Cell-GraphCompass: modeling single cells with graph structure foundation model

Chen Fang

doi:10.1093/nsr/nwaf255

2025-09-09

DOI：10.1093/nsr/nwaf255

原文链接

原文求助

摘要

En 中文

人体细胞受到复杂基因调控网络的调控，这使它们能够实现其细胞命运和功能。受大语言模型进展的启发，已有若干尝试聚焦于构建单细胞转录组数据的基础模型以解析基因调控网络。然而，这些模型倾向于在细胞内对基因施加序列结构，这可能忽略固有的生物学特征，且缺乏利用其他可用先验知识。本文介绍了Cell-GraphCompass（CGCompass），这是首个采用图预训练来建模基因和细胞的基础模型。我们使用三种基因相关信息作为节点特征来构建细胞图，并从三个角度收集数据以描绘基因间关系作为边特征。我们使用超过5000万个人类细胞预训练了该模型，然后将其微调至广泛任务，如批次整合、细胞类型注释、单细胞基因扰动及体外基因敲除预测，取得了出色的性能。总体而言，CGCompass为利用图预训练在构建单细胞分析基础模型中融入先验知识提供了实用架构。

期刊

National Science Review

IF:

17.1

论文数:

3.8K

被引数:

2.0W

机构

暂无机构信息

引用论文

Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods

PLoS ONE

IF0

2011-02-28

OAAI

Chao Chen; Kay Grennan; Judith Badner; Dandan Zhang; Elliot Gershon; Li Jin; Chunyu Liu

Toward subtask-decomposition-based learning and benchmarking for predicting genetic perturbation outcomes and beyond 走向基于子任务分解的学习和基准测试，以预测遗传扰动结果及以后

NATURE COMPUTATIONAL SCIENCE

IF18.3

2024-09-27

PREAI

Gao, Yicheng; Wei, Zhiting; Dong, Kejing; Chen, Ke; Yang, Jingya; Chuai, Guohui; Liu, Qi

GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model Genecoppass: 通过知识知情的跨物种基础模型破译通用基因调控机制

CELL RESEARCH

IF25.9

2024-10-08

OAAI

Yang, Xiaodong; Liu, Guole; Feng, Guihai; Bu, Dechao; Wang, Pengfei; Jiang, Jie; Chen, Shubai; Yang, Qinmeng; Miao, Hefan; Zhang, Yiyang; Man, Zhenpeng; Liang, Zhongming; Wang, Zichen; Li, Yaning; Li, Zheng; Liu, Yana; Tian, Yao; Liu, Wenhao; Li, Cong; Li, Ao; Dong, Jingxi; Hu, Zhilong; Fang, Chen; Cui, Lina; Deng, Zixu; Jiang, Haiping; Cui, Wentao; Zhang, Jiahao; Yang, Zhaohui; Li, Handong; He, Xingjian; Zhong, Liqun; Zhou, Jiaheng; Wang, Zijian; Long, Qingqing; Xu, Ping; Wang, Hongmei; Meng, Zhen; Wang, Xuezhi; Wang, Yangang; Wang, Yong; Zhang, Shihua; Guo, Jingtao; Zhao, Yi; Zhou, Yuanchun; Li, Fei; Liu, Jing; Chen, Yiqiang; Yang, Ge; Li, Xin

A Single-Cell Transcriptome Atlas of the Human Pancreas 人类胰腺的单细胞转录组图谱

CELL SYSTEMS

IF7.7

2016-10-01

875

OAAI

Muraro, Mauro J.; Dharmadhikari, Gitanjali; Gruen, Dominic; Groen, Nathalie; Dielen, Tim; Jansen, Erik; van Gurp, Leon; Engelse, Marten A.; Carlotti, Francoise; de Koning, Eelco J. P.; van Oudenaarden, Alexander

