Last revision: 03 Apr 2017

[1]
Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nikolaos Ignatiadis, Bernd Klaus, Judith Zaugg, and Wolfgang Huber. Nature Methods, 13(7):577-580, 2016.

[2]
Orchestrating high-throughput genomic analysis with Bioconductor. Wolfgang Huber , Vincent J. Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S. Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D. Hansen, Rafael A. Irizarry, Michael Lawrence, Michael I. Love, James MacDonald, Valerie Obenchain, Andrzej K. Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K. Smyth, Dan Tenenbaum, Levi Waldron, and Martin Morgan. Nature Methods, 12:115-121, 2015. (169 citations1).

[3]
A map of directional genetic interactions in a metazoan cell. Bernd Fischer*, Thomas Sandmann*, Thomas Horn*, Maximilian Billmann*, Varun Chaudhary, Wolfgang Huber , and Michael Boutros . eLife, 4, 2015. (14 citations)

[4]
RNA-Seq workflow: gene-level exploratory analysis and differential expression. Michael I. Love, Simon Anders, Vladislav Kim, and Wolfgang Huber. F1000Research, 4(1070), 2015. (12 citations)

[5]
TimerQuant: A modelling approach to tandem fluorescent timer design and data interpretation for measuring protein turnover in embryos. Joseph D. Barry, Erika Donà, Darren Gilmour, and Wolfgang Huber. Development, 143(1):174-179, 2016.

[6]
Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells. Philip Brennecke*, Alejandro Reyes*, Sheena Pinto*, Kristin Rattay*, Michelle Nguyen, Rita Küchler, Wolfgang Huber , Bruno Kyewski , and Lars M. Steinmetz . Nature Immunology, 16:933-941, 2015. (15 citations)

[7]
Covariate-powered weighted multiple testing with false discovery rate control. Nikolaos Ignatiadis and Wolfgang Huber. arχiv, 2017.

[8]
Human haematopoietic stem cell lineage commitment is a continuous process. Lars Velten, Simon F. Haas, Simon Raffel, Sandra Blaszkiewicz, Saiful Islam, Bianca P. Hennig, Christoph Hirche, Christoph Lutz, Eike C. Buss, Daniel Nowak, Tobias Boch, Wolf-Karsten Hofmann, Anthony D. Ho, Wolfgang Huber, Andreas Trumpp, Marieke A. G. Essers, and Lars M. Steinmetz. Nature Cell Biology, 19(4):271-81, 2017.

[9]
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. Cristina Martínez, Bruno K Rodiño-Janeiro, Beatriz Lobo, Megan L Stanifer, Bernd Klaus, Martin Granzow, Ana M González-Castro, Eloisa Salvo-Romero, Carmen Alonso-Cotoner, Marc Pigrau, Ralph Roeth, Gudrun Rappold, Wolfgang Huber, Rosa González-Silos, Justo Lorenzo, Inés de Torres, Fernando Azpiroz, Steeve Boulant, María Vicario, Beate Niesler, and Javier Santos. Gut, 2017.

[10]
Comprehensive identification of RNA-binding proteins by RNA interactome capture. Alfredo Castello, Rastislav Horos, Claudia Strein, Bernd Fischer, Katrin Eichelbaum, Lars M. Steinmetz, Jeroen Krijgsveld, and Matthias W. Hentze. In Erik Dassi, editor, Post-Transcriptional Gene Regulation, pages 131-139. Springer New York, New York, NY, 2016.

[11]
Comprehensive identification of RNA-binding domains in human cells. Alfredo Castello, Bernd Fischer, Christian K. Frese, Rastislav Horos, Anne-Marie Alleaume, Sophia Foehr, Tomaz Curk, Jeroen Krijgsveld, and Matthias W. Hentze. Molecular Cell, 63(4):696-710, 2016.

[12]
Two independent modes of chromosome organization are revealed by cohesin removal. Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian Haering, Leonid Mirny, and François Spitz. bioRχiv, 2016.

[13]
BRAF inhibition in hairy cell leukemia with low-dose vemurafenib. Sascha Dietrich, Andreas Pircher, Volker Endris, Frédéric Peyrade, Clemens-Martin Wendtner, George A. Follows, Jennifer Hüllein, Alexander Jethwa, Elena Ellert, Tatjana Walther, Xiyang Liu, Martin J. S. Dyer, Thomas Elter, Tilman Brummer, Robert Zeiser, Michael Hermann, Michael Herold, Wilko Weichert, Claire Dearden, Torsten Haferlach, Martina Seiffert, Michael Hallek, Christof von Kalle, Anthony D. Ho, Anita Gaehler, Mindaugas Andrulis, Michael Steurer, and Thorsten Zenz. Blood, 127(23):2847-2855, 2016. (10 citations)

[14]
Functional outcomes and quality of life after radical prostatectomy only versus a combination of prostatectomy with radiation and hormonal therapy. Meike Adam, Pierre Tennstedt, Dominik Lanwehr, Derya Tilki, Thomas Steuber, Burkhard Beyer, Imke Thederan, Hans Heinzer, Alexander Haese, Georg Salomon, Lars Budäus, Uwe Michl, Dirk Pehrke, Pär Stattin, Jürgen Bernard, Bernd Klaus, Raisa S. Pompe, Cordula Peterse, Hartwig Huland, Markus Graefen, Rudolf Schwarz, Wolfgang Huber, Stacy Loeb, and Thorsten Schlomm. European Urology, 2016.

[15]
The Shh topological domain facilitates the action of remote enhancers by reducing the effects of genomic distances. Orsolya Symmons, Leslie Pan, Silvia Remeseiro, Tugce Aktas, Felix Klein, Wolfgang Huber, and François Spitz. Developmental Cell, 39(5):529–543, 2016.

[16]
A clash of cultures in discussions of the P value. Wolfgang Huber. Nature Methods, 13(8):607, 2016.

[17]
Exon junction complexes show a distributional bias toward alternatively spliced mRNAs and against mRNAs coding for ribosomal proteins. Christian Hauer, Jana Sieber, Thomas Schwarzl, Ina Hollerer, Tomaz Curk, Anne-Marie Alleaume, Matthias W. Hentze , and Andreas E. Kulozik . Cell Reports, 16(6):1588-1603, 2016.

[18]
Statistical relevance-relevant statistics, part II: presenting experimental data. Bernd Klaus. The EMBO Journal, 35(16):1726-1729, 2016.

[19]
The cardiomyocyte RNA-binding proteome: Links to intermediary metabolism and heart disease. Yalin Liao, Alfredo Castello, Bernd Fischer, Stefan Leicht, Sophia Föehr, Christian K. Frese, Chikako Ragan, Sebastian Kurscheid, Eloisa Pagler, Hao Yang, Jeroen Krijgsveld, Matthias W. Hentze, and Thomas Preiss. Cell Reports, 16(5):1456-1469, 2016.

[20]
DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies. Christophe D. Chabbert, Lars M. Steinmetz, and Bernd Klaus. PeerJ, 4:e1981, 2016.

[21]
A genetic interaction map of cell cycle regulators. Maximilian Billmann*, Thomas Horn*, Bernd Fischer, Thomas Sandmann, Wolfgang Huber, and Michael Boutros. Molecular Biology of the Cell, 2016.

