Not logged in Probe set selection for targeted spatial transcriptomics Kuemmerle, Louis B.; Luecken, Malte D.; Firsova, Alexandra B.; Andrade e Sousa, Lisa Barros de; Strasser, Lena; Mekki, Ilhem Isra; Campi, Francesco; Heumos, Lukas; Shulman, Maiia; Beliaeva, Valentina; Hediyeh-Zadeh, Soroor; Schaar, Anna C.; Mahbubani, Krishnaa T.; Sountoulidis, Alexandros; Balassa, Tamas; Kovacs, Ferenc; Horvath, Peter; Piraud, Marie; Erturk, Ali; Samakovlis, Christos; Theis, Fabian J. Share Save
An open-source framework for end-to-end analysis of electronic health record data Heumos, Lukas; Ehmele, Philipp; Treis, Tim; zu Belzen, Julius Upmeier; Roellin, Eljas; May, Lilly; Namsaraeva, Altana; Horlava, Nastassya; Shitov, Vladimir A.; Zhang, Xinyue; Zappia, Luke; Knoll, Rainer; Lang, Niklas J.; Hetzel, Leon; Virshup, Isaac; Sikkema, Lisa; Curion, Fabiola; Eils, Roland; Schiller, Herbert B.; Hilgendorff, Anne; Theis, Fabian J. Share Save
Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis Curion, Fabiola; Rich-Griffin, Charlotte; Agarwal, Devika; Ouologuem, Sarah; Rue-Albrecht, Kevin; May, Lilly; Garcia, Giulia E. L.; Heumos, Lukas; Thomas, Tom; Lason, Wojciech; Sims, David; Theis, Fabian J.; Dendrou, Calliope A. Share Save
hadge: a comprehensive pipeline for donor deconvolution in single-cell studies Curion, Fabiola; Wu, Xichen; Heumos, Lukas; Andre, Mylene Mariana Gonzales; Halle, Lennard; Ozols, Matiss; Grant-Peters, Melissa; Rich-Griffin, Charlotte; Yeung, Hing-Yuen; Dendrou, Calliope A.; Schiller, Herbert B.; Theis, Fabian J. Share Save
OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data Pfeuffer, Julianus; Bielow, Chris; Wein, Samuel; Jeong, Kyowon; Netz, Eugen; Walter, Axel; Alka, Oliver; Nilse, Lars; Colaianni, Pasquale Domenico; Mccloskey, Douglas; Kim, Jihyung; Rosenberger, George; Bichmann, Leon; Walzer, Mathias; Veit, Johannes; Boudaud, Bertrand; Bernt, Matthias; Patikas, Nikolaos; Pilz, Matteo; Startek, Michal Piotr; Kutuzova, Svetlana; Heumos, Lukas; Charkow, Joshua; Sing, Justin Cyril; Feroz, Ayesha; Siraj, Arslan; Weisser, Hendrik; Dijkstra, Tjeerd M. H.; Perez-Riverol, Yasset; Roest, Hannes; Kohlbacher, Oliver; Sachsenberg, Timo Share Save
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis Lang, Niklas J.; Gote-Schniering, Janine; Porras-Gonzalez, Diana; Yang, Lin; De Sadeleer, Laurens J.; Jentzsch, R. Christoph; Shitov, Vladimir A.; Zhou, Shuhong; Ansari, Meshal; Agami, Ahmed; Mayr, Christoph H.; Hooshiar Kashani, Baharak; Chen, Yuexin; Heumos, Lukas; Pestoni, Jeanine C.; Molnar, Eszter Sarolta; Geeraerts, Emiel; Anquetil, Vincent; Saniere, Laurent; Woegrath, Melanie; Gerckens, Michael; Lehmann, Mareike; Yildirim, Ali Onder; Hatz, Rudolf; Kneidinger, Nikolaus; Behr, Juergen; Wuyts, Wim A.; Stoleriu, Mircea-Gabriel; Luecken, Malte D.; Theis, Fabian J.; Burgstaller, Gerald; Schiller, Herbert B. Share Save
