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1.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

Ziegler, Carly G K; Allon, Samuel J; Nyquist, Sarah K; Mbano, Ian M; Miao, Vincent N; Tzouanas, Constantine N; Cao, Yuming; Yousif, Ashraf S; Bals, Julia; Hauser, Blake M; Feldman, Jared; Muus, Christoph; Wadsworth, Marc H; Kazer, Samuel W; Hughes, Travis K; Doran, Benjamin; Gatter, G James; Vukovic, Marko; Taliaferro, Faith; Mead, Benjamin E; Guo, Zhiru; Wang, Jennifer P; Gras, Delphine; Plaisant, Magali; Ansari, Meshal; Angelidis, Ilias; Adler, Heiko; Sucre, Jennifer M S; Taylor, Chase J; Lin, Brian; Waghray, Avinash; Mitsialis, Vanessa; Dwyer, Daniel F; Buchheit, Kathleen M; Boyce, Joshua A; Barrett, Nora A; Laidlaw, Tanya M; Carroll, Shaina L; Colonna, Lucrezia; Tkachev, Victor; Peterson, Christopher W; Yu, Alison; Zheng, Hengqi Betty; Gideon, Hannah P; Winchell, Caylin G; Lin, Philana Ling; Bingle, Colin D; Snapper, Scott B; Kropski, Jonathan A; Theis, Fabian J.

Cell; 181(5): 1016-1035.e19, 2020 05 28.

Artículo en Inglés | MEDLINE | ID: covidwho-100497

2.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

Ziegler, Carly G K; Allon, Samuel J; Nyquist, Sarah K; Mbano, Ian M; Miao, Vincent N; Tzouanas, Constantine N; Cao, Yuming; Yousif, Ashraf S; Bals, Julia; Hauser, Blake M; Feldman, Jared; Muus, Christoph; Wadsworth, Marc H; Kazer, Samuel W; Hughes, Travis K; Doran, Benjamin; Gatter, G James; Vukovic, Marko; Taliaferro, Faith; Mead, Benjamin E; Guo, Zhiru; Wang, Jennifer P; Gras, Delphine; Plaisant, Magali; Ansari, Meshal; Angelidis, Ilias; Adler, Heiko; Sucre, Jennifer M S; Taylor, Chase J; Lin, Brian; Waghray, Avinash; Mitsialis, Vanessa; Dwyer, Daniel F; Buchheit, Kathleen M; Boyce, Joshua A; Barrett, Nora A; Laidlaw, Tanya M; Carroll, Shaina L; Colonna, Lucrezia; Tkachev, Victor; Peterson, Christopher W; Yu, Alison; Zheng, Hengqi Betty; Gideon, Hannah P; Winchell, Caylin G; Lin, Philana Ling; Bingle, Colin D; Snapper, Scott B; Kropski, Jonathan A; Theis, Fabian J.

Cell; 181(5): 1016-1035.e19, 2020 05 28.

Artículo en Inglés | MEDLINE | ID: mdl-32413319

3.

Deep learning: new computational modelling techniques for genomics.

Eraslan, Gökcen; Avsec, Ziga; Gagneur, Julien; Theis, Fabian J.

Nat Rev Genet; 20(7): 389-403, 2019 07.

Artículo en Inglés | MEDLINE | ID: mdl-30971806

4.

scSLAM-seq reveals core features of transcription dynamics in single cells.

Erhard, Florian; Baptista, Marisa A P; Krammer, Tobias; Hennig, Thomas; Lange, Marius; Arampatzi, Panagiota; Jürges, Christopher S; Theis, Fabian J; Saliba, Antoine-Emmanuel; Dölken, Lars.

Nature; 571(7765): 419-423, 2019 07.

Artículo en Inglés | MEDLINE | ID: mdl-31292545

5.

LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky, Nikolaus; Almouzni, Geneviève; Gorski, Stanislaw A; Aerts, Stein; Amit, Ido; Bertero, Michela G; Bock, Christoph; Bredenoord, Annelien L; Cavalli, Giacomo; Chiocca, Susanna; Clevers, Hans; De Strooper, Bart; Eggert, Angelika; Ellenberg, Jan; Fernández, Xosé M; Figlerowicz, Marek; Gasser, Susan M; Hubner, Norbert; Kjems, Jørgen; Knoblich, Jürgen A; Krabbe, Grietje; Lichter, Peter; Linnarsson, Sten; Marine, Jean-Christophe; Marioni, John C; Marti-Renom, Marc A; Netea, Mihai G; Nickel, Dörthe; Nollmann, Marcelo; Novak, Halina R; Parkinson, Helen; Piccolo, Stefano; Pinheiro, Inês; Pombo, Ana; Popp, Christian; Reik, Wolf; Roman-Roman, Sergio; Rosenstiel, Philip; Schultze, Joachim L; Stegle, Oliver; Tanay, Amos; Testa, Giuseppe; Thanos, Dimitris; Theis, Fabian J; Torres-Padilla, Maria-Elena; Valencia, Alfonso; Vallot, Céline; van Oudenaarden, Alexander; Vidal, Marie; Voet, Thierry.

