Page built: 21 Apr 2024 02:04

[1]

SpatialData: an open and universal data framework for spatial omics. Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Marcella Toth, Rahul B. Shrestha, Harald Vöhringer, Wolfgang Huber, Moritz Gerstung, Josh Moore, Fabian J. Theis, and Oliver Stegle. Nature Methods, March 2024.
PDF - DOI:10.1038/s41592-024-02212-x - Preprint - EuropePMC.

[2]

Restraining Wnt activation and intestinal tumorigenesis by a Rab35 dependent GTPase relay. Siamak Redhai, Tianyu Wang, Kim Boonekamp, Saskia Reuter, Tümay Capraz, Svenja Leible, Shivohum Bahaguna, Fillip Port, Bojana Pavlović, Michaela Holzem, Roman Doll, Niklas Rindtorff, Erica Valentini, Barbara Schmitt, Karsten Richter, Ulrike Engel, Wolfgang Huber, and Michael Boutros. 2024.
DOI:10.1101/2024.02.05.578891 - Preprint - EuropePMC.

[3]

In situ analysis of osmolyte mechanisms of proteome thermal stabilisation. Monika Pepelnjak, Britta Velten, Nicolas Näpflin, Tatjana von Rosen, Umberto Capasso Palmiero, Heather D. Maynard, Paolo Arosio, Eilika Weber-Ban, Natalie de Souza, Wolfgang Huber, and Paola Picotti. Nature Chemical Biology, 2024.
PDF - DOI:10.1038/s41589-024-01568-7 - EuropePMC.

[4]

Multimodal and spatially resolved profiling identifies distinct patterns of T-cell infiltration in nodal B-cell lymphoma entities. Tobias Roider, Marc A. Baertsch, Donnacha Fitzgerald, Harald Vöhringer, Berit J. Brinkmann, Felix Czernilofsky, Mareike Knoll, Laura Llaó-Cid, Peter-Martin Bruch, Nora Liebers, Christian M. Schürch, Verena Passerini, Alexander Brobeil, Gunhild Mechtersheimer, Carsten Müller-Tidow, Oliver Weigert, Martina Seiffert, Garry P. Nolan, Wolfgang Huber^✉, and Sascha Dietrich^✉. Nature Cell Biology, 2024.
PDF - DOI:10.1038/s41556-024-01358-2 - Preprint - EuropePMC.

[5]

Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq. Thomas Schwarzl, Sudeep Sahadevan, Benjamin Lang, Milad Miladi, Rolf Backofen, Wolfgang Huber, Matthias W Hentze^✉, and Gian G Tartaglia^✉. Nucleic Acids Research, 52(1), January 2024.
PDF - DOI:10.1093/nar/gkad998 - Preprint - EuropePMC.

[6]

BioModels Model of the Year 2023. Rahuman S. Malik-Sheriff, Hiroki Asari, Henning Hermjakob, Wolfgang Huber, Thomas Quail, Silvia DM Santos, Amber M Smith, and Virginie Uhlmann. Frontiers in Systems Biology, 2024.
PDF - DOI:10.3389/fsysb.2024.1363884.

[7]

A single-cell multi-omic and spatial atlas of B cell lymphomas reveals differentiation drives intratumor heterogeneity. Donnacha Fitzgerald, Tobias Roider, Marc-Andrea Baertsch, Artur Kibler, Anastasiia Horlova, Erin Chung, Harald Vöhringer, Anna Mathioudaki, Bettina Budeus, Verena Passerini, Mareike Knoll, Johannes Mammen, Linsha Li, Léandra Caillé, Felix Czernilofsky, Peter-Martin Bruch, Nora Liebers, Matthias Meyer-Bender, Oliver Weigert, Judith Zaugg, Garry Nolan, Marc Seifert, Sascha Dietrich^✉, and Wolfgang Huber^✉. bioRχiv, 2023.
DOI:10.1101/2023.11.06.565756 - Preprint - EuropePMC.

[8]

Analysis of multi-condition single-cell data with latent embedding multivariate regression. Constantin Ahlmann-Eltze and Wolfgang Huber. bioRχiv, March 2023.
PDF - DOI:10.1101/2023.03.06.531268 - Preprint - EuropePMC.

[9]

Proteomic profiling identifies Serpin B9 as mediator of resistance to CAR T-cell and bispecific antibody treatment in B-cell lymphoma. Berit J. Brinkmann*, Tümay Capraz*, Tobias Roider*, Mareike Knoll, Carolin Kolb, Yi Liu, Antonia-Eugenia Angeli-Terzidou, Nagarajan Paramasivam, Björn Chapuy, Volker Eckstein, Tim Sauer, Michael Schmitt, Andreas Rosenwald, Carsten Müller-Tidow, Wolfgang Huber^✉, and Sascha Dietrich^✉. bioRχiv, 2023.
DOI:10.1101/2023.06.26.546507 - Preprint - EuropePMC.

[10]

A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens. Hagen M. Gegner*, Thomas Naake*, Karim Aljakouch*, Aurelien Dugourd*, Georg Kliewer, Torsten Müller, Dustin Schilling, Marc A. Schneider, Nina Kunze-Rohrbach, Rüdiger Hell Thomas G.P. Grünewald, Julio Saez-Rodriguez, Wolfgang Huber, Gernot Poschet^✉, and Jeroen Krijgsveld^✉. bioRχiv, 2023.
DOI:10.1101/2023.11.07.561857 - Preprint - EuropePMC.

[11]

Feature selection by replicate reproducibility and non-redundancy. Tümay Capraz and Wolfgang Huber. bioRχiv, 2023.
DOI:10.1101/2023.07.04.547623 - Preprint - EuropePMC.

[12]

Systematic analysis of drug combinations against Gram-positive bacteria. Elisabetta Cacace, Vladislav Kim, Vallo Varik, Michael Knopp, Manuela Tietgen, Amber Brauer-Nikonow, Kemal Inecik, André Mateus, Alessio Milanese, Marita Torrissen Mårli, Karin Mitosch, Joel Selkrig, Ana Rita Brochado, Oscar P. Kuipers, Morten Kjos, Georg Zeller, Mikhail M. Savitski, Stephan Göttig, Wolfgang Huber, and Athanasios Typas. Nature Microbiology, 8:2196, November 2023.
PDF - DOI:10.1038/s41564-023-01486-9 - Preprint - EuropePMC.

[13]

Meta-research: The changing career paths of PhDs and postdocs trained at EMBL. Junyan Lu, Britta Velten, Bernd Klaus, Mauricio Ramm, Wolfgang Huber, and Rachel Coulthard-Graf. eLife, November 2023.
PDF - DOI:10.7554/eLife.78706 - Preprint - EuropePMC.

[14]

MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. Thomas Naake, Johannes Rainer, and Wolfgang Huber. Bioinformatics, 39, October 2023.
PDF - DOI:10.1093/bioinformatics/btad618 - Preprint - EuropePMC.

