SpatialData: an open and universal data framework for spatial omics.

Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B, Pollaris L, Lehner L, Vöhringer H, Kats I, Saeys Y, Saka SK, Huber W, Gerstung M, Moore J, Theis FJ, Stegle O

Nature methods, 2024

doi:10.1038/s41592-024-02212-x.

Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities.

Roider T, Baertsch MA, Fitzgerald D, Vöhringer H, Brinkmann BJ, Czernilofsky F, Knoll M, Llaó-Cid L, Mathioudaki A, Faßbender B, Herbon M, Lautwein T, Bruch PM, Liebers N, Schürch CM, Passerini V, Seifert M, Brobeil A, Mechtersheimer G, Müller-Tidow C, Weigert O, Seiffert M, Nolan GP, Huber W, Dietrich S

Nature cell biology, 2024

doi:10.1038/s41556-024-01358-2.

Restraining Wnt activation and intestinal tumorigenesis by a Rab35 dependent GTPase relay.

Redhai S, Wang T, Boonekamp KE, Reuter S, Capraz T, Leible S, Bahaguna S, Port F, Pavlović B, Holzem M, Doll RM, Rindtorff N, Valentini E, Schmitt B, Richter K, Engel U, Huber W, Boutros M

bioRxiv, 2024

doi:10.1101/2024.02.05.578891.

A single-cell multi-omic and spatial atlas of B cell lymphomas reveals differentiation drives intratumor heterogeneity.

Fitzgerald D, Roider T, Baertsch M, Kibler A, Horlova A, Chung E, Vöhringer H, Mathioudaki A, Budeus B, Passerini V, Knoll M, Mammen J, Li L, Caillé L, Czernilofsky F, Bruch P, Liebers N, Meyer-Bender M, Weigert O, Zaugg J, Nolan G, Seifert M, Dietrich S, Huber W

bioRxiv, 2023

doi:10.1101/2023.11.06.565756.

The changing career paths of PhDs and postdocs trained at EMBL.

Lu J, Velten B, Klaus B, Ramm M, Huber W, Coulthard-Graf R

eLife, 2023

doi:10.7554/elife.78706.

Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq.

Schwarzl T, Sahadevan S, Lang B, Miladi M, Backofen R, Huber W, Hentze MW, Tartaglia GG

Nucleic acids research, 2023

doi:10.1093/nar/gkad998.

MsQuality - an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.

Naake T, Rainer J, Huber W

Bioinformatics , 2023

doi:10.1093/bioinformatics/btad618.

Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: the prospective non-interventional SMARTrial.

Liebers N, Bruch PM, Terzer T, Hernandez-Hernandez M, Paramasivam N, Fitzgerald D, Altmann H, Roider T, Kolb C, Knoll M, Lenze A, Platzbecker U, Röllig C, Baldus C, Serve H, Bornhäuser M, Hübschmann D, Müller-Tidow C, Stölzel F, Huber W, Benner A, Zenz T, Lu J, Dietrich S

Nature cancer, 2023

doi:10.1038/s43018-023-00645-5.

Systematic analysis of drug combinations against Gram-positive bacteria.

Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A

Nature microbiology, 2023

doi:10.1038/s41564-023-01486-9.

Comparing the value of mono- versus coculture for high-throughput compound screening in hematological malignancies.

Herbst SA, Kim V, Roider T, Schitter EC, Bruch PM, Liebers N, Kolb C, Knoll M, Lu J, Dreger P, Müller-Tidow C, Zenz T, Huber W, Dietrich S

Blood advances, 2023

doi:10.1182/bloodadvances.2022009652.

Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia.

Lütge A, Lu J, Hüllein J, Walther T, Sellner L, Wu B, Rosenquist R, Oakes CC, Dietrich S, Huber W, Zenz T

Haematologica, 2023

doi:10.3324/haematol.2022.281869.

Comparison of transformations for single-cell RNA-seq data.

Ahlmann-Eltze C, Huber W

Nature methods, 2023

doi:10.1038/s41592-023-01814-1.

Deep thermal profiling for detection of functional proteoform groups.

Kurzawa N, Leo IR, Stahl M, Kunold E, Becher I, Audrey A, Mermelekas G, Huber W, Mateus A, Savitski MM, Jafari R

Nature chemical biology, 2023

doi:10.1038/s41589-023-01284-8.

Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis.

Gegner HM, Naake T, Dugourd A, Müller T, Czernilofsky F, Kliewer G, Jäger E, Helm B, Kunze-Rohrbach N, Klingmüller U, Hopf C, Müller-Tidow C, Dietrich S, Saez-Rodriguez J, Huber W, Hell R, Poschet G, Krijgsveld J

Frontiers in molecular biosciences, 2022

doi:10.3389/fmolb.2022.961448.

Htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets.

Sahadevan S, Sekaran T, Ashaf N, Fritz M, Hentze MW, Huber W, Schwarzl T

Bioinformatics (Oxford, England), 2022

doi:10.1093/bioinformatics/btac747.

Proteogenomics refines the molecular classification of chronic lymphocytic leukemia.

Herbst SA, Vesterlund M, Helmboldt AJ, Jafari R, Siavelis I, Stahl M, Schitter EC, Liebers N, Brinkmann BJ, Czernilofsky F, Roider T, Bruch PM, Iskar M, Kittai A, Huang Y, Lu J, Richter S, Mermelekas G, Umer HM, Knoll M, Kolb C, Lenze A, Cao X, Österholm C, Wahnschaffe L, Herling C, Scheinost S, Ganzinger M, Mansouri L, Kriegsmann K, Kriegsmann M, Anders S, Zapatka M, Del Poeta G, Zucchetto A, Bomben R, Gattei V, Dreger P, Woyach J, Herling M, Müller-Tidow C, Rosenquist R, Stilgenbauer S, Zenz T, Huber W, Tausch E, Lehtiö J, Dietrich S

Nature communications, 2022

doi:10.1038/s41467-022-33385-8.

Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling.

Batzilla A, Lu J, Kivioja J, Putzker K, Lewis J, Zenz T, Huber W

PLoS computational biology, 2022

doi:10.1371/journal.pcbi.1010438.

Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL.

Bruch PM, Giles HA, Kolb C, Herbst SA, Becirovic T, Roider T, Lu J, Scheinost S, Wagner L, Huellein J, Berest I, Kriegsmann M, Kriegsmann K, Zgorzelski C, Dreger P, Zaugg JB, Müller-Tidow C, Zenz T, Huber W, Dietrich S

Molecular systems biology, 2022

doi:10.15252/msb.202110855.

Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels.

Imkeller K, Ambrosi G, Klemm N, Claveras Cabezudo A, Henkel L, Huber W, Boutros M

Molecular systems biology, 2022

doi:10.15252/msb.202110874.

Systematic discovery of biomolecular condensate-specific protein phosphorylation.

Sridharan S, Hernandez-Armendariz A, Kurzawa N, Potel CM, Memon D, Beltrao P, Bantscheff M, Huber W, Cuylen-Haering S, Savitski MM

Nature chemical biology, 2022

doi:10.1038/s41589-022-01062-y.

Silver clusters of five atoms as highly selective antitumoral agents through irreversible oxidation of thiols.

Porto V, Buceta D, Domínguez B, Carneiro C, Borrajo E, Fraile M, Davila-Ferreira N, Arias IR, Blanco JM, Blanco MC, Devida JM, Giovanetti LJ, Requejo FG, Hernández-Garrido JC, Calvino JJ, López-Haro M, Barone G, James AM, García-Caballero T, González-Castaño DM, Martin Treder, Huber W, Vidal A, Murphy MP, López-Quintela MA, Domínguez F

Advanced Functional Materials, 2022

doi:10.1002/adfm.202113028.

Author Correction: A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles.

Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM

Nature communications, 2021

doi:10.1038/s41467-021-27561-5.

MatrixQCvis: shiny-based interactive data quality exploration for omics data.

Naake T, Huber W

Bioinformatics (Oxford, England), 2021

doi:10.1093/bioinformatics/btab748.

Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake.

Zimoń M, Huang Y, Trasta A, Halavatyi A, Liu JZ, Chen CY, Blattmann P, Klaus B, Whelan CD, Sexton D, John S, Huber W, Tsai EA, Pepperkok R, Runz H

Nature communications, 2021

doi:10.1038/s41467-021-26761-3.

Autologous culture model of nodal B-cell lymphoma identifies ex vivo determinants of response to bispecific antibodies.

Roider T, Brinkmann BJ, Kim V, Knoll M, Kolb C, Roessner PM, Bordas M, Dreger P, Müller-Tidow C, Huber W, Seiffert M, Dietrich S

Blood advances, 2021

doi:10.1182/bloodadvances.2021005400.

Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia.

Lu J, Cannizzaro E, Meier-Abt F, Scheinost S, Bruch PM, Giles HA, Lütge A, Hüllein J, Wagner L, Giacopelli B, Nadeu F, Delgado J, Campo E, Mangolini M, Ringshausen I, Böttcher M, Mougiakakos D, Jacobs A, Bodenmiller B, Dietrich S, Oakes CC, Zenz T, Huber W

Nature cancer, 2021

doi:10.1038/s43018-021-00216-6.

Covariate powered cross-weighted multiple testing.

Ignatiadis N, Huber W

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 2021

doi:10.1111/rssb.12411.

The protein landscape of chronic lymphocytic leukemia (CLL).

Meier-Abt F, Lu J, Cannizzaro E, Pohly MF, Kummer S, Pfammatter S, Kunz L, Collins BC, Nadeu F, Lee KS, Xue P, Gwerder M, Roiss M, Hüllein J, Scheinost S, Dietrich S, Campo E, Huber W, Aebersold R, Zenz T

Blood, 2021

doi:10.1182/blood.2020009741.

SAMHD1 mutations in mantle cell lymphoma are recurrent and confer in vitro resistance to nucleoside analogues.

Bühler MM, Lu J, Scheinost S, Nadeu F, Roos-Weil D, Hensel M, Thavayogarajah T, Moch H, Manz MG, Haralambieva E, Marques Maggio E, Beà S, Giné E, Campo E, Bernard OA, Huber W, Zenz T

Leukemia research, 2021

doi:10.1016/j.leukres.2021.106608.

Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase.

Kong KE, Fischer B, Meurer M, Kats I, Li Z, Rühle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop M, Khmelinskii A

Molecular cell, 2021

doi:10.1016/j.molcel.2021.04.018.

Control of PD-L1 expression in CLL-cells by stromal triggering of the Notch-c-Myc-EZH2 oncogenic signaling axis.

Böttcher M, Bruns H, Völkl S, Lu J, Chartomatsidou E, Papakonstantinou N, Mentz K, Büttner-Herold M, Zenz T, Herling M, Huber W, Ghia P, Stamatopoulos K, Mackensen A, Mougiakakos D

Journal for immunotherapy of cancer, 2021

doi:10.1136/jitc-2020-001889.

Analysis of non-leukemic cellular subcompartments reconstructs clonal evolution of acute myeloid leukemia and identifies therapy-resistant pre-leukemic clones.

Saeed BR, Manta L, Raffel S, Pyl PT, Buss EC, Wang W, Eckstein V, Jauch A, Trumpp A, Huber W, Ho AD, Lutz C

International journal of cancer, 2021

doi:10.1002/ijc.33461.

