Publications

Z. He, L. Dony, J. S. Fleck, A. Szałata, K. X. Li, I. Slišković, H. Lin, M. Santel, A. Atamian, G. Quadrato, J. Sun, S. P. Pașca, Human Cell Atlas Organoid Biological Network, J. G. Camp, F. J. Theis and B. Treutlein
An integrated transcriptomic cell atlas of human neural organoids
Nature 635, 690–698 (2024).external page article

A. Maynard, M. Soretić and B. Treutlein
Single-cell genomic profiling to study regeneration
Current Opinion in Genetics & Development, 87, 102231 (2024).external page article

A. Brazovskaja, T. Gomes, R. Holtackers, P. Wahle, C. Köner, Z. He, T. Schaffer, J. C. Eckel, R. Hänsel, M. Santel, M. Seimiya, 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
Nature Communications, 15 Article number: 5827 (2024).external page article
 

F. Zenk, J. S. Fleck, S. M. J. Jansen, B. Kashanian, B. Eisinger, M. Santel, J. Dupré, J. G. Camp and B. Treutlein
Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems
Nature Neuroscience, 27,  1376–1386 (2024).external page article
 

S. Ahn, A. Jain, K. C. Kasuba, M. Seimiya, R. Okamoto, B. Treutlein and D. J. Müller
Engineering fibronectin-templated multi-component fibrillar extracellular matrices to modulate tissue-specific cell response
Biomaterials, doi: 10.1016/j.biomaterials.2024.122560 (2024).external page article
 

C. Bressan, M. Snapyan, M. Snapyan, J. Klaus, F. di Matteo, S. P. Robertson, B. Treutlein, M. Parent, S. Cappello and A. Saghatelyan
Metformin rescues migratory deficits of cells derived from patients with periventricular heterotopia
EMBO Mol Med, doi: 10.15252/emmm.202216908. (2023).external page article

C. Li, J. S. Fleck, C. Martins-Costa, T. R. Burkard, J. Themann, M. Stuempflen, A. M. Peer, Á. Vertesy, J. B. Littleboy, C. Esk, U. Elling, G. Kasprian, N. S. Corsini, B. Treutlein and J. A. Knoblich
Single-cell brain organoid screening identifies developmental defects in autism
Nature, 621, 373-380. (2023).external page article

 

J. S. Fleck, J. G. Camp and B. Treutlein
What is a cell type?
Science, 381, 6659, 733-734. (2023).external page articleexternal page

P. Wahle, G. Brancati, C. Harmel. Z. He, G. Gut, J.S. Castillo, A. Santos, Q. Yu, P. Noser, J. S. Fleck, B. Gjeta, D. Pavlinić, S. Picelli, M. Hess, G. W. Schmidt, T. Lummen, Y. Jou, P. galliker, D. Goldblum, M. Balogh, C. S. Cowan, H. P. N. Scholl, B. Roska, M. Renner, L. Pelkmans, B. Treutlein and J. G. Camp
Multimodal spatiotemporal phenotyping of human retinal organoid development
Nature biotechnology, DOI: https://doi.org/10.1038/s41587-023-01747-2 . (2023).external page article

P. Cahan and B. Treutlein
A conversation with ChatGPT on the role of computational systems biology in stem cell research
Stem Cell Reports, 18, 1, 1-2. (2023).external page article

J. G. Camp and B. Treutlein
Human brain organoids influence rat behaviour
Nature, Oct; 610 (7931):265-266. doi: 10.1038/d41586-022-02977-1. (2022).external page article
 

J. S. Fleck, S. M. J. Jansen, D. Wollny, F. Zenk, M. Seimiya, A. Jain, R. Okamoto, M. Santel, Z. He, J. G. Camp and B. Treutlein
Inferring and perturbing cell fate regulomes in human brain organoids
Nature, 377, DOI: https://doi.org/10.1038/s41586-022-05279-8 . (2022).external page article


K. Lust, A. Maynard, T Gomes, J. S. Fleck,  J. G. Camp, E. M. Tanaka and B. Treutlein
Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration
Science, 377, DOI: 10.1126/science.abp9262 . (2022).external page article

Z. He, A. Maynard, A. Jain, T. Berber, R. Petri, H. Lin, M. Santel, K. Ly, J. Dupré, L. Sidow, F. Sanchis Callejal, S. Jansen, S. Riesenberg, J. G. Camp and B. Treutlein
Lineage recording in human cerebral organoids
Nat Methods, 19, pages 90–99 . (2022).external page article

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. Ming, A. R. Muorti, I. Park, O. Reiner, H. Song, L. Studer, S. Temple, G. Testa, B. Treutlein and F. M. Vaccarino
A nomenclature consensus for nervous system organoids and assembloids
Nature, 609, pages 907–910 . (2022).external page article