[15]

Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: The prospective non-interventional SMARTrial. Nora Liebers*, Peter-Martin Bruch*, Tobias Terzer, Miguel Hernandez, Nagarajan Paramasivam, Donnacha Fitzgerald, Heidi Altmann, Tobias Roider, Carolin Kolb, Mareike Knoll, Angela Lenze, Uwe Platzbecker, Christoph Röllig, Claudia Baldus, Hubert Serve, Martin Bornhäuser, Daniel Hübschmann, Carsten Müller-Tidow, Friedrich Stölzel, Wolfgang Huber, Axel Benner, Thorsten Zenz, Junyan Lu, and Sascha Dietrich. Nature Cancer, 4:1648, October 2023.
PDF - DOI:10.1038/s43018-023-00645-5 - EuropePMC.

[16]

Deep thermal profiling for detection of functional proteoform groups. Nils Kurzawa, Isabelle Rose Leo, Matthias Stahl, Elena Kunold, Isabelle Becher, Anastasia Audrey, Georgios Mermelekas, Wolfgang Huber, André Mateus, Mikhail M. Savitski, and Rozbeh Jafari. Nature Chemical Biology, 19(8):962-971, August 2023.
PDF - DOI:10.1038/s41589-023-01284-8 - Preprint - EuropePMC.

[17]

Comparing the value of mono- versus coculture for high-throughput compound screening in hematological malignancies. Sophie A. Herbst*, Vladislav Kim*, Tobias Roider, Eva C. Schitter, Peter-Martin Bruch, Nora Liebers, Carolin Kolb, Mareike Knoll, Junyan Lu, Peter Dreger, Carsten Müller-Tidow, Thorsten Zenz, Wolfgang Huber^✉, and Sascha Dietrich^✉. Blood Advances, June 2023.
PDF - DOI:10.1182/bloodadvances.2022009652 - Preprint - EuropePMC.

[18]

Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia. Almut Lütge*, Junyan Lu*, Jennifer Hüllein, Tatjana Walther, Leopold Sellner, Bian Wu, Richard Rosenquist, Christopher C. Oakes, Sascha Dietrich, Wolfgang Huber^✉, and Thorsten Zenz^✉. Haematologica, May 2023.
PDF - DOI:10.3324/haematol.2022.281869 - Preprint - EuropePMC.

[19]

Comparison of transformations for single-cell RNA-seq data. Constantin Ahlmann-Eltze and Wolfgang Huber. Nature Methods, 20(5):665-672, May 2023. (30 citations, source: Semantic Scholar)
PDF - DOI:10.1038/s41592-023-01814-1 - Preprint - EuropePMC.

[20]

htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets. Sudeep Sahadevan, Thileepan Sekaran, Nadia Ashaf, Marko Fritz, Matthias W. Hentze, Wolfgang Huber, and Thomas Schwarzl. Bioinformatics, 39(1), January 2023.
PDF - DOI:10.1093/bioinformatics/btac747 - EuropePMC.

[21]

Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis. Hagen M Gegner*, Thomas Naake*, Aurélien Dugourd*, Torsten Müller*, Felix Czernilofsky, Georg Kliewer, Evelyn Jäger, Barbara Helm, Nina Kunze-Rohrbach, Ursula Klingmüller, Carsten Hopf, Carsten Müller-Tidow, Sascha Dietrich, Julio Saez-Rodriguez, Wolfgang Huber, Rüdiger Hell, Gernot Poschet, and Jeroen Krijgsveld. Frontiers in Molecular Biosciences, 9, December 2022.
PDF - DOI:10.3389/fmolb.2022.961448 - Preprint - EuropePMC.

[22]

Single-cell multi-omic and spatial analysis of nodal B cell non-Hodgkin lymphomas reveals plasticity in B cell maturation as a driver of intratumor heterogeneity. Donnacha Fitzgerald, Tobias Roider, Marc-A. Baertsch, Harald Vöhringer, Mareike Knoll, Bettina Budeus, Artur Kibler, Anna Mathioudaki, Léandra Caillé, Linsha Li, Johannes Mammen, Marc Seifert, Wolfgang Huber, and Sascha Dietrich. Blood, 140:742, November 2022.
DOI:10.1182/blood-2022-156210.

[23]

Viral transduction of primary human lymphoma B cells reveals mechanisms of NOTCH-mediated immune escape. Maurizio Mangolini, Alba Maiques-Diaz, Stella Charalampopoulou, Elena Gerhard-Hartmann, Johannes Bloehdorn, Andrew Moore, Junyan Lu, Valar Nila Roamio Franklin, Chandra Sekhar Reddy Chilamakuri, Ilias Moutsoupoulos, Andreas Rosenwald, Stephan Stilgenbauer, Thorsten Zenz, Irina I. Mohorianu, Clive S. D’Santos, Silvia Deaglio, Daniel J. Hodson, José Ignacio Martín-Subero, and Ingo Ringshausen. Nature Communications, October 2022.
PDF - DOI:10.1038/s41467-022-33739-2 - Preprint - EuropePMC.

[24]

Systematic discovery of biomolecular condensate-specific protein phosphorylation. Sindhuja Sridharan, Alberto Hernandez-Armendariz, Nils Kurzawa, Clement M Potel, Danish Memon, Pedro Beltrao, Marcus Bantscheff, Wolfgang Huber, Sara Cuylen-Haering, and Mikhail M Savitski. Nature Chemical Biology, 18(10):1104, October 2022. (35 citations, source: Semantic Scholar)
PDF - DOI:10.1038/s41589-022-01062-y - EuropePMC.

[25]

Proteogenomics refines the molecular classification of chronic lymphocytic leukemia. Sophie A. Herbst, Mattias Vesterlund, Alexander J. Helmboldt, Rozbeh Jafari, Ioannis Siavelis, Matthias Stahl, Eva C. Schitter, Nora Liebers, Berit J. Brinkmann, Felix Czernilofsky, Tobias Roider, Peter-Martin Bruch, Murat Iskar, Adam Kittai, Ying Huang, Junyan Lu, Sarah Richter, Georgios Mermelekas, Husen Muhammad Umer, Mareike Knoll, Carolin Kolb, Angela Lenze, Xiaofang Cao, Cecilia Österholm, Linus Wahnschaffe, Carmen Herling, Sebastian Scheinost, Matthias Ganzinger, Larry Mansouri, Katharina Kriegsmann, Mark Kriegsmann, Simon Anders, Marc Zapatka, Giovanni Del Poeta, Antonella Zucchetto, Riccardo Bomben, Valter Gattei, Peter Dreger, Jennifer Woyach, Marco Herling, Carsten Müller-Tidow, Richard Rosenquist, Stephan Stilgenbauer, Thorsten Zenz, Wolfgang Huber, Eugen Tausch, Janne Lehtiö^✉, and Sascha Dietrich^✉. Nature Communications, 13(6226), October 2022. (14 citations, source: Semantic Scholar)
PDF - DOI:10.1038/s41467-022-33385-8 - Preprint - EuropePMC.

[26]

Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels. Katharina Imkeller, Giulia Ambrosi, Nancy Klemm, Ainara Claveras Cabezudo, Luisa Henkel, Wolfgang Huber, and Michael Boutros. Molecular Systems Biology, 18(8), August 2022.
PDF - DOI:10.15252/msb.202110874 - EuropePMC.