[22]
Myc depletion induces a pluripotent dormant state mimicking diapause. Roberta Scognamiglio, Nina Cabezas-Wallscheid, Marc Christian Thier, Sandro Altamura, Alejandro Reyes, Áine M. Prendergast, Daniel Baumgärtner, Larissa S. Carnevalli, Ann Atzberger, Simon Haas, Lisa von Paleske, Thorsten Boroviak, Philipp Wörsdörfer, Marieke A.G. Essers, Ulrich Kloz, Robert N. Eisenman, Frank Edenhofer, Paul Bertone, Wolfgang Huber, Franciscus van der Hoeven, Austin Smith, and Andreas Trumpp. Cell, 164(4):668-680, 2016. (13 citations)

[23]
CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma. Elisa M Noll, Christian Eisen, Albrecht Stenzinger, Elisa Espinet, Alexander Muckenhuber, Corinna Klein, Vanessa Vogel, Bernd Klaus, Wiebke Nadler, Christoph Rösli, Christian Lutz, Michael Kulke, Jan Engelhardt, Franziska M Zickgraf, Octavio Espinosa, Matthias Schlesner, Xiaoqi Jiang, Annette Kopp-Schneider, Peter Neuhaus, Marcus Bahra, Bruno V Sinn, Roland Eils, Nathalia A Giese, Thilo Hackert, Oliver Strobel, Jens Werner, Markus W Büchler, Wilko Weichert, Andreas Trumpp, and Martin R Sprick. Nature Medicine, 22:278-287, 2016.

[24]
Nuclear architecture organized by Rif1 underpins the replication-timing program. Rossana Foti, Stefano Gnan, Daniela Cornacchia, Vishnu Dileep, Aydan Bulut-Karslioglu, Sarah Diehl, Andreas Buness, Felix A. Klein, Wolfgang Huber, Ewan Johnstone, Remco Loos, Paul Bertone, David M. Gilbert, Thomas Manke, Thomas Jenuwein, and Sara C.B. Buonomo. Molecular Cell, 61(2):260-273, 2016. (12 citations)

[25]
Landscape and dynamics of transcription initiation in the malaria parasite Plasmodium falciparum. Sophie H. Adjalley, Christophe D. Chabbert, Bernd Klaus, Vicent Pelechano, and Lars M. Steinmetz. Cell Reports, 14(10):2463-2475, 2016.

[26]
An optogenetic method to modulate cell contractility during tissue morphogenesis. Giorgia Guglielmi, Joseph D. Barry, Wolfgang Huber, and Stefano De Renzis. Developmental Cell, 35(5):646-660, 2015.

[27]
BRAF inhibitor therapy in HCL. Sascha Dietrich and Thorsten Zenz. Best Practice & Research Clinical Haematology, 28(4):246-252, 2015.

[28]
Fundamental physical cellular constraints drive self-organization of tissues. Daniel Sánchez-Gutiérrez, Melda Tozluoglu, Joseph D. Barry, Alberto Pascual, Yanlan Mao, and Luis M Escudero. The EMBO Journal, 35(1):77-88, 2015.

[29]
A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells. Marco Breinig*, Felix A. Klein*, Wolfgang Huber , and Michael Boutros . Molecular Systems Biology, 11(12), 2015.

[30]
The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. Benedikt M. Beckmann, Rastislav Horos, Bernd Fischer, Alfredo Castello, Katrin Eichelbaum, Anne-Marie Alleaume, Thomas Schwarzl, Tomaz Curk, Sophia Foehr, Wolfgang Huber, Jeroen Krijgsveld, and Matthias W. Hentze. Nature Communications, 6(10127), 2015. (27 citations)

[31]
Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry. Holger Franken*, Toby Mathieson*, Dorothee Childs*, Gavain M.A. Sweetman*, Thilo Werner, Ina Tögel, Carola Doce, Stephan Gade, Marcus Bantscheff, Gerard Drewes, Friedrich B.M. Reinhard , Wolfgang Huber , and Mikhail M. Savitski . Nature Protocols, 10(10):1567-1593, 2015. (16 citations)

[32]
Thermal proteome profiling monitors ligand interactions with cellular membrane proteins. Friedrich B.M. Reinhard, Dirk Eberhard, Thilo Werner, Holger Franken, Dorothee Childs, Carola Doce, Maria Fälth Savitski, Wolfgang Huber, Marcus Bantscheff, Mikhail M. Savitski, and Gerard Drewes. Nature Methods, 2015. (14 citations)

[33]
FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation. Johannes Popow, Anne-Marie Alleaume, Tomaz Curk, Thomas Schwarzl, Sven Sauer, and Matthias W. Hentze. RNA, 21(11):1873-1884, 2015. (11 citations)

[34]
Statistical relevance-relevant statistics, part I. Bernd Klaus. The EMBO Journal, 34(22):2727-2730, 2015.

[35]
Mutational landscape and complexity in CLL. Thorsten Zenz and Wolfgang Huber. Blood, 126(18):2078-2079, 2015.

[36]
Expression atlas update-an integrated database of gene and protein expression in humans, animals and plants. Robert Petryszak, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Simon Jupp, Satu Koskinen, Oliver Mannion, Laura Huerta, Karine Megy, Catherine Snow, Eleanor Williams, Mitra Barzine, Emma Hastings, Hendrik Weisser, James Wright, Pankaj Jaiswal, Wolfgang Huber, Jyoti Choudhary, Helen E. Parkinson, and Alvis Brazma. Nucleic Acids Research, 44(1):D746-D752, 2016. (27 citations)

[37]
Genetic control of chromatin states in humans involves local and distal chromosomal interactions. Grubert Fabian, Judith B. Zaugg, Maya Kasowski, Oana Ursu, Damek V. Spacek, Alicia R. Martin, Peyton Greenside, Rohith Srivas, Doug H. Phanstiel, Aleksandra Pekowska, Nastaran Heidari, Ghia Euskirchen, Wolfgang Huber, Jonathan K. Pritchard, Carlos D. Bustamante, Lars M. Steinmetz, Anshul Kundaje, and Michael Snyder. Cell, 162(5):1051-1065, 2015. (29 citations)

[38]
A novel inflammatory pathway mediating rapid hepcidin-independent hypoferremia. Claudia Guida, Sandro Altamura, Felix A. Klein, Bruno Galy, Michael Boutros, Artur J. Ulmer, Matthias W. Hentze, and Martina U. Muckenthaler. Blood, 125(14):2265-2275, 2015. (27 citations)

[39]
Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP. Christian Hauer, Tomaz Curk, Simon Anders, Thomas Schwarzl, Anne-Marie Alleaume, Jana Sieber, Ina Hollerer, Madhuri Bhuvanagiri, Wolfgang Huber, Matthias W. Hentze, and Andreas E. Kulozik. Nature Communications, 6(7921), 2015.

[40]
Recurrent CDKN1B (p27) mutations in hairy cell leukemia. Sascha Dietrich, Jennifer Hüllein, Stanley Chun-Wei Lee, Barbara Hutter, David Gonzalez, Sandrine Jayne, Martin J. S. Dyer, Małgorzata Oleś, Monica Else, Xiyang Liu, Mikołaj Słabicki, Bian Wu, Xavier Troussard, Jan Dürig, Mindaugas Andrulis, Claire Dearden, Christof von Kalle, Martin Granzow, Anna Jauch, Stefan Fröhling, Wolfgang Huber, Manja Meggendorfer, Torsten Haferlach, Anthony D. Ho, Daniela Richter, Benedikt Brors, Hanno Glimm, Estella Matutes, Omar Abdel Wahab, and Thorsten Zenz. Blood, 126(8):1005-1008, 2015. (20 citations)

[41]
Single-cell polyadenylation site mapping reveals 3' isoform choice variability. Lars Velten, Simon Anders, Aleksandra Pekowska, Aino I Järvelin, Wolfgang Huber, Vicent Pelechano, and Lars M. Steinmetz. Molecular Systems Biology, 11(6), 2015.

