Survey of metaproteomics software tools for functional microbiome analysis
Sajulga, Ray, Easterly, Caleb, Riffle, Michael, Mesuere, Bart, Muth, Thilo, Mehta, Subina, Kumar, Praveen, Johnson, James, Gruening, Bjoern Andreas, Schiebenhoefer, Henning, Kolmeder, Carolin A, Fuchs, Stephan, Nunn, Brook L, Rudney, Joel, Griffin, Timothy J, Jagtap, Pratik D
Published in PloS one (10.11.2020)
Published in PloS one (10.11.2020)
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Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy
Guerler, Aysam, Baker, Dannon, van den Beek, Marius, Gruening, Bjoern, Bouvier, Dave, Coraor, Nate, Shank, Stephen D, Zehr, Jordan D, Schatz, Michael C, Nekrutenko, Anton
Published in BMC bioinformatics (23.06.2023)
Published in BMC bioinformatics (23.06.2023)
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Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework
Blank, Clemens, Easterly, Caleb, Gruening, Bjoern, Johnson, James, Kolmeder, Carolin A, Kumar, Praveen, May, Damon, Mehta, Subina, Mesuere, Bart, Brown, Zachary, Elias, Joshua E, Hervey, W Judson, McGowan, Thomas, Muth, Thilo, Nunn, Brook, Rudney, Joel, Tanca, Alessandro, Griffin, Timothy J, Jagtap, Pratik D
Published in Proteomes (31.01.2018)
Published in Proteomes (31.01.2018)
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deepTools2: a next generation web server for deep-sequencing data analysis
Ramírez, Fidel, Ryan, Devon P, Grüning, Björn, Bhardwaj, Vivek, Kilpert, Fabian, Richter, Andreas S, Heyne, Steffen, Dündar, Friederike, Manke, Thomas
Published in Nucleic acids research (08.07.2016)
Published in Nucleic acids research (08.07.2016)
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Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization
Wolff, Joachim, Rabbani, Leily, Gilsbach, Ralf, Richard, Gautier, Manke, Thomas, Backofen, Rolf, Grüning, Björn A
Published in Nucleic acids research (02.07.2020)
Published in Nucleic acids research (02.07.2020)
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pyGenomeTracks: reproducible plots for multivariate genomic datasets
Lopez-Delisle, Lucille, Rabbani, Leily, Wolff, Joachim, Bhardwaj, Vivek, Backofen, Rolf, Grüning, Björn, Ramírez, Fidel, Manke, Thomas
Published in Bioinformatics (Oxford, England) (20.04.2021)
Published in Bioinformatics (Oxford, England) (20.04.2021)
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Afgan, Enis, Baker, Dannon, Batut, Bérénice, van den Beek, Marius, Bouvier, Dave, Čech, Martin, Chilton, John, Clements, Dave, Coraor, Nate, Grüning, Björn A, Guerler, Aysam, Hillman-Jackson, Jennifer, Hiltemann, Saskia, Jalili, Vahid, Rasche, Helena, Soranzo, Nicola, Goecks, Jeremy, Taylor, James, Nekrutenko, Anton, Blankenberg, Daniel
Published in Nucleic acids research (02.07.2018)
Published in Nucleic acids research (02.07.2018)
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Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs
Wolff, Joachim, Backofen, Rolf, Grüning, Björn
Published in Bioinformatics (Oxford, England) (18.11.2021)
Published in Bioinformatics (Oxford, England) (18.11.2021)
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
Afgan, Enis, Baker, Dannon, van den Beek, Marius, Blankenberg, Daniel, Bouvier, Dave, Čech, Martin, Chilton, John, Clements, Dave, Coraor, Nate, Eberhard, Carl, Grüning, Björn, Guerler, Aysam, Hillman-Jackson, Jennifer, Von Kuster, Greg, Rasche, Eric, Soranzo, Nicola, Turaga, Nitesh, Taylor, James, Nekrutenko, Anton, Goecks, Jeremy
Published in Nucleic acids research (08.07.2016)
Published in Nucleic acids research (08.07.2016)
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High-resolution TADs reveal DNA sequences underlying genome organization in flies
Ramírez, Fidel, Bhardwaj, Vivek, Arrigoni, Laura, Lam, Kin Chung, Grüning, Björn A, Villaveces, José, Habermann, Bianca, Akhtar, Asifa, Manke, Thomas
Published in Nature communications (15.01.2018)
Published in Nature communications (15.01.2018)
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Strategies for analyzing bisulfite sequencing data
Wreczycka, Katarzyna, Gosdschan, Alexander, Yusuf, Dilmurat, Grüning, Björn, Assenov, Yassen, Akalin, Altuna
Published in Journal of biotechnology (10.11.2017)
Published in Journal of biotechnology (10.11.2017)
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Recent advances in RNA folding
Fallmann, Jörg, Will, Sebastian, Engelhardt, Jan, Grüning, Björn, Backofen, Rolf, Stadler, Peter F.