Nature; 587(7834): 377-386, 2020 Nov.

Artículo en Inglés | MEDLINE | ID: mdl-32894860

6.

Inhibition of LTßR signalling activates WNT-induced regeneration in lung.

Conlon, Thomas M; John-Schuster, Gerrit; Heide, Danijela; Pfister, Dominik; Lehmann, Mareike; Hu, Yan; Ertüz, Zeynep; Lopez, Martin A; Ansari, Meshal; Strunz, Maximilian; Mayr, Christoph; Angelidis, Ilias; Ciminieri, Chiara; Costa, Rita; Kohlhepp, Marlene Sophia; Guillot, Adrien; Günes, Gizem; Jeridi, Aicha; Funk, Maja C; Beroshvili, Giorgi; Prokosch, Sandra; Hetzer, Jenny; Verleden, Stijn E; Alsafadi, Hani; Lindner, Michael; Burgstaller, Gerald; Becker, Lore; Irmler, Martin; Dudek, Michael; Janzen, Jakob; Goffin, Eric; Gosens, Reinoud; Knolle, Percy; Pirotte, Bernard; Stoeger, Tobias; Beckers, Johannes; Wagner, Darcy; Singh, Indrabahadur; Theis, Fabian J; de Angelis, Martin Hrabé; O'Connor, Tracy; Tacke, Frank; Boutros, Michael; Dejardin, Emmanuel; Eickelberg, Oliver; Schiller, Herbert B; Königshoff, Melanie; Heikenwalder, Mathias; Yildirim, Ali Önder.

Nature; 588(7836): 151-156, 2020 12.

Artículo en Inglés | MEDLINE | ID: mdl-33149305

7.

Concepts and limitations for learning developmental trajectories from single cell genomics.

Tritschler, Sophie; Büttner, Maren; Fischer, David S; Lange, Marius; Bergen, Volker; Lickert, Heiko; Theis, Fabian J.

Development; 146(12)2019 Jun 27.

Artículo en Inglés | MEDLINE | ID: mdl-31249007

8.

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.

Bastidas-Ponce, Aimée; Tritschler, Sophie; Dony, Leander; Scheibner, Katharina; Tarquis-Medina, Marta; Salinno, Ciro; Schirge, Silvia; Burtscher, Ingo; Böttcher, Anika; Theis, Fabian J; Lickert, Heiko; Bakhti, Mostafa.

Development; 146(12)2019 Jun 17.

Artículo en Inglés | MEDLINE | ID: mdl-31160421

9.

scGen predicts single-cell perturbation responses.

Lotfollahi, Mohammad; Wolf, F Alexander; Theis, Fabian J.

Nat Methods; 16(8): 715-721, 2019 08.

Artículo en Inglés | MEDLINE | ID: mdl-31363220

10.

A test metric for assessing single-cell RNA-seq batch correction.

Büttner, Maren; Miao, Zhichao; Wolf, F Alexander; Teichmann, Sarah A; Theis, Fabian J.

Nat Methods; 16(1): 43-49, 2019 01.

Artículo en Inglés | MEDLINE | ID: mdl-30573817

11.

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios.

Hoppe, Philipp S; Schwarzfischer, Michael; Loeffler, Dirk; Kokkaliaris, Konstantinos D; Hilsenbeck, Oliver; Moritz, Nadine; Endele, Max; Filipczyk, Adam; Gambardella, Adriana; Ahmed, Nouraiz; Etzrodt, Martin; Coutu, Daniel L; Rieger, Michael A; Marr, Carsten; Strasser, Michael K; Schauberger, Bernhard; Burtscher, Ingo; Ermakova, Olga; Bürger, Antje; Lickert, Heiko; Nerlov, Claus; Theis, Fabian J; Schroeder, Timm.

Nature; 535(7611): 299-302, 2016 07 14.

Artículo en Inglés | MEDLINE | ID: mdl-27411635

12.

Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning.

Chlis, Nikolaos-Kosmas; Rausch, Lisa; Brocker, Thomas; Kranich, Jan; Theis, Fabian J.