[42]
An open data ecosystem for cell migration research. Paola Masuzzo, Lennart Martens, Christophe Ampe, Kurt I. Anderson, Joseph Barry, Olivier De Wever, Olivier Debeir, Christine Decaestecker, Helmut Dolznig, Peter Friedl, Cedric Gaggioli, Benjamin Geiger, Ilya G. Goldberg, Elias Horn, Rick Horwitz, Zvi Kam, Sylvia E. Le Dévédec, Danijela Matic Vignjevic, Josh Moore, Jean-Christophe Olivo-Marin, Erik Sahai, Susanna A. Sansone, Victoria Sanz-Moreno, Staffan Strömblad, Jason Swedlow, Johannes Textor, Marleen Van Troys, and Roman Zantl. Trends in Cell Biology, 25(2):55-58, 2015.

[43]
A discrete transition zone organizes the topological and regulatory autonomy of the adjacent Tfap2c and Bmp7 genes. Taro Tsujimura, Felix A. Klein, Katja Langenfeld, Juliane Glaser, Wolfgang Huber, and François Spitz. PLoS Genetics, 11(1):e1004897, 2015. (17 citations)

[44]
A high-throughput ChIP-Seq for large-scale chromatin studies. Christophe D Chabbert, Sophie H Adjalley, Bernd Klaus, Emilie S Fritsch, Ishaan Gupta, Vicent Pelechano, and Lars M. Steinmetz. Molecular Systems Biology, 11(1), 2015.

[45]
SomaticSignatures: inferring mutational signatures from single-nucleotide variants. Julian S. Gehring, Bernd Fischer, Michael Lawrence, and Wolfgang Huber. Bioinformatics, 31(22):3673-3675, 2015. (10 citations)

[46]
FourCSeq: Analysis of 4C sequencing data. Felix A. Klein, Tibor Pakozdi, Simon Anders, Yad Ghavi-Helm, Eileen E. M. Furlong, and Wolfgang Huber. Bioinformatics, 31(19):3085-3091, 2015.

[47]
h5vc: scalable nucleotide tallies with HDF5. Paul Theodor Pyl, Julian Gehring, Bernd Fischer, and Wolfgang Huber. Bioinformatics, 30(10):1464-1466, 2014.

[48]
Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Michael I. Love, Wolfgang Huber, and Simon Anders. Genome Biology, 15(12):550, 2014. (324 citations).

[49]
Protein quality control at the inner nuclear membrane. Anton Khmelinskii, Marina Pantazopoulou, Bernd Fischer, Deike J. Omnus, Gaëlle Le Dez, Audrey Brossard, Alexander Gunnarsson, Joseph D. Barry, Matthias Meurer, Daniel Kirrmaier, Charles Boone, Wolfgang Huber, Gwenaël Rabut, Per O. Ljungdahl, and Michael Knop. Nature, 516(7531):410-413, 2014. (28 citations)

[50]
HTSeq - a Python framework to work with high-throughput sequencing data. Simon Anders, Paul Theodor Pyl, and Wolfgang Huber. Bioinformatics, 31(2):166-169, 2015. (1001 citations).

[51]
Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages. Yusuke Ohnishi, Wolfgang Huber, Akiko Tsumura, Minjung Kang, Panagiotis Xenopoulos, Kazuki Kurimoto, Andrzej K. Oleś, Marcos J. Araúzo-Bravo, Mitinori Saitou, Anna-Katerina Hadjantonakis, and Takashi Hiiragi. Nature Cell Biology, 16(1):27-37, 2014. (73 citations).

[52]
Measuring genetic interactions in human cells by RNAi and imaging. Christina Laufer, Bernd Fischer, Wolfgang Huber, and Michael Boutros. Nature Protocols, 9(10):2341-2353, 2014. (10 citations)

[53]
Transcriptome-wide profiling and posttranscriptional analysis of hematopoietic stem/progenitor cell differentiation toward myeloid commitment. Daniel Klimmeck*, Nina Cabezas-Wallscheid*, Alejandro Reyes*, Lisa von Paleske, Simon Renders, Jenny Hansson, Jeroen Krijgsveld, Wolfgang Huber , and Andreas Trumpp . Stem Cell Reports, 3(5):858-875, 2014.

[54]
Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis. Nina Cabezas-Wallscheid*, Daniel Klimmeck*, Jenny Hansson*, Daniel B Lipka*, Alejandro Reyes*, Qi Wang, Dieter Weichenhan, Amelie Lier, Lisa von Paleske, Simon Renders, Peer Wünsche, Petra Zeisberger, David Brocks, Lei Gu, Carl Herrmann, Simon Haas, Marieke A.G. Essers, Benedikt Brors, Roland Eils, Wolfgang Huber, Michael D Milsom, Christoph Plass, Jeroen Krijgsveld, and Andreas Trumpp. Cell Stem Cell, 15(4):507-522, 2014. (60 citations).

[55]
A genome-wide map of mitochondrial DNA recombination in yeast. Emilie S. Fritsch, Christophe D. Chabbert, Bernd Klaus, and Lars M. Steinmetz. Genetics, 198(2):755-771, 2014. (12 citations)

[56]
Enhancer loops appear stable during development and are associated with paused polymerase. Yad Ghavi-Helm, Felix A. Klein*, Tibor Pakozdi*, Lucia Ciglar, Daan Noordermeer, Wolfgang Huber, and Eileen E. M. Furlong. Nature, 512(7512):96-100, 2014. (94 citations).

[57]
Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. Ishaan Gupta, Sandra Clauder-Münster, Bernd Klaus, Aino I Järvelin, Raeka S. Aiyar, Vladimir Benes, Stefan Wilkening, Wolfgang Huber, Vicent Pelechano, and Lars M. Steinmetz. Molecular Systems Biology, 10(2), 2014. (23 citations)

[58]
Expression Atlas update-a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Robert Petryszak, Tony Burdett, Benedetto Fiorelli, Nuno A. Fonseca, Mar Gonzalez-Porta, Emma Hastings, Wolfgang Huber, Simon Jupp, Maria Keays, Nataliya Kryvych, Julie McMurry, John C. Marioni, James Malone, Karine Megy, Gabriella Rustici, Amy Y. Tang, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E. Parkinson, and Alvis Brazma. Nucleic Acids Research, 42(1):D926-932, 2014. (101 citations).

[59]
Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization. Aleksandra Pekowska, Bernd Klaus, Felix Alexander Klein, Simon Anders, Małgorzata Oleś, Lars M. Steinmetz, Paul Bertone, and Wolfgang Huber. bioRχiv, 2014.

[60]
Mutated SF3B1 is associated with transcript isoform changes of the genes UQCC and RPL31 both in clls and uveal melanomas. Alejandro Reyes, Carolin Blume, Vicent Pelechano, Petra Jakob, Lars M. Steinmetz, Thorsten Zenz, and Wolfgang Huber. bioRχiv, 2014.

