Nature methods

Keyphrases

Publications

volume 21, number 8, 2024

Carina Prunkl
AI meets biology: a call for community governance. Nature methods 21 (8) (2024)
Tian Tian, Jie Zhang, Xiang Lin, Zhi Wei, Hakon Hakonarson
Dependency-aware deep generative models for multitasking analysis of spatial omics data. Nature methods 21 (8) (2024)
Chenxi Ma, Weimin Tan, Ruian He, Bo Yan
Pretraining a foundation model for generalizable fluorescence microscopy-based image restoration. Nature methods 21 (8) (2024)
Mohammad Lotfollahi
Toward learning a foundational representation of cells and genes. Nature methods 21 (8) (2024)
Wanlu Lei, Caterina Fuster-Barceló, Gabriel K Reder, Arrate Munoz Barrutia, Wei Ouyang
BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging. Nature methods 21 (8) (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods 21 (8) (2024)
Ramya Rangan, Ryan Feathers, Sagar Khavnekar, Adam Lerer, Jake D Johnston, Ron Kelley, Martin Obr, Abhay Kotecha, Ellen D Zhong
CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. Nature methods 21 (8) (2024)
Ramya Rangan, Ryan Feathers, Sagar Khavnekar, Adam Lerer, Jake D Johnston, Ron Kelley, Martin Obr, Abhay Kotecha, Ellen D Zhong
CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. Nature methods 21 (8) (2024)
Vivien Marx
First-gen scientists leap hurdles and give back. Nature methods 21 (8) (2024)
Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma, Xuegong Zhang, Le Song
Large-scale foundation model on single-cell transcriptomics. Nature methods 21 (8) (2024)
Joy Linyue Fan, Achille Nazaret, Elham Azizi
A thousand and one tumors: the promise of AI for cancer biology. Nature methods 21 (8) (2024)
Benjamin M Gyori, Olga Vitek
Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge. Nature methods 21 (8) (2024)
Kyle Coleman, Amelia Schroeder, Mingyao Li
Unlocking the power of spatial omics with AI. Nature methods 21 (8) (2024)
Oded Rotem, Assaf Zaritsky
Visual interpretability of bioimaging deep learning models. Nature methods 21 (8) (2024)
Wenpin Hou, Zhicheng Ji
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. Nature methods 21 (8) (2024)
Yanay Rosen, Maria Brbic, Yusuf Roohani, Kyle Swanson, Ziang Li, Jure Leskovec
Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nature methods 21 (8) (2024)
Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma, Xuegong Zhang, Le Song
Large-scale foundation model on single-cell transcriptomics. Nature methods 21 (8) (2024)
Shanghang Zhang, Gaole Dai, Tiejun Huang, Jianxu Chen
Multimodal large language models for bioimage analysis. Nature methods 21 (8) (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods 21 (8) (2024)
Haotian Cui, Chloe Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Nan Duan, Bo Wang
scGPT: toward building a foundation model for single-cell multi-omics using generative AI. Nature methods 21 (8) (2024)
Loïc Alain Royer
Omega - harnessing the power of large language models for bioimage analysis. Nature methods 21 (8) (2024)
Barrett M Powell, Joseph H Davis
Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. Nature methods 21 (8) (2024)
Chenxi Ma, Weimin Tan, Ruian He, Bo Yan
Pretraining a foundation model for generalizable fluorescence microscopy-based image restoration. Nature methods 21 (8) (2024)
Gustaf Ahdritz, Nazim Bouatta, Christina Floristean, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J O'Donnell, Daniel Berenberg, Ian Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M Stepniewska-Dziubinska, Shang Zhang, Adegoke A Ojewole, Murat Efe Guney, Stella Biderman, Andrew M Watkins, Stephen Ra, Pablo Ribalta Lorenzo, Lucas Nivon, Brian D Weitzner, Yih-En Andrew Ban, Shiyang Chen, Minjia Zhang, Conglong Li, Shuaiwen Leon Song, Yuxiong He, Peter Karl Sorger, Emad Mostaque, Zhao Zhang, Richard Bonneau, Mohammed AlQuraishi
OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization. Nature methods 21 (8) (2024)
