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Staff at EMBL

Dr. Wolfgang Huber

Group Leader and Senior Scientist
Huber Group Joint appointment: EMBL-EBI Hinxton

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail: send a mail
Web page: http://scholar.google.co.uk/citations?user=gI8o6x8AAAAJ&hl=en

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.

Publications

Enhancer loops appear stable during development and are associated with paused polymerase. Ghavi-Helm, Y., Klein, F.A., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W. & Furlong, E.E. Nature. 2014 Jul 2. doi: 10.1038/nature13417. Europe PMC

h5vc: scalable nucleotide tallies with HDF5. Pyl, P.T., Gehring, J., Fischer, B. & Huber, W. Bioinformatics. 2014 May 15;30(10):1464-6. doi: 10.1093/bioinformatics/btu026.Epub 2014 Jan 21. Europe PMC

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Petryszak, R., Burdett, T., Fiorelli, B., Fonseca, N.A., Gonzalez-Porta, M., Hastings, E., Huber, W., Jupp, S., Keays, M., Kryvych, N., McMurry, J., Marioni, J.C., Malone, J., Megy, K., Rustici, G., Tang, A.Y., Taubert, J., Williams, E., Mannion, O., Parkinson, H.E. & Brazma, A. Nucleic Acids Res. 2014 Jan;42(Database issue):D926-32. doi: 10.1093/nar/gkt1270.Epub 2013 Dec 4. Europe PMC

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages. Ohnishi, Y., Huber, W., Tsumura, A., Kang, M., Xenopoulos, P., Kurimoto, K., Oles, A.K., Arauzo-Bravo, M.J., Saitou, M., Hadjantonakis, A.K. & Hiiragi, T. Nat Cell Biol. 2014 Jan;16(1):27-37. doi: 10.1038/ncb2881. Epub 2013 Dec 1. Europe PMC

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. Gupta, I., Clauder-Munster, S., Klaus, B., Jarvelin, A.I., Aiyar, R.S., Benes, V., Wilkening, S., Huber, W., Pelechano, V. & Steinmetz, L.M. Mol Syst Biol. 2014 Feb 25;10(2):719. doi: 10.1002/msb.135068. Print 2014. Europe PMC

Directional tissue migration through a self-generated chemokine gradient. Dona, E., Barry, J.D., Valentin, G., Quirin, C., Khmelinskii, A., Kunze, A., Durdu, S., Newton, L.R., Fernandez-Minan, A., Huber, W., Knop, M. & Gilmour, D. Nature. 2013 Nov 14;503(7475):285-9. doi: 10.1038/nature12635. Epub 2013 Sep 25. Europe PMC

Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay. Pau, G., Walter, T., Neumann, B., Heriche, J.K., Ellenberg, J. & Huber, W. BMC Bioinformatics. 2013 Oct 16;14:308. doi: 10.1186/1471-2105-14-308. Europe PMC

Drift and conservation of differential exon usage across tissues in primate species. Reyes, A., Anders, S., Weatheritt, R.J., Gibson, T.J., Steinmetz, L.M. & Huber, W. Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15377-82. doi:10.1073/pnas.1307202110. Epub 2013 Sep 3. Europe PMC

High-Content siRNA Screen Reveals Global ENaC Regulators and Potential Cystic Fibrosis Therapy Targets. Almaca, J., Faria, D., Sousa, M., Uliyakina, I., Conrad, C., Sirianant, L., Clarke, L.A., Martins, J.P., Santos, M., Heriche, J.K., Huber, W., Schreiber, R., Pepperkok, R., Kunzelmann, K. & Amaral, M.D. Cell. 2013 Sep 12;154(6):1390-400. doi: 10.1016/j.cell.2013.08.045. Europe PMC