Integrated analysis of multimodal single-cell data 多模态单细胞数据的集成分析

Cell

IF0

2021-06-01

OAAI

Yuhan Hao; Stephanie Hao; Erica Andersen-Nissen; William M. Mauck; Shiwei Zheng; Andrew Butler; Maddie J. Lee; Aaron J. Wilk; Charlotte Darby; Michael Zager; Paul Hoffman; Marlon Stoeckius; Efthymia Papalexi; Eleni P. Mimitou; Jaison Jain; Avi Srivastava; Tim Stuart; Lamar M. Fleming; Bertrand Yeung; Angela J. Rogers; Juliana M. McElrath; Catherine A. Blish; Raphael Gottardo; Peter Smibert; Rahul Satija

The new frontier of genome engineering with CRISPR-Cas9 CRISPR-Cas9基因组工程的新领域

Science

IF0

2014-11-28

PREAI

Jennifer A. Doudna; Emmanuelle Charpentier

Transfer learning enables predictions in network biology 迁移学习使网络生物学中的预测成为可能

Nature

IF0

2023-05-31

OAAI

Christina V. Theodoris; Ling Xiao; Anant Chopra; Mark D. Chaffin; Zeina R. Al Sayed; Matthew C. Hill; Helene Mantineo; Elizabeth M. Brydon; Zexian Zeng; X. Shirley Liu; Patrick T. Ellinor

Expanded encyclopaedias of DNA elements in the human and mouse genomes 人类和小鼠基因组中DNA元素的扩展百科全书