A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles.

Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM

Nature communications, 2020

doi:10.1038/s41467-020-19529-8.

glmGamPoi: fitting Gamma-Poisson generalized linearmodels on single cell count data.

Ahlmann-Eltze C, Huber W

Bioinformatics (Oxford, England), 2020

doi:10.1093/bioinformatics/btaa1009.

Transparency and reproducibility in artificial intelligence.

Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Massive Analysis Quality Control (MAQC) Society Board of Directors, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL

Nature, 2020

doi:10.1038/s41586-020-2766-y.

Developmental gene expression differences between humans and mammalian models.

Cardoso-Moreira M, Sarropoulos I, Velten B, Mort M, Cooper DN, Huber W, Kaessmann H

Cell reports, 2020

doi:10.1016/j.celrep.2020.108308.

Miniaturized drug sensitivity and resistance test on patient-derived cells using droplet-microarray.

Popova AA, Dietrich S, Huber W, Reischl M, Peravali R, Levkin PA

SLAS technology, 2020

doi:10.1177/2472630320934432.

A user guide for the online exploration and visualization of PCAWG data.

Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Weinstein JN, Haussler D, Valencia A, Huber W, Papatheodorou I, Park PJ, Ferretti V, Zhu J, Vazquez M

Nature communications, 2020

doi:10.1038/s41467-020-16785-6.

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation.

Kelmer Sacramento E, Kirkpatrick JM, Mazzetto M, Baumgart M, Bartolome A, Di Sanzo S, Caterino C, Sanguanini M, Papaevgeniou N, Lefaki M, Childs D, Bagnoli S, Terzibasi Tozzini E, Di Fraia D, Romanov N, Huber W, Sudmant PH, Vendruscolo M, Chondrogianni N, Ori A, Cellerino A

Molecular systems biology, 2020

doi:10.15252/msb.20209596.

Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels.

Roider T, Seufert J, Uvarovskii A, Frauhammer F, Bordas M, Abedpour N, Stolarczyk M, Mallm JP, Herbst SA, Bruch PM, Balke-Want H, Hundemer M, Rippe K, Goeppert B, Seiffert M, Brors B, Mechtersheimer G, Zenz T, Peifer M, Chapuy B, Schlesner M, Müller-Tidow C, Fröhling S, Huber W, Anders S, Dietrich S

Nature cell biology, 2020

doi:10.1038/s41556-020-0532-x.

Survey of ex vivo drug combination effects in chronic lymphocytic leukemia reveals synergistic drug effects and genetic dependencies.

Lukas M, Velten B, Sellner L, Tomska K, Hüellein J, Walther T, Wagner L, Muley C, Wu B, Oleś M, Dietrich S, Jethwa A, Bohnenberger H, Lu J, Huber W, Zenz T

Leukemia, 2020

doi:10.1038/s41375-020-0846-5.

gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection.

Imkeller K, Ambrosi G, Boutros M, Huber W

Genome biology, 2020

doi:10.1186/s13059-020-1939-1.

Identifying drug targets in tissues and whole blood with thermal-shift profiling.

Perrin J, Werner T, Kurzawa N, Rutkowska A, Childs DD, Kalxdorf M, Poeckel D, Stonehouse E, Strohmer K, Heller B, Thomson DW, Krause J, Becher I, Eberl HC, Vappiani J, Rau CE, Sevin DC, Huber W, Franken H, Savitski MM, Faelth-Savitski M, Bergamini G, Bantscheff M

Nature biotechnology, 2020

doi:10.1038/s41587-019-0388-4.

Publisher correction: orchestrating single-cell analysis with Bioconductor.

Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Hicks SC, Gottardo R

Nature methods, 2019

doi:10.1038/s41592-019-0700-8.

Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTF.

Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB

Cell reports, 2019

doi:10.1016/j.celrep.2019.10.106.

Orchestrating single-cell analysis with Bioconductor.

Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Martini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Hicks SC, Gottardo R

Nature methods, 2019

doi:10.1038/s41592-019-0654-x.

Biological plasticity rescues target activity in CRISPR knock outs.

Smits AH, Ziebell F, Joberty G, Zinn N, Mueller WF, Clauder-Münster S, Eberhard D, Fälth Savitski M, Grandi P, Jakob P, Michon AM, Sun H, Tessmer K, Bürckstümmer T, Bantscheff M, Drewes G, Steinmetz LM, Huber W

Nature methods, 2019

doi:10.1038/s41592-019-0614-5.

Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes.

Velten B, Huber W

Biostatistics (Oxford, England), 2019

doi:10.1093/biostatistics/kxz034.

Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

Childs D, Bach K, Franken H, Anders S, Kurzawa N, Bantscheff M, Savitski M, Huber W

Molecular & cellular proteomics : MCP, 2019

doi:10.1074/mcp.TIR119.001481.

Gene expression across mammalian organ development.

Cardoso-Moreira M, Halbert J, Valloton D, Velten B, Chen C, Shao Y, Liechti A, Ascenção K, Rummel C, Ovchinnikova S, Mazin PV, Xenarios I, Harshman K, Mort M, Cooper DN, Soares MJ, Sandi C, Afonso S, Ferreira PG, Turner JMA, Carneiro M, Fallahshahroudi A, VandeBerg JL, Behr R, Jensen P, Lindsay S, Lisgo S, Huber W, Khaitovich P, Anders S, Baker J, Zhang YE, Kaessmann H

Nature, 2019

doi:10.1038/s41586-019-1338-5.

The RNA-binding protein YBX3 controls amino acid levels by regulating SLC mRNA abundance.