[27]

Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL. Peter-Martin Bruch*, Holly A. R. Giles*, Carolin Kolb, Sophie A Herbst, Tina Becirovic, Tobias Roider, Junyan Lu, Sebastian Scheinost, Lena Wagner, Jennifer Huellein, Ivan Berest, Mark Kriegsmann, Katharina Kriegsmann, Christiane Zgorzelski, Peter Dreger, Judith B Zaugg, Carsten Müller-Tidow, Thorsten Zenz, Wolfgang Huber^✉, and Sascha Dietrich^✉. Molecular Systems Biology, 18:e10855, July 2022.
PDF - DOI:10.15252/msb.202110855 - Preprint - EuropePMC.

[28]

Silver clusters of five atoms as highly selective antitumoral agents through irreversible oxidation of thiols. Vanesa Porto, David Buceta, Blanca Domínguez, Carmen Carneiro, Erea Borrajo, María Fraile, Nerea Davila-Ferreira, Iria R. Arias, José M. Blanco, Maria C. Blanco, Juan M. Devida, Lisandro J. Giovanetti, Félix G. Requejo, Juan C. Hernández-Garrido, José J. Calvino, Miguel López-Haro, Giampaolo Barone, Andrew M. James, Tomás García-Caballero, Diego M. González-Casta no, Martin Treder, Wolfgang Huber, Anxo Vidal, Michael P. Murphy, M. Arturo López-Quintela^✉, and Fernando Domínguez^✉. Advanced Functional Materials, 32(29), July 2022.
PDF - DOI:10.1002/adfm.202113028.

[29]

Networks and graphs discovery in metabolomics data analysis and interpretation. Adam Amara, Clement Frainay, Fabien Jourdan, Thomas Naake, Steffen Neumann, Elva Maria Novoa del Toro, Reza M Salek, Liesa Salzer, Sarah Scharfenberg, and Michael Witting. Frontiers in Molecular Biosciences, 9, March 2022. (32 citations, source: Semantic Scholar)
PDF - DOI:10.3389/fmolb.2022.841373 - EuropePMC.

[30]

MatrixQCvis: shiny-based interactive data quality exploration for omics data. Thomas Naake^✉and Wolfgang Huber^✉. Bioinformatics, February 2022.
PDF - DOI:10.1093/bioinformatics/btab748 - Preprint - EuropePMC.

[31]

The protein landscape of chronic lymphocytic leukemia. Fabienne Meier-Abt*, Junyan Lu*, Ester Cannizzaro, Marcel F Pohly, Sandra Kummer, Sibylle Pfammatter, Laura Kunz, Ben C. Collins, Ferran Nadeu, Kwang S Lee, Peng Xue, Myriam Gwerder, Michael Roiss, Jennifer Hüllein, Sebastian Scheinost, Sascha Dietrich, Elías Campo, Wolfgang Huber^✉, Ruedi Aebersold^✉, and Thorsten Zenz^✉. Blood, The Journal of the American Society of Hematology, 138(24):2514-2525, December 2021. (17 citations, source: Semantic Scholar)
PDF - DOI:10.1182/blood.2020009741 - EuropePMC.

[32]

An autologous culture model of nodal B-cell lymphoma identifies ex vivo determinants of response to bispecific antibodies. Tobias Roider, Berit J. Brinkmann, Vladislav Kim, Mareike Knoll, Carolin Kolb, Philipp M. Roessner, Marie Bordas, Peter Dreger, Carsten Müller-Tidow, Wolfgang Huber, Martina Seiffert, and Sascha Dietrich. Blood Advances, 5(23), December 2021.
PDF - DOI:10.1182/bloodadvances.2021005400 - EuropePMC.

[33]

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting. Rozemarijn Kleinendorst, Guido Barzaghi, Mike L. Smith, Judith B. Zaugg, and Arnaud R. Krebs. Nature Protocols, 16:5673, November 2021.
PDF - DOI:10.1038/s41596-021-00630-1 - EuropePMC.

[34]

Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia. Junyan Lu*, Ester Cannizzaro*, Fabienne Meier-Abt, Sebastian Scheinost, Peter-Martin Bruch, Holly A. R. Giles, Almut Lütge, Jennifer Hüllein, Lena Wagner, Brian John Giacopelli, Ferran Nadeu, Julio Delgado, Elías Campo, Maurizio Mangolini, Ingo Ringshausen, Martin Böttcher, Dimitrios Mougiakakos, Andrea Jacobs, Bernd Bodenmiller, Sascha Dietrich, Christopher C. Oakes, Thorsten Zenz^✉, and Wolfgang Huber^✉. Nature Cancer, 2(8):853-864, July 2021. (30 citations, source: Semantic Scholar)
PDF - DOI:10.1038/s43018-021-00216-6 - EuropePMC.

[35]

Polatuzumab vedotin as a salvage and bridging treatment in relapsed or refractory large B-cell lymphomas. N. Liebers, J. Duell, D. Fitzgerald, A. Kerkhoff, D. Noerenberg, Eva Kaebisch, F. Acker, S. Fuhrmann, C. Leng, M. Welslau, J. Chemnitz, J. Middeke, T. Weber, U. Holtick, R. Trappe, Roald Pfannes, R. Liersch, Christian Spoer, S. Fuxius, N. Gebauer, Léandra Caillé, T. Geer, C. Koenecke, U. Keller, R. Claus, D. Mougiakakos, Stephanie Mayer, A. Huettmann, C. Pott, A. Trummer, G. Wulf, U. Brunnberg, L. Bullinger, G. Hess, C. Mueller-Tidow, B. Glass, G. Lenz, P. Dreger, and S. Dietrich. Blood Advances, 5(13):2707-2716, July 2021. (52 citations, source: Semantic Scholar)
PDF - DOI:10.1182/bloodadvances.2020004155 - EuropePMC.

[36]

CXCR4 hyperactivation cooperates with TCL1 in CLL development and aggressiveness. Richard Lewis, Hans Carlo Maurer, Nikita Singh, Irene González-Menéndez, Matthias Wirth, Markus Schick, Le Zhang, Konstandina Isaakidis, Anna Katharina Scherger, Veronika Schulze, Junyan Lu, Thorsten Zenz, Katja Steiger, Roland Rad, Leticia Quintanilla‐Martinez, Marion Espéli, Karl Balabanian, Ulrich Keller, and Stefan Habringer. Leukemia, 35(10):2895-2905, August 2021.
PDF - DOI:10.1038/s41375-021-01376-1 - EuropePMC.

[37]

Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake. Magdalena Zimoń, Yunfeng Huang, Anthi Trasta, Aliaksandr Halavatyi, Jimmy Z Liu, Chia-Yen Chen, Peter Blattmann, Bernd Klaus, Christopher D Whelan, David Sexton, Sally John, Wolfgang Huber, Ellen A Tsai, Rainer Pepperkok, and Heiko Runz. Nature Communications, November 2021.
PDF - DOI:10.1038/s41467-021-26761-3 - Preprint - EuropePMC.