Nature

IF0

2020-07-29

OAAI

Federico Abascal; Reyes Acosta; Nicholas J. Addleman; Jessika Adrian; Veena Afzal; Rizi Ai; Bronwen Aken; Jennifer A. Akiyama; Omar Al Jammal; Henry Amrhein; Stacie M. Anderson; Gregory R. Andrews; Igor Antoshechkin; Kristin G. Ardlie; Joel Armstrong; Matthew Astley; Budhaditya Banerjee; Amira A. Barkal; If H. A. Barnes; Iros Barozzi; Daniel Barrell; Gemma Barson; Daniel Bates; Ulugbek K. Baymuradov; Cassandra Bazile; Michael A. Beer; Samantha Beik; M. A. Bender; Ruth Bennett; Louis Philip Benoit Bouvrette; Bradley E. Bernstein; Andrew Berry; Anand Bhaskar; Alexandra Bignell; Steven M. Blue; David M. Bodine; Carles Boix; Nathan Boley; Tyler Borrman; Beatrice Borsari; Alan P. Boyle; Laurel A. Brandsmeier; Alessandra Breschi; Emery H. Bresnick; Jason A. Brooks; Michael Buckley; Christopher B. Burge; Rachel Byron; Eileen Cahill; Lingling Cai; Lulu Cao; Mark Carty; Rosa G. Castanon; Andres Castillo; Hassan Chaib; Esther T. Chan; Daniel R. Chee; Sora Chee; Hao Chen; Huaming Chen; Jia-Yu Chen; Songjie Chen; J. Michael Cherry; Surya B. Chhetri; Jyoti S. Choudhary; Jacqueline Chrast; Dongjun Chung; Declan Clarke; Neal A. L. Cody; Candice J. Coppola; Julie Coursen; Anthony M. D’Ippolito; Stephen Dalton; Cassidy Danyko; Claire Davidson; Jose Davila-Velderrain; Carrie A. Davis; Job Dekker; Alden Deran; Gilberto DeSalvo; Gloria Despacio-Reyes; Colin N. Dewey; Diane E. Dickel; Morgan Diegel; Mark Diekhans; Vishnu Dileep; Bo Ding; Sarah Djebali; Alexander Dobin; Daniel Dominguez; Sarah Donaldson; Jorg Drenkow; Timothy R. Dreszer; Yotam Drier; Michael O. Duff; Douglass Dunn; Catharine Eastman; Joseph R. Ecker; Matthew D. Edwards; Nicole El-Ali; Shaimae I. Elhajjajy; Keri Elkins; Andrew Emili; Charles B. Epstein; Rachel C. Evans; Iakes Ezkurdia; Kaili Fan; Peggy J. Farnham; Nina P. Farrell; Elise A. Feingold; Anne-Maud Ferreira; Katherine Fisher-Aylor; Stephen Fitzgerald; Paul Flicek; Chuan Sheng Foo; Kevin Fortier; Adam Frankish; Peter Freese; Shaliu Fu; Xiang-Dong Fu; Yu Fu; Yoko Fukuda-Yuzawa; Mariateresa Fulciniti; Alister P. W. Funnell; Idan Gabdank; Timur Galeev; Mingshi Gao; Carlos Garcia Giron; Tyler H. Garvin; Chelsea Anne Gelboin-Burkhart; Grigorios Georgolopoulos; Mark B. Gerstein; Belinda M. Giardine; David K. Gifford; David M. Gilbert; Daniel A. Gilchrist; Shawn Gillespie; Thomas R. Gingeras; Peng Gong; Alvaro Gonzalez; Jose M. Gonzalez; Peter Good; Alon Goren; David U. Gorkin; Brenton R. Graveley; Michael Gray; Jack F. Greenblatt; Ed Griffiths; Mark T. Groudine; Fabian Grubert; Mengting Gu; Roderic Guigó; Hongbo Guo; Yu Guo; Yuchun Guo; Gamze Gursoy; Maria Gutierrez-Arcelus; Jessica Halow; Ross C. Hardison; Matthew Hardy; Manoj Hariharan; Arif Harmanci; Anne Harrington; Jennifer L. Harrow; Tatsunori B. Hashimoto; Richard D. Hasz; Meital Hatan; Eric Haugen; James E. Hayes; Peng He; Yupeng He; Nastaran Heidari; David Hendrickson; Elisabeth F. Heuston; Jason A. Hilton; Benjamin C. Hitz; Abigail Hochman; Cory Holgren; Lei Hou; Shuyu Hou; Yun-Hua E. Hsiao; Shanna Hsu; Hui Huang; Tim J. Hubbard; Jack Huey; Timothy R. Hughes; Toby Hunt; Sean Ibarrientos; Robbyn Issner; Mineo Iwata; Osagie Izuogu; Tommi Jaakkola; Nader Jameel; Camden Jansen; Lixia Jiang; Peng Jiang; Audra