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Anzahl der Publikationen: 29
Zeitschriftenartikel
Yepez, Vicente A.; Gusic, Mirjana; Kopajtich, Robert; Mertes, Christian; Smith, Nicholas H.; Alston, Charlotte L.; Ban, Rui; Beblo, Skadi; Berutti, Riccardo; Blessing, Holger; Ciara, Elzbieta; Distelmaier, Felix; Freisinger, Peter; Haeberle, Johannes; Hayflick, Susan J.; Hempel, Maja; Itkis, Yulia S.; Kishita, Yoshihito; Klopstock, Thomas; Krylova, Tatiana D.; Lamperti, Costanza; Lenz, Dominic; Makowski, Christine; Mosegaard, Signe; Mueller, Michaela F.; Munoz-Pujol, Gerard; Nadel, Agnieszka; Ohtake, Akira; Okazaki, Yasushi; Procopio, Elena; Schwarzmayr, Thomas; Smet, Joel; Staufner, Christian; Stenton, Sarah L.; Strom, Tim M.; Terrile, Caterina; Tort, Frederic; Coster, Rudy van; Vanlander, Arnaud; Wagner, Matias; Xu, Manting; Fang, Fang; Ghezzi, Daniele; Mayr, Johannes A.; Piekutowska-Abramczuk, Dorota; Ribes, Antonia; Roetig, Agnes; Taylor, Robert W.; Wortmann, Saskia B.; Murayama, Kei; Meitinger, Thomas; Gagneur, Julien und Prokisch, Holger
(2022):
Clinical implementation of RNA sequencing for Mendelian disease diagnostics.
In: Genome Medicine, Bd. 14, Nr. 1, 38
Ringeling, Francisca Rojas; Chakraborty, Shounak; Vissers, Caroline; Reiman, Derek; Patel, Akshay M.; Lee, Ki-Heon; Hong, Ari; Park, Chan-Woo; Reska, Tim; Gagneur, Julien; Chang, Hyeshik; Spletter, Maria L.; Yoon, Ki-Jun; Ming, Guo-li; Song, Hongjun und Canzar, Stefan
(2022):
Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data.
In: Nature Biotechnology, Bd. 40, Nr. 5: S. 741-750
Yepez, Vicente A.; Mertes, Christian; Mueller, Michaela F.; Klaproth-Andrade, Daniela; Wachutka, Leonhard; Fresard, Laure; Gusic, Mirjana; Scheller, Ines F.; Goldberg, Patricia F.; Prokisch, Holger und Gagneur, Julien
(2021):
Detection of aberrant gene expression events in RNA sequencing data.
In: Nature Protocols, Bd. 16, Nr. 2
Mertes, Christian; Scheller, Ines F.; Yepez, Vicente A.; Celik, Muhammed H.; Liang, Yingjiqiong; Kremer, Laura S.; Gusic, Mirjana; Prokisch, Holger und Gagneur, Julien
(2021):
Detection of aberrant splicing events in RNA-seq data using FRASER.
In: Nature Communications, Bd. 12, Nr. 1, 529
Cheng, Jun; Celik, Muhammed Hasan; Thi Yen Duong, Nguyen; Avsec, Ziga und Gagneur, Julien
(2019):
CAGI 5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice.
In: Human Mutation, Bd. 40, Nr. 9: S. 1243-1251
Bonnet, Jacques; Lindeboom, Rik G. H.; Pokrovsky, Daniil; Stricker, Georg; Celik, Muhammed Hasan; Rupp, Ralph A. W.; Gagneur, Julien; Vermeulen, Michiel; Imhof, Axel und Müller, Juerg
(2019):
Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation.
In: Developmental Cell, Bd. 51, Nr. 5
Brechtmann, Felix; Mertes, Christian; Matuseviciute, Agne; Yepez, Vicente A.; Avsec, Ziga; Herzog, Maximilian; Bader, Daniel M.; Prokisch, Holger und Gagneur, Julien
(2018):
OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data.
In: American Journal of Human Genetics, Bd. 103, Nr. 6: S. 907-917
Avsec, Ziga; Barekatain, Mohammadamin; Cheng, Jun und Gagneur, Julien
(2018):
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.
