{"id":4,"date":"2021-04-02T11:44:19","date_gmt":"2021-04-02T15:44:19","guid":{"rendered":"http:\/\/saimalab.com\/?page_id=4"},"modified":"2026-04-03T22:07:26","modified_gmt":"2026-04-04T02:07:26","slug":"publications","status":"publish","type":"page","link":"https:\/\/saimalab.com\/index.php\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n<p class=\"has-text-color\" style=\"color:#0071a1;font-size:18px\">[<a href=\"https:\/\/scholar.google.com\/citations?user=YK3mxLwAAAAJ&amp;hl=en&amp;oi=ao\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/scholar.google.com\/citations?user=YK3mxLwAAAAJ&amp;hl=en&amp;oi=ao\">Google Scholar<\/a>]<\/p>\n\n\n\n<p class=\"has-vivid-red-color has-text-color\" style=\"font-size:22px\"><strong>Selected Publications<\/strong><\/p>\n\n\n\n<ol style=\"list-style-type:1\" class=\"wp-block-list\">\n<li><strong><u>Ma, S.<\/u><\/strong>, Zhang, B., LaFave L., Chiang, Z., Hu Y., Ding, J., Brack, A., Kartha, V., Law, T., Lareau C., Hsu, Y.C., Regev, A. &amp; Buenrostro, J. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0092867420312538\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0092867420312538\">Chromatin potential identified by shared single-cell profiling of RNA and chromatin. <\/a><strong><em>Cell<\/em><\/strong>, 183, 1103-1116 (2020)<strong><em>.<\/em><\/strong><\/li>\n\n\n\n<li><strong><u>Ma, S.<\/u><\/strong>, Revenga, M., Sun, Z., Sun, C., Murphy, T. W., Xie, H., Gonz\u00e1lez-Maeso, J. &amp; Lu. C. <a href=\"https:\/\/www.nature.com\/articles\/s41551-018-0204-3\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.nature.com\/articles\/s41551-018-0204-3\">Cell-type-specific brain methylomes profiled via ultralow-input microfluidics. <\/a><strong><em>Nature Biomedical Engineering<\/em><\/strong>,<strong>\u00a0<\/strong>2, 183-194 (2018).\n<ul class=\"wp-block-list\">\n<li>Featured in VT news \u201c<a href=\"https:\/\/vtnews.vt.edu\/articles\/2018\/03\/eng-epigenomicbreakthrough.html\" title=\"https:\/\/vtnews.vt.edu\/articles\/2018\/03\/eng-epigenomicbreakthrough.html\" target=\"_blank\" rel=\"noreferrer noopener\">Epigenomic tool breakthrough has implications for identifying disease processes<\/a>\u201d<\/li>\n\n\n\n<li>Featured in Behind-the-paper \u201c<a href=\"https:\/\/bioengineeringcommunity.nature.com\/posts\/30839-using-microfluidics-to-map-brain-epigenomes\" title=\"https:\/\/bioengineeringcommunity.nature.com\/posts\/30839-using-microfluidics-to-map-brain-epigenomes\" target=\"_blank\" rel=\"noreferrer noopener\">Using microfluidics to map brain epigenomes<\/a>\u201d<\/li>\n\n\n\n<li>Featured in Nature Biomedical Engineering \u201c<a href=\"https:\/\/www.nature.com\/articles\/s41551-018-0211-4\" title=\"https:\/\/www.nature.com\/articles\/s41551-018-0211-4\" target=\"_blank\" rel=\"noreferrer noopener\">Epigenetic profiling with ultralow DNA amounts<\/a>\u201d<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong><u>Ma, S.<\/u><\/strong>, Hsieh, Y., Ma, J. &amp; Lu, C.<a href=\"https:\/\/advances.sciencemag.org\/content\/4\/4\/eaar8187.full\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/advances.sciencemag.org\/content\/4\/4\/eaar8187.full\"> Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex (SurfaceChIP-seq). <\/a><strong><em>Science Advances<\/em><\/strong>,&nbsp;4, eaar8187<strong><em>&nbsp;<\/em><\/strong>(2018).