Cooke A, Schwarzl T, Huppertz I, Kramer G, Mantas P, Alleaume AM, Huber W, Krijgsveld J, Hentze MW

Cell reports, 2019

doi:10.1016/j.celrep.2019.05.039.

MDM4 is targeted by 1q gain and drives disease in Burkitt lymphoma.

Hüllein J, Słabicki M, Rosolowski M, Jethwa A, Habringer S, Tomska K, Kurilov R, Lu J, Scheinost S, Wagener R, Huang Z, Lukas M, Yavorska O, Helfrich H, Scholtysik R, Tedesco D, Bonneau K, Klapper W, Küppers R, Stilgenbauer S, Pott C, Löffler M, Burkhardt B, Hummel M, Trümper LH, Zapatka M, Brors B, Kreuz M, Siebert R, Huber W, Keller U, Zenz T

Cancer research, 2019

doi:10.1158/0008-5472.CAN-18-3438.

Reporting p values.

Huber W

Cell systems, 2019

doi:10.1016/j.cels.2019.03.001.

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP.

Sridharan S, Kurzawa N, Werner T, Günthner I, Helm D, Huber W, Bantscheff M, Savitski MM

Nature communications, 2019

doi:10.1038/s41467-019-09107-y.

Energy metabolism is co-determined by genetic variants in chronic lymphocytic leukemia and influences drug sensitivity.

Lu J, Böttcher M, Walther T, Mougiakakos D, Zenz T, Huber W

Haematologica, 2019

doi:10.3324/haematol.2018.203067.

The small non-coding vault RNA1-1 acts as a riboregulator of autophagy.

Horos R, Büscher M, Kleinendorst R, Alleaume AM, Tarafder AK, Schwarzl T, Dziuba D, Tischer C, Zielonka EM, Adak A, Castello A, Huber W, Sachse C, Hentze MW

Cell, 2019

doi:10.1016/j.cell.2019.01.030.

Gain of CTCF-anchored chromatin loops marks the exit from naive pluripotency.

Pękowska A, Klaus B, Xiang W, Severino J, Daigle N, Klein FA, Oleś M, Casellas R, Ellenberg J, Steinmetz LM, Bertone P, Huber W

Cell systems, 2018

doi:10.1016/j.cels.2018.09.003.

Drug-based perturbation screen uncovers synergistic drug combinations in Burkitt lymphoma.

Tomska K, Kurilov R, Lee KS, Hüllein J, Lukas M, Sellner L, Walther T, Wagner L, Oleś M, Brors B, Huber W, Zenz T

Scientific reports, 2018

doi:10.1038/s41598-018-30509-3.

TRRAP is essential for regulating the accumulation of mutant and wild-type p53 in lymphoma.

Jethwa A, Słabicki M, Hüllein J, Jentzsch M, Dalal V, Rabe S, Wagner L, Walther T, Klapper W, Bohnenberger H, Rettel M, Lu J, Smits AH, Stein F, Savitski MM, Huber W, Aylon Y, Oren M, Zenz T

Blood, 2018

doi:10.1182/blood-2017-09-806679.

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O

Molecular systems biology, 2018

doi:10.15252/msb.20178124.

Authoring Bioconductor workflows with BiocWorkflowTools.

Smith ML, Oleś AK, Huber W

2018

doi:10.12688/f1000research.14399.1.

Proteome-wide identification of ubiquitin interactions using UbIA-MS.

Zhang X, Smits AH, van Tilburg GB, Ovaa H, Huber W, Vermeulen M

Nature protocols, 2018

doi:10.1038/nprot.2017.147.

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling.

Andersson EI, Pützer S, Yadav B, Dufva O, Khan S, He L, Sellner L, Schrader A, Crispatzu G, Oleś M, Zhang H, Adnan S, Lagström S, Bellanger D, Mpindi JP, Eldfors S, Pemovska T, Pietarinen P, Lauhio A, Tomska K, Cuesta-Mateos C, Faber E, Koschmieder S, Brümmendorf TH, Kytölä S, Savolainen ER, Siitonen T, Ellonen P, Kallioniemi O, Wennerberg K, Ding W, Stern MH, Huber W, Anders S, Tang J, Aittokallio T, Zenz T, Herling M, Mustjoki S

Leukemia, 2017

doi:10.1038/leu.2017.252.

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues.

Reyes A, Huber W

Nucleic acids research, 2017

doi:10.1093/nar/gkx1165.

Expression atlas: gene and protein expression across multiple studies and organisms.

Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R

Nucleic acids research, 2017

doi:10.1093/nar/gkx1158.

Drug-perturbation-based stratification of blood cancer.

Dietrich S, Oleś M, Lu J, Sellner L, Anders S, Velten B, Wu B, Hüllein J, da Silva Liberio M, Walther T, Wagner L, Rabe S, Ghidelli-Disse S, Bantscheff M, Oleś AK, Słabicki M, Mock A, Oakes CC, Wang S, Oppermann S, Lukas M, Kim V, Sill M, Benner A, Jauch A, Sutton LA, Young E, Rosenquist R, Liu X, Jethwa A, Lee KS, Lewis J, Putzker K, Lutz C, Rossi D, Mokhir A, Oellerich T, Zirlik K, Herling M, Nguyen-Khac F, Plass C, Andersson E, Mustjoki S, von Kalle C, Ho AD, Hensel M, Dürig J, Ringshausen I, Zapatka M, Huber W, Zenz T

The Journal of clinical investigation, 2017

doi:10.1172/JCI93801.

Research Techniques Made Simple: Bioinformatics for Genome-Scale Biology.

Foulkes AC, Watson DS, Griffiths CEM, Warren RB, Huber W, Barnes MR

The Journal of investigative dermatology, 2017

doi:10.1016/j.jid.2017.07.095.

Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities.

Bunina D, Štefl M, Huber F, Khmelinskii A, Meurer M, Barry JD, Kats I, Kirrmaier D, Huber W, Knop M

Nucleic acids research, 2017

doi:10.1093/nar/gkx737.

Two independent modes of chromatin organization revealed by cohesin removal

Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F

2017

doi:10.1038/nature24281.

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.

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

Gut, 2017

doi:10.1136/gutjnl-2016-311477.

Human haematopoietic stem cell lineage commitment is a continuous process.

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

Nature cell biology, 2017

doi:10.1038/ncb3493.

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

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

European urology, 2016

doi:10.1016/j.eururo.2016.11.015.

Dissection of CD20 regulation in lymphoma using RNAi.

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

LEUKEMIA, 2016

doi:10.1038/leu.2016.230.

The Shh topological domain facilitates the action of remote enhancers by reducing the effects of genomic distances.

Symmons O, Pan L, Remeseiro S, Aktas T, Klein F, Huber W, Spitz F

Developmental cell, 2016

doi:10.1016/j.devcel.2016.10.015.

Corrigendum: Enhancer loops appear stable during development and are associated with paused polymerase

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EEM

NATURE, 2016

doi:10.1038/nature18962.

A clash of cultures in discussions of the P value.

Huber W

Nature methods, 2016

doi:10.1038/nmeth.3934.

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

Ignatiadis N, Klaus B, Zaugg JB, Huber W

Nature methods, 2016

doi:10.1038/nmeth.3885.

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

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

Leukemia, 2016

doi:10.1038/leu.2016.58.

A genetic interaction map of cell cycle regulators.

Billmann M, Horn T, Fischer B, Sandmann T, Huber W, Boutros M

Molecular biology of the cell, 2016

doi:10.1091/mbc.E15-07-0467.

Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause.

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

Cell, 2016

doi:10.1016/j.cell.2015.12.033.

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

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

MOLECULAR CELL, 2016

doi:10.1016/j.molcel.2015.12.001.

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

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

Nucleic acids research, 2016

doi:10.1093/nar/gkv1045.

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

Barry JD, Donà E, Gilmour D, Huber W

Development (Cambridge, England), 2015

doi:10.1242/dev.125971.

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

Breinig M, Klein FA, Huber W, Boutros M

Molecular systems biology, 2015

doi:10.15252/msb.20156400.

An Optogenetic Method to Modulate Cell Contractility during Tissue Morphogenesis.

Guglielmi G, Barry JD, Huber W, De Renzis S

DEVELOPMENTAL CELL, 2015

doi:10.1016/j.devcel.2015.10.020.

Thermal proteome profiling monitors ligand interactions with cellular membrane proteins.

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

Nature methods, 2015

doi:10.1038/nmeth.3652.

Mutational landscape and complexity in CLL.

Zenz T, Huber W

Blood, 2015

doi:10.1182/blood-2015-09-667584.

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

Love MI, Anders S, Kim V, Huber W

F1000Research, 2015

doi:10.12688/f1000research.7035.1.

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

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

Nature protocols, 2015

doi:10.1038/nprot.2015.101.

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

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

doi:10.1016/j.cell.2015.07.048.

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

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

Nature communications, 2015

doi:10.1038/ncomms8921.

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

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

Nature Immunology, 2015

doi:10.1038/ni.3246.

SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants.

Gehring JS, Fischer B, Lawrence M, Huber W

Bioinformatics (Oxford, England), 2015

doi:10.1093/bioinformatics/btv408.

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

Velten L, Anders S, Pekowska A, Järvelin AI, Huber W, Pelechano V, Steinmetz LM

Molecular systems biology, 2015

doi:10.15252/msb.20156198.

FourCSeq: Analysis of 4C sequencing data.

Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W

Bioinformatics (Oxford, England), 2015

doi:10.1093/bioinformatics/btv335.

A map of directional genetic interactions in a metazoan cell.

Fischer B, Sandmann T, Horn T, Billmann M, Chaudhary V, Huber W, Boutros M

eLife, 2015

doi:10.7554/elife.05464.

Orchestrating high-throughput genomic analysis with Bioconductor.

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

Nature methods, 2015

doi:10.1038/nmeth.3252.

HTSeq - A Python framework to work with high-throughput sequencing data

Anders S, Pyl PT, Huber W

Bioinformatics (Oxford, England), 2014

doi:10.1093/bioinformatics/btu638.

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

Tsujimura T, Klein FA, Langenfeld K, Glaser J, Huber W, Spitz F

PLoS genetics, 2015

doi:10.1371/journal.pgen.1004897.

Protein quality control at the inner nuclear membrane.

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

Nature, 2014

doi:10.1038/nature14096.

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

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

Stem cell reports, 2014

doi:10.1016/j.stemcr.2014.08.012.

Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis

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

Cell stem cell, 2014

doi:10.1016/j.stem.2014.07.005.

Measuring genetic interactions in human cells by RNAi and imaging

Laufer C, Fischer B, Huber W, Boutros M

Nature protocols, 2014

doi:10.1038/nprot.2014.160.

Enhancer loops appear stable during development and are associated with paused polymerase

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE

Nature, 2014

doi:10.1038/nature13417.

The global RNA and protein landscape of hematopoietic stem cells and their immediate progeny.

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

EXPERIMENTAL HEMATOLOGY, 2014

doi:10.1016/j.exphem.2014.07.091.

h5vc: Scalable nucleotide tallies with HDF5

Pyl PT, Gehring J, Fischer B, Huber W

Bioinformatics (Oxford, England), 2014

doi:10.1093/bioinformatics/btu026.

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

Love MI, Huber W, Anders S

Genome biology, 2014

doi:10.1186/s13059-014-0550-8.

