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.

Publications

Total: 124 publication(s)

2015

Fischer B, Sandmann T, Horn T, Billmann M, Chaudhary V, Huber W, Boutros M. (2015)

A map of directional genetic interactions in a metazoan cell.

Elife 4 doi:10.7554/elife.05464
Europe PMC | doi

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. (2015)

Orchestrating high-throughput genomic analysis with Bioconductor.

Nat. Methods 12(2):115-121. doi:10.1038/nmeth.3252
Europe PMC | doi

Tsujimura T, Klein FA, Langenfeld K, Glaser J, Huber W, Spitz F. (2015)

A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes.

PLoS Genet. 11(1) doi:10.1371/journal.pgen.1004897
Europe PMC | doi


2014

Khmelinskii A, Blaszczak E, Pantazopoulou M, Fischer B, Omnus DJ, Le Dez G, Brossard A, Gunnarsson A, Barry JD, Meurer M, Kirrmaier D, Boone C, Huber W, Rabut G, Ljungdahl PO, Knop M. (2014)

Protein quality control at the inner nuclear membrane.

Nature 516(7531):410-413. doi:10.1038/nature14096
Europe PMC | doi

Klimmeck D, Cabezas-Wallscheid N, Reyes A, von Paleske L, Renders S, Hansson J, Krijgsveld J, Huber W, Trumpp A. (2014)

Transcriptome-wide Profiling and Posttranscriptional Analysis of Hematopoietic Stem/Progenitor Cell Differentiation toward Myeloid Commitment.

Stem Cell Reports 3(5):858-875. doi:10.1016/j.stemcr.2014.08.012
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 15(4):507-522. doi:10.1016/j.stem.2014.07.005
Europe PMC | doi

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 31(2):166-169. doi:10.1093/bioinformatics/btu638
Europe PMC | doi

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 512(7512):96-100. 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-D932. 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

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

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

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

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

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

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

Reyes A, Blume Carolin, Pelechano V, Jakob P, Steinmetz LM, Zenz T, Huber W. (2013)

Mutated SF3B1 is associated with transcript isoform changes of the genes UQCC and RPL31 both in CLLs and uveal melanomas

doi:http://dx.doi.org/10.1101/000992
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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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


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

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

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

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

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


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

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

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

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

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

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

Huber W. (2006)

Several articles in the R News special issue on Bioinformatics

R news 6(5)

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

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