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Staff at EMBL

CP-60002619

Dr. Wolfgang Huber

Group Leader and Senior Scientist
Huber Group Joint appointment: Structural and Computational Biology Unit
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

Total: 119 publication(s)

2014

Laufer C, Fischer B, Huber W, Boutros M. (2014)
Measuring genetic interactions in human cells by RNAi and imaging
Nat Protoc 9(10):2341-2353. doi:10.1038/nprot.2014.160
Europe PMC | doi

Anders S, Pyl PT, Huber W. (2014)
HTSeq - A Python framework to work with high-throughput sequencing data
Bioinformatics doi:10.1093/bioinformatics/btu638
Europe PMC | doi

Cabezas-Wallscheid N, Klimmeck D, Hansson J, Lipka DB, Reyes A, Wang Q, Weichenhan D, Lier A, von Paleske L, Renders S, Wünsche P, Zeisberger P, Brocks D, Gu L, Herrmann C, Haas S, Essers MA, Brors B, Eils R, Huber W, Milsom MD, Plass C, Krijgsveld J, Trumpp A. (2014)
Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis
Cell Stem Cell doi:10.1016/j.stem.2014.07.005
Europe PMC | doi

Cabezas-Wallscheid N, Klimmeck D, Hansson J, Reyes A, von Paleske L, Lipka D, Wang Q, Milsom M, Plass C, Huber W, Krijgsveld J, Trumpp A. (2014)
THE GLOBAL RNA AND PROTEIN LANDSCAPE OF HEMATOPOIETIC STEM CELLS AND THEIR IMMEDIATE PROGENY
EXP HEMATOL 42(8):S26.

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. (2014)
Enhancer loops appear stable during development and are associated with paused polymerase
Nature doi:10.1038/nature13417
Europe PMC | doi

Pyl PT, Gehring J, Fischer B, Huber W. (2014)
h5vc: Scalable nucleotide tallies with HDF5
Bioinformatics 30(10):1464-1466. doi:10.1093/bioinformatics/btu026
Europe PMC | doi

Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Wilkening S, Huber W, Pelechano V, Steinmetz LM. (2014)
Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions
Mol. Syst. Biol. 10(2):719. doi:10.1002/msb.135068
Europe PMC | doi

Ohnishi Y, Huber W, Tsumura A, Kang M, Xenopoulos P, Kurimoto K, Oleś AK, Araúzo-Bravo MJ, Saitou M, Hadjantonakis AK, Hiiragi T. (2014)
Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages
Nat. Cell Biol. 16(1):27-37. doi:10.1038/ncb2881
Europe PMC | doi

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


2013

Donà E, Barry JD, Valentin G, Quirin C, Khmelinskii A, Kunze A, Durdu S, Newton LR, Fernandez-Minan A, Huber W, Knop M, Gilmour D. (2013)
Directional tissue migration through a self-generated chemokine gradient
Nature 503(7475):285-289. doi:10.1038/nature12635
Europe PMC | doi

Wells RE, Barry JD, Warrington SJ, Cuhlmann S, Evans P, Huber W, Strutt D, Zeidler MP. (2013)
Control of tissue morphology by Fasciclin III-mediated intercellular adhesion
Development 140(18):3858-3868. doi:10.1242/dev.096214
Europe PMC | doi

Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD. (2013)
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
Nat Protoc 8(9):1765-1786. doi:10.1038/nprot.2013.099
Europe PMC | doi

Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W. (2013)
Drift and conservation of differential exon usage across tissues in primate species
Proc. Natl. Acad. Sci. U.S.A. 110(38):15377-15382. doi:10.1073/pnas.1307202110
Europe PMC | doi

Almaça J, Faria D, Sousa M, Uliyakina I, Conrad C, Sirianant L, Clarke LA, Martins JP, Santos M, Heriché JK, Huber W, Schreiber R, Pepperkok R, Kunzelmann K, Amaral MD. (2013)
High-content siRNA screen reveals global ENaC regulators and potential cystic fibrosis therapy targets
Cell 154(6):1390-1400. doi:10.1016/j.cell.2013.08.045
Europe PMC | doi

Landry JJ, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, Steinmetz LM. (2013)
The genomic and transcriptomic landscape of a HeLa cell line
G3 (Bethesda) 3(8):1213-1224. doi:10.1534/g3.113.005777
Europe PMC | doi