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Wilkening S, Huber W, Pelechano V, Steinmetz LM

Molecular systems biology, 2014

doi:10.1002/msb.135068.

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, Oleś AK, Araúzo-Bravo MJ, Saitou M, Hadjantonakis AK, Hiiragi T

Nature cell biology, 2013

doi:10.1038/ncb2881.

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 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

Nucleic acids research, 2013

doi:10.1093/nar/gkt1270.

Directional tissue migration through a self-generated chemokine gradient

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

Nature, 2013

doi:10.1038/nature12635.

High-content siRNA screen reveals global ENaC regulators and potential cystic fibrosis therapy targets

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

Cell, 2013

doi:10.1016/j.cell.2013.08.045.

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD

Nature protocols, 2013

doi:10.1038/nprot.2013.099.

Drift and conservation of differential exon usage across tissues in primate species

Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W

Proceedings of the National Academy of Sciences of the United States of America, 2013

doi:10.1073/pnas.1307202110.

Control of tissue morphology by Fasciclin III-mediated intercellular adhesion

Wells RE, Barry JD, Warrington SJ, Cuhlmann S, Evans P, Huber W, Strutt D, Zeidler MP

Development (Cambridge, England), 2013

doi:10.1242/dev.096214.

GLOBAL LANDSCAPE OF HEMATOPOIETIC STEM CELLS AND MULTIPOTENT PROGENITORS

Klimmeck D, Cabezas-Wallscheid N, Hansson J, Dohrn L, Reyes A, Huber W, Krijgsveld J, Trumpp A

EXPERIMENTAL HEMATOLOGY, 2013

doi:10.1016/j.exphem.2013.05.048.

The genomic and transcriptomic landscape of a HeLa cell line

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

G3 (Bethesda, Md.), 2013

doi:10.1534/g3.113.005777.

CellH5: a format for data exchange in high-content screening

Sommer C, Held M, Fischer B, Huber W, Gerlich DW

Bioinformatics (Oxford, England), 2013

doi:10.1093/bioinformatics/btt175.

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping

Laufer C, Fischer B, Billmann M, Huber W, Boutros M

Nature methods, 2013

doi:10.1038/nmeth.2436.

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

Yu D, Huber W, Vitek O

Bioinformatics (Oxford, England), 2013

doi:10.1093/bioinformatics/btt143.

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

Reyes A, Blume Carolin, Pelechano V, Jakob P, Steinmetz LM, Zenz T, Huber W

2013

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

Software for computing and annotating genomic ranges

Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ

PLoS computational biology, 2013

doi:10.1371/journal.pcbi.1003118.

Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay.

Pau G, Walter T, Neumann B, Hériché JK, Ellenberg J, Huber W

BMC bioinformatics, 2013

doi:10.1186/1471-2105-14-308.

Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency

Hansson J, Rafiee MR, Reiland S, Polo JM, Gehring J, Okawa S, Huber W, Hochedlinger K, Krijgsveld J

Cell reports, 2012

doi:10.1016/j.celrep.2012.10.014.

Detecting differential usage of exons from RNA-seq data

Anders S, Reyes A, Huber W

Genome research, 2012

doi:10.1101/gr.133744.111.

Tandem fluorescent protein timers for in vivo analysis of protein dynamics

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

Nature biotechnology, 2012

doi:10.1038/nbt.2281.

cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression

Benito E, Valor LM, Jimenez-Minchan M, Huber W, Barco A

The Journal of neuroscience : the official journal of the Society for Neuroscience, 2011

doi:10.1523/jneurosci.4554-11.2011.

Cell-to-cell transfer of HIV-1 via virological synapses leads to endosomal virion maturation that activates viral membrane fusion

Dale BM, McNerney GP, Thompson DL, Hubner W, de Los Reyes K, Chuang FY, Huser T, Chen BK

Cell host & microbe, 2011

doi:10.1016/j.chom.2011.10.015.

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 SM, Huber W, Korbel JO

Genome research, 2011

doi:10.1101/gr.122614.111.

Enterotypes of the human gut microbiome

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

Nature, 2011

doi:10.1038/nature09944.

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi

Horn T, Sandmann T, Fischer B, Axelsson E, Huber W, Boutros M

Nature methods, 2011

doi:10.1038/nmeth.1581.

Antisense expression increases gene expression variability and locus interdependency

Xu Z, Wei W, Gagneur J, Clauder-Münster S, Smolik M, Huber W, Steinmetz LM

Molecular systems biology, 2011

doi:10.1038/msb.2011.1.

Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi

Axelsson E, Sandmann T, Horn T, Boutros M, Huber W, Fischer B

BMC bioinformatics, 2011

doi:10.1186/1471-2105-12-342.

Contributions of the EMERALD project to assessing and improving microarray data quality

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

BioTechniques, 2011

doi:10.2144/000113591.

Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications

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

International journal of molecular epidemiology and genetics, 2011

doi:.

Genome-wide survey of post-meiotic segregation during yeast recombination

Mancera E, Bourgon R, Huber W, Steinmetz LM

Genome biology, 2011

doi:10.1186/gb-2011-12-4-r36.

Assessing affymetrix GeneChip microarray quality

McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA

BMC bioinformatics, 2011

doi:10.1186/1471-2105-12-137.

Organelle proteomics experimental designs and analysis

Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS

Proteomics, 2010

doi:10.1002/pmic.201000244.

Addressing accuracy and precision issues in iTRAQ quantitation

Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, Lilley KS

Molecular & cellular proteomics : MCP, 2010

doi:10.1074/mcp.m900628-mcp200.

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

Molecular systems biology, 2010

doi:10.1038/msb.2010.25.