N. Oskolokov, M. Santel, H. M. Parikh, O. Ekström, G. J. Camp, E. Miyamoto-Mikami, K. Stöm, B.A. Mir, D. Kryvokhyzha, M. Lehtovirta, H. Kobayashi, R. Kakigi, H. Naito, K. Eriksson, B. Nystedt, N. Fuku, B. Treutlein, S. Pääbo and O. Hansson
High-throughput muscle fiber typing from RNA sequencing data
Skeletal Muscle, 12, Article number: 16 . (2022).external page article

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 and B. Treutlein
Characterization of RNA content in individual phase-separated coacervate microdroplets
Nat Commun, May 12;13(1):2626. doi: 10.1038/s41467-022-30158-1. (2022).external page article

J. Krumm, K. Sekine, P. Samaras, A. Brazovskaja, M. Breunig, Y. Yasui, A/ Kleger, H. Taniguchi, M. Wilhelm, B. Treutlein, J. G. Camp and B. Kuster
High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development
Cell Rep., Mar 29;38(13):110604. doi: 10.1016/j.celrep.2022.110604. (2022).external page article

T. Gerber, C. Loureiro, N. Schramma, S. Chen, A. Jain, A. Weber, A. Weigert, M. Santel, K. Alim, B. Treutlein and J. G. Camp
Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium
elife, Feb 23;11:e69745. doi: 10.7554/eLife.69745. (2022).external page article

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C. Kyrousi, A. C. O’Neill, A. Brazovskaja, Z. He, P. Kielkowski, L. Coquand, R. Di Giaimo, P. D’ Andrea, A. Belka, A. F. Echeverry, D. Mei, M. Lenge, C. Cruceanu, I. Y. Buchsbaum, S.Khattak, G. Fabien, E. Binder, F. Elmslie, R. Guerrini, A. D. Baffet, S. A. Sieber, B. Treutlein, P. Robertson and S. Cappello
Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity
Nat Commun, Nov 2;12(1):6298. doi: 10.1038/s41467-021-26447-w. (2021).external page article

M. Haniffa, D. Taylor, S. Linnarsson, B. J. Aronow, G. D. Bader, R. A. Barker, P. G. Camara, J. G. Camp, A. Chédotal, A. Copp, H. C. Etchevers, P. Giacobini, B. Göttgens, G. Guo, A. Hupalowska, K. R. James, E. Kirby, A. Kriegstein, J. Lundeberg, J. C. Marioni, K. B. Meyer, K. K. Niakan, M. Nilsson, B. Olabi, D. Pe’er, A. Regev, J. Rood, O. Rozenblatt-Rosen, R. Satija, S. A. Teichmann, B. Treutlein, R. Vento-Tormo, S. Webb & Human Cell Atlas Developmental Biological Network-Show fewer authors
A roadmap for the Human Developmental Cell Atlas
Nature, Sep;597(7875):196-205(2021).external page article
 

G. Born, M. Nikolova, A. Scherberich, B. Treutlein, A. García-García and I. Martin
Engineering of fully humanized and vascularized 3D bone marrow niches sustaining undifferentiated human cord blood hematopoietic stem and progenitor cells
J. Tissue Eng, Sep 29;12:20417314211044855. doi: 10.1177/20417314211044855(2021).external page article

H. Lin, Z. He. S. Ebert, M. Schörnig, M. Santel, M. T. Nikolova, A. Weigert, W. Hevers, N. N. Kasri, E. Taverna, J. G. Camp and B. Treutlein
NGN2 induces diverse neuron types from human pluripotency
Stem Cell Reports, Jul 22;S2213-6711(21)00372-6 (2021).external page article

Q. Yu, U. Kilik, E. M. Holloway. Y. 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 and J. G. Camp
Charting human development using a multi-endodermal organ atlas and organoid models
Cell, https://doi.org/10.1016/j.cell.2021.04.028(2021).external page article

T. Lin, T. Gerber, Y. Taniguchi-Sugiura, P. Murawala, S. Hermann, L. Grosse, E. Shibata, B. Treutlein and E. M. Tanaka
Fibroblast dedifferentiation as a determinant of successful regeneration
Dev Cell, 56(10):1541-1551.e6(2021).external page article

J. S. Fleck, F. Sanchis-Calleja, Z. He, M. J. Boyle, J. G. Camp and B. Treutlein
Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases
Cell Stem Cell, DOI:https://doi.org/10.1016/j.stem.2021.02.015(2021).external page article

E. M. Holloway, M. Czerwinski, Y. Tsai, J. H. Wu, A. Wu, C. J. Childs, K. D. Walton, C. W. Sweet, Q. Yu, I. Glass, B. Treutlein, J. G. Camp and J. R. Spence
Mapping Development of the Human Intestinal Niche at Single-Cell Resolution
Cell Stem Cell, 28(3):568-580.e4. (2021).external page article

M. Schornig, X. Ju, L. Fast, S. Ebert, A. Weigert, S. Kanton, T. Schaffer, N. Nadif Kasri, B. Treutlein, B. M. Peter, W. Hevers and E. Taverna
Comparison of induced neurons reveals slower structural and functional maturation in humans than in apes
eLife, 10, e59323 (2021).external page article