In: Bioinformatics, Bd. 34, Nr. 8: S. 1261-1269
Yepez, Vicente A.; Kremer, Laura S.; Iuso, Arcangela; Gusic, Mirjana; Kopajtich, Robert; Konarikova, Eliska; Nadel, Agnieszka; Wachutka, Leonhard; Prokisch, Holger und Gagneur, Julien
(2018):
OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer.
In: PLOS One 13(7), e0199938 [PDF, 3MB]
In: PLOS One 13(7), e0199938 [PDF, 3MB]
Hagl, Beate; Spielberger, Benedikt D.; Thoene, Silvia; Bonnal, Sophie; Mertes, Christian; Winter, Christof; Nijman, Isaac J.; Verduin, Shira; Eberherr, Andreas C.; Puel, Anne; Schindler, Detlev; Ruland, Jürgen; Meitinger, Thomas; Gagneur, Julien; Orange, Jordan S.; Gijn, Marielle E. van und Renner, Ellen D.
(2018):
Somatic alterations compromised molecular diagnosis of DOCK8 hyper-IgE syndrome caused by a novel intronic splice site mutation.
In: Scientific Reports, Bd. 8, 16719
[PDF, 3MB]
Zacher, Benedikt; Michel, Margaux; Schwalb, Björn; Cramer, Patrick; Tresch, Achim und Gagneur, Julien
(2017):
Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN.
In: PLOS One 12(1), e0169249 [PDF, 6MB]
In: PLOS One 12(1), e0169249 [PDF, 6MB]
Cheng, Jun; Maier, Kerstin C.; Avsec, Ziga; Rus, Petra und Gagneur, Julien
(2017):
Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast.
In: Rna, Bd. 23, Nr. 11: S. 1648-1659
Michel, Margaux; Demel, Carina; Zacher, Benedikt; Schwalb, Björn; Krebs, Stefan; Blum, Helmut; Gagneur, Julien und Cramer, Patrick
(2017):
TT-seq captures enhancer landscapes immediately after T-cell stimulation.
In: Molecular Systems Biology, Bd. 13, Nr. 3, 920
Kremer, Laura S.; Bader, Daniel M.; Mertes, Christian; Kopajtich, Robert; Pichler, Garwin; Iuso, Arcangela; Haack, Tobias B.; Graf, Elisabeth; Schwarzmayr, Thomas; Terrile, Caterina; Konarikova, Eliska; Repp, Birgit; Kastenmüller, Gabi; Adamski, Jerzy; Lichtner, Peter; Leonhardt, Christoph; Funalot, Benoit; Donati, Alice; Tiranti, Valeria; Lombes, Anne; Jardel, Claude; Glaeser, Dieter; Taylor, Robert W.; Ghezzi, Daniele; Mayr, Johannes A.; Rötig, Agnes; Freisinger, Peter; Distelmaier, Felix; Strom, Tim M.; Meitinger, Thomas; Gagneur, Julien und Prokisch, Holger
(2017):
Genetic diagnosis of Mendelian disorders via RNA sequencing.
In: Nature Communications, Bd. 8, 15824
[PDF, 1MB]
Stricker, Georg; Engelhardt, Alexander; Schulz, Daniel; Schmid, Matthias; Tresch, Achim und Gagneur, Julien
(2017):
GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.
In: Bioinformatics, Bd. 33, Nr. 15: S. 2258-2265
Wei, Hai; Yan, Bo; Gagneur, Julien und Conradt, Barbara
(2017):
Caenorhabditis elegans CES-1 Snail Represses pig-1 MELK Expression To Control Asymmetric Cell Division.
In: Genetics, Bd. 206, Nr. 4: S. 2069-2084
Witzel, Maximilian; Petersheim, Daniel; Fan, Yanxin; Bahrami, Ehsan; Racek, Tomas; Rohlfs, Meino; Puchalka, Jacek; Mertes, Christian; Gagneur, Julien; Ziegenhain, Christoph; Enard, Wolfgang; Stray-Pedersen, AsbJörg; Arkwright, Peter D.; Abboud, Miguel R.; Pazhakh, Vahid; Lieschke, Graham J.; Krawitz, Peter M.; Dahlhoff, Maik; Schneider, Marlon R.; Wolf, Eckhard; Horny, Hans-Peter; Schmidt, Heinrich; Schäffer, Alejandro A. und Klein, Christoph
(2017):
Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes.
