@article{bunne2024optimal,

title = {Optimal transport for single-cell and spatial omics},

author = {Charlotte Bunne and Geoffrey Schiebinger and Andreas Krause and Aviv Regev and Marco Cuturi},

url = {https://rdcu.be/dQTI5},

year  = {2024},

date = {2024-01-01},

journal = {Nature Reviews Methods Primers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ryu2024crossmodality,

title = {Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport},

author = {Jayoung Ryu and Romain Lopez and Charlotte Bunne and Aviv Regev},

url = {https://arxiv.org/pdf/2405.00838.pdf},

year  = {2024},

date = {2024-01-01},

journal = {arXiv Preprint arXiv:2405.00838},

note = {Best Paper Award and Contributed Talk at ICML AI for Science Workshop, 2024},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{van2023equireact,

title = {3DReact: Geometric Deep Learning for Chemical Reactions},

author = {Puck Gerwen and Ksenia R Briling and Charlotte Bunne and Vignesh Ram Somnath and Ruben Laplaza and Andreas Krause and Clemence Corminboeuf},

url = {https://pubs.acs.org/doi/10.1021/acs.jcim.4c00104},

year  = {2024},

date = {2024-01-01},

journal = {Journal of Chemical Information and Modeling},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bunne2024build,

title = {How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities},

author = {Charlotte Bunne and Yusuf Roohani and Yanay Rosen and Ankit Gupta and Xikun Zhang and Marcel Roed and Theo Alexandrov and Mohammed AlQuraishi and Patricia Brennan and Daniel B. Burkhardt and Andrea Califano and Jonah Cool and Abby F. Dernburg and Kirsty Ewing and Emily B. Fox and Matthias Haury and Amy E. Herr and Eric Horvitz and Patrick D. Hsu and Viren Jain and Gregory R. Johnson and Thomas Kalil and David R. Kelley and Shana O. Kelley and Anna Kreshuk and Tim Mitchison and Stephani Otte and Jay Shendure and Nicholas J. Sofroniew and Fabian Theis and Christina V. Theodoris and Srigokul Upadhyayula and Marc Valer and Bo Wang and Eric Xing and Serena Yeung-Levy and Marinka Zitnik and Theofanis Karaletsos and Aviv Regev and Emma Lundberg and Jure Leskovec and Stephen R. Quake},

url = {https://arxiv.org/pdf/2409.11654},

year  = {2024},

date = {2024-01-01},

journal = {arXiv Preprint arXiv:2409.11654},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rohbeck2024modeling,

title = {Modeling Complex System Dynamics with Flow Matching Across Time and Conditions},

author = {Martin Rohbeck and Charlotte Bunne and Edward De Brouwer and Jan-Christian Huetter and Anne Biton and Kelvin Y. Chen and Aviv Regev and Romain Lopez},

year  = {2024},

date = {2024-01-01},

journal = {NeurIPS Workshop on AI for New Drug Modalities},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{plainer2023transition,

title = {Transition Path Sampling with Boltzmann Generator-based MCMC Moves},

author = {Michael Plainer and Hannes Stärk and Charlotte Bunne and Stephan Günnemann},

url = {https://arxiv.org/pdf/2312.05340.pdf},

year  = {2023},

date = {2023-01-01},

journal = {arXiv preprint arXiv:2312.05340},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{serrano2023reproducible,

title = {Reproducible image-based profiling with Pycytominer},

author = {Erik Serrano and Srinivas Niranj Chandrasekaran and Dave Bunten and Kenneth I Brewer and Jenna Tomkinson and Roshan Kern and Michael Bornholdt and Stephen Fleming and Ruifan Pei and John Arevalo and others},

url = {https://arxiv.org/pdf/2311.05340.pdf},

year  = {2023},

date = {2023-01-01},

journal = {arXiv Preprint arXiv:2311.13417},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pariset2023unbalanced,

title = {Unbalanced Diffusion Schrödinger Bridge},

author = {Matteo Pariset and Ya-Ping Hsieh and Charlotte Bunne and Andreas Krause and Valentin De Bortoli},

url = {https://arxiv.org/pdf/2306.09099.pdf},

year  = {2023},

date = {2023-01-01},

journal = {arXiv Preprint arXiv:2306.09099},

note = {ICML Workshop on New Frontiers for Learning, Control, and Dynamical Systems, 2023},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bunne2021learning,

