Edit

Huber Group

Multi-omics and statistical computing

Publications

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

34189564. doi:10.1182/blood.2020009741.

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

33057217. doi:10.1038/s41586-020-2766-y.

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

32636365. doi:10.1038/s41467-020-16785-6.

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

31792435. 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

31659326. doi:10.1038/s41592-019-0614-5.

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

31243369. doi:10.1038/s41586-019-1338-5.

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

31000522. doi:10.1158/0008-5472.CAN-18-3438.

Authoring Bioconductor workflows with BiocWorkflowTools.

Smith ML, Oleś AK, Huber W

2018

doi:10.12688/f1000research.14399.1.

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

28804127. doi:10.1038/leu.2017.252.

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

29227286. doi:10.1172/JCI93801.

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

27560109. doi:10.1038/leu.2016.230.

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

26871632. doi:10.1016/j.cell.2015.12.033.

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

25633503. doi:10.1038/nmeth.3252.

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

25519137. doi:10.1038/nature14096.

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.

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.

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

21508958. doi:10.1038/nature09944.

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

21537400. doi:.

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

20299548. doi:10.1126/science.1183621.

Bioconductor Case Studies

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

2008

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

Low-level analysis of microarray experiments

Huber W, von Heydebreck A, Vingron M

2007

doi:10.1002/9783527619368.ch25.

Several articles in the R News special issue on Bioinformatics

Huber W

2006

doi:.

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

16381901. doi:10.1093/nar/gkj139.

Differential Expression with the Bioconductor Project

Heydebreck A, Huber W, Gentleman R

2005

doi:10.1002/047001153X.g405208.

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:.

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.

On the synthesis of microarray experiments

Gentleman R, Ruschlaupt M, Huber W

Journal of the French Statistical Society 2005

doi:.

Large error models for microarray intensities

Huber W, von Heydebreck A, Vingron M

2005

doi:10.1002/047001153X.g405413.

Analysis of microarray gene expression data

Huber W, von Heydebreck A, Vingron M

2004

doi:10.1002/0470022620.bbc08.

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:.

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:.

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:.

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:.


Edit