Control of tissue morphology by Fasciclin III-mediated intercellular adhesion. Wells, R.E.*, Barry, J.D.*, Warrington, S.J., Cuhlmann, S., Evans, P., Huber, W., Strutt, D. & Zeidler, M.P. Development. 2013 Sep;140(18):3858-68. doi: 10.1242/dev.096214. Epub 2013 Aug 14.
* Contributed equally to this work. Europe PMC

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Anders, S., McCarthy, D.J., Chen, Y., Okoniewski, M., Smyth, G.K., Huber, W. & Robinson, M.D. Nat Protoc. 2013 Sep;8(9):1765-86. doi: 10.1038/nprot.2013.099. Epub 2013 Aug 22. Europe PMC

The genomic and transcriptomic landscape of a HeLa cell line. Landry, J.J., Pyl, P.T., Rausch, T., Zichner, T., Tekkedil, M.M., Stutz, A.M., Jauch, A., Aiyar, R.S., Pau, G., Delhomme, N., Gagneur, J., Korbel, J.O., Huber, W. & Steinmetz, L.M. G3 (Bethesda). 2013 Aug 7;3(8):1213-24. doi: 10.1534/g3.113.005777. Europe PMC

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. Yu, D., Huber, W. & Vitek, O. Bioinformatics. 2013 May 15;29(10):1275-82. doi: 10.1093/bioinformatics/btt143.Epub 2013 Apr 14. Europe PMC

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Laufer, C., Fischer, B., Billmann, M., Huber, W. & Boutros, M. Nat Methods. 2013 May;10(5):427-31. doi: 10.1038/nmeth.2436. Epub 2013 Apr 7. Europe PMC

CellH5: a format for data exchange in high-content screening. Sommer, C., Held, M., Fischer, B., Huber, W. & Gerlich, D.W. Bioinformatics. 2013 Jun 15;29(12):1580-2. doi: 10.1093/bioinformatics/btt175.Epub 2013 Apr 16. Europe PMC

Software for computing and annotating genomic ranges. Lawrence, M., Huber, W., Pages, H., Aboyoun, P., Carlson, M., Gentleman, R., Morgan, M.T. & Carey, V.J. PLoS Comput Biol. 2013 Aug;9(8):e1003118. doi: 10.1371/journal.pcbi.1003118. Epub2013 Aug 8. Europe PMC

Detecting differential usage of exons from RNA-seq data. Anders, S., Reyes, A. & Huber, W. Genome Res. 2012 Oct;22(10):2008-17. doi: 10.1101/gr.133744.111. Epub 2012 Jun21. Europe PMC

Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Khmelinskii, A., Keller, P.J., Bartosik, A., Meurer, M., Barry, J.D., Mardin, B.R., Kaufmann, A., Trautmann, S., Wachsmuth, M., Pereira, G., Huber, W., Schiebel, E. & Knop, M. Nat Biotechnol. 2012 Jun 24;30(7):708-14. doi: 10.1038/nbt.2281. Europe PMC

Highly Coordinated Proteome Dynamics during Reprogramming of Somatic Cells to Pluripotency. Hansson J., Rafiee M.R., Reiland S., Polo J.M., Gehring J., Okawa S., Huber W., Hochedlinger K., Krijgsveld J. Cell Rep. 2012 Dec 27;2(6):1579-92. doi: 10.1016/j.celrep.2012.10.014. Europe PMC

cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression. Benito, E., Valor, L.M., Jimenez-Minchan, M., Huber, W. & Barco, A. J Neurosci. 2011 Dec 14;31(50):18237-50. doi: 10.1523/JNEUROSCI.4554-11.2011. Europe PMC

Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Schlattl, A., Anders, S., Waszak, S.M., Huber, W. & Korbel, J.O. Genome Res. 2011 Dec;21(12):2004-13. doi: 10.1101/gr.122614.111. Epub 2011 Aug23. Europe PMC