[38]

SAMHD1 mutations in mantle cell lymphoma are recurrent and confer in vitro resistance to nucleoside analogues. M. Bühler, Junyan Lu, S. Scheinost, F. Nadeu, D. Roos-Weil, M. Hensel, Tharshika Thavayogarajah, H. Moch, M. Manz, E. Haralambieva, E. Marques Maggio, S. Beà, E. Giné, E. Campo, O. Bernard, W. Huber, and T. Zenz. Leukemia Research, 107:106608, Aug 2021.
PDF - DOI:10.1016/j.leukres.2021.106608 - Preprint - EuropePMC.

[39]

IGLV3-21R110 identifies an aggressive biological subtype of chronic lymphocytic leukemia with intermediate epigenetics. Ferran Nadeu, Romina Royo, Guillem Clot, Martí Duran-Ferrer, Alba Navarro, Silvia Martín, Junyan Lu, Thorsten Zenz, Tycho Baumann, Pedro Jares, Xosé S. Puente, Iñaki Martin-Subero, Julio Delgado, and Elías Campo. Blood, The Journal of the American Society of Hematology, 137(21):2935-2946, May 2021. (46 citations, source: Semantic Scholar)
PDF - DOI:10.1182/blood.2020008311 - EuropePMC.

[40]

The balance between the intronic mir-342 and its host gene evl determines hematopoietic cell fate decision. Friederike Herbst, Tonio Lang, Elias S. P. Eckert, Peer Wünsche, Alexander A. Wurm, Tim Kindinger, Karin Laaber, Shayda Hemmati, Agnes Hotz-Wagenblatt, Oksana Zavidij, Anna Paruzynski, Junyan Lu, Christof von Kalle, Thorsten Zenz, Christoph Klein, Manfred Schmidt, Claudia R. Ball, and Hanno Glimm. Leukemia, 35(10):2948-2963, May 2021. (10 citations, source: Semantic Scholar)
PDF - DOI:10.1038/s41375-021-01267-5 - EuropePMC.

[41]

Control of PD-L1 expression in CLL-cells by stromal triggering of the Notch-c-Myc-EZH2 oncogenic signaling axis. Martin Böttcher, Heiko Bruns, Simon Völkl, Junyan Lu, Elisavet Chartomatsidou, Nikos Papakonstantinou, Kristin Mentz, Maike Büttner-Herold, Thorsten Zenz, Marco Herling, Wolfgang Huber, Paolo Ghia, Kostas Stamatopoulos, Andreas Mackensen, and Dimitrios Mougiakakos. Journal for ImmunoTherapy of Cancer, 9(4), April 2021. (16 citations, source: Semantic Scholar)
PDF - DOI:10.1136/jitc-2020-001889 - EuropePMC.

[42]

Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. K. Kong, Bernd Fischer, M. Meurer, Ilia Kats, Zhaoyan Li, F. Rühle, Joseph Barry, D. Kirrmaier, Veronika Chevyreva, Bryan-Joseph San Luis, M. Costanzo, Wolfgang Huber, Brenda Andrews, Charles Boone, Michael Knop, and Anton Khmelinskii. Molecular Cell, 81(11):2460, June 2021. (27 citations, source: Semantic Scholar)
PDF - DOI:10.1016/j.molcel.2021.04.018 - EuropePMC.

[43]

Covariate powered cross-weighted multiple testing. Nikolaos Ignatiadis and Wolfgang Huber. Journal of the Royal Statistical Society: Series B, 83:720–-751, 2021. (48 citations, source: Semantic Scholar)
PDF - DOI:10.1111/rssb.12411 - Preprint.

[44]

Analysis of nonleukemic cellular subcompartments reconstructs clonal evolution of acute myeloid leukemia and identifies therapy-resistant preleukemic clones. Borhan R Saeed, Linda Manta, Simon Raffel, Paul Theodor Pyl, Eike C Buss, Wenwen Wang, Volker Eckstein, Anna Jauch, Andreas Trumpp, Wolfgang Huber, Anthony D Ho, and Christoph Lutz. International Journal of Cancer, 148(11):2825, June 2021.
PDF - DOI:10.1002/ijc.33461 - EuropePMC.

[45]

glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data. Constantin Ahlmann-Eltze and Wolfgang Huber. Bioinformatics, 36(24):5701-5702, 2020. (109 citations, source: Semantic Scholar)
PDF - DOI:10.1093/bioinformatics/btaa1009 - Preprint - EuropePMC.

[46]

The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome. Martí Duran-Ferrer, Guillem Clot, Ferran Nadeu, Renée Beekman, Tycho Baumann, Jessica Nordlund, Yanara Marincevic-Zuniga, Gudmar Lönnerholm, Alfredo Rivas-Delgado, Silvia Martín, Raquel Ordoñez, Giancarlo Castellano, Marta Kulis, Ana C. Queirós, Seung-Tae Lee, Joseph L. Wiemels, Romina Royo, Montserrat Puiggrós, Junyan Lu, Eva Giné, Sílvia Beà, Pedro Jares, Xabier Agirre, Felipe Prósper, Carlos López-Otín, Xosé S. Puente, Christopher C. Oakes, Thorsten Zenz, Julio Delgado, Armando López-Guillermo, Elías Campo, and José Ignacio Martín-Subero. Nature Cancer, 1(11):1066, November 2020. (54 citations, source: Semantic Scholar)
PDF - DOI:10.1038/s43018-020-00131-2 - EuropePMC.

[47]

A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nils Kurzawa, Isabelle Becher, Sindhuja Sridharan, Holger Franken, André Mateus, Simon Anders, Marcus Bantscheff^✉, Wolfgang Huber^✉, and Mikhail M. Savitski^✉. Nature Communications, 11:5783, Nov 2020. (27 citations, source: Semantic Scholar)
PDF - DOI:10.1038/s41467-020-19529-8 - Preprint - EuropePMC.

[48]

Developmental gene expression differences between humans and mammalian models. Margarida Cardoso-Moreira, Ioannis Sarropoulos, Britta Velten, M. Mort, D. Cooper, Wolfgang Huber, and Henrik Kaessmann. Cell Reports, 33, Oct 2020. (44 citations, source: Semantic Scholar)
PDF - DOI:10.1016/j.celrep.2020.108308 - Preprint - EuropePMC.

[49]

Transparency and reproducibility in artificial intelligence. Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, MAQC Society Board, Levi Waldron, Bo Wang, Chris McIntosh, Anshul Kundaje, Casey S. Greene, Michael M. Hoffman, Jeffrey T. Leek, Wolfgang Huber, Alvis Brazma, Joelle Pineau, Robert Tibshirani, Trevor Hastie, John P.A. Ioannidis, John Quackenbush, and Hugo J.W.L. Aerts. Nature, 586 7829:E14-E16, Oct 2020. (257 citations, source: Semantic Scholar)
PDF - DOI:10.1038/s41586-020-2766-y - Preprint - EuropePMC.

