Last revision: 17 Feb 2020

[1]
Covariate powered cross-weighted multiple testing. Nikolaos Ignatiadis and Wolfgang Huber. arχiv, Feb 2020. PDF, Journal Site.

[2]
Drug-target profiling in tissues and whole blood by thermal shift assays. Jessica Perrin, Thilo Werner, Nils Kurzawa, Anna Rutkowska, Dorothee D. Childs, Mathias Kalxdorf, Daniel Poeckel, Eugenia Stonehouse, Katrin Strohmer, Bianca Heller, Douglas W. Thomson, Jana Krause, Isabelle Becher, H. Christian Eberl, Johanna Vappiani, Daniel C. Sevin, Christina E. Rau, Holger Franken, Wolfgang Huber, Maria Faelth-Savitski, Mikhail M. Savitski, Marcus Bantscheff, and Giovanna Bergamini. Nature Biotechnology, Jan 2020. PDF, Journal Site. Preprint on bioRχiv.

[3]
Modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection. Katharina Imkeller, Giulia Ambrosi, Michael Boutros, and Wolfgang Huber. Genome Biology, in press, 2020. PDF. Preprint on bioRχiv.

[4]
Dissecting intratumor heterogeneity of nodal b cell lymphomas on the transcriptional, genetic, and drug response level. Tobias Roider, Julian Seufert, Alexey Uvarovskii, Felix Frauhammer, Marie Bordas, Nima Abedpour, Marta Stolarczyk, Jan-Philipp Mallm, Sophie Rabe, Peter-Martin Bruch, Hyatt Balke-Want, Michael Hundemer, Karsten Rippe, Benjamin Goeppert, Martina Seiffert, Benedikt Brors, Gunhild Mechtersheimer, Thorsten Zenz, Martin Peifer, Björn Chapuy, Matthias Schlesner, Carsten Müller-Tidow, Stefan Fröhling, Wolfgang Huber, Simon Anders, and Sascha Dietrich. bioRχiv, Dec 2019. PDF, Journal Site.

[5]
Orchestrating single-cell analysis with Bioconductor. Robert A. Amezquita, Aaron T. L. Lun, Etienne Becht, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Hervé Pagès, Mike L. Smith, Wolfgang Huber, Martin Morgan, Raphael Gottardo, and Stephanie C. Hicks. Nature Methods, Dec 2019. PDF, Journal Site. Preprint on bioRχiv.

[6]
Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTF. Ivan Berest, Christian Arnold, Armando Reyes-Palomares, Giovanni Palla, Kasper Dindler Rasmussen, Holly Giles, Peter-Martin Bruch, Wolfgang Huber, Sascha Dietrich, Kristian Helin, and Judith B. Zaugg. Cell Reports, 29(10):3147-3159, Dec 2019. PDF, Journal Site.

[7]
Biological plasticity rescues target activity in CRISPR knock outs. Arne H. Smits*, Frederik Ziebell*, Gerard Joberty, Nico Zinn, William F. Mueller, Sandra Clauder-Münster, Dirk Eberhard, Maria Fälth Savitski, Paola Grandi, Petra Jakob, Anne-Marie Michon, Hanice Sun, Karen Tessmer, Tilmann Burckstummer, Marcus Bantscheff, Lars M. Steinmetz , Gerard Drewes , and Wolfgang Huber . Nature Methods, 16:1087, Nov 2019. PDF, Journal Site. Preprint on bioRχiv.

[8]
Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes. Britta Velten and Wolfgang Huber. Biostatistics, kxz034, Oct 2019. PDF, Journal Site. Preprint on arχiv.

[9]
Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins. Dorothee Childs, Karsten Bach, Holger Franken, Simon Anders, Nils Kurzawa, Marcus Bantscheff, Mikhail Savitski, and Wolfgang Huber. Molecular Cell Proteomics, 2019. PDF, Journal Site. Preprint on bioRχiv.

[10]
Developmental gene expression differences between humans and mammalian models. Margarida Cardoso-Moreira, Britta Velten, Matthew Mort, David N. Cooper, Wolfgang Huber, and Henrik Kaessmann. bioRχiv, Aug 2019. PDF, Journal Site.