[61]
An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae. Stefan Wilkening, Gen Lin, Emilie S. Fritsch, Manu M. Tekkedil, Simon Anders, Raquel Kuehn, Michelle Nguyen, Raeka S. Aiyar, Michael Proctor, Nikita A. Sakhanenko, David J. Galas, Julien Gagneur, Adam Deutschbauer, and Lars M. Steinmetz. Genetics, 196(3):853-865, 2014. (17 citations)

[62]
Accounting for technical noise in single-cell RNA-seq experiments. Philip Brennecke*, Simon Anders*, Jong Kyoung Kim*, Aleksandra A. Kolodziejczyk, Xiuwei Zhang, Valentina Proserpio, Bianka Baying, Vladimir Benes, Sarah A. Teichmann, John C. Marioni, and Marcus G. Heisler. Nature Methods, 10(11):1093-1095, 2013. (135 citations).

[63]
Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay. Gregoire Pau, Thomas Walter, Beate Neumann, Jean-Karim Heriché, Jan Ellenberg, and Wolfgang Huber. BMC Bioinformatics, 14(1):308, 2013.

[64]
Directional tissue migration through a self-generated chemokine gradient. Erika Donà, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, and Darren Gilmour. Nature, 503(7475):285-289, 2013. (94 citations).

[65]
High-content siRNA screen reveals global ENaC regulators and potential cystic fibrosis therapy targets. Joana Almaça*, Diana Faria*, Marisa Sousa, Inna Uliyakina, Christian Conrad, Lalida Sirianant, Luka A. Clarke, José Paulo Martins, Miguel Santos, Jean-Karim Heriché, Wolfgang Huber, Rainer Schreiber, Rainer Pepperkok, Karl Kunzelmann, and Margarida D. Amaral. Cell, 154(6):1390-1400, 2013. (20 citations)

[66]
Drift and conservation of differential exon usage across tissues in primate species. Alejandro Reyes*, Simon Anders*, Robert J. Weatheritt, Toby J. Gibson, Lars M. Steinmetz, and Wolfgang Huber. Proc. Natl. Acad. Sci. U.S.A., 110(38):15377-15382, 2013. (16 citations)

[67]
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Simon Anders, Davis J McCarthy, Yunshun Chen, Michal Okoniewski, Gordon K Smyth, Wolfgang Huber, and Mark D Robinson. Nature Protocols, 8(9):1765-1786, 2013. (223 citations).

[68]
Software for computing and annotating genomic ranges. Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan, and Vincent J. Carey. PLoS Computational Biology, 9(8):e1003118, 2013. (224 citations).

[69]
Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Christina Laufer*, Bernd Fischer*, Maximilian Billmann, Wolfgang Huber , and Michael Boutros . Nature Methods, 10:427-431, 2013. (46 citations)

[70]
CellH5: a format for data exchange in high-content screening. Christoph Sommer, Michael Held, Bernd Fischer, Wolfgang Huber, and Daniel W. Gerlich. Bioinformatics, 29:1580-1582, 2013.

[71]
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. Danni Yu, Wolfgang Huber, and Olga Vitek. Bioinformatics, 29:1275-1282, 2013. (17 citations)

[72]
The Genomic and Transcriptomic Landscape of a HeLa Cell Line. Jonathan Landry*, Paul Theodor Pyl*, Tobias Rausch, Thomas Zichner, Manu M. Tekkedil, Adrian M. Stütz, Anna Jauch, Raeka S. Aiyar, Gregoire Pau, Nicolas Delhomme, Julien Gagneur, Jan O. Korbel, Wolfgang Huber , and Lars M. Steinmetz . G3 (Bethesda), 3(8), 2013. (111 citations).

[73]
Control of tissue morphology by Fasciclin III-mediated intercellular adhesion. Richard E. Wells*, Joseph D. Barry*, Simon Cuhlmann, Paul Evans, Wolfgang Huber, David Strutt, and Martin P. Zeidler. Development, 140:3858-3868, 2013.

[74]
Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Kathi Zarnack, Julian König, Mojca Tajnik, Inigo Martincorena, Sebastian Eustermann, Isabelle Stévant, Alejandro Reyes, Simon Anders, Nicholas M. Luscombe, and Jernej Ule. Cell, 152(3):453-466, 2013. (98 citations).

[75]
An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Stefan Wilkening, Vicent Pelechano, Aino I. Järvelin, Manu M. Tekkedil, Simon Anders, Vladimir Benes, and Lars M. Steinmetz. Nucleic Acids Research, 41(5):e65, 2013. (37 citations)

[76]
Properties of isotope patterns and their utility for peptide identification in large-scale proteomic experiments. Satoshi Okawa, Bernd Fischer, and Jeroen Krijgsveld. Rapid Communications in Mass Spectrometry, 27(9):1067-1075, 2013.

[77]
RNA-binding proteins in Mendelian disease. Alfredo Castello, Bernd Fischer, Matthias W Hentze, and Thomas Preiss. Trends in Genetics, 29:318-327, 2013. (69 citations).

[78]
System-wide identification of RNA-binding proteins by interactome capture. Alfredo Castello, Rastislav Horos, Claudia Strein, Bernd Fischer, Katrin Eichelbaum, Lars M. Steinmetz, Jeroen Krijgsveld, and Matthias W Hentze. Nature Protocols, 8(3):491-500, 2013. (46 citations)

[79]
Biggest challenges in bioinformatics. Jonathan C Fuller, Pierre Khoueiry, Holger Dinkel, Kristoffer Forslund, Alexandros Stamatakis, Joseph Barry, Aidan Budd, Theodoros G Soldatos, Katja Linssen, and Abdul Mateen Rajput. EMBO reports, 14(4):302-304, 2013.

[80]
Detecting differential usage of exons from RNA-Seq data. Simon Anders*, Alejandro Reyes*, and Wolfgang Huber. Genome Research, 22:2008-2017, 2012. (256 citations).

[81]
Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Anton Khmelinskii, Philipp J. Keller, Anna Bartosik, Matthias Meurer, Joseph D. Barry, Balca R. Mardin, Andreas Kaufmann, Susanne Trautmann, Malte Wachsmuth, Gislene Pereira, Wolfgang Huber, Elmar Schiebel, and Michael Knop. Nature Biotechnology, 30:708-714, 2012. (62 citations).

[82]
Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Jenny Hansson, Mahmoud Reza Rafiee, Sonja Reiland, Jose M. Polo, Julian Gehring, Satoshi Okawa, Wolfgang Huber, Konrad Hochedlinger, and Jeroen Krijgsveld. Cell Reports, 2(6):1579-1592, 2012. (88 citations).

[83]
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Alfredo Castello*, Bernd Fischer*, Katrin Eichelbaum, Rastislav Horos, Benedikt M. Beckmann, Claudia Strein, Norman E. Davey, David T. Humphreys, Thomas Preiss, Lars M. Steinmetz, Jeroen Krijgsveld, and Matthias W. Hentze. Cell, 149:1393-1406, 2012. (469 citations).