Published in Journal of biotechnology (10.11.2017)
Published in Journal of biotechnology (10.11.2017)
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Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
Veil, Marina, Yampolsky, Lev Y, Grüning, Björn, Onichtchouk, Daria
Published in Genome research (01.03.2019)
Published in Genome research (01.03.2019)
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Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations
Schubert, Desirée, Bode, Claudia, Kenefeck, Rupert, Hou, Tie Zheng, Wing, James B, Kennedy, Alan, Bulashevska, Alla, Petersen, Britt-Sabina, Schäffer, Alejandro A, Grüning, Björn A, Unger, Susanne, Frede, Natalie, Baumann, Ulrich, Witte, Torsten, Schmidt, Reinhold E, Dueckers, Gregor, Niehues, Tim, Seneviratne, Suranjith, Kanariou, Maria, Speckmann, Carsten, Ehl, Stephan, Rensing-Ehl, Anne, Warnatz, Klaus, Rakhmanov, Mirzokhid, Thimme, Robert, Hasselblatt, Peter, Emmerich, Florian, Cathomen, Toni, Backofen, Rolf, Fisch, Paul, Seidl, Maximilian, May, Annette, Schmitt-Graeff, Annette, Ikemizu, Shinji, Salzer, Ulrich, Franke, Andre, Sakaguchi, Shimon, Walker, Lucy S K, Sansom, David M, Grimbacher, Bodo
Published in Nature medicine (01.12.2014)
Published in Nature medicine (01.12.2014)
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BioContainers: an open-source and community-driven framework for software standardization
da Veiga Leprevost, Felipe, Grüning, Björn A, Alves Aflitos, Saulo, Röst, Hannes L, Uszkoreit, Julian, Barsnes, Harald, Vaudel, Marc, Moreno, Pablo, Gatto, Laurent, Weber, Jonas, Bai, Mingze, Jimenez, Rafael C, Sachsenberg, Timo, Pfeuffer, Julianus, Vera Alvarez, Roberto, Griss, Johannes, Nesvizhskii, Alexey I, Perez-Riverol, Yasset
Published in Bioinformatics (Oxford, England) (15.08.2017)
Published in Bioinformatics (Oxford, England) (15.08.2017)
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Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo
Gilsbach, Ralf, Schwaderer, Martin, Preissl, Sebastian, Grüning, Björn A, Kranzhöfer, David, Schneider, Pedro, Nührenberg, Thomas G, Mulero-Navarro, Sonia, Weichenhan, Dieter, Braun, Christian, Dreßen, Martina, Jacobs, Adam R, Lahm, Harald, Doenst, Torsten, Backofen, Rolf, Krane, Markus, Gelb, Bruce D, Hein, Lutz
Published in Nature communications (26.01.2018)
Published in Nature communications (26.01.2018)
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Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease
Gilsbach, Ralf, Preissl, Sebastian, Grüning, Björn A, Schnick, Tilman, Burger, Lukas, Benes, Vladimir, Würch, Andreas, Bönisch, Ulrike, Günther, Stefan, Backofen, Rolf, Fleischmann, Bernd K, Schübeler, Dirk, Hein, Lutz
Published in Nature communications (22.10.2014)
Published in Nature communications (22.10.2014)
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