EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

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Biography

  • PhD 1998, Statistical Physics, University of Freiburg.
    Postdoctoral research at IBM Research, San Jose, California and at DKFZ Heidelberg.
    Group leader at EMBL-EBI 2004-2009, EMBL Heidelberg since 2009. Senior Scientist since 2011.
    Group leader in the Molecular Medicine Partnership Unit.

Publications

Total: 152 publication(s)

2007

Chiang T, Scholtens D, Sarkar D, Gentleman R, Huber W. (2007)

Coverage and error models of protein-protein interaction data by directed graph analysis

Genome Biol. 8(9):R186. doi: 10.1186/gb-2007-8-9-r186
Europe PMC | doi

Gentleman R, Huber W. (2007)

Making the most of high-throughput protein-interaction data

Genome Biol. 8(10):112. doi: 10.1186/gb-2007-8-10-112
Europe PMC | doi

Huber W, Carey VJ, Long L, Falcon S, Gentleman R. (2007)

Graphs in molecular biology

Paper presented at the Otto Warburg International Summer School and Workshop on Networks and Regulation, Berlin, GERMANY, 2005.BMC Bioinformatics 8 Suppl 6:S8. doi: 10.1186/1471-2105-8-s6-s8
Europe PMC | doi

Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K. (2007)

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions

BMC Biol. 5:25. doi: 10.1186/1741-7007-5-25
Europe PMC | doi

Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W. (2007)

Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts

BMC Bioinformatics 8:221. doi: 10.1186/1471-2105-8-221
Europe PMC | doi


2006

Huber W, Toedling J, Steinmetz LM. (2006)

Transcript mapping with high-density oligonucleotide tiling arrays

Bioinformatics 22(16):1963-1970. doi: 10.1093/bioinformatics/btl289
Europe PMC | doi

David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM. (2006)

A high-resolution map of transcription in the yeast genome

Proc. Natl. Acad. Sci. U.S.A. 103(14):5320-5325. doi: 10.1073/pnas.0601091103
Europe PMC | doi

Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. (2006)

Top-down standards will not serve systems biology

Nature 440(7080):24. doi: 10.1038/440024a
Europe PMC | doi

Gentleman R, Hahne F, Huber W. (2006)

Visualizing genomic data. Technical Report 10

Bioconductor Project Working Papers
Europe PMC

Boutros M, Brás LP, Huber W. (2006)

Analysis of cell-based RNAi screens

Genome Biol. 7(7):R66. doi: 10.1186/gb-2006-7-7-r66
Europe PMC | doi

Hahne F, Arlt D, Sauermann M, Majety M, Poustka A, Wiemann S, Huber W. (2006)

Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts

Genome Biol. 7(8):R77. doi: 10.1186/gb-2006-7-8-r77
Europe PMC | doi

Huber W. (2006)

Several articles in the R News special issue on Bioinformatics

R news 6(5)

Mansmann U, Ruschhaupt M, Huber W. (2006)

Reproducible statistical analysis in microarray profiling studies

Paper presented at the Conference on Statistical Methodology in Bioinformatics and Clinical Trials, Prague, CZECH REPUBLIC, APR, 2004.Methods Inf Med 45(2):139-145. doi: 10.1267/meth06020139
Europe PMC | doi

Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A, Wiemann S. (2006)

The LIFEdb database in 2006

Nucleic Acids Res. 34(Database issue):D415-8. doi: 10.1093/nar/gkj139
Europe PMC | doi


2005

Guilleaume B, Buness A, Schmidt C, Klimek F, Moldenhauer G, Huber W, Arlt D, Korf U, Wiemann S, Poustka A. (2005)

Systematic comparison of surface coatings for protein microarrays

Proteomics 5(18):4705-4712. doi: 10.1002/pmic.200401324
Europe PMC | doi

Heydebreck A, Huber W, Gentleman R. (2005)

Differential Expression with the Bioconductor Project

In: Dunn MJ, Jorde LB, Little PFR, Subramaniam S (eds.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons.doi: 10.1002/047001153X.g405208
doi

Arlt D, Huber W, Liebel U, Schmidt C, Majety M, Sauermann M, Rosenfelder H, Bechtel S, Mehrle A, Bannasch D, Schupp I, Seiler M, Simpson JC, Hahne F, Moosmayer P, Ruschhaupt M, Guilleaume B, Wellenreuther R, Pepperkok R, Sültmann H, Poustka A, Wiemann S. (2005)

Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle

Cancer Res. 65(17):7733-7742. doi: 10.1158/0008-5472.CAN-05-0642
Europe PMC | doi

Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W. (2005)

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

Bioinformatics 21(16):3439-3440. doi: 10.1093/bioinformatics/bti525
Europe PMC | doi

Buness A, Huber W, Steiner K, Sültmann H, Poustka A. (2005)

arrayMagic: two-colour cDNA microarray quality control and preprocessing

Bioinformatics 21(4):554-556. doi: 10.1093/bioinformatics/bti052
Europe PMC | doi

Arlt D, Huber W, Sauermann M, Majety M, Hahne F, Pepperkok R, Poustka A, Wiemann S. (2005)

Novel cancer relevant cell cycle modulators identified in automated cell-based assays

Paper presented at the 30 Jahre Deutsche Gesellschaft für Zellbiologie - Jahrestagung, Heidelberg, 16 - 19 March 2005.Eur. J. Cell Biol. 84:30.
Europe PMC

Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (eds.). (2005)

Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Statistics for Biology and Health. Springer, New York.doi: 10.1007/0-387-29362-0
doi

Gentleman R, Ruschlaupt M, Huber W. (2005)

On the synthesis of microarray experiments

Journal of the French Statistical Society
Europe PMC

Huber W, von Heydebreck A, Vingron M. (2005)

Large error models for microarray intensities

In: Dunn MJ, Jorde LB, Little PFR, Subramaniam S (eds.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons.doi: 10.1002/047001153X.g405413
doi

Sültmann H, von Heydebreck A, Huber W, Kuner R, Buness A, Vogt M, Gunawan B, Vingron M, Füzesí L, Poustka A. (2005)

Gene expression in kidney cancer is associated with cytogenetic abnormalities, metastasis formation, and patient survival

Clin. Cancer Res. 11(2 Pt 1):646-655.
Europe PMC


2004

Wiemann S, Arlt D, Huber W, Wellenreuther R, Schleeger S, Mehrle A, Bechtel S, Sauermann M, Korf U, Pepperkok R, Sültmann H, Poustka A. (2004)

From ORFeome to biology: a functional genomics pipeline

Genome Res. 14(10B):2136-2144. doi: 10.1101/gr.2576704
Europe PMC | doi

Huber W, von Heydebreck A, Vingron M. (2004)

Analysis of microarray gene expression data

In: Balding DJ, Bishop M, Cannings C (eds.), Handbook of Statistical Genetics. John Wiley & Sons.doi: 10.1002/0470022620.bbc08
Europe PMC | doi

Huber W, Gentleman R. (2004)

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements

Bioinformatics 20(10):1651-1652. doi: 10.1093/bioinformatics/bth133
Europe PMC | doi

Schneider J, Buness A, Huber W, Volz J, Kioschis P, Hafner M, Poustka A, Sültmann H. (2004)

Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments

BMC Genomics 5(1):29. doi: 10.1186/1471-2164-5-29
Europe PMC | doi

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. (2004)

Bioconductor: open software development for computational biology and bioinformatics

Genome Biol. 5(10):R80. doi: 10.1186/gb-2004-5-10-r80
Europe PMC | doi

Ruschhaupt M, Huber W, Poustka A, Mansmann U. (2004)

A compendium to ensure computational reproducibility in high-dimensional classification tasks

Stat Appl Genet Mol Biol 3:Article37. doi: 10.2202/1544-6115.1078
Europe PMC | doi


2003

Gunawan B, von Heydebreck A, Fritsch T, Huber W, Ringert RH, Jakse G, Füzesi L. (2003)

Cytogenetic and morphologic typing of 58 papillary renal cell carcinomas: evidence for a cytogenetic evolution of type 2 from type 1 tumors

Cancer Res. 63(19):6200-6205.
Europe PMC

Langer C, Gunawan B, Schüler P, Huber W, Füzesi L, Becker H. (2003)

Prognostic factors influencing surgical management and outcome of gastrointestinal stromal tumours

Br J Surg 90(3):332-339. doi: 10.1002/bjs.4046
Europe PMC | doi

Apic G, Huber W, Teichmann SA. (2003)

Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination

J. Struct. Funct. Genomics 4(2-3):67-78. doi: 10.1023/a:1026113408773
Europe PMC | doi

Heydebreck AV, Gunawan B, Huber W, Vingron M, Füzesi L. (2003)

Mathematical tree models for cytogenetic development in solid tumors

Verh Dtsch Ges Pathol 87:188-192.
Europe PMC

Huber W, von Heydebreck A, Sueltmann H, Poustka A, Vingron M. (2003)

Parameter estimation for the calibration and variance stabilization of microarray data.