[50]

Miniaturized drug sensitivity and resistance test on patient-derived cells using droplet-microarray. A. A. Popova, S. Dietrich, W. Huber, M. Reischl, R. Peravali, and P. Levkin. SLAS Technology, 26(3):274-286, 2021. (10 citations, source: Semantic Scholar)
PDF - DOI:10.1177/2472630320934432 - EuropePMC.

[51]

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation. Erika Kelmer Sacramento, Joanna M Kirkpatrick, Mariateresa Mazzetto, Mario Baumgart, Aleksandar Bartolome, Simone Di Sanzo, Cinzia Caterino, Michele Sanguanini, Nikoletta Papaevgeniou, Maria Lefaki, Dorothee Childs, Sara Bagnoli, Eva Terzibasi Tozzini, Domenico Di Fraia, Natalie Romanov, Peter H Sudmant, Wolfgang Huber, Niki Chondrogianni, Michele Vendruscolo, Alessandro Cellerino, and Alessandro Ori. Molecular Systems Biology, 2020. (119 citations, source: Semantic Scholar)
PDF - DOI:10.15252/msb.20209596 - Preprint - EuropePMC.

[52]

IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms. Ferran Nadeu, Rut Mas de-les Valls, Alba Navarro, Romina Royo, Silvia Martín, Neus Villamor, Helena Suárez-Cisneros, Roso Marés, Junyan Lu, Anna Enjuanes, Alfredo Rivas-Delgado, Marta Aymerich, Tycho Baumann, Dolors Colomer, Julio Delgado, Ryan D. Morin, Thorsten Zenz, Xosé S. Puente, Peter J. Campbell, Sílvia Beà, Francesco Maura, and Elías Campo. Nature Communications, 11(1):1-11, July 2020. (20 citations, source: Semantic Scholar)
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Single cell 3’UTR analysis identifies changes in alternative polyadenylation throughout neuronal differentiation and in autism. Manuel Göpferich*, Nikhil Oommen George*, Ana Domingo Muelas, Alex Bizyn, R. Pascual, Daria Fijalkowska, Georgios Kalamakis, U. Müller, J. Krijgsveld, R. Méndez, I. Fariñas, W. Huber, S. Anders, and A. Martin-Villalba. bioRχiv, August 2020. (10 citations, source: Semantic Scholar)
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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. Nature Cell Biology, 22:896-906, June 2020. (88 citations, source: Semantic Scholar)
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Survey of ex vivo drug combination effects in chronic lymphocytic leukemia reveals synergistic drug effects and genetic dependencies. Marina Lukas*, Britta Velten*, Leopold Sellner, Katarzyna Tomska, Jennifer Hüllein, Tatjana Walther, Lena Wagner, Carolin Muley, Bian Wu, Malgorzata Oles, Sascha Dietrich, Alexander Jethwa, Hanibal Bohnenberger, Junyan Lu, Wolfgang Huber^✉, and Thorsten Zenz^✉. Leukemia, 34:2934, May 2020. (13 citations, source: Semantic Scholar)
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Genome-wide screens implicate loss of cullin ring ligase 3 in persistent proliferation and genome instability in TP53-deficient cells. Alexandros P Drainas, Ruxandra A Lambuta, Irina Ivanova, Özdemirhan Serçin, Ioannis Sarropoulos, Mike L Smith, Theocharis Efthymiopoulos, Benjamin Raeder, Adrian M Stütz, Sebastian M Waszak, Balca R Mardin, and Jan O Korbel. Cell Reports, 31(1):107465, April 2020. (19 citations, source: Semantic Scholar)
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Pan-cancer analysis of whole genomes. PJ Campbell, G Getz, Korbel JO, Stuart JM, ..., Wolfgang Huber, and ... (1341 authors). Nature, 578(7793):82, February 2020. (1789 citations, source: Semantic Scholar)
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Identifying drug targets in tissues and whole blood with thermal-shift profiling. 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, 38:303, January 2020. (94 citations, source: Semantic Scholar)
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gscreend: 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, 21(53), March 2020. (34 citations, source: Semantic Scholar)
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Transcriptional profiling reveals strong impact of major molecular disease subgroups and mixed epistasis in chronic lymphocytic leukemia. Thorsten Zenz, Almut Luetge, Junyan Lu, Jennifer Huellein, Sascha Dietrich, Leopold Sellner, and Wolfgang Huber. Blood, 134:1742, November 2019.
PDF - DOI:10.1182/blood-2019-126388.

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Ex-vivo drug response profiling for tailoring treatment in hematologic malignancies: The prospective non-interventional SMART-trial. Nora Liebers, Peter-Martin Bruch, Agnes Gambietz, Holly Giles, Junyan Lu, Mareike Knoll, Carolin Kolb, Peter Dreger, Carsten Mueller-Tidow, Wolfgang Huber, Axel Benner, Thorsten Zenz, and Sascha Dietrich. Blood, 134(Suppl. 1):376-376, 11 2019.
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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. (470 citations, source: Semantic Scholar)
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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.
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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. (145 citations, source: Semantic Scholar)
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Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes. Britta Velten and Wolfgang Huber. Biostatistics, 22:348-364, April 2021. (17 citations, source: Semantic Scholar)
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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 & Cellular Proteomics, 2019.
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Developmental subtypes assessed by DNA methylation-iPLEX forecast the natural history of chronic lymphocytic leukemia. Brian John Giacopelli, Qiuhong Zhao, Amy S. Ruppert, Akwasi Agyeman, Christoph Weigel, Yue zhong Wu, Madelyn M. Gerber, Kari G. Rabe, Melissa C. Larson, Junyan Lu, James S. Blachly, Kerry A. Rogers, William G. Wierda, Jennifer R. Brown, Kanti R. Rai, Michael J. Keating, Laura Rassenti, Thomas J. Kipps, Thorsten Zenz, Tait D. Shanafelt, Neil E. Kay, Lynne V. Abruzzo, Kevin R. Coombes, Jennifer A. Woyach, John C. Byrd, and Christopher C. Oakes. Blood, 134(8):688, August 2019. (26 citations, source: Semantic Scholar)
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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. (420 citations, source: Semantic Scholar)
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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. (39 citations, source: Semantic Scholar)
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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. (17 citations, source: Semantic Scholar)
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Reporting p Values. Wolfgang Huber. Cell Systems, 8(3):170, 2019.
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[73]

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, March 2019. (166 citations, source: Semantic Scholar)
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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. (17 citations, source: Semantic Scholar)
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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. (119 citations, source: Semantic Scholar)
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Modern Statistics for Modern Biology. Cambridge University Press. Susan Holmes and Wolfgang Huber, February 2019. (101 citations, source: Google Scholar), Online edition url.