Assessing affymetrix GeneChip microarray quality. McCall, M.N., Murakami, P.N., Lukk, M., Huber, W. & Irizarry, R.A. BMC Bioinformatics. 2011 May 7;12:137. doi: 10.1186/1471-2105-12-137. Europe PMC

Enterotypes of the human gut microbiome. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Antolin, M., Artiguenave, F., Blottiere, H.M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Foerstner, K.U., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Huber, W., van Hylckama-Vlieg, J., Jamet, A., Juste, C., Kaci, G., Knol, J., Lakhdari, O., Layec, S., Le Roux, K., Maguin, E., Merieux, A., Melo Minardi, R., M'rini, C., Muller, J., Oozeer, R., Parkhill, J., Renault, P., Rescigno, M., Sanchez, N., Sunagawa, S., Torrejon, A., Turner, K., Vandemeulebrouck, G., Varela, E., Winogradsky, Y., Zeller, G., Weissenbach, J., Ehrlich, S.D. & Bork, P. Nature. 2011 May 12;473(7346):174-80. Epub 2011 Apr 20. Europe PMC

Genome-wide survey of post-meiotic segregation during yeast recombination. Mancera, E., Bourgon, R., Huber, W. & Steinmetz, L.M. Genome Biol. 2011 Apr 11;12(4):R36. Europe PMC

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Horn, T., Sandmann, T., Fischer, B., Axelsson, E., Huber, W. & Boutros, M. Nat Methods. 2011 Apr;8(4):341-6. Epub 2011 Mar 6. Europe PMC

Antisense expression increases gene expression variability and locus interdependency. Xu, Z., Wei, W., Gagneur, J., Clauder-Munster, S., Smolik, M., Huber, W. & Steinmetz, L.M. Mol Syst Biol. 2011 Feb 15;7:468. doi: 10.1038/msb.2011.1. Europe PMC

Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications. Huhn, S., Ingelfinger, D., Bermejo, J.L., Bevier, M., Pardini, B., Naccarati, A., Steinke, V., Rahner, N., Holinski-Feder, E., Morak, M., Schackert, H.K., Gorgens, H., Pox, C.P., Goecke, T., Kloor, M., Loeffler, M., Buttner, R., Vodickova, L., Novotny, J., Demir, K., Cruciat, C.M., Renneberg, R., Huber, W., Niehrs, C., Boutros, M., Propping, P., Vodieka, P., Hemminki, K. & Forsti, A. Int J Mol Epidemiol Genet. 2011 Jan 1;2(1):36-50. Epub 2010 Nov 25. Europe PMC

Contributions of the EMERALD project to assessing and improving microarray data quality. Beisvag, V., Kauffmann, A., Malone, J., Foy, C., Salit, M., Schimmel, H., Bongcam-Rudloff, E., Landegren, U., Parkinson, H., Huber, W., Brazma, A., Sandvik, A.K. & Kuiper, M. Biotechniques. 2011 Jan;50(1):27-31. Europe PMC

Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi. Axelsson, E., Sandmann, T., Horn, T., Boutros, M., Huber, W. & Fischer, B. BMC Bioinformatics. 2011 Aug 17;12:342. Europe PMC

Organelle proteomics experimental designs and analysis. Gatto, L., Vizcaino, J.A., Hermjakob, H., Huber, W. & Lilley, K.S. Proteomics. 2010 Nov;10(22):3957-69. doi: 10.1002/pmic.201000244. Epub2010 Nov 2. Europe PMC

Differential expression analysis for sequence count data. Anders, S. & Huber, W. Genome Biol. 2010 Oct 27;11(10):R106. Europe PMC

Addressing accuracy and precision issues in iTRAQ quantitation. Karp, N.A., Huber, W., Sadowski, P.G., Charles, P.D., Hester, S.V. & Lilley, K.S. Mol Cell Proteomics. 2010 Sep;9(9):1885-97. Epub 2010 Apr 10. Europe PMC

Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3. Schmid, R., Baum, P., Ittrich, C., Fundel-Clemens, K., Huber, W., Brors, B., Eils, R., Weith, A., Mennerich, D. & Quast, K. BMC Genomics. 2010 Jun 2;11:349. doi: 10.1186/1471-2164-11-349. Europe PMC

Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Fuchs, F., Pau, G., Kranz, D., Sklyar, O., Budjan, C., Steinbrink, S., Horn, T., Pedal, A., Huber, W. & Boutros, M. Mol Syst Biol. 2010 Jun 8;6:370. Europe PMC

Independent filtering increases detection power for high-throughput experiments. Bourgon, R., Gentleman, R. & Huber, W. Proc Natl Acad Sci U S A. 2010 May 25;107(21):9546-51. Epub 2010 May 11. Europe PMC

Variation in transcription factor binding among humans. Kasowski, M.*, Grubert, F.*, Heffelfinger, C., Hariharan, M., Asabere, A., Waszak, S.M., Habegger, L., Rozowsky, J., Shi, M., Urban, A.E., Hong, M.Y., Karczewski, K.J., Huber, W., Weissman, S.M., Gerstein, M.B., Korbel, J.O. & Snyder, M. Science. 2010 Apr 9;328(5975):232-5. doi: 10.1126/science.1183621. Epub 2010 Mar18.
(*equal contribution) Europe PMC

A global map of human gene expression. Lukk, M., Kapushesky, M., Nikkila, J., Parkinson, H., Goncalves, A., Huber, W., Ukkonen, E. & Brazma, A. Nat Biotechnol. 2010 Apr;28(4):322-4. doi: 10.1038/nbt0410-322. Europe PMC

EBImage - an R package for image processing with applications to cellular phenotypes. Pau, G., Fuchs, F., Sklyar, O., Boutros, M. & Huber, W. Bioinformatics. 2010 Apr 1;26(7):979-81. Europe PMC

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Neumann, B., Walter, T., Heriche, J.K., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U., Cetin, C., Sieckmann, F., Pau, G., Kabbe, R., Wünsche, A., Satagopam, V., Schmitz, M.H., Chapuis, C., Gerlich, D.W., Schneider, R., Eils, R., Huber, W., Peters, J.M., Hyman, A.A., Durbin, R., Pepperkok, R. & Ellenberg, J. Nature. 2010 Apr 1;464(7289):721-7. Europe PMC

High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Granovskaia, M.V., Jensen, L.J., Ritchie, M.E., Toedling, J., Ning, Y., Bork, P., Huber, W. & Steinmetz, L.M. Genome Biol. 2010 Mar 1;11(3):R24. Europe PMC

Microarray data quality control improves the detection of differentially expressed genes. Kauffmann, A. & Huber, W. Genomics. 2010 Mar;95(3):138-42. Epub 2010 Jan 14. Europe PMC

A large-scale RNAi screen identifies Deaf1 as a regulator of innate immune responses in Drosophila. Kuttenkeuler, D., Pelte, N., Ragab, A., Gesellchen, V., Schneider, L., Blass, C., Axelsson, E., Huber, W. & Boutros, M. J Innate Immun. 2010 Feb;2(2):181-94. Epub 2009 Oct 13. Europe PMC

Genome-wide analysis of mRNA decay patterns during early Drosophila development. Thomsen, S., Anders, S., Janga, S.C., Huber, W. & Alonso, C.R. Genome Biol. 2010;11(9):R93. Epub 2010 Sep 21. Europe PMC

Importing ArrayExpress datasets into R/Bioconductor. Kauffmann, A., Rayner, T.F., Parkinson, H., Kapushesky, M., Lukk, M., Brazma, A. & Huber, W. Bioinformatics. 2009 Aug 15;25(16):2092-4. Epub 2009 Jun 8. Europe PMC