In: Nature Genetics, Bd. 49, Nr. 5: S. 742-752
Gupta, Saumya; Radhakrishnan, Aparna; Nitin, Rachana; Raharja-Liu, Pandu; Lin, Gen; Steinmetz, Lars M.; Gagneur, Julien und Sinha, Himanshu
(2016):
Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant.
In: G3-Genes Genomes Genetics, Bd. 6, Nr. 8: S. 2255-2263
Eser, Philipp; Wachutka, Leonhard; Maier, Kerstin C.; Demel, Carina; Boroni, Mariana; Iyer, Srignanakshi; Cramer, Patrick und Gagneur, Julien
(2016):
Determinants of RNA metabolism in the Schizosaccharomyces pombe genome.
In: Molecular Systems Biology, Bd. 12, Nr. 2, 857
Schwalb, Björn; Michel, Margaux; Zacher, Benedikt; Frühauf, Katja; Demel, Carina; Tresch, Achim; Gagneur, Julien und Cramer, Patrick
(2016):
TT-seq maps the human transient transcriptome.
In: Science, Bd. 352, Nr. 6290: S. 1225-1228
Eser, Philipp; Wachutka, Leonhard; Maier, Kerstin C.; Demel, Carina; Boroni, Mariana; Iyer, Srignanakshi; Cramer, Patrick und Gagneur, Julien
(2016):
Determinants of RNA metabolism in the Schizosaccharomyces pombe genome.
In: Molecular Systems Biology, Bd. 12, Nr. 2, 857
[PDF, 1MB]
Glas, Julia; Dümcke, Sebastian; Zacher, Benedikt; Poron, Don; Gagneur, Julien und Tresch, Achim
(2016):
Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model.
In: Nucleic Acids Research, Bd. 44, Nr. 5, e44
[PDF, 3MB]
Gupta, Saumya; Radhakrishnan, Aparna; Nitin, Rachana; Raharja-Liu, Pandu; Lin, Gen; Steinmetz, Lars M.; Gagneur, Julien und Sinha, Himanshu
(2016):
Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant.
In: G3 - Genes Genomes Genetics, Bd. 6, Nr. 8: S. 2255-2263
[PDF, 2MB]
Bader, Daniel M.; Wilkening, Stefan; Lin, Gen; Tekkedil, Manu M.; Dietrich, Kim; Steinmetz, Lars M. und Gagneur, Julien
(2015):
Negative feedback buffers effects of regulatory variants.
In: Molecular Systems Biology, Bd. 11, Nr. 1
[PDF, 1MB]
Gupta, Saumya; Radhakrishnan, Aparna; Raharja-Liu, Pandu; Lin, Gen; Steinmetz, Lars M.; Gagneur, Julien und Sinha, Himanshu
(2015):
Temporal Expression Profiling Identifies Pathways Mediating Effect of Causal Variant on Phenotype.
In: PLOS Genetics 11(6), e1005195 [PDF, 4MB]
In: PLOS Genetics 11(6), e1005195 [PDF, 4MB]
Bhatia, Aatish; Yadav, Anupama; Zhu, Chenchen; Gagneur, Julien; Radhakrishnan, Aparna; Steinmetz, Lars M.; Bhanot, Gyan und Sinha, Himanshu
(2014):
Yeast Growth Plasticity Is Regulated by Environment-Specific Multi-QTL Interactions.
In: G3-Genes Genomes Genetics, Bd. 4, Nr. 5: S. 769-777
[PDF, 1MB]
Zacher, Benedikt; Lidschreiber, Michael; Cramer, Patrick; Gagneur, Julien und Tresch, Achim
(2014):
Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.
In: Molecular Systems Biology, Bd. 10, Nr. 12, 768
[PDF, 2MB]
Wilkening, Stefan; Tekkedil, Manu M.; Lin, Gen; Fritsch, Emilie S.; Wei, W. u.; Gagneur, Julien; Lazinski, David W.; Camilli, Andrew und Steinmetz, Lars M.
(2013):
Genotyping 1000 yeast strains by next-generation sequencing.
In: BMC Genomics
14:90
[PDF, 1MB]
Gagneur, Julien; Elze, Markus C. und Tresch, Achim
(2011):
Selective Phenotyping, Entropy Reduction, and the Mastermind game.
In: BMC Bioinformatics
12:406
[PDF, 465kB]