PUBLICATIONS

Preprints:

A. Jain, G. Gut, F. Sanchis-Calleja, R. Okamoto, S. Streib, Z. He, F. Zenk, M. Santel, M. Seimiya, R. Holtackers, S. M. J. Jansen, J. G. Camp*, and B. Treutlein. Morphodynamics of human early brain organoid development. BioRxiv (2023). doi: https://doi.org/10.1101/2023.08.21.553827.

M.T. Nikolova, Z. He, R.A. Wimmer, M. Seimiya, J.M. Nikoloff, J.M. Penninger, J.G. Camp*, B. Treutlein. Fate and state transitions during human blood vessel organoid development. BioRxiv (2022), doi: https://doi.org/10.1101/2022.03.23.485329.

R. Okuda, B. Gjeta, D. Popovic, A. Maynard, Q. Yu, Z. He, M. Santel, M. Seimiya, S. Morinaga, Y. Miyagi, T. Yamaguchi, Y. Ueno, H. Taniguichi, B. Treutlein, J.G. Camp*. Reconstructing cell interactions and state trajectories in pancreatic cancer stromal tumoroids. BioRxiv (2022), doi: https://doi.org/10.1101/2022.02.14.480334.

Brazovskaja*, T. Gomes*, C. Körner, Z. He, T. Schaffer, J. C. Eckel, R. Hänsel, M. Santel, T. Denecke, M. Dannemann, M. Brosch, J. Hampe, D. Seehofer, G. Damm, J. G. Camp* and B. Treutlein. Cell atlas of the regenerating human liver after portal vein embolization. BioRxiv (2021), doi: https://doi.org/10.1101/2021.06.03.444016.

Peer reviewed publications:

J.S. Fleck, J.G. Camp*, B. Treutlein. What is a cell type? Science in press (2023).

U. Kilik, A. A. Pollen, C. B. Lowe, J. G. Camp*. Human-specific genetics: New tools to explore the molecular and cellular basis of human evolution. Nature Reviews Genetics. (Accepted).

P. Wahle, G. Brancati, C. Harmel, Z. He, G. Gut, J. Sarabia Del Castillo, A. Xavier da Silveira Dos Santos, Q. Yu, P. Noser, J.S. Fleck, B. Gjeta, D. Pavlinić, S. Picelli, M. Hess, G.W. Schmidt, T.T.A. Lummen, Y. Hou, P. Galliker, D. Goldblum, M. Balogh, C.S. Cowan, H.P.N. Scholl, B. Roska, M. Renner, L. Pelkmans, B. Treutlein, J.G. Camp*. Multimodal spatiotemporal phenotyping of human organoid development. Nature Biotechnology (2023), https://doi.org/10.1038/s41587-023-01747-2

J. G. Camp*, B. Treutlein, Human brain organoids influence rat behaviour. Nature. 610 (2022), pp. 265–266.

J. S. Fleck, S. M. J. Jansen, D. Wollny, F. Zenk, M. Seimiya, A. Jain, R. Okamoto, M. Santel, Z. He, J. G. Camp*, B. Treutlein*, Inferring and perturbing cell fate regulomes in human brain organoids. Nature (2022), doi:10.1038/s41586-022-05279-8.

S. P. Pașca, P. Arlotta, H. S. Bateup, J. G. Camp, S. Cappello, F. H. Gage, J. A. Knoblich, A. R. Kriegstein, M. A. Lancaster, G.-L. Ming, A. R. Muotri, I.-H. Park, O. Reiner, H. Song, L. Studer, S. Temple, G. Testa, B. Treutlein, F. M. Vaccarino, A nomenclature consensus for nervous system organoids and assembloids. Nature. 609, 907–910 (2022).

K. Lust, A. Maynard, T. Gomes, J. S. Fleck, J. G. Camp, E. M. Tanaka, B. Treutlein, Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration. Science. 377, eabp9262 (2022).

J.G. Camp*, and B. Treutlein. “Human Brain Organoids Influence Rat Behaviour.” Nature (2022).

D. Wollny, B. Vernot, J. Wang, M. Hondele, A. Safrastyan, F. Aron, J. Micheel, Z. He, A. Hyman, K. Weis, J. G. Camp, T.-Y. D. Tang, B. Treutlein, Characterization of RNA content in individual phase-separated coacervate microdroplets. Nat. Commun. 13, 2626 (2022).

