Publications

Selected publications from the Sai Ma Lab and collaborators.

Featured

Selected publications

A single-cell spatial transcriptomic census of human skin anatomy

Restrepo, P., Wilder, A., Houser, A., Ramirez, A., …, Gnjatic, S., Ma, S. & Ji, A.L.

Nature Genetics, 58, 903–915 (2026)

Uhrf1 loss alters CTCF-associated topological organization during early mouse embryogenesis

Kurowski, A.†, Zhu, B.†, Sun, Y., Jain, N., Chan, A., Walsh, M.* & Ma, S.*

Nature Communications (accepted) (2026)

Human skin rejuvenation via mRNA

Li, L.*, Tang, Z., Portillo, X., Arora, R., Yang, M., Mintzer, E., Zhang, Z., Sol, S., Boncimino, F., Han, P., Dion, M., Di Cicco, E., Majewski, D.D., Titelman, A.A., Plesa, A.M., Shadpour, M., McNamee, S.M., Restrepo, P., Ji, A.L., Lee, J., Zheng, Y., Li, X., Wang, Y., Tam, J.M., McGee, J.S., Z, Y.S., Artzi, N., Murphy, G.F., Mandinova, A., Kupper, T.S., Ma, S.* & Church, G.*

Nature (accepted) (2026)

HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury

Yuan, W-C., Earl, A., Ma, S., Alcedo, K., Russell, J., Duarte, F., Chu, Y-T., Chang, P-C., Chen, H-H., Chi, H-H., Zhu, Q., Rodriguez-Fraticelli, A., Patel, S., Lee, Y-R., Buenrostro, J. & Camargo, F.

Cell Stem Cell, 32, 6, 990–1005.e8 (2025)

Multiscale footprints reveal the organization of cis-regulatory elements

Hu, Y.*, Horlbeck, M.*, Zhang, R.*, Ma, S., et al.

Nature, 638, 779–786 (2025)

Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours

Hegde, S., Giotti, B.†, Soong, B.†, Halasz, L., Berichel, J., Magen, A., Kloeckner, B., Mattiuz, R., Park, M., Marks, A., Belabed, M., Chin, T., Troncoso, L., Reid, A., Chung, G., D'souza, D., Dawson, T., Kim-Schulze, S., Flores, R., Kaufman, A., Ginhoux, F., Tsankov, A., Marron, T., Ma, S., Brown, B. & Merad, M.

Nature, 646, 1214–1222 (2025)

A transcription factor atlas of directed differentiation

Joung, J., Ma, S.*, Tay, T.*, Geiger-Schuller, K.R.*, Kirchgatterer, P.C., Verdine, V.K., Guo, B., Arias-Garcia, A.A., Allen, E., Singh, A., Kuksenko, O., Abudayyeh, O.O., Gootenberg, J.S., Fu, Z., Macrae, R.K., Buenrostro, J.D., Regev, A. & Zhang, Z.

Cell, 186, 209–229 (2023)

Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes

Zhang, Q., Ma, S., Liu, Z., Zhu, B., Zhou, Z., Li, G., Meana, J.J., González-Maeso, J., Lu, C.

Nature Communications, 14, 4672 (2023)

Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung

Concepcion, C., Ma, S., et al.

Cancer Discovery, 12, 562–585 (2022)

Temporally-divergent regulatory mechanisms govern neuronal development and diversification in the neocortex

Yuan, W., Ma, S., Brown, J., Kim, K., Murek, V., Trastulla, L., Meissner, A., Lodato, S., Shetty, A., Levin, J., Buenrostro, J., Ziller, M. & Arlotta, P.

Nature Neuroscience, 25, 1049–1058 (2022)

Functional inference of gene regulation using single-cell multi-omics

Kartha, V.K., Duarte, F., Hu, Y., Ma, S., Chew, J., Lareau, C., Earl, A., Burkett, Z., Kohlway, A., Lebofsky, R. & Buenrostro, J.

Cell Genomics, 2, 100166 (2022)

Spatial profiling of chromatin accessibility in mouse and human tissues

Deng, Y., Bartosovic, M., Ma, S., et al.

Nature, 609, 375–383 (2022)

Corticosterone inhibits GAS6 to govern hair follicle stem-cell quiescence

Choi, S., Zhang, B., Ma, S., et al.

Nature, 592, 428–432 (2021)

Inference and effects of barcode multiplets in droplet-based single-cell assays

Lareau, C., Ma, S., Duarte, F. & Buenrostro, J.

Nature Communications, 11, 866 (2020)

Epigenomic state transitions characterize tumor progression in mouse lung adenocarcinoma

LaFave, L., Kartha, V.*, Ma, S.*, et al.

Cancer Cell, 38, 212–228 (2020)

Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells

Zhang, B., Ma, S., et al.

