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Decoding Context-Dependent Genetic Networks in vivo

Publicaciones

Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips

Autores: Dan Feng, Zhe Liang, Yifan Wang, Jiaying Yao, Zan Yuan, Guihua Hu, Ruihong Qu, Shang Xie, Dongwei Li, Liwen Yang, Xinai Zhao, Yanfei Ma, Jan U Lohmann, Xiaofeng Gu
Publicado en: BMC Biology, Edición 20/1, 2022, Página(s) 274, ISSN 1471-2229
Editor: BioMed Central
DOI: 10.1186/s12915-022-01473-2

Multiplexed conditional genome editing with Cas12a in Drosophila

Autores: Fillip Port, Maja Starostecka, Michael Boutros
Publicado en: Proceedings of the National Academy of Sciences, Edición 117/37, 2020, Página(s) 22890-22899, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2004655117

Tissue-Specific CRISPR-Cas9 Screening in Drosophila

Autores: Fillip Port, Michael Boutros
Publicado en: Methods in Molecular Biology, Edición 19406029, 2022, Página(s) 157-176, ISSN 1940-6029
Editor: Springer Nature
DOI: 10.1007/978-1-0716-2541-5_7

The Role of Organelles in Intestinal Function, Physiology, and Disease

Autores: Siamak Redhai, Michael Boutros
Publicado en: Trends in Cell Biology, Edición 09628924, 2021, Página(s) 485-499, ISSN 0962-8924
Editor: Elsevier BV
DOI: 10.1016/j.tcb.2021.01.003

Comparison of transformations for single-cell RNA-seq data

Autores: Constantin Ahlmann-Eltze, Wolfgang Huber
Publicado en: Nature Methods, Edición 20/5, 2023, Página(s) 665-672, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-023-01814-1

A global genetic interaction network by single-cell imaging and machine learning

Autores: Florian Heigwer, Christian Scheeder, Josephine Bageritz, Schayan Yousefian, Benedikt Rauscher, Christina Laufer, Sergi Beneyto-Calabuig, Maja Christina Funk, Vera Peters, Maria Boulougouri, Jana Bilanovic, Thilo Miersch, Barbara Schmitt, Claudia Blass, Fillip Port, Michael Boutros
Publicado en: Cell Systems, Edición 14/5, 2023, Página(s) 346–362, ISSN 2405-4712
Editor: Elsevier
DOI: 10.1016/j.cels.2023.03.003

CellRegMap: a statistical framework for mapping context-specific regulatory variants using scRNA-seq

Autores: Anna S E Cuomo, Tobias Heinen, Danai Vagiaki, Danilo Horta, John C Marioni, Oliver Stegle
Publicado en: Molecular Systems Biology, Edición 17444292, 2022, Página(s) e10663, ISSN 1744-4292
Editor: Nature Publishing Group
DOI: 10.15252/msb.202110663

A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila

Autores: Fillip Port, Claudia Strein, Mona Stricker, Benedikt Rauscher, Florian Heigwer, Jun Zhou, Celine Beyersdörffer, Jana Frei, Amy Hess, Katharina Kern, Laura Lange, Nora Langner, Roberta Malamud, Bojana Pavlović, Kristin Rädecke, Lukas Schmitt, Lukas Voos, Erica Valentini, Michael Boutros
Publicado en: eLife, Edición 9, 2020, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.53865

Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels

Autores: Katharina Imkeller; Giulia Ambrosi; Nancy Klemm; Ainara Claveras Cabezudo; Luisa Henkel; Wolfgang Huber; Michael Boutros
Publicado en: Molecular Systems Biology, Edición 17444292, 2022, Página(s) e10874, ISSN 1744-4292
Editor: Nature Publishing Group
DOI: 10.15252/msb.202110874

Conditional CRISPR-Cas Genome Editing in Drosophila to Generate Intestinal Tumors

Autores: Shivohum Bahuguna, Siamak Redhai, Jun Zhou, Tianyu Wang, Fillip Port, Michael Boutros
Publicado en: Cells, Edición 20734409, 2021, Página(s) 3156, ISSN 2073-4409
Editor: MDPI
DOI: 10.3390/cells10113156

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Autores: Britta Velten; Jana M. Braunger; Ricard Argelaguet; Damien Arnol; Jakob Wirbel; Danila Bredikhin; Georg Zeller; Oliver Stegle
Publicado en: Nature Methods, Edición 15487105, 2022, Página(s) 179-186, ISSN 1548-7105
Editor: Springer Nature
DOI: 10.1038/s41592-021-01343-9

scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation

Autores: Tobias Heinen, Stefano Secchia, James P Reddington, Bingqing Zhao, Eileen E M Furlong, Oliver Stegle
Publicado en: Genome Biology, Edición 23/1, 2022, Página(s) 8, ISSN 1474-760X
Editor: BioMed Central Ltd. Part of Springer Nature
DOI: 10.1186/s13059-021-02593-8

MUON: multimodal omics analysis framework

Autores: Danila Bredikhin; Ilia Kats; Oliver Stegle
Publicado en: Genome Biology, Edición 23/1, 2022, Página(s) 42, ISSN 1474-760X
Editor: BioMed Central Ltd. Part of Springer Nature
DOI: 10.1186/s13059-021-02577-8

glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data

Autores: Constantin Ahlmann-Eltze, Wolfgang Huber
Publicado en: Bioinformatics, Edición 36/24, 2020, Página(s) 5701-5702, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1009

Transcriptional landscape of rice roots at the single-cell resolution

Autores: Qing Liu, Zhe Liang, Dan Feng, Sanjie Jiang, Yifan Wang, Zhuoying Du, Ruoxi Li, Guihua Hu, Pingxian Zhang, Yanfei Ma, Jan U. Lohmann, Xiaofeng Gu
Publicado en: Molecular Plant, Edición 14/3, 2021, Página(s) 384-394, ISSN 1674-2052
Editor: Oxford University Press
DOI: 10.1016/j.molp.2020.12.014

A temperature-tolerant CRISPR base editor mediates highly efficient and precise gene editing in Drosophila

Autores: Roman M Doll, Michael Boutros, Fillip Port
Publicado en: Science Advances, Edición 9/35, 2023, Página(s) eadj1568, ISSN 2375-2548
Editor: AAAS
DOI: 10.1126/sciadv.adj1568

FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution

Autores: Florin C. Walter; Oliver Stegle; Britta Velten
Publicado en: Bioinformatics, Edición 39/5, 2023, Página(s) btad183, ISSN 1367-4811
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btad183

Nitric oxide controls shoot meristem activity via regulation of DNA methylation.

Autores: Jian Zeng, Xin’Ai Zhao, Zhe Liang, Inés Hidalgo, Michael Gebert, Pengfei Fan, Christian Wenzl, Sebastian G. Gornik, Jan U. Lohmann
Publicado en: Nature Communications, Edición 14/1, 2023, Página(s) 8001, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-43705-1

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

Autores: Carolin Grones, Thomas Eekhout, Dongbo Shi, Manuel Neumann, Lea S. Berg, Yuji Ke, Rachel Shahan, Kevin L. Cox Jr, Fabio Gomez-Cano, Hilde Nelissen, Jan U. Lohmann, Stefania Giacomello, Olivier C. Martin, Benjamin Cole, Jia-Wei Wang, Kerstin Kaufmann, Michael T. Raissig, Gergo Palfalvi, Thomas Greb, Marc Libault, Bert De Rybel
Publicado en: Plant Cell, Edición 36/4, 2024, Página(s) 812-828, ISSN 1040-4651
Editor: American Society of Plant Biologists
DOI: 10.1093/plcell/koae003

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