Genome-wide allele- and strand-specific expression profiling. Gagneur, J., Sinha, H., Perocchi, F., Bourgon, R., Huber, W. & Steinmetz, L.M. Mol Syst Biol. 2009;5:274. Epub 2009 Jun 16. Europe PMC

Array-based genotyping in S.cerevisiae using semi-supervised clustering. Bourgon, R., Mancera, E., Brozzi, A., Steinmetz, L.M. & Huber, W. Bioinformatics. 2009 Apr 15;25(8):1056-62. doi: 10.1093/bioinformatics/btp104.Epub 2009 Feb 23. Europe PMC

Bidirectional promoters generate pervasive transcription in yeast. Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder-Munster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W. & Steinmetz, L.M. Nature. 2009 Feb 19;457(7232):1033-7. Epub 2009 Jan 25. Europe PMC

arrayQualityMetrics - a bioconductor package for quality assessment of microarray data. Kauffmann, A., Gentleman, R. & Huber, W. Bioinformatics. 2009 Feb 1;25(3):415-6. Epub 2008 Dec 23. Europe PMC

Quality assessment and data analysis for microRNA expression arrays. Sarkar, D., Parkin, R., Wyman, S., Bendoraite, A., Sather, C., Delrow, J., Godwin, A.K., Drescher, C., Huber, W., Gentleman, R. & Tewari, M. Nucleic Acids Res. 2009 Feb;37(2):e17. Epub 2008 Dec 22. Europe PMC

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Durinck, S., Spellman, P.T., Birney, E. & Huber, W. Nat Protoc. 2009;4(8):1184-91. Epub 2009 Jul 23. Europe PMC

Analyzing ChIP-chip data using bioconductor. Toedling, J. & Huber, W. PLoS Comput Biol. 2008 Nov;4(11):e1000227. Epub 2008 Nov 28. Europe PMC

High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Mancera, E., Bourgon, R., Brozzi, A., Huber, W. & Steinmetz, L.M. Nature. 2008 Jul 24;454(7203):479-85. Epub 2008 Jul 9. Europe PMC

Estimating node degree in bait-prey graphs. Scholtens, D., Chiang, T., Huber, W. & Gentleman, R. Bioinformatics. 2008 Jan 15;24(2):218-24. Epub 2007 Nov 19. Europe PMC

Model-based variance-stabilizing transformation for Illumina microarray data. Lin, S.M., Du, P., Huber, W. & Kibbe, W.A. Nucleic Acids Res. 2008 Feb;36(2):e11. Epub 2008 Jan 4. Europe PMC

Bioconductor Case Studies Hahne, F., Huber, W., Gentleman, R. & Falcon, S. Use R. Springer, 2008

Combinatorial effects of four histone modifications in transcription and differentiation. Fischer, J.J., Toedling, J., Krueger, T., Schueler, M., Huber, W. & Sperling, S. Genomics. 2008 Jan;91(1):41-51. Epub 2007 Nov 8. Europe PMC

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Chiang, T., Li, N., Orchard, S., Kerrien, S., Hermjakob, H., Gentleman, R. & Huber, W. Bioinformatics. 2008 Apr 15;24(8):1100-1. Epub 2007 Nov 7. Europe PMC

High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins. Sauermann, M., Hahne, F., Schmidt, C., Majety, M., Rosenfelder, H., Bechtel, S., Huber, W., Poustka, A., Arlt, D. & Wiemann, S. J Biomol Screen. 2007 Jun;12(4):510-20. Epub 2007 May 3. Europe PMC

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data. Girardot, C., Sklyar, O., Grosz, S., Huber, W. & Furlong, E.E. Bioinformatics. 2007 Mar 15;23(6):771-3. Epub 2007 Jan 17. Europe PMC

Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts. Toedling, J., Sklyar, O. & Huber, W. BMC Bioinformatics. 2007 Jun 26;8:221. Europe PMC

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. Steigele, S., Huber, W., Stocsits, C., Stadler, P.F. & Nieselt, K. BMC Biol. 2007 Jun 18;5:25. Europe PMC

Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Purmann, A., Toedling, J., Schueler, M., Carninci, P., Lehrach, H., Hayashizaki, Y., Huber, W. & Sperling, S. Genomics. 2007 May;89(5):580-7. Epub 2007 Mar 21. Europe PMC

Graphs in molecular biology. Huber, W., Carey, V.J., Long, L., Falcon, S. & Gentleman, R. BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S8. Europe PMC

Making the most of high-throughput protein-interaction data. Gentleman, R. & Huber, W. Genome Biol. 2007;8(10):112. Europe PMC

Coverage and error models of protein-protein interaction data by directed graph analysis. Chiang, T., Scholtens, D., Sarkar, D., Gentleman, R. & Huber, W. Genome Biol. 2007;8(9):R186. Europe PMC

In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. Casneuf, T., Van de Peer, Y. & Huber, W. BMC Bioinformatics. 2007 Nov 26;8:461. Europe PMC

Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts. Hahne, F., Arlt, D., Sauermann, M., Majety, M., Poustka, A., Wiemann, S. & Huber, W. Genome Biol. 2006;7(8):R77. Epub 2006 Aug 17. Europe PMC

Transcript mapping with high-density oligonucleotide tiling arrays. Huber, W., Toedling, J. & Steinmetz, L.M. Bioinformatics. 2006 Aug 15;22(16):1963-70. Epub 2006 Jun 20. Europe PMC

Top-down standards will not serve systems biology. Quackenbush, J., Stoeckert, C., Ball, C., Brazma, A., Gentleman, R., Huber, W., Irizarry, R., Salit, M., Sherlock, G., Spellman, P. & Winegarden, N. Nature. 2006 Mar 2;440(7080):24. Europe PMC

Several articles R News special issue on Bioinformatics, 2006 Link

The LIFEdb database in 2006. Mehrle, A., Rosenfelder, H., Schupp, I., del Val, C., Arlt, D., Hahne, F., Bechtel, S., Simpson, J., Hofmann, O., Hide, W., Glatting, K.H., Huber, W., Pepperkok, R., Poustka, A. & Wiemann, S. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D415-8. Europe PMC

Reproducible statistical analysis in microarray profiling studies. Mansmann, U., Ruschhaupt, M. & Huber, W. Methods Inf Med. 2006;45(2):139-45. Europe PMC

Visualizing genomic data. Technical Report 10. Gentleman, R., Hahne, F. & Huber, W. Bioconductor Project Working Papers, 2006 Link

A high-resolution map of transcription in the yeast genome. David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C.J., Bofkin, L., Jones, T., Davis, R.W. & Steinmetz, L.M. Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5. Epub 2006 Mar 28. Europe PMC

Analysis of cell-based RNAi screens. Boutros, M., Bras, L. & Huber, W. Genome Biol. 2006 Jul 25;7(7):R66. Europe PMC

arrayMagic: two-colour cDNA microarray quality control and preprocessing. Buness, A., Huber, W., Steiner, K., Sultmann, H. & Poustka, A. Bioinformatics. 2005 Feb 15;21(4):554-6. Epub 2004 Sep 28. Europe PMC

Gene expression in kidney cancer is associated with cytogenetic abnormalities, metastasis formation, and patient survival. Sultmann, H., von Heydebreck, A., Huber, W., Kuner, R., Buness, A., Vogt, M., Gunawan, B., Vingron, M., Fuzesi, L. & Poustka, A. Clin Cancer Res 2005 Jan 15;11(2 Pt 1):646-55. Europe PMC

Low-level analysis of microarray experiments. Huber, W., von Heydebreck, A. & Vingron, M. Bioinformatics - from Genomes to Therapies, Wiley-VCH, 2005

Large error models for microarray intensities. Huber, W., Heydebreck, A. & Vingron, M. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons, 2004