[84]
A cross-platform toolkit for mass spectrometry and proteomics. Matthew C Chambers, Brendan Maclean, Robert Burke, Dario Amodei, Daniel L Ruderman, Steffen Neumann, Laurent Gatto, Bernd Fischer, Brian Pratt, Jarrett Egertson, Katherine Hoff, Darren Kessner, Natalie Tasman, Nicholas Shulman, Barbara Frewen, Tahmina A Baker, Mi-Youn Brusniak, Christopher Paulse, David Creasy, Lisa Flashner, Kian Kani, Chris Moulding, Sean L Seymour, Lydia M Nuwaysir, Brent Lefebvre, Frank Kuhlmann, Joe Roark, Paape Rainer, Suckau Detlev, Tina Hemenway, Andreas Huhmer, James Langridge, Brian Connolly, Trey Chadick, Krisztina Holly, Josh Eckels, Eric W Deutsch, Robert L Moritz, Jonathan E Katz, David B Agus, Michael MacCoss, David L Tabb, and Parag Mallick. Nature Biotechnology, 30(10):918-920, 2012. (270 citations).

[85]
Personal receptor repertoires: olfaction as a model. Tsviya Olender, Sebastian M. Waszak, Maya Viavant, Miriam Khen, Edna Ben-Asher, Alejandro Reyes, Noam Nativ, Charles J. Wysocki, and Dongliang Geand Doron Lancet. BMC Genomics, 13:414, 2012. (30 citations)

[86]
Mapping of signalling networks through synthetic genetic interaction analysis by RNAi. Thomas Horn*, Thomas Sandmann*, Bernd Fischer*, Elin Axelsson, Wolfgang Huber, and Michael Boutros. Nature Methods, 8(4), 2011. (89 citations).

[87]
Antisense expression increases gene expression variability and locus interdependency. Zhenyu Xu*, Wu Wei*, Julien Gagneur*, Sandra Clauder-Münster, Miłosz Smolik, Wolfgang Huber, and Lars M. Steinmetz. Molecular Systems Biology, 7, 2011. (76 citations).

[88]
Relating CNVs to transcriptome data at fine-resolution: assessment of the effect of variant size, type, and overlap with functional regions. Andreas Schlattl, Simon Anders, Sebastian M. Waszak, Wolfgang Huber, and Jan O. Korbel. Genome Research, 21:2004-2013, 2011. (52 citations).

[89]
Genome-wide survey of post-meiotic segregation during yeast recombination. Eugenio Mancera, Richard Bourgon, Wolfgang Huber, and Lars M. Steinmetz. Genome Biology, 12:R36, 2011. (11 citations)

[90]
cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression. E. Benito, L. M. Valor, M. Jimenez-Minchan, W. Huber, and A. Barco. Journal of Neuroscience, 31:18237-18250, 2011. (38 citations)

[91]
Contributions of the EMERALD project to assessing and improving microarray data quality. Vidar Beisvåg, Audrey Kauffmann, James Malone, Carole Foy, Marc Salit, Heinz Schimmel, Erik Bongcam-Rudloff, Ulf Landegren, Helen Parkinson, Wolfgang Huber, Alvis Brazma, Arne K. Sandvik, and Martin Kuiper. BioTechniques, 50:27-31, 2011.

[92]
Enterotypes of the human gut microbiome. Mani Arumugam, Jeroen Raes, E. Pelletier, D. Le Paslier, T. Yamada, D. R. Mende, G. R. Fernandes, J. Tap, T. Bruls, J. M. Batto, M. Bertalan, N. Borruel, F. Casellas, L. Fernandez, L. Gautier, T. Hansen, M. Hattori, T. Hayashi, M. Kleerebezem, K. Kurokawa, M. Leclerc, F. Levenez, C. Manichanh, H. B. Nielsen, T. Nielsen, N. Pons, J. Poulain, J. Qin, T. Sicheritz-Ponten, S. Tims, D. Torrents, E. Ugarte, E. G. Zoetendal, J. Wang, F. Guarner, O. Pedersen, W. M. de Vos, S. Brunak, J. Dore, J. Weissenbach, S. D. Ehrlich, Peer Bork, Metagenomics Consortium:, M. Antolin, F. Artiguenave, H. M. Blottiere, M. Almeida, C. Brechot, C. Cara, C. Chervaux, A. Cultrone, C. Delorme, G. Denariaz, R. Dervyn, K. U. Foerstner, C. Friss, M. van de Guchte, E. Guedon, F. Haimet, Wolfgang Huber, J. van Hylckama-Vlieg, A. Jamet, C. Juste, G. Kaci, J. Knol, O. Lakhdari, S. Layec, K. Le Roux, E. Maguin, A. Merieux, R. Melo Minardi, C. M'rini, J. Muller, R. Oozeer, J. Parkhill, P. Renault, M. Rescigno, N. Sanchez, S. Sunagawa, A. Torrejon, K. Turner, G. Vandemeulebrouck, E. Varela, Y. Winogradsky, and G. Zeller. Nature, 473:174-180, 2011. (192 citations).

[93]
Assessing Affymetrix GeneChip microarray quality. Matthew M. McCall, Peter N. Murakami, Margus Lukk, Wolfgang Huber, and Rafael A. Irizarry. BMC Bioinformatics, 12:137, 2011. (24 citations)

[94]
Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications. S. Huhn, D. Ingelfinger, J. L. Bermejo, M. Bevier, B. Pardini, A. Naccarati, V. Steinke, N. Rahner, E. Holinski-Feder, M. Morak, H. K. Schackert, H. Gorgens, C. P. Pox, T. Goecke, M. Kloor, M. Loeffler, R. Buttner, L. Vodickova, J. Novotny, K. Demir, C. M. Cruciat, R. Renneberg, W. Huber, C. Niehrs, M. Boutros, P. Propping, P. Vodieka, K. Hemminki, and A. Forsti. Int J Mol Epidemiol Genet, 2:36-50, 2011.

[95]
Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi. Elin Axelsson, Thomas Sandmann, Thomas Horn, Michael Boutros, Wolfgang Huber, and Bernd Fischer. BMC Bioinformatics, 12:342, 2011. (10 citations)

[96]
H3K4 tri-methylation provides an epigenetic signature of active enhancers. Aleksandra Pekowska, Touati Benoukraf, Joaquin Zacarias-Cabeza, Mohamed Belhocine, Frederic Koch, Hélène Holota, Jean Imbert, Jean-Christophe Andrau, Pierre Ferrier, and Salvatore Spicuglia. EMBO Journal, 30(20):4198-4210, 2011. (126 citations).

[97]
Independent filtering increases detection power for high-throughput experiments. Richard Bourgon, Robert Gentleman, and Wolfgang Huber. PNAS, 107(21):9546-9551, 2010. (192 citations).

[98]
Differential expression analysis for sequence count data. Simon Anders and Wolfgang Huber. Genome Biology, 11:R106, 2010. (3395 citations).

[99]
Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Florian Fuchs*, Gregoire Pau*, Dominique Kranz, Oleg Sklyar, Christoph Budjan, Sandra Steinbrink, Thomas Horn, Angelika Pedal, Wolfgang Huber, and Michael Boutros. Molecular Systems Biology, 6(370), 2010. (71 citations).

[100]
EBImage - an R package for image processing with applications to cellular phenotypes. Gregoire Pau, Florian Fuchs, Oleg Sklyar, Michael Boutros, and Wolfgang Huber. Bioinformatics, 26:979-981, 2010. (85 citations).