Johnson; Rory Johnson; Irwin Jungreis; Madhura Kadaba; Maya Kasowski; Mary Kasparian; Momoe Kato; Rajinder Kaul; Trupti Kawli; Michael Kay; Judith C. Keen; Sunduz Keles; Cheryl A. Keller; David Kelley; Manolis Kellis; Pouya Kheradpour; Daniel Sunwook Kim; Anthony Kirilusha; Robert J. Klein; Birgit Knoechel; Samantha Kuan; Michael J. Kulik; Sushant Kumar; Anshul Kundaje; Tanya Kutyavin; Julien Lagarde; Bryan R. Lajoie; Nicole J. Lambert; John Lazar; Ah Young Lee; Donghoon Lee; Elizabeth Lee; Jin Wook Lee; Kristen Lee; Christina S. Leslie; Shawn Levy; Bin Li; Hairi Li; Nan Li; Shantao Li; Xiangrui Li; Yang I. Li; Ying Li; Yining Li; Yue Li; Jin Lian; Maxwell W. Libbrecht; Shin Lin; Yiing Lin; Dianbo Liu; Jason Liu; Peng Liu; Tingting Liu; X. Shirley Liu; Yan Liu; Yaping Liu; Maria Long; Shaoke Lou; Jane Loveland; Aiping Lu; Yuheng Lu; Eric Lécuyer; Lijia Ma; Mark Mackiewicz; Brandon J. Mannion; Michael Mannstadt; Deepa Manthravadi; Georgi K. Marinov; Fergal J. Martin; Eugenio Mattei; Kenneth McCue; Megan McEown; Graham McVicker; Sarah K. Meadows; Alex Meissner; Eric M. Mendenhall; Christopher L. Messer; Wouter Meuleman; Clifford Meyer; Steve Miller; Matthew G. Milton; Tejaswini Mishra; Dianna E. Moore; Helen M. Moore; Jill E. Moore; Samuel H. Moore; Jennifer Moran; Ali Mortazavi; Jonathan M. Mudge; Nikhil Munshi; Rabi Murad; Richard M. Myers; Vivek Nandakumar; Preetha Nandi; Anil M. Narasimha; Aditi K. Narayanan; Hannah Naughton; Fabio C. P. Navarro; Patrick Navas; Jurijs Nazarovs; Jemma Nelson; Shane Neph; Fidencio Jun Neri; Joseph R. Nery; Amy R. Nesmith; J. Scott Newberry; Kimberly M. Newberry; Vu Ngo; Rosy Nguyen; Thai B. Nguyen; Tung Nguyen; Andrew Nishida; William S. Noble; Catherine S. Novak; Eva Maria Novoa; Briana Nuñez; Charles W. O’Donnell; Sara Olson; Kathrina C. Onate; Ericka Otterman; Hakan Ozadam; Michael Pagan; Tsultrim Palden; Xinghua Pan; Yongjin Park; E. Christopher Partridge; Benedict Paten; Florencia Pauli-Behn; Michael J. Pazin; Baikang Pei; Len A. Pennacchio; Alexander R. Perez; Emily H. Perry; Dmitri D. Pervouchine; Nishigandha N. Phalke; Quan Pham; Doug H. Phanstiel; Ingrid Plajzer-Frick; Gabriel A. Pratt; Henry E. Pratt; Sebastian Preissl; Jonathan K. Pritchard; Yuri Pritykin; Michael J. Purcaro; Qian Qin; Giovanni Quinones-Valdez; Ines Rabano; Ernest Radovani; Anil Raj; Nisha Rajagopal; Oren Ram; Lucia Ramirez; Ricardo N. Ramirez; Dylan Rausch; Soumya Raychaudhuri; Joseph Raymond; Rozita Razavi; Timothy E. Reddy; Thomas M. Reimonn; Bing Ren; Alexandre Reymond; Alex Reynolds; Suhn K. Rhie; John Rinn; Miguel Rivera; Juan Carlos Rivera-Mulia; Brian S. Roberts; Jose Manuel Rodriguez; Joel Rozowsky; Russell Ryan; Eric Rynes; Denis N. Salins; Richard Sandstrom; Takayo Sasaki; Shashank Sathe; Daniel Savic; Alexandra Scavelli; Jonathan Scheiman; Christoph Schlaffner; Jeffery A. Schloss; Frank W. Schmitges; Lei Hoon See; Anurag Sethi; Manu Setty; Anthony Shafer; Shuo Shan; Eilon Sharon; Quan Shen; Yin Shen; Richard I. Sherwood; Minyi Shi; Sunyoung Shin; Noam Shoresh; Kyle Siebenthall; Cristina Sisu; Teri Slifer; Cricket A. Sloan; Anna Smith; Valentina Snetkova; Michael P. Snyder; Damek V. Spacek; Sharanya Srinivasan; Rohith Srivas; George Stamatoyannopoulos; John