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The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37719-y
By:
- Loiseau, Chloé;
- Windels, Etthel M.;
- Gygli, Sebastian M.;
- Jugheli, Levan;
- Maghradze, Nino;
- Brites, Daniela;
- Ross, Amanda;
- Goig, Galo;
- Reinhard, Miriam;
- Borrell, Sonia;
- Trauner, Andrej;
- Dötsch, Anna;
- Aspindzelashvili, Rusudan;
- Denes, Rebecca;
- Reither, Klaus;
- Beisel, Christian;
- Tukvadze, Nestani;
- Avaliani, Zaza;
- Stadler, Tanja;
- Gagneux, Sebastien
Publication type:
Article
RNA-Seq of three free-living flatworm species suggests rapid evolution of reproduction-related genes.
Published in:
BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-06862-x
By:
- Brand, Jeremias N.;
- Wiberg, R. Axel W.;
- Pjeta, Robert;
- Bertemes, Philip;
- Beisel, Christian;
- Ladurner, Peter;
- Schärer, Lukas
Publication type:
Article
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers.
Published in:
BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-016-1417-7
By:
- Hofmann, Ariane L.;
- Behr, Jonas;
- Singer, Jochen;
- Kuipers, Jack;
- Beisel, Christian;
- Schraml, Peter;
- Moch, Holger;
- Beerenwinkel, Niko
Publication type:
Article
Single-cell Analysis Reveals Inter- and Intratumour Heterogeneity in Metastatic Breast Cancer.
Published in:
Journal of Mammary Gland Biology & Neoplasia, 2023, v. 28, n. 1, p. 1, doi. 10.1007/s10911-023-09551-z
By:
- Hamelin, Baptiste;
- Obradović, Milan M. S.;
- Sethi, Atul;
- Kloc, Michal;
- Münst, Simone;
- Beisel, Christian;
- Eschbach, Katja;
- Kohler, Hubertus;
- Soysal, Savas;
- Vetter, Marcus;
- Weber, Walter P.;
- Stadler, Michael B.;
- Bentires-Alj, Mohamed
Publication type:
Article
A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila.
Published in:
eLife, 2018, p. 1, doi. 10.7554/eLife.32697.001
By:
- Torres, Joana;
- Monti, Remo;
- Moore, Ariane L.;
- Makiko Seimiya;
- Yanrui Jiang;
- Beerenwinkel, Niko;
- Beisel, Christian;
- Beira, Jorge V.;
- Paro, Renato
Publication type:
Article
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.
Published in:
Nucleic Acids Research, 2014, v. 42, n. 14, p. e115, doi. 10.1093/nar/gku537
By:
- Giallonardo, Francesca Di;
- Töpfer, Armin;
- Rey, Melanie;
- Prabhakaran, Sandhya;
- Duport, Yannick;
- Leemann, Christine;
- Schmutz, Stefan;
- Campbell, Nottania K.;
- Joos, Beda;
- Lecca, Maria Rita;
- Patrignani, Andrea;
- Däumer, Martin;
- Beisel, Christian;
- Rusert, Peter;
- Trkola, Alexandra;
- Günthard, Huldrych F.;
- Roth, Volker;
- Beerenwinkel, Niko;
- Metzner, Karin J.
Publication type:
Article
Quantitative in vivo analysis of chromatin binding of Polycomb and Trithorax group proteins reveals retention of ASH1 on mitotic chromatin.
Published in:
Nucleic Acids Research, 2013, v. 41, n. 10, p. 5235, doi. 10.1093/nar/gkt217
By:
- Steffen, Philipp A.;
- Fonseca, João Pedro;
- Gänger, Cornelia;
- Dworschak, Eva;
- Kockmann, Tobias;
- Beisel, Christian;
- Ringrose, Leonie
Publication type:
Article
Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis.
Published in:
EMBO Journal, 2022, v. 41, n. 24, p. 1, doi. 10.15252/embj.2022111132
By:
- Mukhtar, Tanzila;
- Breda, Jeremie;
- Adam, Manal A;
- Boareto, Marcelo;
- Grobecker, Pascal;
- Karimaddini, Zahra;
- Grison, Alice;
- Eschbach, Katja;
- Chandrasekhar, Ramakrishnan;
- Vermeul, Swen;
- Okoniewski, Michal;
- Pachkov, Mikhail;
- Harwell, Corey C;
- Atanasoski, Suzana;
- Beisel, Christian;
- Iber, Dagmar;
- van Nimwegen, Erik;
- Taylor, Verdon
Publication type:
Article
A chromatin-modifying function of JNK during stem cell differentiation.