Nature, 577, 676–681 (2020)

Chromatin potential identified by shared single-cell profiling of RNA and chromatin

Ma, S., Zhang, B., LaFave, L., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V., Law, T., Lareau, C., Hsu, C.H., Regev, A. & Buenrostro, J.

Cell, 183, 1103–1116 (2020)

Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex (SurfaceChIP-seq)

Ma, S., Hsieh, Y., Ma, J. & Lu, C.

Science Advances, 4, eaar8187 (2018)

Cell-type-specific brain methylomes profiled via ultralow-input microfluidics

Ma, S., Revenga, M., Sun, Z., Sun, C., Murphy, T.W., Xie, H., González-Maeso, J. & Lu, C.

Nature Biomedical Engineering, 2, 183–194 (2018)

Complete list

Other publications

2026

Layering methylome and transcriptome in the same tissue slice

Xiao, Y.* & Ma, S.*

Genomics, Proteomics & Bioinformatics, 24 (1), qzaf136 (2026)

ME-seq protocol V1 a single cell trimodal assay

Zhu, B. & Ma, S.

Protocols.io (2026)

Exploring ADNP syndrome variant pathogenesis through advanced iPSC-derived cortical interneuron models

Hu, R.†, Lee, L.†, …, Ma, S.* & Yang, N.*

Stem Cell Reports (accepted) (2026)

Rationale design in materials and pharmacokinetics for approaches to enable effective brain genome editing (Review)

Lee, S., Shrestha, S., Huang, Z., Chi, C.-W., Mintz, R.L., He, S., Ma, S., Straubinger, R.M., Chavez, A., Mager, D.E.* & Lao, Y-H.*

Cell Biomaterials (accepted) (2026)

A CRISPR-Based Humanized Model Reveals Cooperative Role of STAG2 Loss in Familial GATA2-Deficient MDS Progression

Freed, G., Quijada-Alamo, M., Lee, L., Poddar, N., Autar, S., Carcamo, S., Fiore, P., Wang, K., Martinez, I.G., Zhang, M., Saniei, S., Chao, C., Mekerishvili, L., Diaz, Z., Ma, S., Hasson, D. & Wagenblast, E.

Blood Advances (accepted) (2026)

2024

Chromatin-based mechanisms of diversification of regulatory and pro-inflammatory states reveal a role for BACH2 in Th17-based autoimmunity

Thakore, P., Schnell, A., Zhao, M., Huang, L., Hou, Y., Christian, E., Zaghouani, S., Wang, C., Singh, V., Ma, S., et al.

Nature Immunology, 25, 1395–1410 (2024)

Multi-Omics profiling of human hippocampus reveals increased inflammation and transcription instability in major depressive disorder

Xiao, Y., Mariani, M., …, Ma, S., …, Boldrini, M.

Biological Psychiatry, 95 (10), S68–S69 (2024)

2023

Spatially resolved co-sequencing of epigenome and transcriptome at cellular level

Zhang, D.*, Deng, Y.*, Kukanja, P., Bartosovic, M., Su, G., Bao, S., Liu, Y., Xiao, Y., Ma, S., et al.

Nature, 616, 113–122 (2023)

Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens

Otto, J.*, Ursu, O.*, Wu, A., Cuocco, M., Ma, S., et al.

Molecular Cell, 83, 1–18 (2023)

Epigenetic memory of coronavirus infection in innate immune cells and their progenitors

Cheong, J.G.*, Ravishankar, A.*, Sharma, S.*, Parkhurst, C.*, Grassmann, S., Wingert, C.K., Laurent, P., Ma, S., et al.

Cell, 186 (18), 3882–3902 (2023)

2022

Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues

Hsieh, Y.P., Naler, L., Ma, S. & Lu, C.

NAR Genomics and Bioinformatics, 4(1), lqac006 (2022)

2021

ELF3 activated by a superenhancer and an autoregulatory feedback loop is required for high-level HLA-C expression on extravillous trophoblasts

Li, Q., Meissner, T., Wang, F., Du, Z., Ma, S., et al.

PNAS, 118, e2025512118 (2021)

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

Biancalani, T., Scalia, G., Buffoni, L., Avasthi, R., Lu, Z., Sanger, A., Tokcan, N., Vanderburg, C., Segerstolpe, A., Zhang, M., Avraham-Davidi, I., Vickovic, S., Nitzan, M., Ma, S., et al.

Nature Methods, 18, 1352–1362 (2021)

Single-cell ATAC-seq reveals GATA2-dependent priming defect in myeloid and a maturation bottleneck in lymphoid lineages

Avagyan, S., Weber, M.C., Ma, S., Prasad, M., Mannherz, W.P., Yang, S., Buenrostro, J.D. & Zon, L.I.