Bioinformatics - from Genomes to Therapies, chapter Low-level analysis of microarray experiments. Huber, W., Heydebreck A. & Vingron, M. Wiley-VCH, 2005

Systematic comparison of surface coatings for protein microarrays. Guilleaume, B., Buness, A., Schmidt, C., Klimek, F., Moldenhauer, G., Huber, W., Arlt, D., Korf, U., Wiemann, S. & Poustka, A. Proteomics. 2005 Dec;5(18):4705-12. Europe PMC

On the synthesis of microarray experiments. Gentleman, R., Ruschhaupt, M. & Huber, W. Journal de la Société Française de Statistique, 146(1-2), 2005

Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman, R., Carey, V., Huber, W., Irizarry, R., Dudoit, S. Springer, 2005 Link

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A. & Huber, W. Bioinformatics 2005 Aug 15;21(16):3439-40. Europe PMC

Novel cancer relevant cell cycle modulators identified in automated cell-based assays Dorit Arlt, Huber, W., Mamatha Sauermann, Meher Majety, Florian Hahne, Pepperkok, R., Annemarie Poustka, and Stefan Wiemann European Journal of Cell Biology, 84(Suppl. 55):30, 2005

Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle. 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, J.C., Hahne, F., Moosmayer, P., Ruschhaupt, M., Guilleaume, B., Wellenreuther, R., Pepperkok, R., Sultmann, H., Poustka, A. & Wiemann, S. Cancer Res 2005 Sep 1;65(17):7733-42. Europe PMC

From ORFeome to biology: a functional genomics pipeline. Wiemann, S., Arlt, D., Huber, W., Wellenreuther, R., Schleeger, S., Mehrle, A., Bechtel, S., Sauermann, M., Korf, U., Pepperkok, R., Sultmann, H. & Poustka, A. Genome Res. 2004 Oct;14(10B):2136-44. Europe PMC

Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments. Schneider, J., Buness, A., Huber, W., Volz, J., Kioschis, P., Hafner, M., Poustka, A. & Sultmann, H. BMC Genomics. 2004 Apr 30;5(1):29. Europe PMC

A compendium to ensure computational reproducibility in high-dimensional classification tasks. Ruschhaupt, M., Huber, W., Poustka, A. & Mansmann, U. Stat Appl Genet Mol Biol. 2004;3:Article37. Epub 2004 Dec 19. Europe PMC

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. Huber, W. & Gentleman, R. Bioinformatics 2004 Jul 10;20(10):1651-2. Epub 2004 Feb 26. Europe PMC

Differential Expression with the Bioconductor Project. Heydebreck, A., Huber, W. & Gentleman, R. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons, 2004

Bioconductor: open software development for computational biology and bioinformatics. Gentleman, R.C., Carey, V.J., Bates, D.M., 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, A.J., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, J.Y. & Zhang, J. Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. Europe PMC

Cytogenetic and morphologic typing of 58 papillary renal cell carcinomas: evidence for a cytogenetic evolution of type 2 from type 1 tumors. Gunawan, B., von Heydebreck, A., Fritsch, T., Huber, W., Ringert, R.H., Jakse, G. & Fuzesi, L. Cancer Res. 2003 Oct 1;63(19):6200-5. Europe PMC

Parameter estimation for the calibration and variance stabilization of microarray data. Huber, W., von Heydebreck, A., Sueltmann, H., Poustka, A. & Vingron, M. Stat Appl Genet Mol Biol. 2003;2:Article3. Epub 2003 Apr 5. Europe PMC

Prognostic factors influencing surgical management and outcome of gastrointestinal stromal tumours. Langer, C., Gunawan, B., Schuler, P., Huber, W., Fuzesi, L. & Becker, H. Br J Surg. 2003 Mar;90(3):332-9. Europe PMC

Analysis of microarray gene expression data. Huber W., von Heydebreck, A. & Vingron, M. Handbook of Statistical Genetics 2003, John Wiley & Sons.