[11]
Gene expression across mammalian organ development. Margarida Cardoso-Moreira, Jean Halbert, Delphine Valloton, Britta Velten, Chunyan Chen, Yi Shao, Angélica Liechti, Kelly Ascenção, Coralie Rummel, Svetlana Ovchinnikova, Pavel V. Mazin, Ioannis Xenarios, Keith Harshman, Matthew Mort, David N. Cooper, Carmen Sandi, Michael J. Soares, Paula G. Ferreira, Sandra Afonso, Miguel Carneiro, James M. A. Turner, John L. VandeBerg, Amir Fallahshahroudi, Per Jensen, Rüdiger Behr, Steven Lisgo, Susan Lindsay, Philipp Khaitovich, Wolfgang Huber, Julie Baker, Simon Anders, Yong E. Zhang, and Henrik Kaessmann. Nature, 571(7766):505-509, Jun 2019. PDF, Journal Site.

[12]
The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance. Amy Cooke, Thomas Schwarzl, Ina Huppertz, Gertjan Kramer, Panagiotis Mantas, Anne-Marie Alleaume, Wolfgang Huber, Jeroen Krijgsveld, and Matthias W Hentze. Cell Reports, 27(11):3097-3106, Jun 2019. PDF, Journal Site.

[13]
MDM4 is targeted by 1q gain and drives disease in Burkitt lymphoma. Jennifer Hüllein, Mikoaj Sabicki, Maciej Rosolowski, Alexander Jethwa, Stefan Habringer, Katarznya Tomska, Roma Kurilov, Junyan Lu, Sebastian Scheinost, Rabea Wagener, Zhiqin Huang, Marina Lukas, Olena Yavorska, Hanne Helfrich, René Scholtysik, Kyle Bonneau, Donato Tedesco, Ralf Küppers, Wolfram Klapper, Christiane Pott, Stephan Stilgenbauer, Birgit Burkhardt, Markus Löffler, Lorenz H Trümper, Michael Hummel, Benedikt Brors, Marc Zapatka, Reiner Siebert, Markus Kreuz, Ulrich Keller, Wolfgang Huber, and Thorsten Zenz. Cancer Research, 2019. PDF, Journal Site. Preprint on bioRχiv.

[14]
Reporting p Values. Wolfgang Huber. Cell Systems, 8(3):170, 2019. PDF, Journal Site.

[15]
Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation. Erika Kelmer Sacramento, Joanna M. Kirkpatrick, Mariateresa Mazzetto, Simone Di Sanzo, Cinzia Caterino, Michele Sanguanini, Nikoletta Papaevgeniou, Maria Lefaki, Dorothee Childs, Sara Bagnoli, Eva Terzibasi Tozzini, Aleksandar Bartolome, Natalie Romanov, Mario Baumgart, Wolfgang Huber, Niki Chondrogianni, Michele Vendruscolo, Alessandro Cellerino, and Alessandro Ori. bioRχiv, Mar 2019. PDF, Journal Site.

[16]
Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP. Sindhuja Sridharan, Nils Kurzawa, Thilo Werner, Ina Guenthner, Dominic Helm, Wolfgang Huber, Marcus Bantscheff, and Mikhail M Savitski. Nature Communications, 10(1):1155, Mar 2019. PDF, Journal Site.

[17]
Energy metabolism is co-determined by genetic variants in chronic lymphocytic leukemia and influences drug sensitivity. Junyan Lu, Martin Böttcher, Tatjana Walther, Dimitrios Mougiakakos, Thorsten Zenz, and Wolfgang Huber. Haematologica, Feb 2019. PDF, Journal Site.

[18]
The small non-coding vault RNA1-1 acts as a riboregulator of autophagy. Rastislav Horos, Magdalena Büscher, Rozemarijn Kleinendorst, Anne-Marie Alleaume, Abul K Tarafder, Thomas Schwarzl, Dmytro Dziuba, Christian Tischer, Elisabeth M Zielonka, Asli Adak, Alfredo Castello, Wolfgang Huber, Carsten Sachse, and Matthias W Hentze. Cell, 176(5):1054-1067, 2019. PDF, Journal Site. Preprint on bioRχiv.

[19]
Modern Statistics for Modern Biology. Cambridge University Press. Susan Holmes and Wolfgang Huber, February 2019. Journal Site, Online edition .

[20]
The human RNA-binding proteome and its dynamics during translational arrest. Jakob Trendel, Thomas Schwarzl, Rastislav Horos, Ananth Prakash, Alex Bateman, Matthias W. Hentze, and Jeroen Krijgsveld. Cell, 176(1):391 - 403.e19, 2019. PDF, Journal Site (20 citations1).