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

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

M. Dannemann, Z. He, C. Heide, B. Vernot, L. Sidow, S. Kanton, A. Weigert, B. Treutlein, S. Paabo, J. Kelso and J. G. Camp
Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions
Stem Cell Reports, 15, 214-225 (2020). external page articl

B. Treutlein and J. G. Camp
Sequencing perturbed cortex development
Science, 370(6520):1038-1039 doi: 10.1126/science.abf3661(2020). external page article

Z. He, A. Brazovskaja, S. Ebert, J. G. Camp and B. Treutlein
CSS: cluster similarity spectrum integration of single-cell genomics data
Genome Biology, 21, Article number: 224 (2020). external page article

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

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. C. Sherwood, J. G. Camp, S. Paabo, B. Treutlein and P. Khaitovich
Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
Genome research, 30, 776-789 (2020). external page article

A. L. McGuire, S. Gabriel, S. A. Tishkoff, A. Wonkam, A. Chakravarti, E. E. M. Furlong, B. Treutlein, A. Meissner, H. Y. Chang, N. Lopez-Bigas, E. Segal and J. S. Kim
The road ahead in genetics and genomics
Nat Rev Genet, 21, 581-596 (2020). external page article

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 and J. R. Spence
In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution
Developmental Cell, DOI:https://doi.org/10.1016/j.devcel.2020.01.033 (2020). external page article

K. Sekine, S. Tsuzuki, R. Yasui, T. Kobayashi, K. Ikeda, Y. Hamada, E. Kanai, J. G. Camp, B. Treutlein, Y. Ueno, S. Okamoto and H. Taniguchi
Robust detection of undifferentiated iPSC among differentiated cells
Scientific reports, 10, 10293 (2020). external page article

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S. Kanton, M. Boyle, Z. He, M. Santel, A. Weigert, F. Sanchis Calleja, L. Sidow, J. Fleck, P. Guijarro, D. Han, Z. Qian, M. Heide, W. B. Huttner, P. Khaitovich, S. Pääbo, B. Treutlein and J.G. Camp
Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development
Nature, 574 418-422 (2019). external page article

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

R.G Parra, N. Papadopoulos, L. Ahumada-Arranz, J.E. Kholtei, N. Mottelson, Y. Horokhovsky, B. Treutlein and J. Soeding.
Reconstructing complex lineage trees from scRNA-seq data using MERLoT
Nucleic Acids Res., 47(17), 8961-8974. doi: 10.1093/nar/gkz706. (2019). external page article

A.M. Klein and B. Treutlein
Single cell analyses of development in the modern era
Development, 146(12), pii: dev181396. doi: 10.1242/dev.181396. (2019). external page article

W. Koh, A. Wu, L. Penland, B. Treutlein, N. F. Neff, G. L. Mantalas, Y. J. Blumenfeld, Y. Y. El-Sayed, D. K. Stevenson, G. M. Shaw, and S. R. Quake
Single Cell Transcriptomes Derived from Human Cervical and Uterine Tissue during Pregnancy
Adv Biosyst, 3, e1800336 (2019). external page article

J. Klaus, S. Kanton, C. Kyrousi, A.C. Ayo-Martin, R. Di 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 and S. Cappello
Altered neuronal migratory trajectories in human cerebral organoids derived from individuals with neuronal heterotopia
Nature Medicine, 25, 561-568 (2019). external page article

J.G.Camp and B. Treutlein
Evaluation of Wu et al.: Strengthening Single-Cell Bioinformatic Comparisons for Improving Organoid Differentiation
Cell stem Cell, 24(3),343-344 (2019). external page article

A. Brazovskaja, B. Treutlein and G. Camp.
High-throughput single-cell transcriptomics on organoids
Currrent Opinion in Biotechnology, 55, 167-171 (2019). external page article

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

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

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* and B. Berninger*.
Pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program.
Nature Neuroscience, 21, 932-940 (2018). external page article

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 and H. Taniguchi.
Optimal Hypoxia Regulates Human iPSC-Derived Liver Bud Differentiation through Intercellular TGFB Signaling.
Stem Cell Reports, 11(2), 306-316 (2018). external page external page article

J.M. Churko, P. Garg, B. Treutlein, M. Venkatasubramanian, H. Wu, J. Lee, Q. N. Wessells, S. Y. Chen, W. Y. Chen, K. Chetal, G. Mantalas, N. Neff, E. Jabart, A. Sharma, G. P. Nolan, N. Salomonis and J. C. Wu.
Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis.
Nat Commun, 9(1), 4906 (2018). external page article

S. Vaid, J. G. Camp, L. Hersemann, C. Eugster Oegema, A. K. Heninger, S. Winkler, H. Brandl, M. Sarov, B. Treutlein, W. B. Huttner and T. Namba.
A novel population of Hopx-dependent basal radial glial cells in the developing mouse neocortex.
Development, 145(20) (2018). external page article

J. Kageyama, D. Wollny, B. Treutlein* and J. G. Camp*.
ShinyCortex: Exploring Single-Cell Transcriptome Data From the Developing Human Cortex.
Front Neurosci, 12, 315 (2018). external page article

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