Angerer, Philipp, Laleh Haghverdi, Maren Büttner, Fabian J. Theis, Carsten Marr, and Florian Buettner. 2016. “Destiny: Diffusion Maps for Large-Scale Single-Cell Data in R.” Bioinformatics 32 (8): 1241–43. https://doi.org/10.1093/bioinformatics/btv715.

Angerer, Philipp, Lukas Simon, Sophie Tritschler, F. Alexander Wolf, David Fischer, and Fabian J. Theis. 2017. “Single Cells Make Big Data: New Challenges and Opportunities in Transcriptomics.” Current Opinion in Systems Biology 4: 85–91.

Bajikar, Sameer S., Christiane Fuchs, Andreas Roller, Fabian J. Theis, and Kevin A. Janes. 2014. “Parameterizing Cell-to-Cell Regulatory Heterogeneities via Stochastic Transcriptional Profiles.” Proceedings of the National Academy of Sciences of the United States of America 111 (5): E626–35. https://doi.org/10.1073/pnas.1311647111.

Beyer, Marc, Zeinab Abdullah, Jens M. Chemnitz, Daniela Maisel, Jil Sander, Clara Lehmann, Yasser Thabet, et al. 2016. “Tumor-Necrosis Factor Impairs CD4+ T Cell–mediated Immunological Control in Chronic Viral Infection.” Nature Immunology 17 (March): 593. https://doi.org/10.1038/ni.3399.

Beyer, Marc, Yasser Thabet, Roman-Ulrich Müller, Timothy Sadlon, Sabine Classen, Katharina Lahl, Samik Basu, et al. 2011. “Repression of the Genome Organizer SATB1 in Regulatory T Cells Is Required for Suppressive Function and Inhibition of Effector Differentiation.” Nature Immunology 12 (9): 898–907. https://doi.org/10.1038/ni.2084.

Bilkei-Gorzo, Andras, Onder Albayram, Astrid Draffehn, Kerstin Michel, Anastasia Piyanova, Hannah Oppenheimer, Mona Dvir-Ginzberg, et al. 2017. “A Chronic Low Dose of Δ9-Tetrahydrocannabinol (THC) Restores Cognitive Function in Old Mice.” Nature Medicine 23 (6): 782–87. https://doi.org/10.1038/nm.4311.

Buettner, Florian, Victoria Moignard, Berthold Göttgens, and Fabian J. Theis. 2014. “Probabilistic PCA of Censored Data: Accounting for Uncertainties in the Visualization of High-Throughput Single-Cell qPCR Data.” Bioinformatics 30 (13): 1867–75. https://doi.org/10.1093/bioinformatics/btu134.

Camell, Christina D., Jil Sander, Olga Spadaro, Aileen Lee, Kim Y. Nguyen, Allison Wing, Emily L. Goldberg, et al. 2017. “Inflammasome-Driven Catecholamine Catabolism in Macrophages Blunts Lipolysis during Ageing.” Nature 550 (7674): 119–23. https://doi.org/10.1038/nature24022.

Christ, Anette, Patrick Günther, Mario A. R. Lauterbach, Peter Duewell, Debjani Biswas, Karin Pelka, Claus J. Scholz, et al. 2018. “Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming.” Cell 172 (1-2): 162–75.e14. https://doi.org/10.1016/j.cell.2017.12.013.

De Nardo, Dominic, Larisa I. Labzin, Hajime Kono, Reiko Seki, Susanne V. Schmidt, Marc Beyer, Dakang Xu, et al. 2014. “High-Density Lipoprotein Mediates Anti-Inflammatory Reprogramming of Macrophages via the Transcriptional Regulator ATF3.” Nature Immunology 15 (2): 152–60. https://doi.org/10.1038/ni.2784.

Deltcheva, Elitza, Krzysztof Chylinski, Cynthia M. Sharma, Karine Gonzales, Yanjie Chao, Zaid A. Pirzada, Maria R. Eckert, Jörg Vogel, and Emmanuelle Charpentier. 2011. “CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III.” Nature 471 (7340): 602–7. https://doi.org/10.1038/nature09886.

Durek, Pawel, Karl Nordström, Gilles Gasparoni, Abdulrahman Salhab, Christopher Kressler, Melanie de Almeida, Kevin Bassler, et al. 2016. “Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development.” Immunity 45 (5): 1148–61. https://doi.org/10.1016/j.immuni.2016.10.022.

Haghverdi, Laleh, Maren Buettner, F. Alexander Wolf, Florian Buettner, and Fabian J. Theis. 2016. “Diffusion Pseudotime Robustly Reconstructs Lineage Branching.” Nature Methods 13 (10): 845–48.

Heidkamp, Gordon F., Jil Sander, Christian H. K. Lehmann, Lukas Heger, Nathalie Eissing, Anna Baranska, Jennifer J. Lühr, et al. 2016. “Human Lymphoid Organ Dendritic Cell Identity Is Predominantly Dictated by Ontogeny, Not Tissue Microenvironment.” Science Immunology 1 (6). https://doi.org/10.1126/sciimmunol.aai7677.

Hilsenbeck, Oliver, Michael Schwarzfischer, Stavroula Skylaki, Bernhard Schauberger, Philipp S. Hoppe, Dirk Loeffler, Konstantinos D. Kokkaliaris, et al. 2016. “Software Tools for Single-Cell Tracking and Quantification of Cellular and Molecular Properties.” Nature Biotechnology 34 (7): 703–6. https://doi.org/10.1038/nbt.3626.

