Benchmarking cell type and gene set annotation by large language models with AnnDictionary

G George Crowley (Department of Bioengineering, Stanford University) R Robert C. Jones M Mark Krasnow A Angela Oliveira Pisco J Julia Salzman N Nir Yosef S Siyu He M Madhav Mantri (Meinig School of Biomedical Engineering, Cornell University) J Jessie Aguirre R Ron Garner S Sal Guerrero W William Harper R Resham Irfan S Sophia Mahfouz R Ravi Ponnusamy B Bhavani A. Sanagavarapu A Ahmad Salehi I Ivan Sampson C Chloe Tang A Alan G. Cheng J James M. Gardner (Department of Surgery, University of California San Francisco) B Burnett Kelly T Thurman Slone Z Zifa Wang A Anika Choudhury S Sheela Crasta C Chen Dong (State Key Laboratory of Drug Research) M Marcus L. Forst D Douglas E. Henze J Jaeyoon Lee M Maurizio Morri S Serena Y. Tan S Sevahn K. Vorperian L Lynn Yang M Marcela Alcántara-Hernádez J Julian Berg D Dhruv Bhatt S Sara Billings A Andrès Gottfried-Blackmore J Jamie Bozeman S Simon Bucher E Elisa Caffrey A Amber Casillas R Rebecca Chen M Matthew Choi R Rebecca N. Culver I Ivana Cvijović (Department of Applied Physics) K Ke Ding H Hala Shakib Dhowre H Hua Dong K Kenneth Donaville L Lauren Duan X Xiaochen Fan M Mariko H. Foecke F Francisco X. Galdos E Eliza A. Gaylord K Karen Gonzales W William R. Goodyer M Michelle Griffin Y Yuchao Gu (College of Biological Engineering, Qingdao University of Science and Technology) S Shuo Han J Jun Yan He P Paul Heinrich R Rebeca Arroyo Hornero K Keliana Hui J Juan C. Irwin S SoRi Jang A Annie Jensen S Saswati Karmakar J Jengmin Kang H Hailey Kang S Soochi Kim (Department of Neurology and Neurological Sciences, Stanford University School of Medicine) S Stewart J. Kim W William Kong M Mallory A. Laboulaye D Daniel Lee G Gyehyun Lee E Elise Lelou A Anping Li B BaoXiang Li W Wan-Jin Lu H Hayley Raquer-McKay E Elvira Mennillo L Lindsay Moore E Elena Montauti K Karim Mrouj S Shravani Mukherjee P Patrick Neuhöfer S Saphia Nguyen H Honor Paine J Jennifer B. Parker J Julia Pham K Kiet T. Phong P Pratima Prabala Z Zhen Qi J Joshua Quintanilla I Iulia Rusu A Ali Reza Rais Sadati B Bronwyn Scott D David Seong H Hosu Sin H Hanbing Song B Bikem Soyur S Sean Spencer V Varun R. Subramaniam M Michael Swift (Department of Chemical and Systems Biology) A Aditi Swarup G Greg Szot A Aris Taychameekiatchai E Emily Trimm S Stefan Veizades S Sivakamasundari Vijayakumar K Kim Chi Vo T Tian Wang (School of Chinese Materia Medica) T Timothy Wu Y Yinghua Xie W William Yue (Department of Medicine and Division of Gastroenterology, University of California San Francisco) Z Zue Zhang A Angela Detweiler H Honey Mekonen N Norma F. Neff (Chan Zuckerberg Biohub SF) S Sheryl Paul A Amanda Seng J Jia Yan D Deana Rae Crystal Colburg B Balint Laszlo Forgo L Luca Ghita F Frank McCarthy A Aditi Agrawal A Alina Isakova K Kavita Murthy A Alexandra Psaltis W Wenfei Sun K Kyle Awayan P Pierre Boyeau R Robrecht Cannoodt L Leah Dorman S Samuel D’Souza C Can Ergen J Justin Hong H Harper Hua E Erin McGeever A Antoine de Morree L Luise A. Seeker A Alexander J. Tarashansky A Astrid Gillich T Taha A. Jan A Angela Ling A Abhishek Murti N Nikita Sajai R Ryan M. Samuel J Juliane Winkler S Steven E. Artandi P Philip A. Beachy M Mike F. Clarke Z Zev Gartner L Linda C. Giudice F Franklin W. Huang J Juliana Idoyaga M Michael G. Kattah C Christin S. Kuo D Diana J. Laird M Michael T. Longaker P Patricia Nguyen D David Y. Oh (Division of Hematology/Oncology, Department of Medicine, University of California) T Thomas A. Rando K Kristy Red-Horse B Bruce Wang A Albert Y. Wu S Sean M. Wu B Bo Yu J James Zou S Stephen R. Quake