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis Lang, Niklas Jonathan; Gote-Schniering, Janine; Porras-Gonzalez, Diana; Yang, Lin; De Sadeleer, Laurens J.; Jentzsch, R. Christoph; Shitov, Vladimir A.; Zhou, Shuhong; Ansari, Meshal; Agami, Ahmed; Mayr, Christoph H.; Kashani, Baharak Hooshiar; Chen, Yuexin; Heumos, Lukas; Pestoni, Jeanine C.; Geeraerts, Emil; Anquetil, Vincent; Saniere, Laurent; Woegrath, Melanie; Gerckens, Michael; Hatz, Rudolf; Kneidinger, Nikolaus; Behr, Juergen; Wuyts, Wim A.; Stoleriu, Mircea-Gabriel; Luecken, Malte D.; Theis, Fabian J.; Burgstaller, Gerald; Schiller, Herbert. B. Share Save
Myeloid-dependent immunosuppressive features drive IPF progression Kapellos, Theodoros; Viteri, Valeria; Sirokha, Dmytro; Greiffo, Flavia; Namsaraeva, Altana; Heumos, Lukas; Dietel, Daniela; Frankenberger, Marion; Eickelberg, Oliver; Kneidinger, Nikolaus; Yildirim, Ali Oeender; Schiller, Herbert; Behr, Juergen; Fernandez, Isis Enlil Share Save
A spatially resolved extracellular matrix proteome atlas of the distal human lung Chen, Yuexin; Gote-Schniering, Janine; Mueller, Michaela; Albanese, Pascal; Jankevics, Andris; Jentzsch, R. Christoph; Tata, Aleksandra; Ansari, Meshal; De Sadeleer, Laurens; Yang, Lin; Heumos, Lukas; Agami, Ahmed; Zhou, Shuhong; Mayr, Christoph H.; Hatz, Rudolf; Schneider, Christian P.; Behr, Juergen; Hilgendorff, Anne; Yildirim, Ali Oender; Stoleriu, Mircea-Gabriel; Dorfmueller, Peter; Theis, Fabian J.; Tata, Purushothama Rao; Luecken, Malte D.; Scheltema, Richard A.; Schiller, Herbert B. Share Save
An integrated cell atlas of the lung in health and disease Sikkema, Lisa; Ramirez-Suastegui, Ciro; Strobl, Daniel C.; Gillett, Tessa E.; Zappia, Luke; Madissoon, Elo; Markov, Nikolay S.; Zaragosi, Laure-Emmanuelle; Ji, Yuge; Ansari, Meshal; Arguel, Marie-Jeanne; Apperloo, Leonie; Banchero, Martin; Becavin, Christophe; Berg, Marijn; Chichelnitskiy, Evgeny; Chung, Mei-i; Collin, Antoine; Gay, Aurore C. A.; Gote-Schniering, Janine; Kashani, Baharak Hooshiar; Inecik, Kemal; Jain, Manu; Kapellos, Theodore S.; Kole, Tessa M.; Leroy, Sylvie; Mayr, Christoph H.; Oliver, Amanda J.; von Papen, Michael; Peter, Lance; Taylor, Chase J.; Walzthoeni, Thomas; Xu, Chuan; Bui, Linh T.; De Donno, Carlo; Dony, Leander; Faiz, Alen; Guo, Minzhe; Gutierrez, Austin J.; Heumos, Lukas; Huang, Ni; Ibarra, Ignacio L.; Jackson, Nathan D.; Murthy, Preetish Kadur Lakshminarasimha; Lotfollahi, Mohammad; Tabib, Tracy; Talavera-Lopez, Carlos; Travaglini, Kyle J.; Wilbrey-Clark, Anna; Worlock, Kaylee B.; Yoshida, Masahiro; van den Berge, Maarten; Bosse, Yohan; Desai, Tushar J.; Eickelberg, Oliver; Kaminski, Naftali; Krasnow, Mark A.; Lafyatis, Robert; Nikolic, Marko Z.; Powell, Joseph E.; Rajagopal, Jayaraj; Rojas, Mauricio; Rozenblatt-Rosen, Orit; Seibold, Max A.; Sheppard, Dean; Shepherd, Douglas P.; Sin, Don D.; Timens, Wim; Tsankov, Alexander M.; Whitsett, Jeffrey; Xu, Yan; Banovich, Nicholas E.; Barbry, Pascal; Duong, Thu Elizabeth; Falk, Christine S.; Meyer, Kerstin B.; Kropski, Jonathan A.; Pe'er, Dana; Schiller, Herbert B.; Tata, Purushothama Rao; Schultze, Joachim L.; Teichmann, Sara A.; Misharin, Alexander, V; Nawijn, Martijn C.; Luecken, Malte D.; Theis, Fabian J.; Chen, Yuexin; Hagood, James S.; Agami, Ahmed; Horvath, Peter; Lundeberg, Joakim; Marquette, Charles-Hugo; Pryhuber, Gloria; Samakovlis, Chistos; Sun, Xin; Ware, Lorraine B.; Zhang, Kun Share Save