Mathematical tree models for cytogenetic development in solid tumors. Heydebreck, A.V., Gunawan, B., Huber, W., Vingron, M. & Fuzesi, L. Verh Dtsch Ges Pathol. 2003;87:188-92. Europe PMC

Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. Apic, G., Huber, W. & Teichmann, S.A. J Struct Funct Genomics. 2003;4(2-3):67-78. Europe PMC

Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A. & Vingron, M. Bioinformatics. 2002;18 Suppl 1:S96-104. Europe PMC

Transcription profiling of renal cell carcinoma. Huber, W., Boer, J.M., von Heydebreck, A., Gunawan, B., Vingron, M., Fuzesi, L., Poustka, A. & Sultmann, H. Verh Dtsch Ges Pathol. 2002;86:153-64. Europe PMC

Prognostic impacts of cytogenetic findings in clear cell renal cell carcinoma: gain of 5q31-qter predicts a distinct clinical phenotype with favorable prognosis. Gunawan, B., Huber, W., Holtrup, M., von Heydebreck, A., Efferth, T., Poustka, A., Ringert, R.H., Jakse, G. & Fuzesi, L. Cancer Res. 2001 Nov 1;61(21):7731-8. Europe PMC

FLASHFLOOD: a 3D field-based similarity search and alignment method for flexible molecules. Pitman, M.C., Huber, W.K., Horn, H., Kramer, A., Rice, J.E. & Swope, W.C. J Comput Aided Mol Des. 2001 Jul;15(7):587-612. Europe PMC

Identifying splits with clear separation: a new class discovery method for gene expression data. von Heydebreck, A., Huber, W., Poustka, A. & Vingron, M. Bioinformatics. 2001;17 Suppl 1:S107-14. Europe PMC

Gene expression profiling of kidney cancer using a tumor-specific cdna microarray Sultmann, H., Huber, W., Fuzesi, L., Gunawan, B., von Heydebreck, A., Vingron, M., Poustka, A. Clinical Cancer Research, 7(11, Suppl. S):155, 2001

Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array. Boer J.M. et al. Genome Res. 2001 11 1861-1870 Europe PMC

Quasistationary distributions of dissipative nonlinear quantum oscillators in strong periodic driving fields Breuer, H.P., Huber, W. & Petruccione, F. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000May;61(5A):4883-9. Europe PMC

Dynamics of strongly driven open quantum systems. Huber, W. PhD thesis, University of Freiburg 1998

Vestibular-neck interaction and transformation of sensory coordinates. Mergner, T., Huber, W. & Becker, W. J Vestib Res. 1997 Jul-Aug;7(4):347-67. Europe PMC

Stochastic wave function method versus density matrix: a numerical comparison. Breuer, H.P., Huber, W. & Petruccione, F. Computer Physics Communications, 104:, 1997

Fast Monte Carlo algorithm for nonequilibrium systems. Breuer, H.P., Huber, W. & Petruccione, F. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996Apr;53(4):4232-4235. Europe PMC

Ortsaufgelöste Messung und Modellierung der Permeabilität der Blut-Hirn-Schranke [Spatially resolved measurement and modeling of blood brain barrier permeability]. Huber, W., Kopitzki, K., Timmer, J. & Warnke, P.C. Biomedizinische Technik 1996 41(s1) 160-161

The three-loop model: a neural network for the generation of saccadic reaction times. Fischer, B., Gezeck, S. & Huber, W. Biol Cybern. 1995;72(3):185-96. Europe PMC

The macroscopic limit in a stochastic reaction-diffusion process. Breuer, H.P., Huber, W. & Petruccione, F. Europhys Lett 1995 30(2) 69-74

Fluctuation effects on wave propagation in a reaction-diffusion process. Breuer, H.P., Huber, W. & Petruccione, F. Physica D, 73:259-273, 1994