Stat Appl Genet Mol Biol 2:Article3. doi: 10.2202/1544-6115.1008
Europe PMC | doi


2002

Huber W, Boer JM, von Heydebreck A, Gunawan B, Vingron M, Füzesi L, Poustka A, Sültmann H. (2002)

Transcription profiling of renal cell carcinoma

Verh Dtsch Ges Pathol 86:153-164.
Europe PMC

Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M. (2002)

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

Bioinformatics 18 Suppl 1:S96-104.
Europe PMC


2001

Boer JM, Huber WK, Sültmann H, Wilmer F, von Heydebreck A, Haas S, Korn B, Gunawan B, Vente A, Füzesi L, Vingron M, Poustka A. (2001)

Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array

Genome Res. 11(11):1861-1870.
Europe PMC

Gunawan B, Huber W, Holtrup M, von Heydebreck A, Efferth T, Poustka A, Ringert RH, Jakse G, Füzesi L. (2001)

Prognostic impacts of cytogenetic findings in clear cell renal cell carcinoma: gain of 5q31-qter predicts a distinct clinical phenotype with favorable prognosis

Cancer Res. 61(21):7731-7738.
Europe PMC

Pitman MC, Huber WK, Horn H, Krämer A, Rice JE, Swope WC. (2001)

FLASHFLOOD: a 3D field-based similarity search and alignment method for flexible molecules

J. Comput. Aided Mol. Des. 15(7):587-612. doi: 10.1023/a:1011921423829
Europe PMC | doi

Sultmann H, Huber W, Fuzesi L, Gunawan B, von Heydebreck A, Vingron M, Poustka A. (2001)

Gene expression profiling of kidney cancer using a tumor-specific cDNA microarray

Clin. Cancer Res. 7(11):3684S.
Europe PMC

von Heydebreck A, Huber W, Poustka A, Vingron M. (2001)

Identifying splits with clear separation: a new class discovery method for gene expression data

Bioinformatics 17 Suppl 1:S107-14.
Europe PMC


2000

Breuer HP, Huber W, Petruccione F. (2000)

Quasistationary distributions of dissipative nonlinear quantum oscillators in strong periodic driving fields

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 61(5A):4883-4889. doi: 10.1103/physreve.61.4883
Europe PMC | doi


1998

Huber W. (1998)

Dynamics of strongly driven open quantum systems



1997

Breuer HP, Huber W, Petruccione F. (1997)

Stochastic wave-function method versus density matrix: a numerical comparison

Comput Phys Commun 104(1-3):46-58.
Europe PMC

Mergner T, Huber W, Becker W. (1997)

Vestibular-neck interaction and transformation of sensory coordinates

Paper presented at the 3rd International Symposium on the Head/Neck System, VAIL, CO, JUL 02-06, 1995.J Vestib Res 7(4):347-367.
Europe PMC


1996

Breuer HP, Huber W, Petruccione F. (1996)

Fast Monte Carlo algorithm for nonequilibrium systems

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 53(4):4232-4235. doi: 10.1103/physreve.53.4232
Europe PMC | doi

Huber W, Kopitzki K, Timmer J, Warnke PC. (1996)

Ortsaufgelöste Messung und Modellierung der Permeabilität der Blut-Hirn-Schranke

Biomedical Engineering / Biomedizinische Technik 41(s1):160-161. doi: 10.1515/bmte.1996.41.s1.160
doi


1995

Breuer HP, Huber W, Petruccione F. (1995)

The macroscopic limit in a stochastic reaction-diffusion process

Europhys Lett 30(2):69-74.
Europe PMC

Fischer B, Gezeck S, Huber W. (1995)

The three-loop model: a neural network for the generation of saccadic reaction times

Biol Cybern 72(3):185-196. doi: 10.1007/s004220050123
Europe PMC | doi


1994

Breuer HP, Huber W, Petruccione F. (1994)

Fluctuation effects on wave propagation in a reaction-diffusion process

Physica D 73(3):259-273. doi: 10.1016/0167-2789(94)90161-9
Europe PMC | doi

Huber W. (1994)

The description of reaction diffusion processes by master equations