title = {Learning Single-Cell Perturbation Responses using Neural Optimal Transport},

author = {Charlotte Bunne and Stefan Stark and Gabriele Gut and ... and Mitchell Levesque and Kjong Van Lehmann and Lucas Pelkmans and Andreas Krause and Gunnar Rätsch},

url = {https://www.nature.com/articles/s41592-023-01969-x},

year  = {2023},

date = {2023-01-01},

journal = {Nature Methods},

note = {Highlighted as Research Briefing in Nature Methods. Also presented at the NeurIPS Workshop on Optimal Transport and Machine Learning (OTML), 2021},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{luebeck2023neural,

title = {Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings},

author = {Frederike Lübeck and Charlotte Bunne and Gabriele Gut and Jacobo Sarabia Castillo and Lucas Pelkmans and David Alvarez Melis},

url = {https://arxiv.org/pdf/2209.15621.pdf},

year  = {2023},

date = {2023-01-01},

journal = {arXiv Preprint arXiv:2209.15621},

note = {Spotlight Talk at NeurIPS Meaningful Representations of Life Workshop, 2022},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{schwaller2022machine,

title = {Machine intelligence for chemical reaction space},

author = {Philippe Schwaller and Alain C Vaucher and Ruben Laplaza and Charlotte Bunne and Andreas Krause and Clemence Corminboeuf and Teodoro Laino},

url = {https://wires.onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1604},

year  = {2022},

date = {2022-01-01},

journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},

publisher = {Wiley Online Library},

note = {Selected as Featured Cover of Volume 12, Issue 5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cuturi2022optimal,

title = {Optimal Transport Tools (OTT): A JAX Toolbox for all things Wasserstein},

author = {Marco Cuturi and Laetitia Meng-Papaxanthos and Yingtao Tian and Charlotte Bunne and Geoff Davis and Olivier Teboul},

url = {https://arxiv.org/pdf/2201.12324.pdf},

year  = {2022},

date = {2022-01-01},

journal = {arXiv Preprint arXiv:2201.12324},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chevalley2022invariant,

title = {Invariant Causal Mechanisms through Distribution Matching},

author = {Mathieu Chevalley and Charlotte Bunne and Andreas Krause and Stefan Bauer},

url = {https://arxiv.org/pdf/2206.11646.pdf},

year  = {2022},

date = {2022-01-01},

journal = {arXiv Preprint arXiv:2206.11646},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{manica2021cosifer,

title = {COSIFER: a Python package for the consensus inference of molecular interaction networks},

author = {Matteo Manica and Charlotte Bunne and Roland Mathis and Joris Cadow and Mehmet Eren Ahsen and Gustavo A Stolovitzky and Maria Rodriguez Martinez},

url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa942/5949000},

year  = {2020},

date = {2020-01-01},

journal = {Bioinformatics},

volume = {37},

number = {14},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{buchauer2019exponential,

title = {Exponential Growth of Glioblastoma In Vivo Driven by Rapidly Dividing and Outwardly Migrating Cancer Stem Cells},

author = {Lisa Buchauer and Muhammad Amir Khan and Yue Zhuo and Chunxuan Shao and Peng Zou and Weijun Feng and Mengran Qian and Gözde Bekki and Charlotte Bunne and Anna Neuerburg and Azer Aylin Acikgöz and Mona Tomaschko and Zhe Zhu and Heike Alter and Katharina Hartmann and Olga Friesen and Klaus Hexel and Thomas Höfer and Hai-Kun Liu},

url = {https://www.biorxiv.org/content/10.1101/723601v1.full.pdf},

year  = {2019},

date = {2019-01-01},

journal = {bioRxiv Preprint bioRxiv:10.1101/723601v1},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{waldhauer2015backbone,

title = {Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation},

author = {Max C Waldhauer and Silvan N Schmitz and Constantin Ahlmann-Eltze and Jan G Gleixner and Carolin C Schmelas and Anna G Huhn and Charlotte Bunne and Magdalena Büscher and Max Horn and Nils Klughammer and others},

url = {https://pubs.rsc.org/en/Content/ArticleLanding/2015/MB/C5MB00341E},

year  = {2015},

date = {2015-01-01},

journal = {Molecular BioSystems},

volume = {11},

number = {12},

publisher = {Royal Society of Chemistry},

keywords = {},

pubstate = {published},

tppubtype = {article}

}