Published in:
Nature Genetics, 2012, v. 44, n. 1, p. 94, doi. 10.1038/ng.1036
By:
- Tiwari, Vijay K;
- Stadler, Michael B;
- Wirbelauer, Christiane;
- Paro, Renato;
- Schübeler, Dirk;
- Beisel, Christian
Publication type:
Article
Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing.
Published in:
Nature Structural & Molecular Biology, 2010, v. 17, n. 7, p. 894, doi. 10.1038/nsmb.1825
By:
- Bell, Oliver;
- Schwaiger, Michaela;
- Oakeley, Edward J;
- Lienert, Florian;
- Beisel, Christian;
- Stadler, Michael B.;
- Schübeler, Dirk
Publication type:
Article
Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa.
Published in:
Nature Structural & Molecular Biology, 2010, v. 17, n. 6, p. 679, doi. 10.1038/nsmb.1821
By:
- Brykczynska, Urszula;
- Hisano, Mizue;
- Erkek, Serap;
- Ramos, Liliana;
- Oakeley, Edward J.;
- Roloff, Tim C.;
- Beisel, Christian;
- Schübeler, Dirk;
- Stadler, Michael B.;
- Peters, Antoine H. F. M.
Publication type:
Article
Laser fluorescence of dentin caries covered with a novel nano-filled sealant.
Published in:
Lasers in Medical Science, 2013, v. 28, n. 1, p. 133, doi. 10.1007/s10103-012-1087-2
By:
- Braun, Andreas;
- Beisel, Christian;
- Brede, Olivier;
- Krause, Felix
Publication type:
Article
gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis.
Published in:
Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad329
By:
- Grob, Linda;
- Bertolini, Anne;
- Carrara, Matteo;
- Lischetti, Ulrike;
- Tastanova, Aizhan;
- Beisel, Christian;
- Levesque, Mitchell P;
- Stekhoven, Daniel J;
- Singer, Franziska
Publication type:
Article
The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study.
Published in:
Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.633396
By:
- Ticlla, Monica R.;
- Hella, Jerry;
- Hiza, Hellen;
- Sasamalo, Mohamed;
- Mhimbira, Francis;
- Rutaihwa, Liliana K.;
- Droz, Sara;
- Schaller, Sarah;
- Reither, Klaus;
- Hilty, Markus;
- Comas, Inaki;
- Beisel, Christian;
- Schmid, Christoph D.;
- Fenner, Lukas;
- Gagneux, Sebastien
Publication type:
Article
Convergent network effects along the axis of gene expression during prostate cancer progression.
Published in:
Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02188-9
By:
- Charmpi, Konstantina;
- Guo, Tiannan;
- Zhong, Qing;
- Wagner, Ulrich;
- Sun, Rui;
- Toussaint, Nora C.;
- Fritz, Christine E.;
- Yuan, Chunhui;
- Chen, Hao;
- Rupp, Niels J.;
- Christiansen, Ailsa;
- Rutishauser, Dorothea;
- Rüschoff, Jan H.;
- Fankhauser, Christian;
- Saba, Karim;
- Poyet, Cedric;
- Hermanns, Thomas;
- Oehl, Kathrin;
- Moore, Ariane L.;
- Beisel, Christian
Publication type:
Article
Read length versus Depth of Coverage for Viral Quasispecies Reconstruction.
Published in:
PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0047046
By:
- Zagordi, Osvaldo;
- Däumer, Martin;
- Beisel, Christian;
- Beerenwinkel, Niko
Publication type:
Article
Silencing chromatin: comparing modes and mechanisms.
Published in:
2011
By:
- Beisel, Christian;
- Paro, Renato
Publication type:
journal article
Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma.
Published in:
Cancers, 2021, v. 13, n. 9, p. 2163, doi. 10.3390/cancers13092163
By:
- Moore, Ariane L.;
- Batavia, Aashil A.;
- Kuipers, Jack;
- Singer, Jochen;
- Burcklen, Elodie;
- Schraml, Peter;
- Beisel, Christian;
- Moch, Holger;
- Beerenwinkel, Niko;
- Furney, Simon J.