Sommer C, Held M, Fischer B, Huber W, Gerlich DW. (2013)
CellH5: a format for data exchange in high-content screening
Bioinformatics 29(12):1580-1582. doi:10.1093/bioinformatics/btt175
Europe PMC | doi

Laufer C, Fischer B, Billmann M, Huber W, Boutros M. (2013)
Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping
Nat. Methods 10(5):427-431. doi:10.1038/nmeth.2436
Europe PMC | doi

Yu D, Huber W, Vitek O. (2013)
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Bioinformatics 29(10):1275-1282. doi:10.1093/bioinformatics/btt143
Europe PMC | doi

Pau G, Walter T, Neumann B, Hériché JK, Ellenberg J, Huber W. (2013)
Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay
BMC Bioinformatics 14:308. doi:10.1186/1471-2105-14-308
Europe PMC | doi

Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ. (2013)
Software for computing and annotating genomic ranges
PLoS Comput. Biol. 9(8):e1003118. doi:10.1371/journal.pcbi.1003118
Europe PMC | doi


2012

Hansson J, Rafiee MR, Reiland S, Polo JM, Gehring J, Okawa S, Huber W, Hochedlinger K, Krijgsveld J. (2012)
Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency
Cell Rep 2(6):1579-1592. doi:10.1016/j.celrep.2012.10.014
Europe PMC | doi

Anders S, Reyes A, Huber W. (2012)
Detecting differential usage of exons from RNA-seq data
Genome Res. 22(10):2008-2017. doi:10.1101/gr.133744.111
Europe PMC | doi

Khmelinskii A, Keller PJ, Bartosik A, Meurer M, Barry JD, Mardin BR, Kaufmann A, Trautmann S, Wachsmuth M, Pereira G, Huber W, Schiebel E, Knop M. (2012)
Tandem fluorescent protein timers for in vivo analysis of protein dynamics
Nat. Biotechnol. 30(7):708-714. doi:10.1038/nbt.2281
Europe PMC | doi


2011

Benito E, Valor LM, Jimenez-Minchan M, Huber W, Barco A. (2011)
cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression
J. Neurosci. 31(50):18237-18250. doi:10.1523/jneurosci.4554-11.2011
Europe PMC | doi

Dale BM, McNerney GP, Thompson DL, Hubner W, de Los Reyes K, Chuang FY, Huser T, Chen BK. (2011)
Cell-to-cell transfer of HIV-1 via virological synapses leads to endosomal virion maturation that activates viral membrane fusion
Cell Host Microbe 10(6):551-562. doi:10.1016/j.chom.2011.10.015
Europe PMC | doi

Schlattl A, Anders S, Waszak SM, Huber W, Korbel JO. (2011)
Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions
Genome Res. 21(12):2004-2013. doi:10.1101/gr.122614.111
Europe PMC | doi

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, 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 HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, 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, Mérieux 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 SD, Bork P. (2011)
Enterotypes of the human gut microbiome
Nature 473(7346):174-180. doi:10.1038/nature09944
Europe PMC | doi

Horn T, Sandmann T, Fischer B, Axelsson E, Huber W, Boutros M. (2011)
Mapping of signaling networks through synthetic genetic interaction analysis by RNAi
Nat. Methods 8(4):341-346. doi:10.1038/nmeth.1581
Europe PMC | doi

Xu Z, Wei W, Gagneur J, Clauder-Münster S, Smolik M, Huber W, Steinmetz LM. (2011)
Antisense expression increases gene expression variability and locus interdependency
Mol. Syst. Biol. 7:468. doi:10.1038/msb.2011.1
Europe PMC | doi

McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. (2011)
Assessing affymetrix GeneChip microarray quality
BMC Bioinformatics 12:137. doi:10.1186/1471-2105-12-137
Europe PMC | doi

Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M. (2011)
Contributions of the EMERALD project to assessing and improving microarray data quality
BioTechniques 50(1):27-31. doi:10.2144/000113591
Europe PMC | doi

Axelsson E, Sandmann T, Horn T, Boutros M, Huber W, Fischer B. (2011)
Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi
BMC Bioinformatics 12:342. doi:10.1186/1471-2105-12-342
Europe PMC | doi

