EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

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  • 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.


Total: 150 publication(s)


Velten L, Haas SF, Raffel S, Blaszkiewicz S, Islam S, Hennig BP, Hirche C, Lutz C, Buss EC, Nowak D, Boch T, Hofmann WK, Ho AD, Huber W, Trumpp A, Essers MA, Steinmetz LM. (2017)

Human haematopoietic stem cell lineage commitment is a continuous process

Nat. Cell Biol. 19(4):1-271. doi: 10.1038/ncb3493
Europe PMC | doi

Adam M, Tennstedt P, Lanwehr D, Tilki D, Steuber T, Beyer B, Thederan I, Heinzer H, Haese A, Salomon G, Budäus L, Michl U, Pehrke D, Stattin P, Bernard J, Klaus B, Pompe RS, Petersen C, Huland H, Graefen M, Schwarz R, Huber W, Loeb S, Schlomm T. (2017)

Functional Outcomes and Quality of Life After Radical Prostatectomy Only Versus a Combination of Prostatectomy with Radiation and Hormonal Therapy.

Eur. Urol. 71(3):330-336. doi: 10.1016/j.eururo.2016.11.015
Europe PMC | doi

Martínez C, Rodiño-Janeiro BK, Lobo B, Stanifer ML, Klaus B, Granzow M, González-Castro AM, Salvo-Romero E, Alonso-Cotoner C, Pigrau M, Roeth R, Rappold G, Huber W, González-Silos R, Lorenzo J, de Torres I, Azpiroz F, Boulant S, Vicario M, Niesler B, Santos J. (2017)

miR-16 and miR-125b are involved in barrier function dysregulation through the modulation of claudin-2 and cingulin expression in the jejunum in IBS with diarrhoea.

Gut doi: 10.1136/gutjnl-2016-311477
Europe PMC | doi


Słabicki M, Lee KS, Jethwa A, Sellner L, Sacco F, Walther T, Hüllein J, Dietrich S, Wu B, Lipka DB, Oakes CC, Mamidi S, Pyrzyńska B, Winiarska M, Oleś M, Seifert M, Plass C, Kirschfink M, Boettcher M, Gołąb J, Huber W, Fröhling S, Zenz T. (2016)

Dissection of CD20 regulation in lymphoma using RNAi.

Leukemia 30(12):2409-2412. doi: 10.1038/leu.2016.230
Europe PMC | doi

Symmons O, Pan L, Remeseiro S, Aktas T, Klein F, Huber W, Spitz F. (2016)

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances.

Dev. Cell 39(5):529-543. doi: 10.1016/j.devcel.2016.10.015
Europe PMC | doi

Huber W. (2016)

A clash of cultures in discussions of the P value.

Nat. Methods 13(8) doi: 10.1038/nmeth.3934
Europe PMC | doi

Ignatiadis N, Klaus B, Zaugg JB, Huber W. (2016)

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing.

Nat. Methods 13(7):577-580. doi: 10.1038/nmeth.3885
Europe PMC | doi

Braun M, Qorraj M, Büttner M, Klein FA, Saul D, Aigner M, Huber W, Mackensen A, Jitschin R, Mougiakakos D. (2016)

CXCL12 promotes glycolytic reprogramming in acute myeloid leukemia cells via the CXCR4/mTOR axis.

Leukemia doi: 10.1038/leu.2016.58
Europe PMC | doi

Billmann M, Horn T, Fischer B, Sandmann T, Huber W, Boutros M. (2016)

A genetic interaction map of cell cycle regulators.

Mol. Biol. Cell doi: 10.1091/mbc.E15-07-0467
Europe PMC | doi

Scognamiglio R, Cabezas-Wallscheid N, Thier MC, Altamura S, Reyes A, Prendergast ÁM, Baumgärtner D, Carnevalli LS, Atzberger A, Haas S, von Paleske L, Boroviak T, Wörsdörfer P, Essers MA, Kloz U, Eisenman RN, Edenhofer F, Bertone P, Huber W, van der Hoeven F, Smith A, Trumpp A. (2016)

Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause.