[21]
Gain of CTCF-anchored chromatin loops marks the exit from naive pluripotency. Aleksandra Pękowska , Bernd Klaus, Wanqing Xiang, Jacqueline Severino, Nathalie Daigle, Felix A. Klein, Małgorzata Oleś, Rafael Casellas, Jan Ellenberg, Lars M. Steinmetz, Paul Bertone , and Wolfgang Huber . Cell Systems, 11 2018. PDF, Journal Site.

[22]
Condensin II inactivation in interphase does not affect chromatin folding or gene expression. Nezar Abdennur, Wibke Schwarzer, Aleksandra Pękowska, Indra Alon Shaltiel, Wolfgang Huber, Christian H Haering, Leonid Mirny, and Francois Spitz. bioRχiv, Oct 2018. PDF, Journal Site.

[23]
Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture. Joel I Perez-Perri, Birgit Rogell, Thomas Schwarzl, Frank Stein, Yang Zhou, Mandy Rettel, Annika Brosig, and Matthias W Hentze. Nature Communications, 9, 10 2018. PDF, Journal Site.

[24]
Machine learning predicts the yeast metabolome from the quantitative proteome of kinase knockouts. Aleksej Zelezniak, Jakob Vowinckel, Floriana Capuano, Christoph B. Messner, Vadim Demichev, Nicole Polowsky, Michael Mülleder, Stephan Kamrad, Bernd Klaus, Markus A. Keller, and Markus Ralser. Cell Systems, 7(3):269 - 283.e6, 9 2018. PDF, Journal Site.

[25]
Clonal diversity predicts adverse outcome in chronic lymphocytic leukemia. Alexander C. Leeksma, Justin Taylor, Bian Wu, Jeffrey R. Gardner, Jie He, Michelle Nahas, Mithat Gonen, Wendimagegn G. Alemayehu, Doreen te Raa, Tatjana Walther, Jennifer Hüllein, Sascha Dietrich, Rainer Claus, Fransien de Boer, Koen de Heer, Julie Dubois, Maria Dampmann, Jan Dürig, Marinus H. J. van Oers, Christian H. Geisler, Eric Eldering, Ross L. Levine, Vincent Miller, Tariq Mughal, Nicole Lamanna, Mark G. Frattini, Mark L. Heaney, Andrew Zelenetz, Thorsten Zenz, Omar Abdel-Wahab, and Arnon P. Kater. Leukemia, 33(2):390-402, 2019. PDF, Journal Site.

[26]
A combinatorial extracellular code tunes the intracellular signaling network activity to distinct cellular responses. Dmitry Kuchenov, Frederik Ziebell, Florian Salopiata, Mevlut Citir, Ursula Klingmueller, Wolfgang Huber, and Carsten Schultz. bioRχiv, 6 2018. PDF, Journal Site.

[27]
Multi-Omics Factor Analysis - a framework for unsupervised integration of multi-omics data sets. Ricard Argelaguet*, Britta Velten*, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner , Wolfgang Huber , and Oliver Stegle . Molecular Systems Biology, 14(6):e8124, 6 2018. PDF, Journal Site (29 citations) Preprint on bioRχiv.

[28]
TRRAP is essential for regulating the accumulation of mutant and wild-type p53 in lymphoma. Alexander Jethwa, Mikoaj Sabicki, Jennifer Hüllein, Marius Jentzsch, Vineet Dalal, Sophie Rabe, Lena Wagner, Tatjana Walther, Wolfram Klapper, Hanibal Bohnenberger, Mandy Rettel, Junyan Lu, Arne H Smits, Frank Stein, Mikhail M. Savitski, Wolfgang Huber, Yael Aylon, Moshe Oren, and Thorsten Zenz. Blood, 6 2018. PDF, Journal Site.

[29]
beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types. Aaron TL Lun, Hervé Pagès, and Mike L Smith. PLoS Computational Biology, 14(5):e1006135, 5 2018. PDF, Journal Site.

[30]
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Laleh Haghverdi, Aaron TL Lun, Michael D Morgan, and John C Marioni. Nature Biotechnology, 36(5):421, 4 2018. PDF, Journal Site (100 citations).

[31]
Authoring Bioconductor workflows with BiocWorkflowTools. Mike L Smith, Andrzej K Oleś, and Wolfgang Huber. F1000Research, 7, 2018. PDF, Journal Site.