Mass, Elvira, Ivan Ballesteros, Matthias Farlik, Florian Halbritter, Patrick Günther, Lucile Crozet, Christian E. Jacome-Galarza, et al. 2016. “Specification of Tissue-Resident Macrophages during Organogenesis.” Science 353 (6304). https://doi.org/10.1126/science.aaf4238.

Moignard, Victoria, Iain C. Macaulay, Gemma Swiers, Florian Buettner, Judith Schütte, Fernando J. Calero-Nieto, Sarah Kinston, et al. 2013. “Characterization of Transcriptional Networks in Blood Stem and Progenitor Cells Using High-Throughput Single-Cell Gene Expression Analysis.” Nature Cell Biology 15 (4): 363–72. https://doi.org/10.1038/ncb2709.

Papenfort, Kai, Yan Sun, Masatoshi Miyakoshi, Carin K. Vanderpool, and Jörg Vogel. 2013. “Small RNA-Mediated Activation of Sugar Phosphatase mRNA Regulates Glucose Homeostasis.” Cell 153 (2): 426–37. https://doi.org/10.1016/j.cell.2013.03.003.

Plass, M. et al. 2018, in press. “Cell Type Atlas and Lineage Tree of A Whole Complex Animal by Single-Cell Transcriptomics.” Science

Saliba, Antoine-Emmanuel, Lei Li, Alexander J. Westermann, Silke Appenzeller, Daphne A. C. Stapels, Leon N. Schulte, Sophie Helaine, and Jörg Vogel. 2016. “Single-Cell RNA-Seq Ties Macrophage Polarization to Growth Rate of Intracellular Salmonella.” Nature Microbiology 2 (November): 16206. https://doi.org/10.1038/nmicrobiol.2016.206.

Sander, Jil, Susanne V. Schmidt, Branko Cirovic, Naomi McGovern, Olympia Papantonopoulou, Anna-Lena Hardt, Anna C. Aschenbrenner, et al. 2017. “Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.” Immunity 47 (6): 1051–66.e12. https://doi.org/10.1016/j.immuni.2017.11.024.

See, Peter, Charles-Antoine Dutertre, Jinmiao Chen, Patrick Günther, Naomi McGovern, Sergio Erdal Irac, Merry Gunawan, et al. 2017. “Mapping the Human DC Lineage through the Integration of High-Dimensional Techniques.” Science 356 (6342). https://doi.org/10.1126/science.aag3009.

Sharma, Cynthia M., Steve Hoffmann, Fabien Darfeuille, Jérémy Reignier, Sven Findeiss, Alexandra Sittka, Sandrine Chabas, et al. 2010. “The Primary Transcriptome of the Major Human Pathogen Helicobacter Pylori.” Nature 464 (7286): 250–55. https://doi.org/10.1038/nature08756.

Simon, L. M., S. Karg, A. J. Westermann, M. Engel, A. H. A. Elbehery, B. Hense, M. Heinig, L. Deng, and F. J. Theis. 2018. “MetaMap: An Atlas of Metatranscriptomic Reads in Human Disease-Related RNA-Seq Data.” GigaScience 7 (6). https://doi.org/10.1093/gigascience/giy070.

Tedeschi, Andrea, Sebastian Dupraz, Claudia J. Laskowski, Jia Xue, Thomas Ulas, Marc Beyer, Joachim L. Schultze, and Frank Bradke. 2016. “The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS.” Neuron 92 (2): 419–34. https://doi.org/10.1016/j.neuron.2016.09.026.

Tritschler, Sophie, Fabian J. Theis, Heiko Lickert, and Anika Böttcher. 2017. “Systematic Single-Cell Analysis Provides New Insights into Heterogeneity and Plasticity of the Pancreas.” Molecular Metabolism 6 (9): 974–90. https://doi.org/10.1016/j.molmet.2017.06.021.

Ulas, Thomas, Sabine Pirr, Beate Fehlhaber, Marie S. Bickes, Torsten G. Loof, Thomas Vogl, Lara Mellinger, et al. 2017. “S100-Alarmin-Induced Innate Immune Programming Protects Newborn Infants from Sepsis.” Nature Immunology 18 (6): 622–32. https://doi.org/10.1038/ni.3745.

Wendeln, Ann-Christin, Karoline Degenhardt, Lalit Kaurani, Michael Gertig, Thomas Ulas, Gaurav Jain, Jessica Wagner, et al. 2018. “Innate Immune Memory in the Brain Shapes Neurological Disease Hallmarks.” Nature 556 (7701): 332–38. https://doi.org/10.1038/s41586-018-0023-4.

Westermann, Alexander J., Konrad U. Förstner, Fabian Amman, Lars Barquist, Yanjie Chao, Leon N. Schulte, Lydia Müller, Richard Reinhardt, Peter F. Stadler, and Jörg Vogel. 2016. “Dual RNA-Seq Unveils Noncoding RNA Functions in Host-Pathogen Interactions.” Nature 529 (7587): 496–501. https://doi.org/10.1038/nature16547.

Wolf, F. Alexander, Philipp Angerer, and Fabian J. Theis. 2018. “SCANPY: Large-Scale Single-Cell Gene Expression Data Analysis.” Genome Biology 19 (1): 15. https://doi.org/10.1186/s13059-017-1382-0.

Xue, Jia, Susanne V. Schmidt, Jil Sander, Astrid Draffehn, Wolfgang Krebs, Inga Quester, Dominic De Nardo, et al. 2014. “Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation.” Immunity 40 (2): 274–88. https://doi.org/10.1016/j.immuni.2014.01.006.