Blood Advances, 5, 2673–1686 (2021)

Protocol for single-cell ATAC-sequencing using combinatorial indexing

Del Priore, I.*, Ma, S.*, Strecker, J., Jacks, T., LaFave, L. & Buenrostro, J.

STAR Protocols, 2, 100583 (2021)

SHARE-seq V1

Ma, S., Regev, A. & Buenrostro, J.

Protocols.io (2021)

2020

Sustained activation of ampk enhances differentiation of human iPSC-derived cardiomyocytes via sirtuin activation

Sarikhani, M., Garbern, J., Ma, S., et al.

Stem Cell Report, 20, 498–514 (2020)

2019

A diffusion-based microfluidic device for single-cell RNA-seq

Sarma, M., Lee, J., Ma, S., Li, S. & Lu, C.

Lab on a Chip, 19, 1247–1256 (2019)

Transcriptional atlas of intestinal immune cells reveals that neuropeptide α-cgrp modulates group 2 innate lymphoid cell responses

Xu, H., Ding, J., Porter, C., Wallrapp, A., Tabaka, M., Ma, S., et al.

Immunity, 51, 696–708 (2019)

2018

Microfluidic low-Input fluidized-bed enabled ChIP-seq device for automated and parallel analysis of histone modifications

Murphy, T.W., Hsieh, Y., Ma, S., Zhu, Y. & Lu, C.

Analytical Chemistry, 90, 7666–7674 (2018)

Recent advances in the use of microfluidic technologies for single cell analysis

Murphy, T.W., Zhang, Q., Naler, L., Ma, S. & Lu, C.

Analyst, 143, 60–80 (review) (2018)

2017

Microfluidics for genome-wide studies involving next generation sequencing

Ma, S., Murphy, T.W. & Lu, C.

Biomicrofluidics, 11, 021501 (review, Editor’s Picks) (2017)

Immunomagnetic separation of tumor initiating cells by screening two surface markers

Sun, C., Hsieh, Y., Ma, S., Geng, S., Cao, Z., Li, L. & Lu, C.

Scientific Reports, 7, 40632 (2017)

2016

RNA extraction from a mycobacterium under ultrahigh electric field intensity

Ma, S., Bryson, B.D., Sun, C., Fortune, S.M. & Lu, C.

Analytical Chemistry, 88, 5053–5057 (2016)

Paramagnetic structures within a microfluidic channel for enhanced immunomagnetic isolation and surface patterning of cells

Sun, C., Hassanisaber, H., Yu, R., Ma, S., Verbridge, S.S. & Lu, C.

Scientific Reports, 6, 29407 (2016)

2015

Optimal design of microfluidic platforms for diffusion-based PCR for “one-pot” analysis of cells

Crowa, J., Achenie, L.E.K., Lu, C., Ma, S., Loufakis, D.N., Cao, Z. & Chang, Y.

Computer Aided Chemical Engineering, 37, 1199–1204 (2015)

2014

Visible paper chip immunoassay for rapid determination of bacteria in water distribution system

Ma, S., Tang, Y., Liu, J. & Wu, J.

Talanta, 120, 135–140 (2014)

Electroporation-based delivery of cell-penetrating peptide conjugates of peptide nucleic acids for antisense inhibition of intracellular bacteria

Ma, S., Schroeder, B., Sun, C., Loufakis, D.N., Cao, Z., Sriranganathan, N. & Lu, C.

Integrative Biology, 2014, 973–978 (2014)

Diffusion-based microfluidic PCR for “one-pot” analysis of cells

Ma, S., Loufakis, D.N., Cao, Z., Chang, Y., Achenie, L.E.K. & Lu, C.

Lab on a Chip, 14, 2905–2909 (selected as cover; hot article) (2014)

Electroporation-delivered fluorescent protein biosensors for probing molecular activities in cells without genetic encoding

Sun, C., Ouyang, M., Cao, Z., Ma, S., Alqublan, H., Sriranganathan, N., Wang, Y. & Lu, C.

Chemical Communications, 50, 11536–11539 (2014)

Focusing of mammalian cells under an ultrahigh pH gradient created by unidirectional electropulsation in a confined microchamber

Loufakis, D.N., Cao, Z., Ma, S., Mittelman, D. & Lu, C.

Chemical Science, 5, 3331–3337 (2014)

2012

Capture, enrichment, and mass spectrometric detection of low‐molecular‐weight biomarkers with nanoporous silicon microparticles

Tan, J., Zhao, W., Yu, J., Ma, S., Sailor, M.J. & Wu, J.

Advanced Healthcare Materials, 1, 742–750 (2012)

2009

Solid high-proton conductors based on heteropoly acids

Liu, Z., Wu, Q., Song, X. & Ma, S.

Progress in Chemistry, 21, 982–989 (2009)