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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. (259 citations, source: Semantic Scholar)
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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. (61 citations, source: Semantic Scholar)
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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. (15 citations, source: Semantic Scholar)
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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. (130 citations, source: Semantic Scholar)
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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, September 2018. (74 citations, source: Semantic Scholar)
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Drug-based perturbation screen uncovers synergistic drug combinations in Burkitt lymphoma. K. Tomska, R. Kurilov, K. S. Lee, J. Hüllein, M. Lukas, L. Sellner, T. Walther, L. Wagner, M. Oleś, B. Brors, W. Huber, and T. Zenz. Scientific Reports, 8, Aug 2018. (22 citations, source: Semantic Scholar)
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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. (48 citations, source: Semantic Scholar)
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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, Jun 2018.
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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, Jun 2018. (603 citations, source: Semantic Scholar)
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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, Jun 2018. (27 citations, source: Semantic Scholar)
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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, May 2018. (10 citations, source: Semantic Scholar)
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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, April 2018. (1443 citations, source: Semantic Scholar)
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Authoring Bioconductor workflows with BiocWorkflowTools. Mike L Smith, Andrzej K Oleś, and Wolfgang Huber. F1000Research, 7, 2018.
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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, February 2018. (388 citations, source: Semantic Scholar)
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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. (52 citations, source: Semantic Scholar)
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A brave new world of RNA-binding proteins. Matthias W. Hentze, Alfredo Castello, Thomas Schwarzl, and Thomas Preiss. Nature Reviews Molecular Cell Biology, January 2018. (1033 citations, source: Semantic Scholar)
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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. (79 citations, source: Semantic Scholar)
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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.
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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. (180 citations, source: Semantic Scholar)
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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. (305 citations, source: Semantic Scholar)
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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. (14 citations, source: Semantic Scholar)
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Two independent modes of chromatin organization revealed by cohesin removal. Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pękowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian Haering, Leonid Mirny, and Francois Spitz. Nature, 2017. (854 citations, source: Semantic Scholar)
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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. (13 citations, source: Semantic Scholar)
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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.
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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. (125 citations, source: Semantic Scholar)
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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. (690 citations, source: Semantic Scholar)
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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. (100 citations, source: Semantic Scholar)
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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. (65 citations, source: Semantic Scholar)
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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. (181 citations, source: Semantic Scholar)
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A clash of cultures in discussions of the P value. Wolfgang Huber. Nature Methods, 13:607, 2016. (10 citations, source: Semantic Scholar)
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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. (63 citations, source: Semantic Scholar)
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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. (120 citations, source: Semantic Scholar)
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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. (475 citations, source: Semantic Scholar)
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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.
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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.
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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.
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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. (21 citations, source: Semantic Scholar)
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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. (213 citations, source: Semantic Scholar)
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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. (176 citations, source: Semantic Scholar)
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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, Jan 2016. (145 citations, source: Semantic Scholar)
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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. (53 citations, source: Semantic Scholar)
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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. (73 citations, source: Semantic Scholar)
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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. (375 citations, source: Semantic Scholar)
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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. (15 citations, source: Semantic Scholar)
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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. (104 citations, source: Semantic Scholar)
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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. (154 citations, source: Semantic Scholar)
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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. (224 citations, source: Semantic Scholar)
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Mutational landscape and complexity in CLL. Thorsten Zenz and Wolfgang Huber. Blood, 126(18):2078-2079, 2015.
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BRAF inhibitor therapy in HCL. Sascha Dietrich and Thorsten Zenz. Best Practice & Research Clinical Haematology, 28(4):246-252, 2015. (13 citations, source: Semantic Scholar)
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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. (487 citations, source: Semantic Scholar)
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RNA-Seq workflow: gene-level exploratory analysis and differential expression. Michael I. Love, Simon Anders, Vladislav Kim, and Wolfgang Huber. F1000Research, 4(1070), 2015. (325 citations, source: Semantic Scholar)
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Statistical relevance-relevant statistics, part I. Bernd Klaus. The EMBO Journal, 34(22):2727-2730, 2015. (10 citations, source: Semantic Scholar)
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Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry. H. Franken, T. Mathieson, D. Childs, G. M. Sweetman, T. Werner, I. Tögel, C. Doce, S. Gade, M. Bantscheff, G. Drewes, F. B. Reinhard, W. Huber, and M. M. Savitski. Nature Protocols, 10(10):1567-1593, 2015. (440 citations, source: Semantic Scholar)
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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. (77 citations, source: Semantic Scholar)
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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. (82 citations, source: Semantic Scholar)
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Genetic control of chromatin states in humans involves local and distal chromosomal interactions. F. Grubert, J. B. Zaugg, M. Kasowski, O. Ursu, D. V. Spacek, A. R. Martin, P. Greenside, R. Srivas, D. H. Phanstiel, A. Pekowska, N. Heidari, G. Euskirchen, W. Huber, J. K. Pritchard, C. D. Bustamante, L. M. Steinmetz, A. Kundaje, and M. Snyder. Cell, 162(5):1051-1065, 2015. (290 citations, source: Semantic Scholar)
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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. (31 citations, source: Semantic Scholar)
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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. (119 citations, source: Semantic Scholar)
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SomaticSignatures: inferring mutational signatures from single-nucleotide variants. Julian S. Gehring, Bernd Fischer, Michael Lawrence, and Wolfgang Huber. Bioinformatics, 31(22):3673-3675, 2015. (269 citations, source: Semantic Scholar)
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Single-cell polyadenylation site mapping reveals 3' isoform choice variability. Lars Velten, Simon Anders, Aleksandra Pękowska, Aino I Järvelin, Wolfgang Huber, Vicent Pelechano, and Lars M. Steinmetz. Molecular Systems Biology, 11(6), 2015.
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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. (86 citations, source: Semantic Scholar)
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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. (148 citations, source: Semantic Scholar)
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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. (78 citations, source: Semantic Scholar)
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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. (2787 citations, source: Semantic Scholar)
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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.
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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. (55 citations, source: Semantic Scholar)
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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. (24 citations, source: Semantic Scholar)
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h5vc: scalable nucleotide tallies with HDF5. Paul Theodor Pyl, Julian Gehring, Bernd Fischer, and Wolfgang Huber. Bioinformatics, 30(10):1464-1466, 2014.
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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. (9998 citations, source: Semantic Scholar)
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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. (174 citations, source: Semantic Scholar)
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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. (9998 citations, source: Semantic Scholar)
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Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages. Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oleś, M. J. Ara?zo-Bravo, M. Saitou, A. K. Hadjantonakis, and T. Hiiragi. Nature Cell Biology, 16(1):27-37, 2014. (261 citations, source: Semantic Scholar)
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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. (18 citations, source: Semantic Scholar)
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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. (28 citations, source: Semantic Scholar)
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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. (274 citations, source: Semantic Scholar)
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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. (64 citations, source: Semantic Scholar)
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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. (451 citations, source: Semantic Scholar)
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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.
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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. (322 citations, source: Semantic Scholar)
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Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization. Aleksandra Pękowska, Bernd Klaus, Felix Alexander Klein, Simon Anders, Małgorzata Oleś, Lars M. Steinmetz, Paul Bertone, and Wolfgang Huber. bioRχiv, 2014.
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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, July 2014.
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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. (74 citations, source: Semantic Scholar)
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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. (881 citations, source: Semantic Scholar)
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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.
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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. (333 citations, source: Semantic Scholar)
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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, R. Schreiber, R. Pepperkok, K. Kunzelmann, and M. D. Amaral. Cell, 154(6):1390-1400, 2013. (51 citations, source: Semantic Scholar)
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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. (107 citations, source: Semantic Scholar)
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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. (1037 citations, source: Semantic Scholar)
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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. (3006 citations, source: Semantic Scholar)
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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. (127 citations, source: Semantic Scholar)
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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. (13 citations, source: Semantic Scholar)
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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. (124 citations, source: Semantic Scholar)
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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. (408 citations, source: Semantic Scholar)
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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. (30 citations, source: Semantic Scholar)
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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. (386 citations, source: Semantic Scholar)
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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. (106 citations, source: Semantic Scholar)
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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.
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RNA-binding proteins in Mendelian disease. Alfredo Castello, Bernd Fischer, Matthias W Hentze, and Thomas Preiss. Trends in Genetics, 29:318-327, 2013. (218 citations, source: Semantic Scholar)
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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. (176 citations, source: Semantic Scholar)
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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. (421 citations, source: Semantic Scholar)
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Detecting differential usage of exons from RNA-Seq data. Simon Anders*, Alejandro Reyes*, and Wolfgang Huber. Genome Research, 22:2008-2017, 2012. (1375 citations, source: Semantic Scholar)
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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. (246 citations, source: Semantic Scholar)
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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. (245 citations, source: Semantic Scholar)
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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. (1797 citations, source: Semantic Scholar)
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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. (2559 citations, source: Semantic Scholar)
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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.
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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. (172 citations, source: Semantic Scholar)
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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. (188 citations, source: Semantic Scholar)
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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. (107 citations, source: Semantic Scholar)
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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. (21 citations, source: Semantic Scholar)
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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. (107 citations, source: Semantic Scholar)
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Contributions of the EMERALD project to assessing and improving microarray data quality. Vidar Beisvag, Audrey Kauffmann, James Malone, Carole Foy, Marc Salit, Heinz Schimmel, Erik Bongcam-Rudloff, Ulf Landegren, Helen Parkinson, Wolfgang Huber, Alvis Brazma, Arne Sandvik, and Martin Kuiper. BioTechniques, 50:27-31, 2011. (13 citations, source: Semantic Scholar)
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Enterotypes of the human gut microbiome. M. Arumugam, J. 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. Doré, MetaHIT Consortium:, M. Antolín, 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, W. Huber, J. van Hylckama-Vlieg, A. Jamet, C. Juste, G. Kaci, J. Knol, O. Lakhdari, S. Layec, K. Le Roux, E. Maguin, A. Mérieux, 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, G. Zeller, J. Weissenbach, S. D. Ehrlich, and P. Bork. Nature, 473:174-180, 2011.
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[193]