J. Krumm, K. Sekine, P. Samaras, A. Brazovskaja, M. Breunig, R. Yasui, A. Kleger, H. Taniguchi, M. Wilhelm, B. Treutlein, J. G. Camp, B. Kuster, High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Rep. 38, 110604 (2022).

Z. He, T. Gerber, A. Maynard, A. Jain, R. Petri, M. Santel, K. Ly, L. Sidow, F. Sanchís-Calleja, S. Riesenberg, J. G. Camp*, B. Treutlein*. Lineage recording reveals dynamics of cerebral organoid regionalization. Nature Methods. 19, 90–99 (2022).

T. Gerber, C. Loureiro, N. Schramma, S. Chen, A. Jain, A. Weber, A. Weigert, M. Santel, K. Alim*, B. Treutlein*, J. G. Camp*. Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium. eLife 2022; 11:e69745 DOI: 10.7554/eLife.69745

Q. Yu, U. Kilik, E. M. Holloway, Y.-H. Tsai, C. Harmel, A. Wu, J. H. Wu, M. Czerwinski, C. J. Childs, Z. He, M. M. Capeling, S. Huang, I. A. Glass, P. D. R. Higgins, B. Treutlein*, J. R. Spence*, J. G. Camp*, Charting human development using a multi-endodermal organ atlas and organoid models. Cell. 184, 3281-3298.e22 (2021).

E. M. Holloway, M. Czerwinski, Y.-H. Tsai, J. H. Wu, A. Wu, C. J. Childs, K. D. Walton, C. W. Sweet, Q. Yu, I. Glass, B. Treutlein, J. G. Camp*, J. R. Spence*, Mapping Development of the Human Intestinal Niche at Single-Cell Resolution. Cell Stem Cell. 28, 568-580.e4 (2021).

C. Bock, M. Boutros, J. G. Camp, L. Clarke, H. Clevers, J. A. Knoblich, P. Liberali, A. Regev, A. C. Rios, O. Stegle, H. G. Stunnenberg, S. A. Teichmann, B. Treutlein, R. G. J. Vries, H. C. A. Biological N. Organoids, The Organoid Cell Atlas. Nature Biotechnology. 39, 13-17 (2021).

J. S. Fleck, F. Sanchís-Calleja, Z. He, M. Santel, M. J. Boyle, J. G. Camp*, B. Treutlein*, Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases. Cell Stem Cell. 28, 1148-1159.e8 (2021).

M. Haniffa, D. Taylor, S. Linnarsson, B. J. Aronow, G. D. Bader,…, A roadmap for the Human Developmental Cell Atlas. Nature. 597, 196–205 (2021).

H.-C. Lin, Z. He, S. Ebert, M. Schörnig, M. Santel, M. T. Nikolova, A. Weigert, W. Hevers, N. N. Kasri, E. Taverna, J. G. Camp*, B. Treutlein*, NGN2 induces diverse neuron types from human pluripotency. Stem Cell Rep. 16, 2118–2127 (2021).

Y.-H. Hung, S. Huang, M. K. Dame, Q. Yu, Q. C. Yu, Y. A. Zeng, J. G. Camp, J. R. Spence, P. Sethupathy, Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model. Nucleic Acids Res. 49, gkaa1204- (2021).

Z. He*, A. Brazovskaja, S. Ebert, J. G. Camp*, B. Treutlein*, CSS: cluster similarity spectrum integration of single-cell genomics data. Genome Biol. 21, 224 (2020).

G. Brancati, B. Treutlein, J. G. Camp*, Resolving Neurodevelopmental and Vision Disorders Using Organoid Single-Cell Multi-omics. Neuron. 107, 1000–1013 (2020).

A. J. Miller, Q. Yu, M. Czerwinski, Y.-H. Tsai, R. F. Conway, A. Wu, E. M. Holloway, T. Walker, I. A. Glass, B. Treutlein, J. G. Camp*, J. R. Spence*, In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution. Dev Cell. 53, 117-128.e6 (2020).