[101]
Genome-wide analysis of mRNA decay patterns during early Drosophila development. Stefan Thomsen, Simon Anders, Sarath Chandra Janga, Wolfgang Huber, and Claudio R. Alonso. Genome Biology, 11:R93, 2010. (43 citations)

[102]
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Beate Neumann, Thomas Walter, Jean-Karim Heriché, Jutta Bulkescher, Holger Erfle, Christian Conrad, Phill Rogers, Ina Poser, Michael Held, Urban Liebel, Cihan Cetin, Frank Sieckmann, Gregoire Pau, Rolf Kabbe, Annelie Wuensche, Venkata Satagopam, Michael H. A. Schmitz, Catherine Chapuis, Daniel W. Gerlich, Reinhard Schneider, Roland Eils, Wolfgang Huber, Jan-Michael Peters, Anthony A. Hyman, Richard Durbin, Rainer Pepperkok, and Jan Ellenberg. Nature, 464(7289):721-727, 2010. (416 citations).

[103]
Addressing accuracy and precision issues in iTRAQ quantitation. Natasha A. Karp, Wolfgang Huber, Pawel G. Sadowski, Philip D. Charles, Svenja V. Hester, and Kathryn S. Lilley. Molecular and Cellular Proteomics, 9:1885-97, 2010. (211 citations).

[104]
Organelle proteomics experimental designs and analysis. Laurent Gatto, Juan Antonio Vizcaíno, Henning Hermjakob, Wolfgang Huber, and Kathryn S. Lilley. Proteomics, 2010. (28 citations)

[105]
High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Marina V. Granovskaia, Lars J. Jensen, Matthew E. Ritchie, Jörn Tödling, Ye Ning, Peer Bork, Wolfgang Huber, and Lars M. Steinmetz. Genome Biology, 11:R24, 2010. (49 citations)

[106]
Variation in transcription factor binding among humans. Maya Kasowski, Fabian Grubert, Christopher Heffelfinger, Manoj Hariharan, Akwasi Asabere, Sebastian M. Waszak, Lukas Habegger, Joel Rozowsky, Minyi Shi, Alexander E. Urban, Mi-Young Hong, Konrad J. Karczewski, Wolfgang Huber, Sherman M. Weissman, Mark B. Gerstein, Jan O. Korbel, and Michael Snyder. Science, 328:232-235, 2010. (297 citations).

[107]
Microarray data quality control improves the detection of differentially expressed genes. Audrey Kauffmann and Wolfgang Huber. Genomics, 95:138-142, 2010. (33 citations)

[108]
A large-scale RNAi screen identifies Deaf1 as a regulator of innate immune responses in Drosophila. David Kuttenkeuler, Nadege Pelte, Anan Ragab, Viola Gesellchen, Lena Schneider, Claudia Blass, Elin Axelsson, Wolfgang Huber, and Michael Boutros. Journal of Innate Immunity, 2:181-194, 2010. (21 citations)

[109]
Comparison of normalization methods for Illumina BeadChip(R) HumanHT-12 v3. Ramona Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel-Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich, and Karsten Quast. BMC Genomics, 11:349, 2010. (37 citations)

[110]
A global map of human gene expression. Margus Lukk, Misha Kapushesky, Janne Nikkila, Helen Parkinson, Angela Goncalves, Wolfgang Huber, Esko Ukkonen, and Alvis Brazma. Nature Biotechnology, 28:322-324, 2010. (183 citations).

[111]
Fully automatic stitching and distortion correction of transmission electron microscope images. Verena Kaynig, Bernd Fischer, Elisabeth Müller, and Joachim M Buhmann. Journal of Structural Biology, 171(2):163-173, 2010. (21 citations)

[112]
Bidirectional promoters generate pervasive transcription in yeast. Zhenyu Xu*, Wu Wei*, Julien Gagneur, Fabiana Perocchi, Sandra Clauder-Muenster, Jurgi Camblong, Elisa Guffanti, Francoise Stutz, Wolfgang Huber, and Lars M. Steinmetz. Nature, 457(7232):1033-1037, 2009. (427 citations).

[113]
Genome-wide allele- and strand-specific expression profiling. Julien Gagneur, Himanshu Sinha, Fabiana Perocchi, Richard Bourgon, Wolfgang Huber, and Lars M. Steinmetz. Molecular Systems Biology, 5:274, 2009. (24 citations)

[114]
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Steffen Durinck, Paul T. Spellman, Ewan Birney, and Wolfgang Huber. Nature Protocols, 4(8):1184-1191, 2009. (169 citations).

[115]
Quality assessment and data analysis for microRNA expression arrays. Deepayan Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, Wolfgang Huber, Robert Gentleman, and Munesh Tewari. Nucleic Acids Research, 37(2), 2009. (31 citations)

[116]
arrayQualityMetrics - a Bioconductor package for quality assessment of microarray data. Audrey Kauffmann, Robert Gentleman, and Wolfgang Huber. Bioinformatics, 25:415-416, 2009. (80 citations).

[117]
Importing ArrayExpress datasets into R/Bioconductor. Audrey Kauffmann, Tim F. Rayner, Helen Parkinson, Misha Kapushesky, Margus Lukk, Alvis Brazma, and Wolfgang Huber. Bioinformatics, 25:2092-2094, 2009. (80 citations).

[118]
The hwriter package. Gregoire Pau and Wolfgang Huber. The R Journal, 1(1):22-24, 2009.

[119]
Visualisation of genomic data with the Hilbert curve. Simon Anders. Bioinformatics, 25:1231-1235, 2009. (28 citations)

[120]
ShortRead: a Bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Martin Morgan, Simon Anders, Michael Lawrence, Patrick Aboyoun, Hervé Pagés, and Robert Gentleman. Bioinformatics, 25:2607, 2009. (145 citations).

[121]
CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. Michael Held, M. H. Schmitz, Bernd Fischer, Thomas Walter, Beate Neumann, M. H. Olma, M. Peter, Jan Ellenberg, and Daniel W. Gerlich. Nature Methods, 7(9):747-754, 2010. (127 citations).

[122]
High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Eugenio Mancera*, Richard Bourgon*, Alessandro Brozzi, Wolfgang Huber, and Lars M. Steinmetz. Nature, 454(7203):479-485, 2008. (278 citations).

[123]
Array-based genotyping in S. cerevisiae using semi-supervised clustering. Richard Bourgon, Eugenio Mancera, Alessandro Brozzi, Lars M. Steinmetz, and Wolfgang Huber. Bioinformatics, 25(8):1056-1062, 2009.

[124]
Analyzing ChIP-chip data using Bioconductor. Jörn Tödling and Wolfgang Huber. PLoS Computational Biology, 4(11), 2008. (13 citations)

[125]
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Tony Chiang, Nianhua Li, Sandra Orchard, Samuel Kerrien, Henning Hermjakob, Robert Gentleman, and Wolfgang Huber. Bioinformatics, 24(8):1100-1101, 2008.

[126]
Model-based variance-stabilizing transformation for Illumina microarray data. Simon M. Lin, Pan Du, Wolfgang Huber, and Warren A. Kibbe. Nucleic Acids Res, 36(2), 2008. (259 citations).

[127]
Combinatorial effects of four histone modifications in transcription and differentiation. Jenny J. Fischer, Jörn Tödling, Tammo Krüger, Markus Schüler, Wolfgang Huber, and Silke Sperling. Genomics, 91(1):41-51, 2008. (26 citations)

[128]
Estimating node degree in bait-prey graphs. Denise Scholtens, Tony Chiang, Wolfgang Huber, and Robert Gentleman. Bioinformatics, 24(2):218-224, 2008. (10 citations)

[129]
Bioconductor Case Studies. Use R. Springer. Florian Hahne, Wolfgang Huber, Robert Gentleman, and Seth Falcon, 2008. (101 citations).