[32]
Proteome-wide identification of ubiquitin interactions using UbIA-MS. Xiaofei Zhang*, Arne H Smits*, Gabrielle BA van Tilburg*, Huib Ovaa, Wolfgang Huber, and Michiel Vermeulen. Nature Protocols, 13(3):530-550, 2018. PDF, Journal Site (10 citations)

[33]
Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data. James H. R. Farmery, Mike L. Smith, and Andy G. Lynch. Scientific Reports, 8(1), 2018. PDF, Journal Site.

[34]
A brave new world of RNA-binding proteins. Matthias W. Hentze, Alfredo Castello, Thomas Schwarzl, and Thomas Preiss. Nature Reviews Molecular Cell Biology, 2018. PDF, Journal Site (101 citations).

[35]
Landscape of nuclear transport receptor cargo specificity. Marie-Therese Mackmull, Bernd Klaus, Ivonne Heinze, Manopriya Chokkalingam, Andreas Beyer, Robert B Russell, Alessandro Ori, and Martin Beck. Molecular Systems Biology, 13(12), 2017. PDF, Journal Site (14 citations)

[36]
Drug-perturbation-based stratification of blood cancer. Sascha Dietrich*, Małgorzata Oleś*, Junyan Lu*, Leopold Sellner, Simon Anders, Britta Velten, Bian Wu, Jennifer Hüllein, Michelle da Silva Liberio, Tatjana Walther, Lena Wagner, Sophie Rabe, Sonja Ghidelli-Disse, Marcus Bantscheff, Andrzej K. Oleś, Mikołaj Słabicki, Andreas Mock, Christopher C. Oakes, Shihui Wang, Sina Oppermann, Marina Lukas, Vladislav Kim, Martin Sill, Axel Benner, Anna Jauch, Lesley Ann Sutton, Emma Young, Richard Rosenquist, Xiyang Liu, Alexander Jethwa, Kwang Seok Lee, Joe Lewis, Kerstin Putzker, Christoph Lutz, Davide Rossi, Andriy Mokhir, Thomas Oellerich, Katja Zirlik, Marco Herling, Florence Nguyen-Khac, Christoph Plass, Emma Andersson, Satu Mustjoki, Christof von Kalle, Anthony D. Ho, Manfred Hensel, Jan Dürig, Ingo Ringshausen, Marc Zapatka, Wolfgang Huber , and Thorsten Zenz . The Journal of Clinical Investigation, 128(1):427-445, 2018. PDF, Journal Site (11 citations)

[37]
Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Alejandro Reyes and Wolfgang Huber. Nucleic Acids Research, 46(2):582-592, 2018. PDF, Journal Site (25 citations) Preprint on bioRχiv.

[38]
Expression Atlas: gene and protein expression across multiple studies and organisms. Irene Papatheodorou, Nuno A. Fonseca, Maria Keays, Y. Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen, Suhaib Mohammed, Matthew Geniza, Justin Preece, Pankaj Jaiswal, Andrew F. Jarnuczak, Wolfgang Huber, Oliver Stegle, Juan Antonio Vizcaino, Alvis Brazma, and Robert Petryszak. Nucleic Acids Research, 2017. PDF, Journal Site (63 citations).

[39]
Online resources for PCAWG data exploration, visualization, and discovery. Mary Goldman*, Junjun Zhang*, Nuno A. Fonseca*, Qian Xiang, Brian Craft, Elena Piñeiro-Yáñez, Brian O'Connor, Wojciech Bazant, Elisabet Barrera, Alfonso Muñoz, Robert Petryszak, Anja Füllgrabe, Fatima Al-Shahrour, Maria Keays, David Haussler, John Weinstein, Wolfgang Huber, Alfonso Valencia, Irene Papatheodorou , Jingchun Zhu , Vincent Ferreti , and Miguel Vazquez . bioRχiv, 2017. PDF, Journal Site.

[40]
voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data. Gokmen Zararsiz, Dincer Goksuluk, Bernd Klaus, Selcuk Korkmaz, Vahap Eldem, Erdem Karabulut, and Ahmet Ozturk. PeerJ, 5:e3890, 2017. PDF, Journal Site.

[41]
Two independent modes of chromatin organization revealed by cohesin removal. Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra P ekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian Haering, Leonid Mirny, and Francois Spitz. Nature, 2017. PDF, Journal Site (179 citations). Preprint on bioRχiv.

