@ARTICLE{Figueredo:2009dg,
   author = {Figueredo, A.~J. and Wolf, P. S.~A.},
   title = {Assortative pairing and life history strategy -- a cross-cultural study},
   journal = {Human Nature},
   volume = {20},
   pages = {317-330},
   year = {2009},
   doi={https://doi.org/10.1007/s12110-009-9068-2}
}

@MISC{Hao:gidmaps:2014,
  author = {Hao, Z. and AghaKouchak, A. and Nakhjiri, N. and Farahmand, A},
  year = {2014},
  title = {Global integrated drought monitoring and prediction system ({GIDMaPS}) data sets},
  howpublished = {\emph{figshare} \url{http://dx.doi.org/10.6084/m9.figshare.853801}}
}




@article{sauer2023stylegan,
  title={StyleGAN-t: Unlocking the power of GANs for fast large-scale text-to-image synthesis},
  author={Sauer, Axel and Karras, Tero and Laine, Samuli and Geiger, Andreas and Aila, Timo},
  journal={International Conference on Machine Learning},
  year={2023}
}

@article{xia2022gan,
  title={GAN Inversion: A survey},
  author={Xia, Weihao and Zhang, Yulun and Yang, Yujiu and Xue, Jing-Hao and Zhou, Bolei and Yang, Ming-Hsuan},
  journal={IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year={2022},
  publisher={IEEE}
}

@inproceedings{bermano2022state,
  title={State-of-the-Art in the Architecture, Methods and Applications of StyleGAN},
  author={Bermano, Amit H and Gal, Rinon and Alaluf, Yuval and Mokady, Ron and Nitzan, Yotam and Tov, Omer and Patashnik, Oren and Cohen-Or, Daniel},
  booktitle={Computer Graphics Forum},
  volume={41},
  pages={591--611},
  year={2022},
  organization={Wiley Online Library}
}

@article{zhang2023text,
  title={Text-to-image Diffusion Model in Generative AI: A Survey},
  author={Zhang, Chenshuang and Zhang, Chaoning and Zhang, Mengchun and Kweon, In So},
  journal={arXiv preprint arXiv:2303.07909},
  year={2023}
}

@article{doudna2020promise,
  title={The promise and challenge of therapeutic genome editing},
  author={Doudna, Jennifer A},
  journal={Nature},
  volume={578},
  number={7794},
  pages={229--236},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@article{jinek2012programmable,
  title={A programmable dual-RNA--guided DNA endonuclease in adaptive bacterial immunity},
  author={Jinek, Martin and Chylinski, Krzysztof and Fonfara, Ines and Hauer, Michael and Doudna, Jennifer A and Charpentier, Emmanuelle},
  journal={science},
  volume={337},
  number={6096},
  pages={816--821},
  year={2012},
  publisher={American Association for the Advancement of Science}
}

@article{komor2016programmable,
  title={Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage},
  author={Komor, Alexis C and Kim, Yongjoo B and Packer, Michael S and Zuris, John A and Liu, David R},
  journal={Nature},
  volume={533},
  number={7603},
  pages={420--424},
  year={2016},
  publisher={Nature Publishing Group UK London}
}

@article{naeem2020latest,
  title={Latest developed strategies to minimize the off-target effects in CRISPR-Cas-mediated genome editing},
  author={Naeem, Muhammad and Majeed, Saman and Hoque, Mubasher Zahir and Ahmad, Irshad},
  journal={Cells},
  volume={9},
  number={7},
  pages={1608},
  year={2020},
  publisher={MDPI}
}

@article{de2019ethics,
  title={The ethics of genome editing in non-human animals: a systematic review of reasons reported in the academic literature},
  author={de Graeff, Nienke and Jongsma, Karin R and Johnston, Josephine and Hartley, Sarah and Bredenoord, Annelien L},
  journal={Philosophical Transactions of the Royal Society B},
  volume={374},
  number={1772},
  pages={20180106},
  year={2019},
  publisher={The Royal Society}
}


@inproceedings{kang2023scaling,
  title={Scaling up gans for text-to-image synthesis},
  author={Kang, Minguk and Zhu, Jun-Yan and Zhang, Richard and Park, Jaesik and Shechtman, Eli and Paris, Sylvain and Park, Taesung},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  year={2023}
}

@article{moses2022museum,
  title={Museum of spatial transcriptomics},
  author={Moses, Lambda and Pachter, Lior},
  journal={Nature Methods},
  volume={19},
  number={5},
  pages={534--546},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

@article{he2022high,
  title={High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging},
  author={He, Shanshan and Bhatt, Ruchir and Brown, Carl and Brown, Emily A and Buhr, Derek L and Chantranuvatana, Kan and Danaher, Patrick and Dunaway, Dwayne and Garrison, Ryan G and Geiss, Gary and others},
  journal={Nature Biotechnology},
  volume={40},
  number={12},
  pages={1794--1806},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