E. Khrameeva, I. Kurochkin, D. Han, P. Guijarro, S. Kanton, M. Santel, Z. Qian, S. Rong, P. Mazin, M. Sabirov, M. Bulat, O. Efimova, A. Tkachev, S. Guo, C. Sherwood, G. Camp, S. Paabo, B. Treutlein, P. Khaitovich, Genome Research, doi:10.1101/gr.256958.119. (2021)

S. Kanton, B. Treutlein, J. G. Camp, Single-cell genomic analysis of human cerebral organoids. Methods Cell Biol. 159, 229–256 (2020).

M. Dannemann, Z. He, C. Heide, B. Vernot, L. Sidow, S. Kanton, A. Weigert, B. Treutlein, S. Pääbo, J. Kelso, J. G. Camp*, Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions. Stem Cell Rep. 15, 214–225 (2020).

B. Treutlein, J. G. Camp*, Sequencing perturbed cortex development. Science. 370, 1038–1039 (2020).

S. Kanton, M. J. Boyle, Z. He, M. Santel, A. Weigert, F. Sanchís-Calleja, P. Guijarro, L. Sidow, J. S. Fleck, D. Han, Z. Qian, M. Heide, W. B. Huttner, P. Khaitovich, S. Pääbo, B. Treutlein*, J. G. Camp*, Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature. 574, 418–422 (2019).

A. Brazovskaja, B. Treutlein, J. G. Camp*, High-throughput single-cell transcriptomics on organoids. Curr Opin Biotech. 55, 167–171 (2019).

J. G. Camp*, R. Platt, B. Treutlein, Mapping human cell phenotypes to genotypes with single-cell genomics. Science. 365, 1401–1405 (2019).

J. Klaus, S. Kanton, C. Kyrousi, A. C. Ayo-Martin, R. D. Giaimo, S. Riesenberg, A. C. O’Neill, J. G. Camp, C. Tocco, M. Santel, E. Rusha, M. Drukker, M. Schroeder, M. Götz, S. P. Robertson, B. Treutlein, S. Cappello, Altered neuronal migratory trajectories in human cerebral organoids derived from individuals with neuronal heterotopia. Nature Medicine. 25, 561–568 (2019).

T. Gerber, P. Murawala, D. Knapp, W. Masselink, M. Schuez, S. Hermann, M. Gac-Santel, S. Nowoshilow, J. Kageyama, S. Khattak, J. D. Currie, J. G. Camp, E. M. Tanaka, B. Treutlein, Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration. Science. 362, eaaq0681 (2018).

B. Treutlein*, J. G. Camp*, Evaluation of Wu et al.: Strengthening Single-Cell Bioinformatic Comparisons for Improving Organoid Differentiation. Cell Stem Cell. 24, 343–344 (2019).

J. Kageyama, D. Wollny, B. Treutlein, J. G. Camp*, ShinyCortex: Exploring Single-Cell Transcriptome Data From the Developing Human Cortex. Frontiers in Neuroscience. 12, 315 (2018).

M. Karow*, J. G. Camp*, S. Falk, T. Gerber, A. Pataskar, M. Gac-Santel, J. Kageyama, A. Brazovskaja, A. Garding, W. Fan, T. Riedemann, A. Casamassa, A. Smiyakin, C. Schichor, M. Götz, V. K. Tiwari, B. Treutlein, B. Berninger, Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. Nature Neuroscience. 21, 932-940 (2018).

J. G. Camp*, D. Wollny, B. Treutlein, Single-cell genomics to guide human stem cell and tissue engineering. Nature Methods. 15, 661–667 (2018).

H. Ayabe, T. Anada, T. Kamoya, T. Sato, M. Kimura, E. Yoshizawa, S. Kikuchi, Y. Ueno, K. Sekine, J. G. Camp, B. Treutlein, A. Ferguson, O. Suzuki, T. Takebe, H. Taniguchi, Optimal Hypoxia Regulates Human iPSC-Derived Liver Bud Differentiation through Intercellular TGFB Signaling. Stem Cell Rep. 11, 306–316 (2018).

S. Vaid, J. G. Camp, L. Hersemann, C. E. Oegema, A.-K. Heninger, S. Winkler, H. Brandl, M. Sarov, B. Treutlein, W. B. Huttner, T. Namba, A novel population of Hopx-dependent basal radial glial cells in the developing mouse neocortex. Development. 145, dev169276 (2018).