Mancera E, Bourgon R, Huber W, Steinmetz LM. (2011)
Genome-wide survey of post-meiotic segregation during yeast recombination
Genome Biol. 12(4):R36. doi:10.1186/gb-2011-12-4-r36
Europe PMC | doi

Huhn S, Ingelfinger D, Bermejo JL, Bevier M, Pardini B, Naccarati A, Steinke V, Rahner N, Holinski-Feder E, Morak M, Schackert HK, Görgens H, Pox CP, Goecke T, Kloor M, Loeffler M, Büttner R, Vodickova L, Novotny J, Demir K, Cruciat CM, Renneberg R, Huber W, Niehrs C, Boutros M, Propping P, Vodièka P, Hemminki K, Försti A. (2011)
Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications
Int J Mol Epidemiol Genet 2(1):36-50.
Europe PMC


2010

Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS. (2010)
Organelle proteomics experimental designs and analysis
Proteomics 10(22):3957-3969. doi:10.1002/pmic.201000244
Europe PMC | doi

Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, Lilley KS. (2010)
Addressing accuracy and precision issues in iTRAQ quantitation
Mol. Cell Proteomics 9(9):1885-1897. doi:10.1074/mcp.m900628-mcp200
Europe PMC | doi

Fuchs F, Pau G, Kranz D, Sklyar O, Budjan C, Steinbrink S, Horn T, Pedal A, Huber W, Boutros M. (2010)
Clustering phenotype populations by genome-wide RNAi and multiparametric imaging
Mol. Syst. Biol. 6:370. doi:10.1038/msb.2010.25
Europe PMC | doi

Bourgon R, Gentleman R, Huber W. (2010)
Independent filtering increases detection power for high-throughput experiments
Proc. Natl. Acad. Sci. U.S.A. 107(21):9546-9551. doi:10.1073/pnas.0914005107
Europe PMC | doi

Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A. (2010)
A global map of human gene expression
Nat. Biotechnol. 28(4):322-324. doi:10.1038/nbt0410-322
Europe PMC | doi

Pau G, Fuchs F, Sklyar O, Boutros M, Huber W. (2010)
EBImage--an R package for image processing with applications to cellular phenotypes
Bioinformatics 26(7):979-981. doi:10.1093/bioinformatics/btq046
Europe PMC | doi

Neumann B, Walter T, Hériché JK, 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 MH, Chapuis C, Gerlich DW, Schneider R, Eils R, Huber W, Peters JM, Hyman AA, Durbin R, Pepperkok R, Ellenberg J. (2010)
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes
Nature 464(7289):721-727. doi:10.1038/nature08869
Europe PMC | doi

Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M. (2010)
Variation in transcription factor binding among humans
Science 328(5975):232-235. doi:10.1126/science.1183621
Europe PMC | doi

Kauffmann A, Huber W. (2010)
Microarray data quality control improves the detection of differentially expressed genes
Genomics 95(3):138-142. doi:10.1016/j.ygeno.2010.01.003
Europe PMC | doi

Kuttenkeuler D, Pelte N, Ragab A, Gesellchen V, Schneider L, Blass C, Axelsson E, Huber W, Boutros M. (2010)
A large-scale RNAi screen identifies Deaf1 as a regulator of innate immune responses in Drosophila
J Innate Immun 2(2):181-194. doi:10.1159/000248649
Europe PMC | doi

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

Anders S, Huber W. (2010)
Differential expression analysis for sequence count data
Genome Biol. 11(10):R106. doi:10.1186/gb-2010-11-10-r106
Europe PMC | doi

Thomsen S, Anders S, Janga SC, Huber W, Alonso CR. (2010)
Genome-wide analysis of mRNA decay patterns during early Drosophila development
Genome Biol. 11(9):R93. doi:10.1186/gb-2010-11-9-r93
Europe PMC | doi

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. (2010)
High-resolution transcription atlas of the mitotic cell cycle in budding yeast
Genome Biol. 11(3):R24. doi:10.1186/gb-2010-11-3-r24
Europe PMC | doi


2009

Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W. (2009)
Importing ArrayExpress datasets into R/Bioconductor
Bioinformatics 25(16):2092-2094. doi:10.1093/bioinformatics/btp354
Europe PMC | doi