Cell 164(4):668-680. doi: 10.1016/j.cell.2015.12.033
Europe PMC | doi

Foti R, Gnan S, Cornacchia D, Dileep V, Bulut-Karslioglu A, Diehl S, Buness A, Klein FA, Huber W, Johnstone E, Loos R, Bertone P, Gilbert DM, Manke T, Jenuwein T, Buonomo SCB. (2016)

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

MOL CELL 61(2):260-273. doi: 10.1016/j.molcel.2015.12.001
Europe PMC | doi

Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A. (2016)

Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants.

Nucleic Acids Res. 44(D1):D746-52. doi: 10.1093/nar/gkv1045
Europe PMC | doi

Barry JD, Donà E, Gilmour D, Huber W. (2016)

TimerQuant: a modelling approach to tandem fluorescent timer design and data interpretation for measuring protein turnover in embryos.

Development 143(1):174-9. doi: 10.1242/dev.125971
Europe PMC | doi


Breinig M, Klein FA, Huber W, Boutros M. (2015)

A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells.

Mol. Syst. Biol. 11(12) doi: 10.15252/msb.20156400
Europe PMC | doi

Guglielmi G, Barry JD, Huber W, De Renzis S. (2015)

An Optogenetic Method to Modulate Cell Contractility during Tissue Morphogenesis.

Dev Cell 35(5):646-660. doi: 10.1016/j.devcel.2015.10.020
Europe PMC | doi

Reinhard FB, Eberhard D, Werner T, Franken H, Childs D, Doce C, Savitski MF, Huber W, Bantscheff M, Savitski MM, Drewes G. (2015)

Thermal proteome profiling monitors ligand interactions with cellular membrane proteins.

Nat. Methods 12(12):1129-1131. doi: 10.1038/nmeth.3652
Europe PMC | doi

Zenz T, Huber W. (2015)

Mutational landscape and complexity in CLL.

Blood 126(18):2078-2079. doi: 10.1182/blood-2015-09-667584
Europe PMC | doi

Love MI, Anders S, Kim V, Huber W. (2015)

RNA-Seq workflow: gene-level exploratory analysis and differential expression.

F1000Res 4 doi: 10.12688/f1000research.7035.1
Europe PMC | doi

Franken H, Mathieson T, Childs D, Sweetman GM, Werner T, Tögel I, Doce C, Gade S, Bantscheff M, Drewes G, Reinhard FB, Huber W, Savitski MM. (2015)

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

Nat Protoc 10(10):1567-1593. doi: 10.1038/nprot.2015.101
Europe PMC | doi

Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M. (2015)

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

Cell 162(5):1051-1065. doi: 10.1016/j.cell.2015.07.048
Europe PMC | doi

Hauer C, Curk T, Anders S, Schwarzl T, Alleaume AM, Sieber J, Hollerer I, Bhuvanagiri M, Huber W, Hentze MW, Kulozik AE. (2015)

Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP.

Nat Commun 6:7921. doi: 10.1038/ncomms8921
Europe PMC | doi

Brennecke P, Reyes A, Pinto S, Rattay K, Nguyen M, Küchler R, Huber W, Kyewski B, Steinmetz LM. (2015)

Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells.

Nat. Immunol. 16(9):933-941. doi: 10.1038/ni.3246
Europe PMC | doi

Gehring JS, Fischer B, Lawrence M, Huber W. (2015)

SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants.

Bioinformatics doi: 10.1093/bioinformatics/btv408
Europe PMC | doi

Velten L, Anders S, Pekowska A, Järvelin AI, Huber W, Pelechano V, Steinmetz LM. (2015)

Single-cell polyadenylation site mapping reveals 3' isoform choice variability.

Mol. Syst. Biol. 11(6) doi: 10.15252/msb.20156198
Europe PMC | doi

Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W. (2015)

FourCSeq: Analysis of 4C sequencing data.

Bioinformatics 31(19):3085-3091. doi: 10.1093/bioinformatics/btv335
Europe PMC | doi

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


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

Love MI, Huber W, Anders S. (2014)

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

Genome Biol. 15(12):550. doi: 10.1186/s13059-014-0550-8
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


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


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


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


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


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


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

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


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