Independent filtering increases detection power for high-throughput experiments

Bourgon R, Gentleman R, Huber W

Proceedings of the National Academy of Sciences of the United States of America, 2010

doi:10.1073/pnas.0914005107.

Variation in transcription factor binding among humans

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

Science (New York, N.Y.), 2010

doi:10.1126/science.1183621.

A global map of human gene expression

Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A

Nature biotechnology, 2010

doi:10.1038/nbt0410-322.

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

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

Nature, 2010

doi:10.1038/nature08869.

EBImage--an R package for image processing with applications to cellular phenotypes

Pau G, Fuchs F, Sklyar O, Boutros M, Huber W

Bioinformatics (Oxford, England), 2010

doi:10.1093/bioinformatics/btq046.

Microarray data quality control improves the detection of differentially expressed genes

Kauffmann A, Huber W

Genomics, 2010

doi:10.1016/j.ygeno.2010.01.003.

Differential expression analysis for sequence count data

Anders S, Huber W

Genome biology, 2010

doi:10.1186/gb-2010-11-10-r106.

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM

Genome biology, 2010

doi:10.1186/gb-2010-11-3-r24.

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

Journal of innate immunity, 2010

doi:10.1159/000248649.

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

doi:10.1186/1471-2164-11-349.

Genome-wide analysis of mRNA decay patterns during early Drosophila development

Thomsen S, Anders S, Janga SC, Huber W, Alonso CR

Genome biology, 2010

doi:10.1186/gb-2010-11-9-r93.

Importing ArrayExpress datasets into R/Bioconductor

Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W

Bioinformatics (Oxford, England), 2009

doi:10.1093/bioinformatics/btp354.

Array-based genotyping in S.cerevisiae using semi-supervised clustering

Bourgon R, Mancera E, Brozzi A, Steinmetz LM, Huber W

Bioinformatics (Oxford, England), 2009

doi:10.1093/bioinformatics/btp104.

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data

Kauffmann A, Gentleman R, Huber W

Bioinformatics (Oxford, England), 2009

doi:10.1093/bioinformatics/btn647.

Quality assessment and data analysis for microRNA expression arrays

Sarkar D, Parkin R, Wyman S, Bendoraite A, Sather C, Delrow J, Godwin AK, Drescher C, Huber W, Gentleman R, Tewari M

Nucleic acids research, 2009

doi:10.1093/nar/gkn932.

Bidirectional promoters generate pervasive transcription in yeast

Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM

Nature, 2009

doi:10.1038/nature07728.

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Durinck S, Spellman PT, Birney E, Huber W

Nature protocols, 2009

doi:10.1038/nprot.2009.97.

Genome-wide allele- and strand-specific expression profiling

Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM

Molecular systems biology, 2009

doi:10.1038/msb.2009.31.

Analyzing ChIP-chip data using bioconductor

Toedling J, Huber W

PLoS computational biology, 2008

doi:10.1371/journal.pcbi.1000227.

High-resolution mapping of meiotic crossovers and non-crossovers in yeast

Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM

Nature, 2008

doi:10.1038/nature07135.

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 (Oxford, England), 2008

doi:10.1093/bioinformatics/btm518.

Model-based variance-stabilizing transformation for Illumina microarray data

Lin SM, Du P, Huber W, Kibbe WA

Nucleic acids research, 2008

doi:10.1093/nar/gkm1075.

Bioconductor Case Studies

Hahne F, Huber W, Gentleman R, Falcon S (eds.)

2008

doi:10.1007/978-0-387-77240-0.

Combinatorial effects of four histone modifications in transcription and differentiation

Fischer JJ, Toedling J, Krueger T, Schueler M, Huber W, Sperling S

Genomics, 2008

doi:10.1016/j.ygeno.2007.08.010.

Estimating node degree in bait-prey graphs

Scholtens D, Chiang T, Huber W, Gentleman R

Bioinformatics (Oxford, England), 2008

doi:10.1093/bioinformatics/btm565.

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

Journal of biomolecular screening, 2007

doi:10.1177/1087057107301271.

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

doi:10.1016/j.ygeno.2007.01.010.

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 EE

Bioinformatics (Oxford, England), 2007

doi:10.1093/bioinformatics/btl641.

Low-level analysis of microarray experiments

Huber W, von Heydebreck A, Vingron M

2007

doi:10.1002/9783527619368.ch25.

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

doi:10.1186/1471-2105-8-461.

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

Chiang T, Scholtens D, Sarkar D, Gentleman R, Huber W

Genome biology, 2007

doi:10.1186/gb-2007-8-9-r186.

Making the most of high-throughput protein-interaction data

Gentleman R, Huber W

Genome biology, 2007

doi:10.1186/gb-2007-8-10-112.

Graphs in molecular biology

Huber W, Carey VJ, Long L, Falcon S, Gentleman R

BMC bioinformatics, 2007

doi:10.1186/1471-2105-8-s6-s8.

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

Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K

BMC biology, 2007

doi:10.1186/1741-7007-5-25.

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

Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W

BMC bioinformatics, 2007

doi:10.1186/1471-2105-8-221.

Transcript mapping with high-density oligonucleotide tiling arrays

Huber W, Toedling J, Steinmetz LM

Bioinformatics (Oxford, England), 2006

doi:10.1093/bioinformatics/btl289.

A high-resolution map of transcription in the yeast genome

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

Proceedings of the National Academy of Sciences of the United States of America, 2006

doi:10.1073/pnas.0601091103.

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

doi:10.1038/440024a.

Visualizing genomic data. Technical Report 10.

Gentleman R, Hahne F, Huber W

2006

doi:.

Several articles in the R News special issue on Bioinformatics

Huber W

2006

doi:.