Publication type:
Article
Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors.
Published in:
EMBO Journal, 2017, v. 36, n. 24, p. 3619, doi. 10.15252/embj.201797105
By:
- Alberti‐Servera, Llucia;
- Muenchow, Lilly;
- Tsapogas, Panagiotis;
- Capoferri, Giuseppina;
- Eschbach, Katja;
- Beisel, Christian;
- Ceredig, Rhodri;
- Ivanek, Robert;
- Rolink, Antonius
Publication type:
Article
Statistical tests for intra-tumour clonal co-occurrence and exclusivity.
Published in:
PLoS Computational Biology, 2021, v. 17, n. 12, p. 1, doi. 10.1371/journal.pcbi.1009036
By:
- Kuipers, Jack;
- Moore, Ariane L.;
- Jahn, Katharina;
- Schraml, Peter;
- Wang, Feng;
- Morita, Kiyomi;
- Futreal, P. Andrew;
- Takahashi, Koichi;
- Beisel, Christian;
- Moch, Holger;
- Beerenwinkel, Niko
Publication type:
Article
Tead transcription factors differentially regulate cortical development.
Published in:
Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-61490-5
By:
- Mukhtar, Tanzila;
- Breda, Jeremie;
- Grison, Alice;
- Karimaddini, Zahra;
- Grobecker, Pascal;
- Iber, Dagmar;
- Beisel, Christian;
- van Nimwegen, Erik;
- Taylor, Verdon
Publication type:
Article
Genome assemblies of the simultaneously hermaphroditic flatworms Macrostomum cliftonense and Macrostomum hystrix.
Published in:
G3: Genes | Genomes | Genetics, 2023, v. 13, n. 9, p. 1, doi. 10.1093/g3journal/jkad149
By:
- Wiberg, R. Axel W.;
- Brand, Jeremias N.;
- Viktorin, Gudrun;
- Mitchell, Jack O.;
- Beisel, Christian;
- Schärer, Lukas
Publication type:
Article
Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction.
Published in:
Molecular Systems Biology, 2018, v. 14, n. 8, p. 1, doi. 10.15252/msb.20188266
By:
- Rzepiela, Andrzej J;
- Ghosh, Souvik;
- Breda, Jeremie;
- Vina-Vilaseca, Arnau;
- Syed, Afzal P;
- Gruber, Andreas J;
- Eschbach, Katja;
- Beisel, Christian;
- Nimwegen, Erik;
- Zavolan, Mihaela
Publication type:
Article
Detection of SARS-CoV-2 RNA in a Zoo-Kept Red Fox (Vulpes vulpes).
Published in:
Viruses (1999-4915), 2024, v. 16, n. 4, p. 521, doi. 10.3390/v16040521
By:
- Chan, Tatjana;
- Ginders, Julia;
- Kuhlmeier, Evelyn;
- Meli, Marina L.;
- Bönzli, Eva;
- Meili, Theres;
- Hüttl, Julia;
- Hatt, Jean-Michel;
- Hindenlang Clerc, Karin;
- Kipar, Anja;
- Wyss, Fabia;
- Wenker, Christian;
- Ryser-Degiorgis, Marie-Pierre;
- Valenzuela Agüí, Cecilia;
- Urban, Christian;
- Beisel, Christian;
- Stadler, Tanja;
- Hofmann-Lehmann, Regina
Publication type:
Article
Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland.
Published in:
Viruses (1999-4915), 2023, v. 15, n. 1, p. 245, doi. 10.3390/v15010245
By:
- Kuhlmeier, Evelyn;
- Chan, Tatjana;
- Agüí, Cecilia Valenzuela;
- Willi, Barbara;
- Wolfensberger, Aline;
- Beisel, Christian;
- Topolsky, Ivan;
- Beerenwinkel, Niko;
- Stadler, Tanja;
- Jones, Sarah;
- Tyson, Grace;
- Hosie, Margaret J.;
- Reitt, Katja;
- Hüttl, Julia;
- Meli, Marina L.;
- Hofmann-Lehmann, Regina
Publication type:
Article
Detection and Genome Sequencing of SARS-CoV-2 in a Domestic Cat with Respiratory Signs in Switzerland.