@article{janesick2022high,
  title={High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue},
  author={Janesick, Amanda and Shelansky, Robert and Gottscho, Andrew D and Wagner, Florian and Rouault, Morgane and Beliakoff, Ghezal and de Oliveira, Michelli Faria and Kohlway, Andrew and Abousoud, Jawad and Morrison, Carolyn A and others},
  journal={bioRxiv},
  pages={2022--10},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{croitoru2023diffusion,
  title={Diffusion models in vision: A survey},
  author={Croitoru, Florinel-Alin and Hondru, Vlad and Ionescu, Radu Tudor and Shah, Mubarak},
  journal={IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year={2023},
  publisher={IEEE}
}

@inproceedings{karras2020analyzing,
  title={Analyzing and improving the image quality of stylegan},
  author={Karras, Tero and Laine, Samuli and Aittala, Miika and Hellsten, Janne and Lehtinen, Jaakko and Aila, Timo},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={8110--8119},
  year={2020}
}

@article{karras2021alias,
  title={Alias-free generative adversarial networks},
  author={Karras, Tero and Aittala, Miika and Laine, Samuli and H{\"a}rk{\"o}nen, Erik and Hellsten, Janne and Lehtinen, Jaakko and Aila, Timo},
  journal={Advances in Neural Information Processing Systems},
  volume={34},
  pages={852--863},
  year={2021}
}

@article{wu2023gilea,
  title={GILEA: GAN Inversion-enabled latent eigenvalue analysis for phenome profiling and editing},
  author={Wu, Jiqing and Koelzer, Viktor H},
  journal={bioRxiv},
  pages={2023--02},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}

@article{campa2019multiplexed,
  title={Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts},
  author={Campa, Carlo C and Weisbach, Niels R and Santinha, Ant{\'o}nio J and Incarnato, Danny and Platt, Randall J},
  journal={Nature Methods},
  volume={16},
  number={9},
  pages={887--893},
  year={2019},
  publisher={Nature Publishing Group US New York}
}


@article{heusel2017gans,
  title={Gans trained by a two time-scale update rule converge to a local nash equilibrium},
  author={Heusel, Martin and Ramsauer, Hubert and Unterthiner, Thomas and Nessler, Bernhard and Hochreiter, Sepp},
  journal={Advances in neural information processing systems},
  volume={30},
  year={2017}
}

@inproceedings{sauer2022stylegan,
  title={Stylegan-xl: Scaling stylegan to large diverse datasets},
  author={Sauer, Axel and Schwarz, Katja and Geiger, Andreas},
  booktitle={ACM SIGGRAPH 2022 conference proceedings},
  pages={1--10},
  year={2022}
}

@software{Shariatnia_Simple_CLIP_2021,
author = {Shariatnia, M. Moein},
doi = {10.5281/zenodo.6845731; https://github.com/moein-shariatnia/OpenAI-CLIP},
month = {4},
title = {{Simple CLIP}},
version = {1.0.0},
year = {2021},
}

@inproceedings{richardson2021encoding,
  title={Encoding in style: a stylegan encoder for image-to-image translation},
  author={Richardson, Elad and Alaluf, Yuval and Patashnik, Or and Nitzan, Yotam and Azar, Yaniv and Shapiro, Stav and Cohen-Or, Daniel},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={2287--2296},
  year={2021}
}

@inproceedings{alaluf2021restyle,
  title={Restyle: A residual-based stylegan encoder via iterative refinement},
  author={Alaluf, Yuval and Patashnik, Or and Cohen-Or, Daniel},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},
  pages={6711--6720},
  year={2021}
}

@inproceedings{zhang2018unreasonable,
  title={The unreasonable effectiveness of deep features as a perceptual metric},
  author={Zhang, Richard and Isola, Phillip and Efros, Alexei A and Shechtman, Eli and Wang, Oliver},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={586--595},
  year={2018}
}

@article{stuart2019integrative,
  title={Integrative single-cell analysis},
  author={Stuart, Tim and Satija, Rahul},
  journal={Nature reviews genetics},
  volume={20},
  number={5},
  pages={257--272},
  year={2019},
  publisher={Nature Publishing Group UK London}
}

@inproceedings{wu2022sorted,
  title={Sorted eigenvalue comparison $d_{Eig}$: A simple alternative to $d_{FID}$},
  year={2022},
  author={Wu, Jiqing and Koelzer, Viktor},
  booktitle={NeurIPS 2022 Workshop on Distribution Shifts: Connecting Methods and Applications}
}

@article{vert2023will,
  title={How will generative AI disrupt data science in drug discovery?},
  author={Vert, Jean-Philippe},
  journal={Nature Biotechnology},
  pages={1--2},
  year={2023},
  publisher={Nature Publishing Group US New York}
}