Analysis of cell-based RNAi screens

Boutros M, Brás LP, Huber W

Genome biology, 2006

doi:10.1186/gb-2006-7-7-r66.

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 biology, 2006

doi:10.1186/gb-2006-7-8-r77.

Reproducible statistical analysis in microarray profiling studies

Mansmann U, Ruschhaupt M, Huber W

Methods of information in medicine, 2006

doi:10.1267/meth06020139.

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 KH, Huber W, Pepperkok R, Poustka A, Wiemann S

Nucleic acids research, 2006

doi:10.1093/nar/gkj139.

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

doi:10.1002/pmic.200401324.

Differential Expression with the Bioconductor Project

Heydebreck A, Huber W, Gentleman R

2005

doi:10.1002/047001153X.g405208.

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 JC, Hahne F, Moosmayer P, Ruschhaupt M, Guilleaume B, Wellenreuther R, Pepperkok R, Sültmann H, Poustka A, Wiemann S

Cancer research, 2005

doi:10.1158/0008-5472.CAN-05-0642.

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 (Oxford, England), 2005

doi:10.1093/bioinformatics/bti525.

arrayMagic: two-colour cDNA microarray quality control and preprocessing

Buness A, Huber W, Steiner K, Sültmann H, Poustka A

Bioinformatics (Oxford, England), 2005

doi:10.1093/bioinformatics/bti052.

Large error models for microarray intensities

Huber W, von Heydebreck A, Vingron M

2005

doi:10.1002/047001153X.g405413.

Bioinformatics and Computational Biology Solutions Using R and Bioconductor

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

2005

doi:10.1007/0-387-29362-0.

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

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

European journal of cell biology, 2005

doi:.

On the synthesis of microarray experiments

Gentleman R, Ruschlaupt M, Huber W

Journal of the French Statistical Society, 2005

doi:.

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

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

Clinical cancer research : an official journal of the American Association for Cancer Research, 2005

doi:.

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, Sültmann H, Poustka A

Genome research, 2004

doi:10.1101/gr.2576704.

Analysis of microarray gene expression data

Huber W, von Heydebreck A, Vingron M

2004

doi:10.1002/0470022620.bbc08.

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

Huber W, Gentleman R

Bioinformatics (Oxford, England), 2004

doi:10.1093/bioinformatics/bth133.

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, Sültmann H

BMC genomics, 2004

doi:10.1186/1471-2164-5-29.

Bioconductor: open software development for computational biology and bioinformatics

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

Genome biology, 2004

doi:10.1186/gb-2004-5-10-r80.

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

Ruschhaupt M, Huber W, Poustka A, Mansmann U

Statistical applications in genetics and molecular biology, 2004

doi:10.2202/1544-6115.1078.

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 RH, Jakse G, Füzesi L

Cancer research, 2003

doi:.

Prognostic factors influencing surgical management and outcome of gastrointestinal stromal tumours

Langer C, Gunawan B, Schüler P, Huber W, Füzesi L, Becker H

The British journal of surgery, 2003

doi:10.1002/bjs.4046.

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

Apic G, Huber W, Teichmann SA

Journal of structural and functional genomics, 2003

doi:10.1023/a:1026113408773.

Mathematical tree models for cytogenetic development in solid tumors

Heydebreck AV, Gunawan B, Huber W, Vingron M, Füzesi L

Verhandlungen der Deutschen Gesellschaft fur Pathologie, 2003

doi:.

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

Huber W, von Heydebreck A, Sueltmann H, Poustka A, Vingron M

Statistical applications in genetics and molecular biology, 2003

doi:10.2202/1544-6115.1008.

Transcription profiling of renal cell carcinoma

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

Verhandlungen der Deutschen Gesellschaft fur Pathologie, 2002

doi:.

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

Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M

Bioinformatics (Oxford, England), 2002

doi:.

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

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

Genome research, 2001

doi:10.1101/gr.184501.

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 RH, Jakse G, Füzesi L

Cancer research, 2001

doi:.

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

Pitman MC, Huber WK, Horn H, Krämer A, Rice JE, Swope WC

Journal of computer-aided molecular design, 2001

doi:10.1023/a:1011921423829.

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 : an official journal of the American Association for Cancer Research, 2001

doi:.

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

von Heydebreck A, Huber W, Poustka A, Vingron M

Bioinformatics (Oxford, England), 2001

doi:.

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

Breuer HP, Huber W, Petruccione F

Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, 2000

doi:10.1103/physreve.61.4883.

Dynamics of strongly driven open quantum systems

Huber W

1998

doi:.

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

Breuer HP, Huber W, Petruccione F

Computer physics communications, 1997

doi:.

Vestibular-neck interaction and transformation of sensory coordinates

Mergner T, Huber W, Becker W

Journal of vestibular research : equilibrium & orientation, 1997

doi:.

Fast Monte Carlo algorithm for nonequilibrium systems

Breuer HP, Huber W, Petruccione F

Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, 1996

doi:10.1103/physreve.53.4232.

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

Huber W, Kopitzki K, Timmer J, Warnke PC

Biomedical Engineering / Biomedizinische Technik, 1996

doi:10.1515/bmte.1996.41.s1.160.

The macroscopic limit in a stochastic reaction-diffusion process

Breuer HP, Huber W, Petruccione F

Europhysics letters, 1995

doi:.

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

Fischer B, Gezeck S, Huber W

Biological cybernetics, 1995

doi:10.1007/s004220050123.

Fluctuation effects on wave propagation in a reaction-diffusion process

Breuer HP, Huber W, Petruccione F

Physica D. Nonlinear phenomena, 1994

doi:10.1016/0167-2789(94)90161-9.

The description of reaction diffusion processes by master equations

Huber W

1994

doi:.