Published in:
Viruses (1999-4915), 2021, v. 13, n. 3, p. 496, doi. 10.3390/v13030496
By:
- Klaus, Julia;
- Meli, Marina L.;
- Willi, Barbara;
- Nadeau, Sarah;
- Beisel, Christian;
- Stadler, Tanja;
- Egberink, Herman;
- Zhao, Shan;
- Lutz, Hans;
- Riond, Barbara;
- Rösinger, Nina;
- Stalder, Hanspeter;
- Renzullo, Sandra;
- Hofmann-Lehmann, Regina;
- Martinez-Sobrido, Luis
Publication type:
Article
The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila.
Published in:
Genome Biology, 2013, v. 14, n. 2, p. 1, doi. 10.1186/gb-2013-14-2-r18
By:
- Kockmann, Tobias;
- Gerstung, Moritz;
- Schlumpf, Tommy;
- Zhu Xhinzhou;
- Hess, Daniel;
- Beerenwinkel, Niko;
- Beisel, Christian;
- Paro, Renato
Publication type:
Article
Histone methylation by the Drosophila epigenetic transcriptional regulator Ash1.
Published in:
Nature, 2002, v. 419, n. 6909, p. 857, doi. 10.1038/nature01126
By:
- Beisel, Christian;
- Imhof, Axel;
- Greene, Jaime;
- Kremmer, Elisabeth;
- Sauer, Frank
Publication type:
Article
Retraction: Histone methylation by the Drosophila epigenetic transcriptional regulator Ash1.
Published in:
2015
By:
- Beisel, Christian;
- Imhof, Axel;
- Greene, Jaime;
- Kremmer, Elisabeth;
- Sauer, Frank
Publication type:
Correction Notice
Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs.
Published in:
Nature, 2014, v. 511, n. 7507, p. 46, doi. 10.1038/nature13289
By:
- Lopez-Rios, Javier;
- Duchesne, Amandine;
- Speziale, Dario;
- Andrey, Guillaume;
- Peterson, Kevin A.;
- Germann, Philipp;
- Ünal, Erkan;
- Liu, Jing;
- Floriot, Sandrine;
- Barbey, Sarah;
- Gallard, Yves;
- Müller-Gerbl, Magdalena;
- Courtney, Andrew D.;
- Klopp, Christophe;
- Rodriguez, Sabrina;
- Ivanek, Robert;
- Beisel, Christian;
- Wicking, Carol;
- Iber, Dagmar;
- Robert, Benoit
Publication type:
Article
Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity.
Published in:
BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2164-8
By:
- Menardo, Fabrizio;
- Loiseau, Chloé;
- Brites, Daniela;
- Coscolla, Mireia;
- Gygli, Sebastian M.;
- Rutaihwa, Liliana K.;
- Trauner, Andrej;
- Beisel, Christian;
- Borrell, Sonia;
- Gagneux, Sebastien
Publication type:
Article
High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm.
Published in:
PLoS Genetics, 2011, v. 7, n. 6, p. 1, doi. 10.1371/journal.pgen.1002126
By:
- Wolff, Philip;
- Weinhofer, Isabelle;
- Seguin, Jonathan;
- Roszak, Pawel;
- Beisel, Christian;
- Donoghue, Mark T. A.;
- Spillane, Charles;
- Nordborg, Magnus;
- Rehmsmeier, Marc;
- Köhler, Claudia
Publication type:
Article
Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development.
Published in:
PLoS ONE, 2019, v. 14, n. 3, p. 1, doi. 10.1371/journal.pone.0214088
By:
- Borrell, Sònia;
- Trauner, Andrej;
- Brites, Daniela;
- Rigouts, Leen;
- Loiseau, Chloe;
- Coscolla, Mireia;
- Niemann, Stefan;
- De Jong, Bouke;
- Yeboah-Manu, Dorothy;
- Kato-Maeda, Midori;
- Feldmann, Julia;
- Reinhard, Miriam;
- Beisel, Christian;
- Gagneux, Sebastien
Publication type:
Article
Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits.
Published in:
Frontiers in Zoology, 2015, v. 12, n. 1, p. 1, doi. 10.1186/s12983-015-0106-0
By:
- Arbore, Roberto;
- Sekii, Kiyono;
- Beisel, Christian;
- Ladurner, Peter;
- Berezikov, Eugene;
- Schärer, Lukas
Publication type:
Article
SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics.