Bourgon R, Mancera E, Brozzi A, Steinmetz LM, Huber W. (2009)
Array-based genotyping in S.cerevisiae using semi-supervised clustering
Bioinformatics 25(8):1056-1062. doi:10.1093/bioinformatics/btp104
Europe PMC | doi

Kauffmann A, Gentleman R, Huber W. (2009)
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data
Bioinformatics 25(3):415-416. doi:10.1093/bioinformatics/btn647
Europe PMC | doi

Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. (2009)
Bidirectional promoters generate pervasive transcription in yeast
Nature 457(7232):1033-1037. doi:10.1038/nature07728
Europe PMC | doi

Sarkar D, Parkin R, Wyman S, Bendoraite A, Sather C, Delrow J, Godwin AK, Drescher C, Huber W, Gentleman R, Tewari M. (2009)
Quality assessment and data analysis for microRNA expression arrays
Nucleic Acids Res. 37(2):e17. doi:10.1093/nar/gkn932
Europe PMC | doi

Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM. (2009)
Genome-wide allele- and strand-specific expression profiling
Mol. Syst. Biol. 5:274. doi:10.1038/msb.2009.31
Europe PMC | doi

Durinck S, Spellman PT, Birney E, Huber W. (2009)
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt
Nat Protoc 4(8):1184-1191. doi:10.1038/nprot.2009.97
Europe PMC | doi


2008

Toedling J, Huber W. (2008)
Analyzing ChIP-chip data using bioconductor
PLoS Comput. Biol. 4(11):e1000227. doi:10.1371/journal.pcbi.1000227
Europe PMC | doi

Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM. (2008)
High-resolution mapping of meiotic crossovers and non-crossovers in yeast
Nature 454(7203):479-485. doi:10.1038/nature07135
Europe PMC | doi

Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W. (2008)
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository
Bioinformatics 24(8):1100-1101. doi:10.1093/bioinformatics/btm518
Europe PMC | doi

Lin SM, Du P, Huber W, Kibbe WA. (2008)
Model-based variance-stabilizing transformation for Illumina microarray data
Nucleic Acids Res. 36(2):e11. doi:10.1093/nar/gkm1075
Europe PMC | doi

Hahne F, Huber W, Gentleman R, Falcon S (eds.). (2008)
Bioconductor Case Studies
Use R!. Springer, New York.doi:10.1007/978-0-387-77240-0
doi

Fischer JJ, Toedling J, Krueger T, Schueler M, Huber W, Sperling S. (2008)
Combinatorial effects of four histone modifications in transcription and differentiation
Genomics 91(1):41-51. doi:10.1016/j.ygeno.2007.08.010
Europe PMC | doi

Scholtens D, Chiang T, Huber W, Gentleman R. (2008)
Estimating node degree in bait-prey graphs
Bioinformatics 24(2):218-224. doi:10.1093/bioinformatics/btm565
Europe PMC | doi


2007

Sauermann M, Hahne F, Schmidt C, Majety M, Rosenfelder H, Bechtel S, Huber W, Poustka A, Arlt D, Wiemann S. (2007)
High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins
J Biomol Screen 12(4):510-520. doi:10.1177/1087057107301271
Europe PMC | doi

Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, Hayashizaki Y, Huber W, Sperling S. (2007)
Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality
Genomics 89(5):580-587. doi:10.1016/j.ygeno.2007.01.010
Europe PMC | doi

Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE. (2007)
CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data
Bioinformatics 23(6):771-773. doi:10.1093/bioinformatics/btl641
Europe PMC | doi

Huber W, von Heydebreck A, Vingron M. (2007)
Low-level analysis of microarray experiments
In: Lengauer T (ed.), Bioinformatics - From Genomes to Therapies. Wiley-VCH Verlag GmbH, Weinheim. pp 929-956.doi:10.1002/9783527619368.ch25
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

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

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

Casneuf T, Van de Peer Y, Huber W. (2007)
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
BMC Bioinformatics 8:461. doi:10.1186/1471-2105-8-461
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

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

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

Huber W. (2006)
Several articles in the R News special issue on Bioinformatics
R news 6(5)

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

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

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

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

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

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. doi:10.1016/j.ejcb.2005.02.001
Europe PMC | doi

Gentleman R, Ruschlaupt M, Huber W. (2005)
On the synthesis of microarray experiments
Journal of the French Statistical Society 146(1-2):173-194.
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
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

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

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


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

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