[130]
Overexpression of dna repair genes is associated with metastasis: A new hypothesis. Alain Sarasin and Audrey Kauffmann. Mutation Research/Reviews in Mutation Research, 659(1-2):49-55, 2008. (50 citations).

[131]
Coverage and error models of protein-protein interaction data by directed graph analysis. Tony Chiang, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, and Wolfgang Huber. Genome Biology, 8(9), 2007. (23 citations)

[132]
Making the most of high-throughput protein-interaction data. Robert Gentleman and Wolfgang Huber. Genome Biology, 8(10):112-112, 2007. (25 citations)

[133]
Graphs in molecular biology. Wolfgang Huber, Vincent J. Carey, Li Long, Seth Falcon, and Robert Gentleman. BMC Bioinformatics, 8(Suppl. 6), 2007. (46 citations)

[134]
Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts. Jörn Tödling, Oleg Sklyar, Tammo Krüger, Jenny J. Fischer, Silke Sperling, and Wolfgang Huber. BMC Bioinformatics, 8:221-221, 2007.

[135]
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. Tineke Casneuf, Yves Van de Peer, and Wolfgang Huber. BMC Bioinformatics, 8:461-461, 2007. (41 citations)

[136]
CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data. Charles Girardot, Oleg Sklyar, Sophie Grosz, Wolfgang Huber, and Eileen E. M. Furlong. Bioinformatics, 23(6):771-773, 2007.

[137]
Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Antje Purmann, Jörn Tödling, Markus Schüler, Piero Carninci, Hans Lehrach, Yoshihide Hayashizaki, Wolfgang Huber, and Silke Sperling. Genomics, 89(5):580-587, 2007. (36 citations)

[138]
High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins. Mamatha Sauermann, Florian Hahne, Christian Schmidt, Meher Majety, Heiko Rosenfelder, Stephanie Bechtel, Wolfgang Huber, Annemarie Poustka, Dorit Arlt, and Stefan Wiemann. Journal of Biomolecular Screening, 12(4):510-520, 2007.

[139]
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. Stephan Steigele, Wolfgang Huber, Claudia Stocsits, Peter F. Stadler, and Kay Nieselt. BMC Biology, 5:25-25, 2007. (22 citations)

[140]
Analysis of cell-based RNAi screens. Michael Boutros, Lígia P. Brás, and Wolfgang Huber. Genome Biology, 7(7), 2006. (160 citations).

[141]
A high-resolution map of transcription in the yeast genome. Lior David*, Wolfgang Huber*, Marina Granovskaia, Jörn Tödling, Curtis J. Palm, Lee Bofkin, T. Jones, Ron W. Davis, and Lars M. Steinmetz. PNAS, 103(14):5320-5325, 2006. (418 citations).

[142]
Transcript mapping with high-density oligonucleotide tiling arrays. Wolfgang Huber, Jörn Tödling, and Lars M. Steinmetz. Bioinformatics, 22(16):1963-1970, 2006. (96 citations).

[143]
Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts. Florian Hahne, Dorit Arlt, Mamatha Sauermann, Meher Majety, Annemarie Poustka, Stefan Wiemann, and Wolfgang Huber. Genome Biology, 7(8), 2006. (14 citations)

[144]
Reproducible statistical analysis in microarray profiling studies. Ulrich Mansmann, Markus Ruschhaupt, and Wolfgang Huber. Methods of Information in Medicine, 45:139-145, 2006.

[145]
The LIFEdb database in 2006. Alexander Mehrle, Heiko Rosenfelder, Ingo Schupp, Coral del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, Jeremy Simpson, Oliver Hofmann, Winston Hide, Karl-Heinz Glatting, Wolfgang Huber, Rainer Pepperkok, Annemarie Poustka, and Stefan Wiemann. Nucleic Acids Research, 34(Database issue):415-418, 2006. (22 citations)

[146]
Visualizing genomic data. Robert Gentleman, Florian Hahne, and Wolfgang Huber. Technical Report 10, Bioconductor Project Working Papers, 2006.

[147]
Image analysis for microscopy screens. Oleg Sklyar and Wolfgang Huber. R News, 6(5):12-16, 2006.

[148]
Transcript mapping with high-density tiling arrays. Matthew Ritchie and Wolfgang Huber. R News, 6(5):23-27, 2006.

[149]
Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle. Dorit Arlt, Wolfgang Huber, Urban Liebel, C. Schmidt, Meher Majety, Mamatha Sauermann, Heiko Rosenfelder, Stefanie Bechtel, Alexander Mehrle, Detlev Bannasch, Ingo Schupp, Markus Seiler, Jeremy C. Simpson, Florian Hahne, Petra Moosmayer, Markus Ruschhaupt, Birgit Guilleaume, Ruth Wellenreuther, Rainer Pepperkok, Holger Sültmann, Annemarie Poustka, and Stefan Wiemann. Cancer Research, 65(17):7733-7742, 2005. (19 citations)

[150]
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma, and Wolfgang Huber. Bioinformatics, 21:3439-3440, 2005. (336 citations).

[151]
Systematic comparison of surface coatings for protein microarrays. Birgit Guilleaume, Andreas Buness, C. Schmidt, F. Klimek, G. Moldenhauer, Wolfgang Huber, Dorit Arlt, Ulrike Korf, Stefan Wiemann, and Annemarie Poustka. Proteomics, 5:4705-4712, 2005. (33 citations)

[152]
Gene expression in kidney cancer is associated with cytogenetic abnormalities, metastasis formation, and patient survival. Holger Sültmann, Anja von Heydebreck, Wolfgang Huber, Rupert Kuner, Andreas Buness, Markus Vogt, Bastian Gunawan, Martin Vingron, Laszlo Fuzesi, and Annemarie Poustka. Clinical Cancer Research, 11:646-655, 2005. (54 citations).

[153]
arrayMagic: two-colour cDNA microarray quality control and preprocessing. Andreas Buness, Wolfgang Huber, Klaus Steiner, Holger Sültmann, and Annemarie Poustka. Bioinformatics, 21(4):554-556, 2005. (36 citations)

[154]
Novel cancer relevant cell cycle modulators identified in automated cell-based assays. Dorit Arlt, Wolfgang Huber, Mamatha Sauermann, Meher Majety, Florian Hahne, Rainer Pepperkok, Annemarie Poustka, and Stefan Wiemann. European Journal of Cell Biology, 84(Suppl. 55):30, 2005.

[155]
Bioinformatics - from Genomes to Therapies, chapter Low-level analysis of microarray experiments. Wolfgang Huber, Anja von Heydebreck, and Martin Vingron. Wiley-VCH, 2005.

[156]
On the synthesis of microarray experiments. Robert Gentleman, Markus Ruschhaupt, and Wolfgang Huber. Journal de la Société Française de Statistique, 146(1-2), 2005.

[157]
Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer. Robert Gentleman, Vincent J. Carey, Wolfgang Huber, Rafael Irizarry, and Sandrine Dudoit, editors, 2005. (2120 citations).

[158]
Bioconductor: open software development for computational biology and bioinformatics. Robert C. Gentleman, Vincent J. Carey, Douglas M. Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Y.C. Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J. Rossini, Günther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean Y.H. Yang, and J.H. Zhang. Genome Biology, 5(10), 2004. (6093 citations).