[42]
Research techniques made simple: Bioinformatics for genome-scale biology. Amy C. Foulkes, David S. Watson, Christopher E.M. Griffiths, Richard B. Warren, Wolfgang Huber, and Michael R. Barnes. Journal of Investigative Dermatology, 137(9):e163-e168, 2017. PDF, Journal Site.

[43]
Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities. Daria Bunina*, Martin Stefl*, Florian Huber*, Anton Khmelinskii, Matthias Meurer, Joseph D. Barry, Ilia Kats, Daniel Kirrmaier, Wolfgang Huber, and Michael Knop. Nucleic Acids Research, 45(19):11144-11158, 2017. PDF, Journal Site.

[44]
Metabolic shifts in residual breast cancer drive tumor recurrence. Kristina M. Havas, Vladislava Milchevskaya, Ksenija Radic, Ashna Alladin, Eleni Kafkia, Marta Garcia, Jens Stolte, Bernd Klaus, Nicole Rotmensz, Toby J. Gibson, Barbara Burwinkel, Andreas Schneeweiss, Giancarlo Pruneri, Kiran R. Patil, Rocio Sotillo, and Martin Jechlinger. The Journal of Clinical Investigation, 127(6):2091-2105, 2017. PDF, Journal Site (19 citations)

[45]
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. PDF, Journal Site (152 citations).

[46]
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, 66(9):1597-1610, 2017. PDF, Journal Site (20 citations)

[47]
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. PDF, Journal Site (21 citations)

[48]
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. PDF, Journal Site (47 citations)

[49]
A clash of cultures in discussions of the P value. Wolfgang Huber. Nature Methods, 13:607, 2016. PDF, Journal Site.

[50]
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. PDF, Journal Site (22 citations)

[51]
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. PDF, Journal Site (46 citations)

[52]
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. PDF, Journal Site (123 citations).

[53]
Statistical relevance-relevant statistics, part II: presenting experimental data. Bernd Klaus. The EMBO Journal, 35(16):1726-1729, 2016. PDF, Journal Site.

[54]
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. PDF, Journal Site (35 citations)

[55]
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. PDF, Journal Site (52 citations). Preprint on bioRχiv.

[56]
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. PDF, Journal Site.

[57]
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. PDF, Journal Site (12 citations)

[58]
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. PDF, Journal Site.

[59]
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. PDF, Journal Site (78 citations).

[60]
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. PDF, Journal Site (66 citations).

[61]
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. PDF, Journal Site (59 citations).

[62]
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. PDF, Journal Site (25 citations)

[63]
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. PDF, Journal Site (23 citations)

[64]
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. PDF, Journal Site (140 citations).

[65]
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. PDF, Journal Site.

[66]
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. PDF, Journal Site (30 citations)

[67]
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. PDF, Journal Site (55 citations).

[68]
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. PDF, Journal Site (75 citations).

[69]
Mutational landscape and complexity in CLL. Thorsten Zenz and Wolfgang Huber. Blood, 126(18):2078-2079, 2015. PDF, Journal Site.

[70]
BRAF inhibitor therapy in HCL. Sascha Dietrich and Thorsten Zenz. Best Practice & Research Clinical Haematology, 28(4):246-252, 2015. Journal Site (10 citations)

[71]
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. PDF, Journal Site (222 citations).

[72]
RNA-Seq workflow: gene-level exploratory analysis and differential expression. Michael I. Love, Simon Anders, Vladislav Kim, and Wolfgang Huber. F1000Research, 4(1070), 2015. PDF, Journal Site (112 citations).

[73]
Statistical relevance-relevant statistics, part I. Bernd Klaus. The EMBO Journal, 34(22):2727-2730, 2015. PDF, Journal Site.

[74]
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. PDF, Journal Site (87 citations).

[75]
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. PDF, Journal Site (37 citations)

[76]
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. PDF, Journal Site (39 citations)

[77]
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 P ekowska, 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. PDF, Journal Site (121 citations).

[78]
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. PDF, Journal Site (15 citations)

[79]
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. PDF, Journal Site (50 citations).

[80]
SomaticSignatures: inferring mutational signatures from single-nucleotide variants. Julian S. Gehring, Bernd Fischer, Michael Lawrence, and Wolfgang Huber. Bioinformatics, 31(22):3673-3675, 2015. PDF, Journal Site (95 citations). Preprint on bioRχiv.

