The paper presents the MIND model, showing that competing induction and exclusion programs shape the sensorimotor-to-association axis in the neocortex across species.

Nature · Jul 1, 2026Peer-reviewedNeuroscience

Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

Archibald Enninful, Zhaojun Zhang, Dmytro Klymyshyn, Matthew H. Ingalls, Mingyu Yang, Hailing Zong, Zhiliang Bai, Negin Farzad, Graham Su, Alev Baysoy, Jungmin Nam, Yao Lu, Shuozhen Bao, Siyan Deng, Nancy Ruonan Zhang, , Rong Fan

Thermostable RNaseH release of barcoded cDNA keeps sections intact for CODEX imaging, yielding same-section whole-transcriptome and protein maps plus CODEX-guided spot deconvolution in FFPE tissues.

Nature Methods · Jan 15, 2026Peer-reviewedSystems Biology✦ In-depth digest

SPACEc: A Streamlined, Interactive Python Workflow for Multiplexed Image Processing and Analysis

Yuqi Tan, Tim Noah Kempchen, Martin Becker, Maximilian Haist, Dorien Feyaerts, Jiaqi Liu, Marieta Ioana Toma, Yang Xiao, Graham Su, Andrew J. Rech, Michael Hölzel, Rong Fan, John W. Hickey, Garry P. Nolan

SPACEc provides a Python workflow for analyzing multiplexed imaging data with interactive tools for image processing, segmentation, and spatial analysis.

Nature Communications · Nov 27, 2025Peer-reviewedBioinformatics

Spatial epigenomic niches underlie glioblastoma cell state plasticity

Sam Kint, Subhi Talal Younes, Shuozhen Bao, Gretchen Long, David Wouters, Erin L. Stephenson, Xing Lou, Mei Zhong, Di Zhang, Graham Su, Archibald Enninful, Mingyu Yang, Huey‐Miin Chen, Katrina I Ellestad, Colleen Anderson, , Marco Gallo

This study identifies two epigenetically-defined spatial niches in glioblastoma that influence cell state plasticity through local and long-range molecular signals.

bioRxiv · May 9, 2025 · PreprintGenomics

Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues

Zhiliang Bai, Dingyao Zhang, Yan Ping Gao, Bo Tao, Daiwei Zhang, Shuozhen Bao, Archibald Enninful, Yadong Wang, Haikuo Li, Graham Su, Xiaolong Tian, Ningning Zhang, Yang Xiao, Yang Liu, Mark Gerstein, , Rong Fan

This paper introduces Patho-DBiT, a method for spatial transcriptomics in FFPE tissues, enabling RNA biology analysis including splicing, variants, and regulatory networks in clinical samples.

Cell · Sep 30, 2024Peer-reviewedSystems Biology

Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level

Yanxiang Deng, Marek Bartošovič, Sai Ma, Di Zhang, Petra Kukanja, Yang Xiao, Graham Su, Yang Liu, Xiaoyu Qin, Gorazd B. Rosoklija, Andrew J. Dwork, J. John Mann, Mina L. Xu, Stephanie Halene, Joseph E. Craft, , Rong Fan

This paper introduces spatial-ATAC-seq, a method for spatially resolved chromatin accessibility profiling at the cellular level, and demonstrates its application in mouse embryos and human tonsil tissue.

Nature · Aug 17, 2022Peer-reviewedGenomics

Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping

Yang Liu, Marcello DiStasio, Graham Su, Hiromitsu Asashima, Archibald Enninful, Xiaoyu Qin, Yanxiang Deng, Pino Bordignon, Marco Cassano, Mary M. Tomayko, Mina L. Xu, Stephanie Halene, Joseph E. Craft, David A. Hafler, Rong Fan

Spatial-CITE-seq profiles proteins and transcriptomes in tissues, revealing spatially distinct immune responses in mouse and human tissues.

bioRxiv · Apr 1, 2022 · PreprintGenomics

Spatial Epigenome Sequencing at Tissue Scale and Cellular Level

Yanxiang Deng, Marek Bartošovič, Petra Kukanja, Di Zhang, Yang Liu, Graham Su, Archibald Enninful, Zhiliang Bai, Gonçalo Castelo‐Branco, Rong Fan

This paper presents spatial epigenome profiling using CUT&Tag and microfluidic barcoding to map histone modifications at tissue scale and single-cell level in mouse embryos and olfactory bulbs.

Science · Feb 10, 2022Peer-reviewedGenomics

High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue

Yang Liu, Mingyu Yang, Yanxiang Deng, Graham Su, Archibald Enninful, Cindy C. Guo, Toma Tebaldi, Di Zhang, Dongjoo Kim, Zhiliang Bai, Eileen Norris, Alisia Pan, Jiatong Li, Yang Xiao, Stephanie Halene, Rong Fan

DBiT-seq enables high-spatial-resolution multi-omics mapping of mouse embryos by deterministic barcoding, revealing tissue types and fine features like retinal pigmented epithelium and microvasculature.

Cell · Nov 13, 2020Peer-reviewedGenomics

High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue

The paper was withdrawn due to a duplicate posting and directs readers to the current version on bioRxiv.

bioRxiv · Aug 1, 2020 · PreprintGenomics