The scverse project provides a computational ecosystem for single-cell omics data analysis Virshup, Isaac; Bredikhin, Danila; Heumos, Lukas; Palla, Giovanni; Sturm, Gregor; Gayoso, Adam; Kats, Ilia; Koutrouli, Mikaela; Berger, Bonnie; Pe'er, Dana; Regev, Aviv; Teichmann, Sarah; Finotello, Francesca; Wolf, F. Alexander; Yosef, Nir; Stegle, Oliver; Theis, Fabian; Angerer, Philipp; Bergen, Volker; Boyeau, Pierre D.; Buettner, Maren; Eraslan, Gokcen; Fischer, David; Frank, Max C.; Hong, Justin; Klein, Michal; Lange, Marius; Lopez, Romain; Lotfollahi, Mohammad; Luecken, Malte; Ramirez, Fidel A.; Regier, Jeffrey; Rybakov, Sergei; Schaar, Anna; Valiollah Pour Amiri, Valeh; Weiler, Philipp J.; Xing, Galen Share Save
Best practices for single-cell analysis across modalities Heumos, Lukas; Schaar, Anna C.; Lance, Christopher; Litinetskaya, Anastasia; Drost, Felix; Zappia, Luke; Luecken, Malte; Strobl, Daniel; Henao, Juan; Curion, Fabiola B.; Schiller, Herbert; Theis, Fabian Share Save
A Mutation-Agnostic Hematopoietic Stem Cell Gene Therapy for Metachromatic Leukodystrophy Antony, Justin S.; Daniel-Moreno, Alberto; Lamsfus-Calle, Andres; Raju, Janani; Kaftancioglu, Merve; Urena-Bailen, Guillermo; Rottenberger, Jennifer; Hou, Yujuan; Santhanakumaran, Vidiyaah; Lee, Jun-Hoe; Heumos, Lukas; Boehringer, Judith; Kraegeloh-Mann, Ingeborg; Handgretinger, Rupert; Mezger, Markus Share Save
The AIMe registry for artificial intelligence in biomedical research Matschinske, Julian; Alcaraz, Nicolas; Benis, Arriel; Golebiewski, Martin; Grimm, Dominik G.; Heumos, Lukas; Kacprowski, Tim; Lazareva, Olga; List, Markus; Louadi, Zakaria; Pauling, Josch K.; Pfeifer, Nico; Roettger, Richard; Schwaemmle, Veit; Sturm, Gregor; Traverso, Alberto; Van Steen, Kristel; de Freitas, Martiela Vaz; Villalba Silva, Gerda Cristal; Wee, Leonard; Wenke, Nina K.; Zanin, Massimiliano; Zolotareva, Olga; Baumbach, Jan; Blumenthal, David B. Share Save
Sfaira accelerates data and model reuse in single cell genomics Fischer, David S.; Dony, Leander; Konig, Martin; Moeed, Abdul; Zappia, Luke; Heumos, Lukas; Tritschler, Sophie; Holmberg, Olle; Aliee, Hananeh; Theis, Fabian J. Share Save
Universal Gene Correction Approaches for β-hemoglobinopathies Using CRISPR-Cas9 and Adeno-Associated Virus Serotype 6 Donor Templates Lamsfus-Calle, Andres; Daniel-Moreno, Alberto; Urena-Bailen, Guillermo; Rottenberger, Jennifer; Raju, Janani; Epting, Thomas; Marciano, Sabina; Heumos, Lukas; Baskaran, Praveen; Antony, Justin S.; Handgretinger, Rupert; Mezger, Markus Share Save
Comparative targeting analysis of KLF1, BCL11A, and HBG1/2 in CD34+ HSPCs by CRISPR/Cas9 for the induction of fetal hemoglobin Lamsfus-Calle, Andres; Daniel-Moreno, Alberto; Antony, Justin S.; Epting, Thomas; Heumos, Lukas; Baskaran, Praveen; Admard, Jakob; Casadei, Nicolas; Latifi, Ngadhnjim; Siegmund, Darina M.; Kormann, Michael S. D.; Handgretinger, Rupert; Mezger, Markus Share Save
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