[81]
Single-cell polyadenylation site mapping reveals 3' isoform choice variability. Lars Velten, Simon Anders, Aleksandra P ekowska, Aino I Järvelin, Wolfgang Huber, Vicent Pelechano, and Lars M. Steinmetz. Molecular Systems Biology, 11(6), 2015. PDF, Journal Site (19 citations)

[82]
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. PDF, Journal Site (33 citations)

[83]
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. PDF, Journal Site (70 citations).

[84]
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. PDF, Journal Site (39 citations)

[85]
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. PDF, Journal Site (826 citations).

[86]
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. PDF, Journal Site (15 citations)

[87]
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. PDF, Journal Site (33 citations)

[88]
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. PDF, Journal Site (11 citations)

[89]
h5vc: scalable nucleotide tallies with HDF5. Paul Theodor Pyl, Julian Gehring, Bernd Fischer, and Wolfgang Huber. Bioinformatics, 30(10):1464-1466, 2014. PDF, Journal Site.

[90]
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. PDF, Journal Site (6751 citations). Preprint on bioRχiv.

[91]
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. PDF, Journal Site (72 citations).

[92]
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. PDF, Journal Site (4756 citations).

[93]
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. PDF, Journal Site (147 citations).

[94]
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. PDF, Journal Site (11 citations)

[95]
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. PDF, Journal Site (14 citations)

[96]
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. PDF, Journal Site (190 citations).

[97]
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. PDF, Journal Site (31 citations)

[98]
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. PDF, Journal Site (206 citations).

[99]
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. PDF, Journal Site (45 citations)

[100]
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. PDF, Journal Site (183 citations).

[101]
Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization. Aleksandra P ekowska, Bernd Klaus, Felix Alexander Klein, Simon Anders, Małgorzata Oleś, Lars M. Steinmetz, Paul Bertone, and Wolfgang Huber. bioRχiv, 2014. PDF, Journal Site.

[102]
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, 7 2014. PDF, Journal Site.

[103]
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. PDF, Journal Site (40 citations)

[104]
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. PDF, Journal Site (346 citations).

[105]
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. PDF, Journal Site.

[106]
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. PDF, Journal Site (161 citations).

[107]
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. PDF, Journal Site (34 citations)

[108]
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. PDF, Journal Site (36 citations)

[109]
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. PDF, Journal Site (501 citations).

[110]
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. PDF, Journal Site (746 citations).

[111]
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. PDF, Journal Site (67 citations).

[112]
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. PDF, Journal Site.

[113]
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. PDF, Journal Site (41 citations)

[114]
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. PDF, Journal Site (202 citations).

[115]
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. PDF, Journal Site (12 citations)

[116]
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. PDF, Journal Site (178 citations).

[117]
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. PDF, Journal Site (57 citations).

[118]
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. Journal Site.

[119]
RNA-binding proteins in Mendelian disease. Alfredo Castello, Bernd Fischer, Matthias W Hentze, and Thomas Preiss. Trends in Genetics, 29:318-327, 2013. PDF, Journal Site (123 citations).

[120]
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. PDF, Journal Site (84 citations).

[121]
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. PDF, Journal Site.

[122]
The RNA-binding protein repertoire of embryonic stem cells. S Chul Kwon, Hyerim Yi, Katrin Eichelbaum, Sophia Föhr, Bernd Fischer, Kwon Tae You, Alfredo Castello, Jeroen Krijgsveld, Matthias W Hentze, and V Narry Kim. Nature Structural and Molecular Biology, page 1122, 2013. PDF, Journal Site (214 citations).

[123]
Detecting differential usage of exons from RNA-Seq data. Simon Anders*, Alejandro Reyes*, and Wolfgang Huber. Genome Research, 22:2008-2017, 2012. PDF, Journal Site (502 citations).

[124]
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. PDF, Journal Site (113 citations).

[125]
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. PDF, Journal Site (135 citations).

[126]
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. PDF, Journal Site (848 citations).

[127]
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. PDF, Journal Site (700 citations).

[128]
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. PDF, Journal Site (44 citations)

[129]
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. PDF, Journal Site (119 citations).

[130]
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. PDF, Journal Site (108 citations).

[131]
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. PDF, Journal Site (64 citations).

[132]
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. PDF, Journal Site (12 citations)

[133]
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. PDF, Journal Site (60 citations).

[134]
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. PDF, Journal Site (10 citations)

[135]
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. PDF, Journal Site (332 citations).