A. Stamatoyannopoulos; Rebecca Stanton; Dave Steffan; Sandra Stehling-Sun; J. Seth Strattan; Amanda Su; Balaji Sundararaman; Marie-Marthe Suner; Tahin Syed; Matt Szynkarek; Forrest Y. Tanaka; Danielle Tenen; Mingxiang Teng; Jeffrey A. Thomas; Dave Toffey; Michael L. Tress; Diane E. Trout; Gosia Trynka; Junko Tsuji; Sean A. Upchurch; Oana Ursu; Barbara Uszczynska-Ratajczak; Mia C. Uziel; Alfonso Valencia; Benjamin Van Biber; Arjan G. van der Velde; Eric L. Van Nostrand; Yekaterina Vaydylevich; Jesus Vazquez; Alec Victorsen; Jost Vielmetter; Jeff Vierstra; Axel Visel; Anna Vlasova; Christopher M. Vockley; Simona Volpi; Shinny Vong; Hao Wang; Mengchi Wang; Qin Wang; Ruth Wang; Tao Wang; Wei Wang; Xiaofeng Wang; Yanli Wang; Nathaniel K. Watson; Xintao Wei; Zhijie Wei; Hendrik Weisser; Sherman M. Weissman; Rene Welch; Robert E. Welikson; Zhiping Weng; Harm-Jan Westra; John W. Whitaker; Collin White; Kevin P. White; Andre Wildberg; Brian A. Williams; David Wine; Heather N. Witt; Barbara Wold; Maxim Wolf; James Wright; Rui Xiao; Xinshu Xiao; Jie Xu; Jinrui Xu; Koon-Kiu Yan; Yongqi Yan; Hongbo Yang; Xinqiong Yang; Yi-Wen Yang; Galip Gürkan Yardımcı; Brian A. Yee; Gene W. Yeo; Taylor Young; Tianxiong Yu; Feng Yue; Chris Zaleski; Chongzhi Zang; Haoyang Zeng; Weihua Zeng; Daniel R. Zerbino; Jie Zhai; Lijun Zhan; Ye Zhan; Bo Zhang; Jialing Zhang; Jing Zhang; Kai Zhang; Lijun Zhang; Peng Zhang; Qi Zhang; Xiao-Ou Zhang; Yanxiao Zhang; Zhizhuo Zhang; Yuan Zhao; Ye Zheng; Guoqing Zhong; Xiao-Qiao Zhou; Yun Zhu; Jared Zimmerman; Jill E. Moore; Michael J. Purcaro; Henry E. Pratt; Charles B. Epstein; Noam Shoresh; Jessika Adrian; Trupti Kawli; Carrie A. Davis; Alexander Dobin; Rajinder Kaul; Jessica Halow; Eric L. Van Nostrand; Peter Freese; David U. Gorkin; Yin Shen; Yupeng He; Mark Mackiewicz; Florencia Pauli-Behn; Brian A. Williams; Ali Mortazavi; Cheryl A. Keller; Xiao-Ou Zhang; Shaimae I. Elhajjajy; Jack Huey; Diane E. Dickel; Valentina Snetkova; Xintao Wei; Xiaofeng Wang; Juan Carlos Rivera-Mulia; Joel Rozowsky; Jing Zhang; Surya B. Chhetri; Jialing Zhang; Alec Victorsen; Kevin P. White; Axel Visel; Gene W. Yeo; Christopher B. Burge; Eric Lécuyer; David M. Gilbert; Job Dekker; John Rinn; Eric M. Mendenhall; Joseph R. Ecker; Manolis Kellis; Robert J. Klein; William S. Noble; Anshul Kundaje; Roderic Guigó; Peggy J. Farnham; J. Michael Cherry; Richard M. Myers; Bing Ren; Brenton R. Graveley; Mark B. Gerstein; Len A. Pennacchio; Michael P. Snyder; Bradley E. Bernstein; Barbara Wold; Ross C. Hardison; Thomas R. Gingeras; John A. Stamatoyannopoulos; Zhiping Weng

Transcriptomic diversity of cell types across the adult human brain 成人大脑中细胞类型的转录组多样性

Science

IF0

2023-10-13

OAAI

Kimberly Siletti; Rebecca Hodge; Alejandro Mossi Albiach; Ka Wai Lee; Song-Lin Ding; Lijuan Hu; Peter Lönnerberg; Trygve Bakken; Tamara Casper; Michael Clark; Nick Dee; Jessica Gloe; Daniel Hirschstein; Nadiya V. Shapovalova; C. Dirk Keene; Julie Nyhus; Herman Tung; Anna Marie Yanny; Ernest Arenas; Ed S. Lein; Sten Linnarsson

Gene2vec: distributed representation of genes based on co-expression Gene2vec: 基于共表达的基因分布式表示

BMC GENOMICS

IF3.7

2019-02-04

109

OAAI

Du, Jingcheng; Jia, Peilin; Dai, Yulin; Tao, Cui; Zhao, Zhongming; Zhi, Degui

查看更多内容