@article{chowdhury2022single,
  title={Single-sequence protein structure prediction using a language model and deep learning},
  author={Chowdhury, Ratul and Bouatta, Nazim and Biswas, Surojit and Floristean, Christina and Kharkar, Anant and Roy, Koushik and Rochereau, Charlotte and Ahdritz, Gustaf and Zhang, Joanna and Church, George M and others},
  journal={Nature Biotechnology},
  volume={40},
  number={11},
  pages={1617--1623},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

@article{llinares2023deep,
  title={Deep embedding and alignment of protein sequences},
  author={Llinares-L{\'o}pez, Felipe and Berthet, Quentin and Blondel, Mathieu and Teboul, Olivier and Vert, Jean-Philippe},
  journal={Nature Methods},
  volume={20},
  number={1},
  pages={104--111},
  year={2023},
  publisher={Nature Publishing Group US New York}
}

@inproceedings{radford2021learning,
  title={Learning transferable visual models from natural language supervision},
  author={Radford, Alec and Kim, Jong Wook and Hallacy, Chris and Ramesh, Aditya and Goh, Gabriel and Agarwal, Sandhini and Sastry, Girish and Askell, Amanda and Mishkin, Pamela and Clark, Jack and others},
  booktitle={International conference on machine learning},
  pages={8748--8763},
  year={2021},
  organization={PMLR}
}

@article{johnson2023building,
  title={Building the next generation of virtual cells to understand cellular biology},
  author={Johnson, Graham T and Agmon, Eran and Akamatsu, Matthew and Lundberg, Emma and Lyons, Blair and Ouyang, Wei and Quintero-Carmona, Omar A and Riel-Mehan, Megan and Rafelski, Susanne and Horwitz, Rick},
  journal={Biophysical Journal},
  year={2023},
  publisher={Elsevier}
}

@article{vandereyken2023methods,
  title={Methods and applications for single-cell and spatial multi-omics},
  author={Vandereyken, Katy and Sifrim, Alejandro and Thienpont, Bernard and Voet, Thierry},
  journal={Nature Reviews Genetics},
  pages={1--22},
  year={2023},
  publisher={Nature Publishing Group UK London}
}

@article{ruan2020circulating,
  title={Circulating tumor cell characterization of lung cancer brain metastases in the cerebrospinal fluid through single-cell transcriptome analysis},
  author={Ruan, Haoyu and Zhou, Yihang and Shen, Jie and Zhai, Yue and Xu, Ying and Pi, Linyu and Huang, Ruofan and Chen, Kun and Li, Xiangyu and Ma, Weizhe and others},
  journal={Clinical and translational medicine},
  volume={10},
  number={8},
  pages={e246},
  year={2020},
  publisher={Wiley Online Library}
}


@ARTICLE{edit2023what,
  title={What’s next for bioimage analysis?},
  journal={Nature Methods},
  volume={20},
  pages={945-946},
  year={2023},
  doi={https://doi.org/10.1038/s41592-023-01950-8}
}

@inproceedings{patashnik2021styleclip,
  title={Styleclip: Text-driven manipulation of stylegan imagery},
  author={Patashnik, Or and Wu, Zongze and Shechtman, Eli and Cohen-Or, Daniel and Lischinski, Dani},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},
  pages={2085--2094},
  year={2021}
}

@article{goodfellow2014generative,
  title={Generative adversarial nets},
  author={Goodfellow, Ian and Pouget-Abadie, Jean and Mirza, Mehdi and Xu, Bing and Warde-Farley, David and Ozair, Sherjil and Courville, Aaron and Bengio, Yoshua},
  journal={Advances in neural information processing systems},
  volume={27},
  year={2014}
}

@article{royer2023future,
  title={The future of bioimage analysis: a dialog between mind and machine},
  author={Royer, Lo{\"\i}c A},
  journal={Nature Methods},
  volume={20},
  number={7},
  pages={951--952},
  year={2023},
  publisher={Nature Publishing Group US New York}
}

@article{lamiable2023revealing,
  title={Revealing invisible cell phenotypes with conditional generative modeling},
  author={Lamiable, Alexis and Champetier, Tiphaine and Leonardi, Francesco and Cohen, Ethan and Sommer, Peter and Hardy, David and Argy, Nicolas and Massougbodji, Achille and Del Nery, Elaine and Cottrell, Gilles and others},
  journal={Nature Communications},
  volume={14},
  number={1},
  pages={6386},
  year={2023},
  publisher={Nature Publishing Group UK London}
}