[136]
Assessing Affymetrix GeneChip microarray quality. Matthew M. McCall, Peter N. Murakami, Margus Lukk, Wolfgang Huber, and Rafael A. Irizarry. BMC Bioinformatics, 12:137, 2011. PDF, Journal Site (37 citations)

[137]
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. PDF, Journal Site.

[138]
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. PDF, Journal Site (10 citations)

[139]
H3K4 tri-methylation provides an epigenetic signature of active enhancers. Aleksandra P ekowska, 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. PDF, Journal Site (177 citations).

[140]
Independent filtering increases detection power for high-throughput experiments. Richard Bourgon, Robert Gentleman, and Wolfgang Huber. PNAS, 107(21):9546-9551, 2010. PDF, Journal Site (298 citations).

[141]
Differential expression analysis for sequence count data. Simon Anders and Wolfgang Huber. Genome Biology, 11:R106, 2010. PDF, Journal Site (6399 citations).

[142]
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. PDF, Journal Site (96 citations).

[143]
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. PDF, Journal Site (200 citations).

[144]
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. PDF, Journal Site (77 citations).

[145]
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. PDF, Journal Site (529 citations).

[146]
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. PDF, Journal Site (310 citations).

[147]
Organelle proteomics experimental designs and analysis. Laurent Gatto, Juan Antonio Vizcaíno, Henning Hermjakob, Wolfgang Huber, and Kathryn S. Lilley. Proteomics, 2010. PDF, Journal Site (32 citations)

[148]
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. PDF, Journal Site (68 citations).

[149]
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. PDF, Journal Site (369 citations).

[150]
Microarray data quality control improves the detection of differentially expressed genes. Audrey Kauffmann and Wolfgang Huber. Genomics, 95:138-142, 2010. PDF, Journal Site (46 citations)

[151]
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. PDF, Journal Site (25 citations)

[152]
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. PDF, Journal Site (47 citations)

[153]
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. PDF, Journal Site (225 citations).

[154]
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. PDF, Journal Site (30 citations)

[155]
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. PDF, Journal Site.

[156]
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. PDF, Journal Site.

[157]
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. PDF, Journal Site.

[158]
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. PDF, Journal Site.

[159]
arrayQualityMetrics - a Bioconductor package for quality assessment of microarray data. Audrey Kauffmann, Robert Gentleman, and Wolfgang Huber. Bioinformatics, 25:415-416, 2009. PDF, Journal Site.

[160]
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. PDF, Journal Site.

[161]
The hwriter package. Gregoire Pau and Wolfgang Huber. The R Journal, 1(1):22-24, 2009. PDF, Journal Site.

[162]
Visualisation of genomic data with the Hilbert curve. Simon Anders. Bioinformatics, 25:1231-1235, 2009. PDF, Journal Site.

[163]
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. PDF, Journal Site (218 citations).

[164]
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. PDF, Journal Site (181 citations).

[165]
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. PDF, Journal Site.

[166]
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. PDF, Journal Site.

[167]
Analyzing ChIP-chip data using Bioconductor. Jörn Tödling and Wolfgang Huber. PLoS Computational Biology, 4(11), 2008. PDF, Journal Site.

[168]
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. PDF, Journal Site.

[169]
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. PDF, Journal Site.

[170]
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. PDF, Journal Site.

[171]
Estimating node degree in bait-prey graphs. Denise Scholtens, Tony Chiang, Wolfgang Huber, and Robert Gentleman. Bioinformatics, 24(2):218-224, 2008. PDF, Journal Site.

[172]
Bioconductor Case Studies. Use R. Springer. Florian Hahne, Wolfgang Huber, Robert Gentleman, and Seth Falcon, 2008. PDF, Journal Site (130 citations).

[173]
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. PDF, Journal Site.

[174]
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. PDF, Journal Site.

[175]
Making the most of high-throughput protein-interaction data. Robert Gentleman and Wolfgang Huber. Genome Biology, 8(10):112-112, 2007. PDF, Journal Site.

[176]
Graphs in molecular biology. Wolfgang Huber, Vincent J. Carey, Li Long, Seth Falcon, and Robert Gentleman. BMC Bioinformatics, 8(Suppl. 6), 2007. PDF, Journal Site.

[177]
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. PDF, Journal Site.

[178]
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. PDF, Journal Site.

[179]
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. PDF, Journal Site.

[180]
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. PDF, Journal Site.