Assessing Affymetrix GeneChip microarray quality. Matthew M. McCall, Peter N. Murakami, Margus Lukk, Wolfgang Huber, and Rafael A. Irizarry. BMC Bioinformatics, 12:137, 2011. (79 citations, source: Semantic Scholar)
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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.
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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. (14 citations, source: Semantic Scholar)
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H3K4 tri-methylation provides an epigenetic signature of active enhancers. Aleksandra Pękowska, 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. (305 citations, source: Semantic Scholar)
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Independent filtering increases detection power for high-throughput experiments. Richard Bourgon, Robert Gentleman, and Wolfgang Huber. PNAS, 107(21):9546-9551, 2010. (697 citations, source: Semantic Scholar)
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Differential expression analysis for sequence count data. Simon Anders and Wolfgang Huber. Genome Biology, 11:R106, 2010. (1680 citations, source: Semantic Scholar)
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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. (155 citations, source: Semantic Scholar)
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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. (600 citations, source: Semantic Scholar)
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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. (120 citations, source: Semantic Scholar)
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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. (810 citations, source: Semantic Scholar)
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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. (469 citations, source: Semantic Scholar)
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Organelle proteomics experimental designs and analysis. Laurent Gatto, Juan Antonio Vizcaíno, Henning Hermjakob, Wolfgang Huber, and Kathryn S. Lilley. Proteomics, 2010. (60 citations, source: Semantic Scholar)
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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. (115 citations, source: Semantic Scholar)
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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. (596 citations, source: Semantic Scholar)
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Microarray data quality control improves the detection of differentially expressed genes. Audrey Kauffmann and Wolfgang Huber. Genomics, 95:138-142, 2010. (91 citations, source: Semantic Scholar)
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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. (43 citations, source: Semantic Scholar)
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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.
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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. (382 citations, source: Semantic Scholar)
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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. (73 citations, source: Semantic Scholar)
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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. (951 citations, source: Semantic Scholar)
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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. (34 citations, source: Semantic Scholar)
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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. (2774 citations, source: Semantic Scholar)
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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. (50 citations, source: Semantic Scholar)
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arrayQualityMetrics - a Bioconductor package for quality assessment of microarray data. Audrey Kauffmann, Robert Gentleman, and Wolfgang Huber. Bioinformatics, 25:415-416, 2009. (95 citations, source: Semantic Scholar)
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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. (95 citations, source: Semantic Scholar)
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The hwriter package: Composing HTML documents with R objects. Gregoire Pau and Wolfgang Huber. The R Journal, 1(1):22-24, 2009.
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Visualisation of genomic data with the Hilbert curve. Simon Anders. Bioinformatics, 25:1231-1235, 2009. (25 citations, source: Semantic Scholar)
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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.
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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. (348 citations, source: Semantic Scholar)
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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. (554 citations, source: Semantic Scholar)
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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.
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Analyzing ChIP-chip data using Bioconductor. Jörn Tödling. PLoS Computational Biology, 4(11), 2008. (26 citations, source: Semantic Scholar)
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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.
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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. (545 citations, source: Semantic Scholar)
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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. (61 citations, source: Semantic Scholar)
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Estimating node degree in bait-prey graphs. Denise Scholtens, Tony Chiang, Wolfgang Huber, and Robert Gentleman. Bioinformatics, 24(2):218-224, 2008. (18 citations, source: Semantic Scholar)
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Bioconductor Case Studies. Use R. Springer. Florian Hahne, Wolfgang Huber, Robert Gentleman, and Seth Falcon, 2008. (111 citations, source: Semantic Scholar)
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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. (93 citations, source: Semantic Scholar)
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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. (49 citations, source: Semantic Scholar)
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Making the most of high-throughput protein-interaction data. Robert Gentleman and Wolfgang Huber. Genome Biology, 8(10):112-112, 2007. (47 citations, source: Semantic Scholar)
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Graphs in molecular biology. Wolfgang Huber, Vincent J. Carey, Li Long, Seth Falcon, and Robert Gentleman. BMC Bioinformatics, 8(Suppl. 6), 2007. (137 citations, source: Semantic Scholar)
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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. (14 citations, source: Semantic Scholar)
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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. (75 citations, source: Semantic Scholar)
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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.
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[237]

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. (70 citations, source: Semantic Scholar)
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[238]

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 - DOI:10.1177/1087057107301271 - EuropePMC.