@article{wu2023silico,
    author = {Wu, Jiqing and Koelzer, Viktor H},
    title = "{SST-editing: in silico spatial transcriptomic editing at single-cell resolution}",
    journal = {Bioinformatics},
    volume = {40},
    number = {3},
    pages = {btae077},
    year = {2024},
    month = {02},
    issn = {1367-4811},
    doi = {10.1093/bioinformatics/btae077},
    url = {https://doi.org/10.1093/bioinformatics/btae077},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/40/3/btae077/56850944/btae077.pdf},
}

@inproceedings{lin2021infinitygan,
  title={InfinityGAN: Towards Infinite-Pixel Image Synthesis},
  author={Lin, Chieh Hubert and Lee, Hsin-Ying and Cheng, Yen-Chi and Tulyakov, Sergey and Yang, Ming-Hsuan},
  booktitle={International Conference on Learning Representations},
  year={2022}
}

@inproceedings{kulikov2023sinddm,
  title={Sinddm: A single image denoising diffusion model},
  author={Kulikov, Vladimir and Yadin, Shahar and Kleiner, Matan and Michaeli, Tomer},
  booktitle={International Conference on Machine Learning},
  pages={17920--17930},
  year={2023},
  organization={PMLR}
}

@article{naddaf2023europe,
  title={Europe spent€ 600 million to recreate the human brain in a computer. How did it go?},
  author={Naddaf, Miryam},
  journal={Nature},
  volume={620},
  number={7975},
  pages={718--720},
  year={2023}
}

@article{carrillo2023synthetic,
  title={Synthetic whole-slide image tile generation with gene expression profile-infused deep generative models},
  author={Carrillo-Perez, Francisco and Pizurica, Marija and Ozawa, Michael G and Vogel, Hannes and West, Robert B and Kong, Christina S and Herrera, Luis Javier and Shen, Jeanne and Gevaert, Olivier},
  journal={Cell Reports Methods},
  volume={3},
  number={8},
  year={2023},
  publisher={Elsevier}
}

@article{bankhead2017qupath,
  title={QuPath: Open source software for digital pathology image analysis},
  author={Bankhead, Peter and Loughrey, Maurice B and Fern{\'a}ndez, Jos{\'e} A and Dombrowski, Yvonne and McArt, Darragh G and Dunne, Philip D and McQuaid, Stephen and Gray, Ronan T and Murray, Liam J and Coleman, Helen G and others},
  journal={Scientific reports},
  volume={7},
  number={1},
  pages={1--7},
  year={2017},
  publisher={Nature Publishing Group}
}

@inproceedings{shaham2019singan,
  title={Singan: Learning a generative model from a single natural image},
  author={Shaham, Tamar Rott and Dekel, Tali and Michaeli, Tomer},
  booktitle={Proceedings of the IEEE/CVF international conference on computer vision},
  pages={4570--4580},
  year={2019}
}


@article{haniffa2021roadmap,
  title={A roadmap for the human developmental cell atlas},
  author={Haniffa, Muzlifah and Taylor, Deanne and Linnarsson, Sten and Aronow, Bruce J and Bader, Gary D and Barker, Roger A and Camara, Pablo G and Camp, J Gray and Ch{\'e}dotal, Alain and Copp, Andrew and others},
  journal={Nature},
  volume={597},
  number={7875},
  pages={196--205},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@article{zhang2021survey,
  title={A survey on neural network interpretability},
  author={Zhang, Yu and Ti{\v{n}}o, Peter and Leonardis, Ale{\v{s}} and Tang, Ke},
  journal={IEEE Transactions on Emerging Topics in Computational Intelligence},
  volume={5},
  number={5},
  pages={726--742},
  year={2021},
  publisher={IEEE}
}

@article{harkonen2020ganspace,
  title={Ganspace: Discovering interpretable gan controls},
  author={H{\"a}rk{\"o}nen, Erik and Hertzmann, Aaron and Lehtinen, Jaakko and Paris, Sylvain},
  journal={Advances in neural information processing systems},
  volume={33},
  pages={9841--9850},
  year={2020}
}

@article{kynkaanniemi2022role,
  title={The Role of ImageNet Classes in Fr\'echet Inception Distance},
  author={Kynk{\"a}{\"a}nniemi, Tuomas and Karras, Tero and Aittala, Miika and Aila, Timo and Lehtinen, Jaakko},
  journal={arXiv preprint arXiv:2203.06026},
  year={2022}
}


@article{yao2023high,
  title={A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain},
  author={Yao, Zizhen and van Velthoven, Cindy TJ and Kunst, Michael and Zhang, Meng and McMillen, Delissa and Lee, Changkyu and Jung, Won and Goldy, Jeff and Abdelhak, Aliya and Aitken, Matthew and others},
  journal={Nature},
  volume={624},
  number={7991},
  pages={317--332},
  year={2023},
  publisher={Nature Publishing Group UK London}
}
