Pesquisa | Biblioteca Virtual em Saúde

1.

Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma.

Kirschenbaum, Daniel; Xie, Ken; Ingelfinger, Florian; Katzenelenbogen, Yonatan; Abadie, Kathleen; Look, Thomas; Sheban, Fadi; Phan, Truong San; Li, Baoguo; Zwicky, Pascale; Yofe, Ido; David, Eyal; Mazuz, Kfir; Hou, Jinchao; Chen, Yun; Shaim, Hila; Shanley, Mayra; Becker, Soeren; Qian, Jiawen; Colonna, Marco; Ginhoux, Florent; Rezvani, Katayoun; Theis, Fabian J; Yosef, Nir; Weiss, Tobias; Weiner, Assaf; Amit, Ido.

Cell ; 187(1): 149-165.e23, 2024 01 04.

Artigo em Inglês | MEDLINE | ID: mdl-38134933

2.

The challenges in finding your home as a multidisciplinary scientist.

Wang, Sijia; Marr, Linsey C; Contreras, Lydia M; Theis, Fabian J; Nurse, Paul.

Cell ; 185(15): 2623-2625, 2022 07 21.

Artigo em Inglês | MEDLINE | ID: mdl-35868266

3.

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.

Artigo em Inglês | MEDLINE | ID: mdl-32413319

4.

Best practices for single-cell analysis across modalities.

Heumos, Lukas; Schaar, Anna C; Lance, Christopher; Litinetskaya, Anastasia; Drost, Felix; Zappia, Luke; Lücken, Malte D; Strobl, Daniel C; Henao, Juan; Curion, Fabiola; Schiller, Herbert B; Theis, Fabian J.

Nat Rev Genet ; 24(8): 550-572, 2023 08.

Artigo em Inglês | MEDLINE | ID: mdl-37002403

5.

Modeling fragment counts improves single-cell ATAC-seq analysis.

Martens, Laura D; Fischer, David S; Yépez, Vicente A; Theis, Fabian J; Gagneur, Julien.

Nat Methods ; 21(1): 28-31, 2024 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-38049697

6.

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells.

Gayoso, Adam; Weiler, Philipp; Lotfollahi, Mohammad; Klein, Dominik; Hong, Justin; Streets, Aaron; Theis, Fabian J; Yosef, Nir.

Nat Methods ; 21(1): 50-59, 2024 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-37735568

7.

SpatialData: an open and universal data framework for spatial omics.

Marconato, Luca; Palla, Giovanni; Yamauchi, Kevin A; Virshup, Isaac; Heidari, Elyas; Treis, Tim; Vierdag, Wouter-Michiel; Toth, Marcella; Stockhaus, Sonja; Shrestha, Rahul B; Rombaut, Benjamin; Pollaris, Lotte; Lehner, Laurens; Vöhringer, Harald; Kats, Ilia; Saeys, Yvan; Saka, Sinem K; Huber, Wolfgang; Gerstung, Moritz; Moore, Josh; Theis, Fabian J; Stegle, Oliver.

Nat Methods ; 2024 Mar 20.

Artigo em Inglês | MEDLINE | ID: mdl-38509327

8.

CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data.

Lubatti, Gabriele; Stock, Marco; Iturbide, Ane; Ruiz Tejada Segura, Mayra L; Riepl, Melina; Tyser, Richard C V; Danese, Anna; Colomé-Tatché, Maria; Theis, Fabian J; Srinivas, Shankar; Torres-Padilla, Maria-Elena; Scialdone, Antonio.

Development ; 150(11)2023 Jun 01.

Artigo em Inglês | MEDLINE | ID: mdl-37294170

9.

Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps.

Spitzer, Hannah; Berry, Scott; Donoghoe, Mark; Pelkmans, Lucas; Theis, Fabian J.

Nat Methods ; 20(7): 1058-1069, 2023 07.

Artigo em Inglês | MEDLINE | ID: mdl-37248388

10.

Population-level integration of single-cell datasets enables multi-scale analysis across samples.

De Donno, Carlo; Hediyeh-Zadeh, Soroor; Moinfar, Amir Ali; Wagenstetter, Marco; Zappia, Luke; Lotfollahi, Mohammad; Theis, Fabian J.

Nat Methods ; 20(11): 1683-1692, 2023 Nov.