[239]

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. (43 citations, source: Semantic Scholar)
PDF - DOI:10.1186/1741-7007-5-25 - EuropePMC.

[240]

Analysis of cell-based RNAi screens. Michael Boutros, Lígia P. Brás, and Wolfgang Huber. Genome Biology, 7(7), 2006. (312 citations, source: Semantic Scholar)
PDF - DOI:10.1186/gb-2006-7-7-r66 - EuropePMC.

[241]

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. (726 citations, source: Semantic Scholar)
PDF - DOI:10.1073/pnas.0601091103 - EuropePMC.

[242]

Transcript mapping with high-density oligonucleotide tiling arrays. Wolfgang Huber, Jörn Tödling, and Lars M. Steinmetz. Bioinformatics, 22(16):1963-1970, 2006.
PDF - DOI:10.1093/bioinformatics/btl289 - EuropePMC.

[243]

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. (28 citations, source: Semantic Scholar)
PDF - DOI:10.1186/gb-2006-7-8-r77 - EuropePMC.

[244]

Reproducible statistical analysis in microarray profiling studies. Ulrich Mansmann, Markus Ruschhaupt, and Wolfgang Huber. Methods of Information in Medicine, 45:139-145, 2006.
PDF - DOI:10.1007/11558958_114.

[245]

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. (40 citations, source: Semantic Scholar)
PDF - DOI:10.1093/nar/gkj139 - EuropePMC.

[246]

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

[247]

Image analysis for microscopy screens. Oleg Sklyar and Wolfgang Huber. R News, 6(5):12-16, 2006. (12 citations, source: Google Scholar)
PDF.

[248]

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

[249]

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. (20 citations, source: Semantic Scholar)
PDF - DOI:10.1158/0008-5472.CAN-05-0642 - EuropePMC.

[250]

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. (1723 citations, source: Semantic Scholar)
PDF - DOI:10.1093/bioinformatics/bti525 - EuropePMC.

[251]

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. (44 citations, source: Semantic Scholar)
PDF - DOI:10.1002/pmic.200401324 - EuropePMC.

[252]

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. (107 citations, source: Google Scholar)
PDF.

[253]

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. (58 citations, source: Semantic Scholar)
PDF - DOI:10.1093/bioinformatics/bti052 - EuropePMC.

[254]

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.
DOI:10.1016/j.ejcb.2005.02.001.

[255]

Bioinformatics - from Genomes to Therapies, chapter Low-level analysis of microarray experiments. Wolfgang Huber, Anja von Heydebreck, and Martin Vingron. Wiley-VCH, 2005.
PDF - DOI:10.1002/9783527619368.ch25 - EuropePMC.

[256]

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.

[257]

Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer. Robert Gentleman, Vincent J. Carey, Wolfgang Huber, Rafael Irizarry, and Sandrine Dudoit, editors, 2005. (172 citations, source: Semantic Scholar)
DOI:10.1007/0-387-29362-0.

[258]

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. (9999 citations, source: Semantic Scholar)
PDF - DOI:10.1186/gb-2004-5-10-r80 - EuropePMC.

[259]

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. Wolfgang Huber and Robert Gentleman. Bioinformatics, 20:1651-1652, 2004. (38 citations, source: Semantic Scholar)
PDF - DOI:10.1093/bioinformatics/bth133 - EuropePMC.

[260]

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. (100 citations, source: Semantic Scholar)
PDF - DOI:10.2202/1544-6115.1078 - EuropePMC.

[261]

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. (87 citations, source: Semantic Scholar)
PDF - DOI:10.1186/1471-2164-5-29 - EuropePMC.

[262]

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. (50 citations, source: Semantic Scholar)
PDF - DOI:10.1101/gr.2576704 - EuropePMC.

[263]

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 - DOI:10.1002/047001153X.g405413.

[264]

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. (54 citations, source: Semantic Scholar)
PDF - DOI:10.1002/047001153X.g405208.

[265]

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. (92 citations, source: Semantic Scholar)
PDF - DOI:10.1023/A:1026113408773 - EuropePMC.

[266]

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. (107 citations, source: Semantic Scholar)
PDF - DOI:10.1016/S0344-0338(04)80586-7.

[267]

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.

[268]

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 - DOI:10.2202/1544-6115.1008 - EuropePMC.

[269]

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 - DOI:10.1002/9780470061619.ch6.

[270]

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. (181 citations, source: Semantic Scholar)
PDF - DOI:10.1002/bjs.4046 - EuropePMC.

[271]

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. (2334 citations, source: Semantic Scholar)
PDF - DOI:10.1093/bioinformatics/18.suppl_1.S96 - EuropePMC.

[272]

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.

[273]

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 K Huber, Holger Sültmann, Friederike Wilmer, Anja von Heydebreck, Stefan Haas, Bernhard Korn, Bastian Gunawan, Andreas Vente, Laszlo Füzesi, Martin Vingron, and Annemarie Poustka. Genome Research, 11(11):1861-1870, 2001. (42 citations, source: Semantic Scholar)
PDF - DOI:10.1101/gr.184501 - EuropePMC.

[274]

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.

[275]

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. (17 citations, source: Semantic Scholar)
PDF - DOI:10.1023/A:1011921423829 - EuropePMC.

[276]

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. (67 citations, source: Semantic Scholar)
PDF - DOI:10.1093/bioinformatics/17.suppl_1.S107 - EuropePMC.

[277]

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.

[278]

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. (44 citations, source: Semantic Scholar)
PDF - DOI:10.1103/PhysRevE.61.4883 - EuropePMC.

[279]

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. (20 citations, source: Semantic Scholar)
PDF - DOI:10.1016/S0010-4655(97)00050-7.

[280]

Vestibular-neck interaction and transformation of sensory coordinates. Thomas Mergner, Wolfgang Huber, and Wolfgang Becker. Journal of Vestibular Research, 7:347-367, 1997.
DOI:10.1016/S0957-4271(96)00176-0.

[281]

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.

[282]

Fast Monte Carlo algorithm for nonequilibrium systems. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Physical Review E, 53:4232-4235, 1996.
PDF - DOI:10.1103/PhysRevE.53.4232 - EuropePMC.

[283]

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. (21 citations, source: Semantic Scholar)
PDF - DOI:10.1007/BF00201483.

[284]

The macroscopic limit in a stochastic reaction-diffusion process. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Europhysics Letters, 30:69-74, 1995.
PDF - DOI:10.1209/0295-5075/30/2/002 - EuropePMC.

[285]

Fluctuation effects on wave propagation in a reaction-diffusion process. Heinz Peter Breuer, Wolfgang Huber, and Francesco Petruccione. Physica D, 73:259-273, 1994. (53 citations, source: Semantic Scholar)
PDF - DOI:10.1016/0167-2789(94)90161-9.

[286]

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

[287]

The description of reaction diffusion processes by master equations. Wolfgang Huber. Diploma thesis, University of Freiburg, 1994.
PDF.

* indicates equal contributions
^✉ co-corresponding authorships

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