Published in:
2018
By:
- Singer, Franziska;
- Irmisch, Anja;
- Toussaint, Nora C.;
- Grob, Linda;
- Singer, Jochen;
- Thurnherr, Thomas;
- Beerenwinkel, Niko;
- Levesque, Mitchell P.;
- Dummer, Reinhard;
- Quagliata, Luca;
- Rothschild, Sacha I.;
- Wicki, Andreas;
- Beisel, Christian;
- Stekhoven, Daniel J.
Publication type:
journal article
An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits.
Published in:
BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-1033
By:
- Routtu, Jarkko;
- Hall, Matthew D.;
- Albere, Brian;
- Beisel, Christian;
- Daniel Bergeron, R.;
- Chaturvedi, Anurag;
- Jeong-Hyeon Choi;
- Colbourne, John;
- De Meester, Luc;
- Stephens, Melissa T.;
- Stelzer, Claus-Peter;
- Solorzano, Eleanne;
- Kelley Thomas, W.;
- Pfrender, Michael E.;
- Ebert, Dieter
Publication type:
Article
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis.
Published in:
Bioinformatics, 2018, v. 34, n. 1, p. 107, doi. 10.1093/bioinformatics/btx540
By:
- Singer, Jochen;
- Ruscheweyh, Hans-Joachim;
- Hofmann, Ariane L;
- Thurnherr, Thomas;
- Singer, Franziska;
- Toussaint, Nora C;
- Ng, Charlotte K Y;
- Piscuoglio, Salvatore;
- Beisel, Christian;
- Christofori, Gerhard
Publication type:
Article
Live slow-frozen human tumor tissues viable for 2D, 3D, ex vivo cultures and single-cell RNAseq.
Published in:
Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-04025-0
By:
- Restivo, Gaetana;
- Tastanova, Aizhan;
- Balázs, Zsolt;
- Panebianco, Federica;
- Diepenbruck, Maren;
- Ercan, Caner;
- Preca, Bodgan-T.;
- Hafner, Jürg;
- Weber, Walter P.;
- Kurzeder, Christian;
- Vetter, Marcus;
- Soysal, Simone Münst;
- Beisel, Christian;
- Bentires-Alj, Mohamed;
- Piscuoglio, Salvatore;
- Krauthammer, Michael;
- Levesque, Mitchell P.
Publication type:
Article
A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex.
Published in:
Frontiers in Microbiology, 2018, p. N.PAG, doi. 10.3389/fmicb.2018.02820
By:
- Brites, Daniela;
- Loiseau, Chloé;
- Menardo, Fabrizio;
- Borrell, Sonia;
- Boniotti, Maria Beatrice;
- Warren, Robin;
- Dippenaar, Anzaan;
- Parsons, Sven David Charles;
- Beisel, Christian;
- Behr, Marcel A.;
- Fyfe, Janet A.;
- Coscolla, Mireia;
- Gagneux, Sebastien
Publication type:
Article
Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17222-4
By:
- Höllerer, Simon;
- Papaxanthos, Laetitia;
- Gumpinger, Anja Cathrin;
- Fischer, Katrin;
- Beisel, Christian;
- Borgwardt, Karsten;
- Benenson, Yaakov;
- Jeschek, Markus
Publication type:
Article
DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.
Published in:
BMC Genomics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12864-022-08403-0
By:
- Yermanos, Alexander;
- Hong, Kai-Lin;
- Agrafiotis, Andreas;
- Han, Jiami;
- Nadeau, Sarah;
- Valenzuela, Cecilia;
- Azizoglu, Asli;
- Ehling, Roy;
- Gao, Beichen;
- Spahr, Michael;
- Neumeier, Daniel;
- Chang, Ching-Hsiang;
- Dounas, Andreas;
- Petrillo, Ezequiel;
- Nissen, Ina;
- Burcklen, Elodie;
- Feldkamp, Mirjam;
- Beisel, Christian;
- Oxenius, Annette;
- Savic, Miodrag
Publication type:
Article
Dissection of gene regulatory networks in embryonic stem cells by means of high-throughput sequencing.
Published in:
Biological Chemistry, 2009, v. 390, n. 11, p. 1139, doi. 10.1515/BC.2009.116
By:
- Beisel, Christian;
- Paro, Renato
Publication type:
Article

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