Artigo em Inglês | MEDLINE | ID: mdl-37813989

11.

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.

Artigo em Inglês | MEDLINE | ID: mdl-33149305

12.

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 11.

Artigo em Inglês | MEDLINE | ID: mdl-32894860

13.

Benchmarking atlas-level data integration in single-cell genomics.

Luecken, Malte D; Büttner, M; Chaichoompu, K; Danese, A; Interlandi, M; Mueller, M F; Strobl, D C; Zappia, L; Dugas, M; Colomé-Tatché, M; Theis, Fabian J.

Nat Methods ; 19(1): 41-50, 2022 01.

Artigo em Inglês | MEDLINE | ID: mdl-34949812

14.

Squidpy: a scalable framework for spatial omics analysis.

Palla, Giovanni; Spitzer, Hannah; Klein, Michal; Fischer, David; Schaar, Anna Christina; Kuemmerle, Louis Benedikt; Rybakov, Sergei; Ibarra, Ignacio L; Holmberg, Olle; Virshup, Isaac; Lotfollahi, Mohammad; Richter, Sabrina; Theis, Fabian J.

Nat Methods ; 19(2): 171-178, 2022 02.

Artigo em Inglês | MEDLINE | ID: mdl-35102346

15.

CellRank for directed single-cell fate mapping.

Lange, Marius; Bergen, Volker; Klein, Michal; Setty, Manu; Reuter, Bernhard; Bakhti, Mostafa; Lickert, Heiko; Ansari, Meshal; Schniering, Janine; Schiller, Herbert B; Pe'er, Dana; Theis, Fabian J.

Nat Methods ; 19(2): 159-170, 2022 02.

Artigo em Inglês | MEDLINE | ID: mdl-35027767

16.

longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types.

Hagenberg, Jonas; Budde, Monika; Pandeva, Teodora; Kondofersky, Ivan; Schaupp, Sabrina K; Theis, Fabian J; Schulze, Thomas G; Müller, Nikola S; Heilbronner, Urs; Batra, Richa; Knauer-Arloth, Janine.

Bioinformatics ; 40(4)2024 Mar 29.

Artigo em Inglês | MEDLINE | ID: mdl-38485697

17.

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.

Artigo em Inglês | MEDLINE | ID: mdl-30971806

18.

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.

Artigo em Inglês | MEDLINE | ID: mdl-31292545

19.

Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts.

Mayr, Christoph H; Sengupta, Arunima; Asgharpour, Sara; Ansari, Meshal; Pestoni, Jeanine C; Ogar, Paulina; Angelidis, Ilias; Liontos, Andreas; Rodriguez-Castillo, José Alberto; Lang, Niklas J; Strunz, Maximilian; Porras-Gonzalez, Diana; Gerckens, Michael; De Sadeleer, Laurens J; Oehrle, Bettina; Viteri-Alvarez, Valeria; Fernandez, Isis E; Tallquist, Michelle; Irmler, Martin; Beckers, Johannes; Eickelberg, Oliver; Stoleriu, Gabriel Mircea; Behr, Jürgen; Kneidinger, Nikolaus; Wuyts, Wim A; Wasnick, Roxana Maria; Yildirim, Ali Önder; Ahlbrecht, Katrin; Morty, Rory E; Samakovlis, Christos; Theis, Fabian J; Burgstaller, Gerald; Schiller, Herbert B.

Eur Respir J ; 63(2)2024 Feb.

Artigo em Inglês | MEDLINE | ID: mdl-38212077

20.

Predicting cellular responses to complex perturbations in high-throughput screens.

Lotfollahi, Mohammad; Klimovskaia Susmelj, Anna; De Donno, Carlo; Hetzel, Leon; Ji, Yuge; Ibarra, Ignacio L; Srivatsan, Sanjay R; Naghipourfar, Mohsen; Daza, Riza M; Martin, Beth; Shendure, Jay; McFaline-Figueroa, Jose L; Boyeau, Pierre; Wolf, F Alexander; Yakubova, Nafissa; Günnemann, Stephan; Trapnell, Cole; Lopez-Paz, David; Theis, Fabian J.

Mol Syst Biol ; 19(6): e11517, 2023 06 12.

Artigo em Inglês | MEDLINE | ID: mdl-37154091

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