Nucleic Acids Res; 48(20): 11335-11346, 2020 11 18.

Artículo en Inglés | MEDLINE | ID: mdl-33119742

13.

Prospective identification of hematopoietic lineage choice by deep learning.

Buggenthin, Felix; Buettner, Florian; Hoppe, Philipp S; Endele, Max; Kroiss, Manuel; Strasser, Michael; Schwarzfischer, Michael; Loeffler, Dirk; Kokkaliaris, Konstantinos D; Hilsenbeck, Oliver; Schroeder, Timm; Theis, Fabian J; Marr, Carsten.

Nat Methods; 14(4): 403-406, 2017 Apr.

Artículo en Inglés | MEDLINE | ID: mdl-28218899

14.

Copy number aberrations from Affymetrix SNP 6.0 genotyping data-how accurate are commonly used prediction approaches?

Pitea, Adriana; Kondofersky, Ivan; Sass, Steffen; Theis, Fabian J; Mueller, Nikola S; Unger, Kristian.

Brief Bioinform; 2018 Oct 23.

Artículo en Inglés | MEDLINE | ID: mdl-30351397

15.

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data.

Angerer, Philipp; Fischer, David S; Theis, Fabian J; Scialdone, Antonio; Marr, Carsten.

Bioinformatics; 36(15): 4291-4295, 2020 Aug 01.

Artículo en Inglés | MEDLINE | ID: mdl-32207520

16.

Conditional out-of-distribution generation for unpaired data using transfer VAE.

Lotfollahi, Mohammad; Naghipourfar, Mohsen; Theis, Fabian J; Wolf, F Alexander.

Bioinformatics; 36(Supplement_2): i610-i617, 2020 Dec 30.

Artículo en Inglés | MEDLINE | ID: mdl-33381839

17.

Current best practices in single-cell RNA-seq analysis: a tutorial.

Luecken, Malte D; Theis, Fabian J.

Mol Syst Biol; 15(6): e8746, 2019 06 19.

Artículo en Inglés | MEDLINE | ID: mdl-31217225

18.

Predicting antigen specificity of single T cells based on TCR CDR3 regions.

Fischer, David S; Wu, Yihan; Schubert, Benjamin; Theis, Fabian J.

Mol Syst Biol; 16(8): e9416, 2020 08.

Artículo en Inglés | MEDLINE | ID: mdl-32779888

19.

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines.

Raimúndez, Elba; Keller, Simone; Zwingenberger, Gwen; Ebert, Karolin; Hug, Sabine; Theis, Fabian J; Maier, Dieter; Luber, Birgit; Hasenauer, Jan.

PLoS Comput Biol; 16(3): e1007147, 2020 03.

Artículo en Inglés | MEDLINE | ID: mdl-32119655

20.

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.

Arloth, Janine; Eraslan, Gökcen; Andlauer, Till F M; Martins, Jade; Iurato, Stella; Kühnel, Brigitte; Waldenberger, Melanie; Frank, Josef; Gold, Ralf; Hemmer, Bernhard; Luessi, Felix; Nischwitz, Sandra; Paul, Friedemann; Wiendl, Heinz; Gieger, Christian; Heilmann-Heimbach, Stefanie; Kacprowski, Tim; Laudes, Matthias; Meitinger, Thomas; Peters, Annette; Rawal, Rajesh; Strauch, Konstantin; Lucae, Susanne; Müller-Myhsok, Bertram; Rietschel, Marcella; Theis, Fabian J; Binder, Elisabeth B; Mueller, Nikola S.

PLoS Comput Biol; 16(2): e1007616, 2020 02.

Artículo en Inglés | MEDLINE | ID: mdl-32012148

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SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

Deep learning: new computational modelling techniques for genomics.

scSLAM-seq reveals core features of transcription dynamics in single cells.

LifeTime and improving European healthcare through cell-based interceptive medicine.

Inhibition of LTßR signalling activates WNT-induced regeneration in lung.

Concepts and limitations for learning developmental trajectories from single cell genomics.

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.

scGen predicts single-cell perturbation responses.

A test metric for assessing single-cell RNA-seq batch correction.

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios.

Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning.

Prospective identification of hematopoietic lineage choice by deep learning.

Copy number aberrations from Affymetrix SNP 6.0 genotyping data-how accurate are commonly used prediction approaches?

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data.

Conditional out-of-distribution generation for unpaired data using transfer VAE.

Current best practices in single-cell RNA-seq analysis: a tutorial.

Predicting antigen specificity of single T cells based on TCR CDR3 regions.

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines.

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.