J. G. Camp*, B. Treutlein, Human organomics: a fresh approach to understanding human development using single-cell transcriptomics. Development. 144, 1584–1587 (2017).

J. G. Camp*, B. Treutlein, Advances in mini-brain technology. Nature. 545, 39–40 (2017).

J. G. Camp*, K. Sekine*, T. Gerber, H. Loeffler-Wirth, H. Binder, M. Gac, S. Kanton, J. Kageyama, G. Damm, D. Seehofer, L. Belicova, M. Bickle, R. Barsacchi, R. Okuda, E. Yoshizawa, M. Kimura, H. Ayabe, H. Taniguchi, T. Takebe, B. Treutlein, Multilineage communication regulates human liver bud development from pluripotency. Nature. 546, 533–538 (2017).

C. R. Lickwar, J. G. Camp, M. Weiser, J. L. Cocchiaro, D. M. Kingsley, T. S. Furey, S. Z. Sheikh, J. F. Rawls, Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. Plos Biology. 15, e2002054 (2017).

F. Mora-Bermúdez*, F. Badsha*, S. Kanton*, J. G. Camp*, B. Vernot, K. Köhler, B. Voigt, K. Okita, T. Maricic, Z. He, R. Lachmann, S. Pääbo, B. Treutlein, W. B. Huttner, Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development. Elife. 5, e18683 (2016).

O. Gokce, G. M. Stanley, B. Treutlein, N. F. Neff, J. G. Camp, R. C. Malenka, P. E. Rothwell, M. V. Fuccillo, T. C. Südhof, S. R. Quake, Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. Cell Reports. 16, 1126–1137 (2016).

B. Treutlein, Q. Y. Lee, J. G. Camp, M. Mall, W. Koh, S. A. M. Shariati, S. Sim, N. F. Neff, J. M. Skotheim, M. Wernig, S. R. Quake, Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature. 534, 391–395 (2016).

J. G. Camp*, F. Badsha*, M. Florio, S. Kanton, T. Gerber, M. Wilsch-Bräuninger, E. Lewitus, A. Sykes, W. Hevers, M. Lancaster, J. A. Knoblich, R. Lachmann, S. Pääbo, W. B. Huttner, B. Treutlein, Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc National Acad Sci. 112, 15672–15677 (2015).

K. Atarashi, T. Tanoue, M. Ando, N. Kamada, Y. Nagano, S. Narushima, W. Suda, A. Imaoka, H. Setoyama, T. Nagamori, E. Ishikawa, T. Shima, T. Hara, S. Kado, T. Jinnohara, H. Ohno, T. Kondo, K. Toyooka, E. Watanabe, S. Yokoyama, S. Tokoro, H. Mori, Y. Noguchi, H. Morita, I. I. Ivanov, T. Sugiyama, G. Nuñez, J. G. Camp, M. Hattori, Y. Umesaki, K. Honda, Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells. Cell. 163, 367–380 (2015).

B. A. Braun, A. Marcovitz, J. G. Camp, R. Jia, G. Bejerano, Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales. Proc National Acad Sci. 112, 8036–8040 (2015).

J. G. Camp*, C. L. Frank*, C. R. Lickwar, H. Guturu, T. Rube, A. M. Wenger, J. Chen, G. Bejerano, G. E. Crawford, J. F. Rawls, Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Research. 24, 1504–1516 (2014).

J. G. Camp*, A. L. Jazwa, C. M. Trent, J. F. Rawls, Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription. Plos Genetics. 8, e1002585 (2012).

D. C. Rinker, P. L. Jones, R. J. Pitts, M. Rutzler, J. G. Camp, L. Sun, P. Xu, D. Weaver, L. J. Zwiebel, Novel high-throughput screens of Anopheles gambiae odorant receptors reveal candidate behaviour-modifying chemicals for mosquitoes. Physiol. Entomol. 37, 33–41 (2012).

J. G. Camp*, M. Kanther, I. Semova, J. F. Rawls, Patterns and Scales in Gastrointestinal Microbial Ecology. Gastroenterology. 136, 1989–2002 (2009).