[181]
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. PDF, Journal Site.

[182]
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. PDF, Journal Site.

[183]
Analysis of cell-based RNAi screens. Michael Boutros, Lígia P. Brás, and Wolfgang Huber. Genome Biology, 7(7), 2006. PDF, Journal Site.

[184]
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. PDF, Journal Site.

[185]
Transcript mapping with high-density oligonucleotide tiling arrays. Wolfgang Huber, Jörn Tödling, and Lars M. Steinmetz. Bioinformatics, 22(16):1963-1970, 2006. PDF, Journal Site.

[186]
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. PDF, Journal Site.

[187]
Reproducible statistical analysis in microarray profiling studies. Ulrich Mansmann, Markus Ruschhaupt, and Wolfgang Huber. Methods of Information in Medicine, 45:139-145, 2006. PDF, Journal Site.

[188]
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. PDF, Journal Site.

[189]
Visualizing genomic data. Robert Gentleman, Florian Hahne, and Wolfgang Huber. Technical Report 10, Bioconductor Project Working Papers, 2006. PDF, Journal Site.

[190]
Image analysis for microscopy screens. Oleg Sklyar and Wolfgang Huber. R News, 6(5):12-16, 2006. PDF, Journal Site.

[191]
Transcript mapping with high-density tiling arrays. Matthew Ritchie and Wolfgang Huber. R News, 6(5):23-27, 2006. PDF, Journal Site.

[192]
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. PDF, Journal Site.

[193]
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. PDF, Journal Site.

[194]
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. PDF, Journal Site.

[195]
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. PDF, Journal Site.

[196]
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. PDF, Journal Site.

[197]
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.

[198]
Bioinformatics - from Genomes to Therapies, chapter Low-level analysis of microarray experiments. Wolfgang Huber, Anja von Heydebreck, and Martin Vingron. Wiley-VCH, 2005. PDF.

[199]
On the synthesis of microarray experiments. Robert Gentleman, Markus Ruschhaupt, and Wolfgang Huber. Journal de la Société Française de Statistique, 146(1-2), 2005. PDF, Journal Site.

[200]
Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer. Robert Gentleman, Vincent J. Carey, Wolfgang Huber, Rafael Irizarry, and Sandrine Dudoit, editors, 2005. Journal Site (2635 citations).

[201]
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. PDF, Journal Site.

[202]
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. Wolfgang Huber and Robert Gentleman. Bioinformatics, 20:1651-1652, 2004. PDF, Journal Site.

[203]
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. PDF, Journal Site (98 citations).

[204]
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. PDF, Journal Site.

[205]
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. PDF, Journal Site.

[206]
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 (17 citations)

[207]
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 (63 citations).

[208]
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 (89 citations).

[209]
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. PDF, Journal Site.

[210]
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.

[211]
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. PDF, Journal Site (193 citations).

[212]
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 (59 citations).

[213]
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. PDF, Journal Site.

[214]
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. PDF, Journal Site (2062 citations).

[215]
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.

[216]
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. PDF, Journal Site.

[217]
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. PDF, Journal Site.

[218]
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. PDF, Journal Site.

[219]
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. PDF, Journal Site (83 citations).

[220]
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. PDF, Journal Site.

[221]
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. PDF, Journal Site.

[222]
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. PDF, Journal Site.

[223]
Vestibular-neck interaction and transformation of sensory coordinates. Thomas Mergner, Wolfgang Huber, and Wolfgang Becker. Journal of Vestibular Research, 7:347-367, 1997.

[224]
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. PDF.

[225]
Fast Monte Carlo algorithm for nonequilibrium systems. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Physical Review E, 53:4232-4235, 1996. PDF, Journal Site.

[226]
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. PDF, Journal Site.

[227]
The macroscopic limit in a stochastic reaction-diffusion process. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Europhysics Letters, 30:69-74, 1995. PDF, Journal Site.

[228]
Fluctuation effects on wave propagation in a reaction-diffusion process. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Physica D, 73:259-273, 1994. PDF, Journal Site.

[229]
Dynamics of strongly driven open quantum systems. Wolfgang Huber. PhD thesis, University of Freiburg, 1998. PDF.

[230]
The description of reaction diffusion processes by master equations. Wolfgang Huber. Diploma thesis, University of Freiburg, 1994. PDF.
* indicates equal contributions
 co-corresponding authorships
1Source: ISI Web of Science.


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