Wenpin Hou, Zhicheng Ji
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. Nature methods 21 (8) (2024)
Artur Szałata, Karin Hrovatin, Sören Becker, Alejandro Tejada-Lapuerta, Haotian Cui, Bo Wang, Fabian Joachim Theis
Transformers in single-cell omics: a review and new perspectives. Nature methods 21 (8) (2024)
Jean Nakhle
Splicing inhibition unlocks human totipotency. Nature methods 21 (8) (2024)
Nina Vogt
Studying naturalistic behavior virtually. Nature methods 21 (8) (2024)
Eloise Berson, Philip Chung, Camilo A Espinosa, Thomas J Montine, Nima Aghaeepour
Unlocking human immune system complexity through AI. Nature methods 21 (8) (2024)
Valerie Chen, Muyu Yang, Wenbo Cui, Joon Sik Kim, Ameet Talwalkar, Jian Ma
Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. Nature methods 21 (8) (2024)
Omar O Abudayyeh, Jonathan Samuel Gootenberg
Programmable biology through artificial intelligence: from nucleic acids to proteins to cells. Nature methods 21 (8) (2024)
Minkyung Baek
Towards the prediction of general biomolecular interactions with AI. Nature methods 21 (8) (2024)
Lei Tang
Epigenetic editing with CHARM. Nature methods 21 (8) (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods 21 (8) (2024)
Vivien Marx
Quest for AI literacy. Nature methods 21 (8) (2024)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data. Nature methods 21 (8) (2024)
Alexander Sasse, Maria Chikina, Sara Mostafavi
Unlocking gene regulation with sequence-to-function models. Nature methods 21 (8) (2024)
Loïc Alain Royer
Omega - harnessing the power of large language models for bioimage analysis. Nature methods 21 (8) (2024)
Vivien Marx
First-gen scientists leap hurdles and give back. Nature methods 21 (8) (2024)
Gustaf Ahdritz, Nazim Bouatta, Christina Floristean, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J O'Donnell, Daniel Berenberg, Ian Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M Stepniewska-Dziubinska, Shang Zhang, Adegoke A Ojewole, Murat Efe Guney, Stella Biderman, Andrew M Watkins, Stephen Ra, Pablo Ribalta Lorenzo, Lucas Nivon, Brian D Weitzner, Yih-En Andrew Ban, Shiyang Chen, Minjia Zhang, Conglong Li, Shuaiwen Leon Song, Yuxiong He, Peter Karl Sorger, Emad Mostaque, Zhao Zhang, Richard Bonneau, Mohammed AlQuraishi
OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization. Nature methods 21 (8) (2024)
Elana Simon, Kyle Swanson, James Y Zou
Language models for biological research: a primer. Nature methods 21 (8) (2024)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data. Nature methods 21 (8) (2024)
Yanay Rosen, Maria Brbic, Yusuf Roohani, Kyle Swanson, Ziang Li, Jure Leskovec
Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nature methods 21 (8) (2024)
Haotian Cui, Chloe Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Nan Duan, Bo Wang
scGPT: toward building a foundation model for single-cell multi-omics using generative AI. Nature methods 21 (8) (2024)
Arunima Singh
Proximity-triggered protein trans-splicing. Nature methods 21 (8) (2024)
Michał Januszewski, Viren Jain
Next-generation AI for connectomics. Nature methods 21 (8) (2024)
Wenpin Hou, Zhicheng Ji
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. Nature methods 21 (8) (2024)
Tian Tian, Jie Zhang, Xiang Lin, Zhi Wei, Hakon Hakonarson
Dependency-aware deep generative models for multitasking analysis of spatial omics data. Nature methods 21 (8) (2024)

volume 21, number 9, 2024

Zhexin Wang, Tanmay A M Bharat
Serial lift-out for in situ structural biology of multicellular specimens. Nature methods 21 (9) (2024)
Ho Thuy Dung Nguyen, Gaia Perone, Nikolai Klena, Roberta Vazzana, Flaminia Kaluthantrige Don, Malan Silva, Simona Sorrentino, Paolo Swuec, Frederic Leroux, Nereo Kalebic, Francesca Coscia, Philipp S Erdmann
Serialized on-grid lift-in sectioning for tomography (SOLIST) enables a biopsy at the nanoscale. Nature methods 21 (9) (2024)