[159]
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. Wolfgang Huber and Robert Gentleman. Bioinformatics, 20:1651-1652, 2004. (25 citations)

[160]
A compendium to ensure computational reproducibility in high-dimensional classification tasks. Markus Ruschhaupt, Wolfgang Huber, Annemarie Poustka, and Ulrich Mansmann. Statistical Applications in Genetics and Molecular Biology, 3(37), 2004. (96 citations).

[161]
Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments. Jörg Schneider, Andreas Buness, Wolfgang Huber, Joachim Volz, Petra Kioschis, Mathias Hafner, Annemarie Poustka, and Holger Sültmann. BMC Genomics, 5(1):29, 2004. (60 citations).

[162]
From ORFeome to biology: a functional genomics pipeline. Stefan Wiemann, Dorit Arlt, Wolfgang Huber, Ruth Wellenreuther, Simone Schleeger, Alexander Mehrle, Stephanie Bechtel, Mamatha Sauermann, Ulrike Korf, Rainer Pepperkok, Holger Sültmann, and Annemarie Poustka. Genome Research, 108:2136-44, 2004. (35 citations)

[163]
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, chapter Error models for microarray intensities. Wolfgang Huber, Anja von Heydebreck, and Martin Vingron. John Wiley & Sons, 2004. pdf (13 citations)

[164]
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, chapter Differential Expression with the Bioconductor Project. Anja von Heydebreck, Wolfgang Huber, and Robert Gentleman. John Wiley & Sons, 2004. pdf (58 citations).

[165]
Multi-domain protein families and domain pairs: Comparison with known structures and a random model of domain recombination. Gordana Apic, Wolfgang Huber, and Sarah A. Teichmann. Journal of Structural and Functional Genomics, 4:67-78, 2003. pdf (76 citations).

[166]
Cytogenetic and morphologic typing of 58 papillary renal cell carcinomas: Evidence for a cytogenetic evolution of type 2 from type 1 tumors. Bastian Gunawan, Anja von Heydebreck, Thekla Fritsch, Wolfgang Huber, Rolf-Hermann Ringert, Gerhard Jakse, and László Füzesi. Cancer Research, 63:6200-6205, 2003. (67 citations).

[167]
Mathematical tree models for cytogenetic development in solid tumors. Anja von Heydebreck, Bastian Gunawan, Wolfgang Huber, Martin Vingron, and Laszlo Füzesi. Verhandlungen der Deutschen Gesellschaft für Pathologie, 2003.

[168]
Parameter estimation for the calibration and variance stabilization of microarray data. Wolfgang Huber, Anja von Heydebreck, Holger Sültmann, Annemarie Poustka, and Martin Vingron. Statistical Applications in Genetics and Molecular Biology, 2(1):Article 3, 2003. (164 citations).

[169]
Analysis of microarray gene expression data. Wolfgang Huber, Anja von Heydebreck, and Martin Vingron. In Martin Bishop et al., editor, Handbook of Statistical Genetics. John Wiley & Sons, Ltd, Chichester, UK, 2003. pdf (60 citations).

[170]
Prognostic factors influencing surgical management and outcome of gastrointestinal stromal tumours. C. Langer, Bastian Gunawan, P. Schüler, Wolfgang Huber, Laszlo Füzesi, and H. Becker. British Journal of Surgery, 90:332-399, 2003. (121 citations).

[171]
Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Wolfgang Huber, Anja von Heydebreck, Holger Sültmann, Annemarie Poustka, and Martin Vingron. Bioinformatics, 18 Suppl 1:96-104, 2002. (1801 citations).

[172]
Transcription profiling of renal cell carcinoma. Wolfgang Huber, Judith M. Boer, Anja von Heydebreck, Bastian Gunawan, Martin Vingron, László Füzesí, Annemarie Poustka, and Holger Sültmann. Verhandlungen der Deutschen Gesellschaft für Pathologie, 86:153-164, 2002.

[173]
Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array. Judith M. Boer, Wolfgang Huber, Holger Sültmann, Friederike Wilmer, Anja von Heydebreck, Stefan Haas, Bernhard Korn, Bastian Gunawan, Astrid Vente, Laszlo Füzesi, Martin Vingron, and Annemarie Poustka. Genome Research, 11(11):1861-1870, 2001. (146 citations).

[174]
Prognostic impacts of cytogenetic findings in clear cell renal cell carcinoma: Chromosome translocation der(3)t(3;5) or gain of 5q predict a distinct clinical phenotype with favourable prognosis. Bastian Gunawan, Wolfgang Huber, Meike Holtrup, Anja von Heydebreck, Thomas Efferth, Annemarie Poustka, Rolf-Hermann Ringert, Gerhard Jakse, and László Füzesi. Cancer Research, 61:7731-7738, 2001. (70 citations).

[175]
FLASHFLOOD: A 3D field-based similarity search and alignment method for flexible molecules. Michael C. Pitman, Wolfgang Huber, Hans Horn, Andreas Krämer, Julia E. Rice, and William C. Swope. Journal of Computer-Aided Molecular Design, 15:587-612, 2001. (18 citations)

[176]
Identifying splits with clear separation: A new class discovery method for gene expression data. Anja von Heydebreck, Wolfgang Huber, Annemarie Poustka, and Martin Vingron. Bioinformatics, 17 Suppl. 1:S107-114, 2001. (79 citations).

[177]
Gene expression profiling of kidney cancer using a tumor-specific cDNA microarray. Holger Sültmann, Wolfgang Huber, Laszlo Fuzesi, Bastian Gunawan, Anja von Heydebreck, Martin Vingron, and Annemarie Poustka. Clinical Cancer Research, 7(11, Suppl. S):155, 2001.

[178]
Quasistationary distributions of dissipative nonlinear quantum oscillators in strong periodic driving fields. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Physical Review E, 61:4883-4889, 2000. (33 citations)

[179]
Stochastic wave function method versus density matrix: a numerical comparison. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Computer Physics Communications, 104:46-58, 1997. (18 citations)

[180]
Vestibular-neck interaction and transformation of sensory coordinates. Thomas Mergner, Wolfgang Huber, and Wolfgang Becker. Journal of Vestibular Research, 7:347-367, 1997. (102 citations).

[181]
Spatially resolved measurement and modeling of blood brain barrier permeability. Wolfgang Huber, Klaus Kopitzki, Jens Timmer, and Peter Warnke. Biomedizinische Technik, 41 suppl. 1:160, 1996.

[182]
Fast Monte Carlo algorithm for nonequilibrium systems. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Physical Review E, 53:4232-4235, 1996.

[183]
The three-loop model: a neural network for the generation of saccadic reaction times. Burkhart Fischer, Stefan Gezeck, and Wolfgang Huber. Biological Cybernetics, 72:185-196, 1995. (28 citations)

[184]
The macroscopic limit in a stochastic reaction-diffusion process. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Europhysics Letters, 30:69-74, 1995. (26 citations)

[185]
Fluctuation effects on wave propagation in a reaction-diffusion process. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Physica D, 73:259-273, 1994. (50 citations).

[186]
Dynamics of strongly driven open quantum systems. Wolfgang Huber. PhD thesis, University of Freiburg, 1998.

[187]
The description of reaction diffusion processes by master equations. Wolfgang Huber. Diploma thesis, University of Freiburg, 1994.
* indicates equal contributions
 co-corresponding authorships
1 S o u r c e : I S I W e b o f S c i e n c e .


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