninci and M. Armaka and W. Witke and V. Harokopos and N. Pavelka and D. Koczan and C. Argyropoulos and M.M. Thwin and S. M{\"o}ller and W. Kazunori and P. Gopalakrishnakone and P. Ricciardi-Castagnoli and H.-J. Thiesen and Y. Hayashizaki and G. Kollias},
    title = {Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.},
    journal = {PLoS Genet.},
    volume = {1},
    number = {4},
    pages = {e48},
    year = {2005},
    url = {http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=16254600},
    }
    
    
  • A. Tille and S. Möller: Debian-Med Free Software in Health Care. in MAS*BIOMED Workshop, AAMAS, Utrecht, NL, pp. 72-85, 2005
    BibTeX Link
    @inproceedings{TiMo05,
    author = {A. Tille and S. M{\"o}ller},
    title = {Debian-{M}ed {F}ree {S}oftware in {H}ealth {C}are},
    booktitle = {MAS*BIOMED Workshop, AAMAS, Utrecht, NL},
    editor = {Guiliano Admano and J{\"o}rg Denzinger and Andrew Martin and Emanuela Merelli and Simon Miles and Huaglory Tianfield and Rainer Unland},
    pages = {72--85},
    year = {2005},
    url = {http://people.debian.org/~tille/debian-med/talks/200507_biomed/index_en.html},
    pdf = {http://www.diee.unica.it/biomed05/pdf/proceedings.pdf},
    }
    
    
  • P. Gierer and S. M. Ibrahim and T. Mittlmeier and D. Koczan and S. Möller and J. Landes and G. Gradl and B. Vollmar: Gene expression profile and synovial microcirculation at early stages of collagen-induced arthritis. Arthritis Research and Therapy, pp. R868-R876, 2005
    BibTeX Link
    @misc{GiIbMiKoMo05,
    author = {P. Gierer and S. M. Ibrahim and T. Mittlmeier and D. Koczan and S. M{\"o}ller and J. Landes and G. Gradl and B. Vollmar},
    title = {Gene expression profile and synovial microcirculation at early stages of collagen-induced arthritis},
    journal = {Arthritis Research and Therapy},
    number = {7},
    pages = {R868--R876},
    year = {2005},
    url={http://arthritis-research.com/content/7/4/R868},
    pdf={http://arthritis-research.com/content/pdf/ar1754.pdf},
    }
    
    
  • M. Johannesson and L. M. Olsson and A. K. Lindqvist and S. Möller and D. Koczan and L. Wester-Rosenlof and H. J. Thiesenand S. Ibrahim and R. Holmdahl: Gene expression profiling of arthritis using a QTL chip reveals a complex gene regulation of the Cia5 region in mice. Genes Immun., no. 6, pp. 575-583, 2005
    BibTeX Link
    @article{JoOlLiMoKoWeThIbHo05,
    author = {M. Johannesson and L. M. Olsson and A. K. Lindqvist and S. M{\"o}ller and D. Koczan and L. Wester-Rosenlof and H. J. Thiesenand S. Ibrahim and R. Holmdahl},
    title = {Gene expression profiling of arthritis using a {QTL} chip reveals a complex gene regulation of the {Cia5} region in mice},
    journal = {Genes Immun.},
    volume = {6},
    year = {2005},
    pages= {575--583},
    url = {http://www.nature.com/gene/journal/v6/n7/abs/6364242a.html},
    }
    
    
  • P. Serrano-Fernández and S. M. Ibrahim and D. Koczan and U. K. Zettl and S. Möller: In silico fine-mapping: narrowing disease-associated loci by intergenomics. Bioinformatics, no. 21, pp. 1737-1738, 2005
    BibTeX Link
    @article{SeIbKoZeMo05,
    author = {P. Serrano-Fern{\'a}ndez and S. M. Ibrahim and D. Koczan and U. K. Zettl and S. M{\"o}ller},
    title = {In silico fine-mapping: narrowing disease-associated loci by intergenomics},
    journal = {Bioinformatics},
    volume = {21},
    number = {8},
    pages = {1737--1738},
    year = {2005},
    url = {http://bioinformatics.oxfordjournals.org/cgi/content/full/21/8/1737},
    }
    
    
  • E. Bartocci and E. Merelli and S. Möller: Integration of EnsEMBL with BioAgent.. Technical Report, 2005
    BibTeX
    @techreport{BaMeMoe05,
    author = {E. Bartocci and E. Merelli and S. M{\"o}ller},
    title = {Integration of EnsEMBL with BioAgent.},
    journal = {Technical Report},
    number = {TR02-2005},
    institution = {Dipartimento di Matematica e Informatica, Universita di Camerino},
    year = {2005},
    }