\n<ul class=\"wp-block-list\">\n<li>Featured in GenomeWeb \u201c<a href=\"https:\/\/www.genomeweb.com\/sequencing\/virginia-tech-team-develops-microfluidic-technique-low-input-chip-seq#.YGihOy2ZNBw\" title=\"https:\/\/www.genomeweb.com\/sequencing\/virginia-tech-team-develops-microfluidic-technique-low-input-chip-seq#.YGihOy2ZNBw\">Virginia tech team develops microfluidic technique for low-input ChIP-seq<\/a>\u201d<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Restrepo, P. Wilder, A., Houser, A. Ramirez, A., \u2026,&nbsp;Gnjatic, S.,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>&nbsp;&amp; Ji, A. L. <a href=\"https:\/\/www.nature.com\/articles\/s41588-026-02552-8\" target=\"_blank\" rel=\"noopener\" title=\"A single-cell spatial transcriptomic census of human skin anatomy.\">A single-cell spatial transcriptomic census of human skin anatomy.<\/a>&nbsp;<strong>bioRxiv<\/strong>&nbsp;|&nbsp;<strong><em>Nature Genetics<\/em><\/strong>, accepted, 2026.<\/li>\n\n\n\n<li>Hegde, S., Giotti, B.\u2020, Soong, B.\u2020, 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&#8217;souza, D., Dawson, T., Kim-Schulze, S., Flores, R., Kaufman, A., Ginhoux, F., Tsankov, A., Marron, T.,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S<\/span>.<\/strong>,<strong>&nbsp;<\/strong>Brown, B. &amp; Merad, M. <a href=\"https:\/\/www.nature.com\/articles\/s41586-025-09493-y\" target=\"_blank\" rel=\"noopener\" title=\"Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours\">Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours<\/a>.&nbsp;<strong><em>Nature<\/em><\/strong>, 646,&nbsp;1214\u20131222&nbsp;(2025).<\/li>\n\n\n\n<li>Yuan, W-C., Earl, A.,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, 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. &amp; Camago, F.&nbsp;<a href=\"https:\/\/www.cell.com\/cell-stem-cell\/fulltext\/S1934-5909(25)00177-8\" target=\"_blank\" rel=\"noopener\" title=\"HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury\">HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury<\/a>.&nbsp;<strong><em>Cell Stem Cell<\/em><\/strong>, 32, 6, 990- 1005.e8 (2025).<\/li>\n\n\n\n<li>Hu, Y.*, Horlbeck, M.*, Zhang, R.*,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>&nbsp;et al. <a href=\"https:\/\/www.nature.com\/articles\/s41586-024-08443-4\" target=\"_blank\" rel=\"noopener\" title=\"Multiscale footprints reveal the organization of&nbsp;cis-regulatory elements\">Multiscale footprints reveal the organization of&nbsp;<em>cis<\/em>-regulatory elements<\/a>.&nbsp;<strong><em>Nature,&nbsp;<\/em><\/strong>638, 779\u2013786 (2025).<\/li>\n\n\n\n<li>Zhang, Q., <strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong> Liu, Z., <span style=\"text-decoration: underline;\"><strong>Zhu, B<\/strong>.<\/span>, Zhou, Z., Li, G., Meana, J. J., Gonz\u00e1lez-Maeso, J., Lu, C. <a href=\"https:\/\/www.nature.com\/articles\/s41467-023-40411-w\" target=\"_blank\" rel=\"noopener\" title=\"\">Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes<\/a>. <strong><em>Nature Communication<\/em><\/strong><em><strong>s<\/strong><\/em>, 14, 4672 (2023).<\/li>\n\n\n\n<li>Joung, J.,\u00a0<strong><span style=\"text-decoration: underline;\">Ma, S.*<\/span><\/strong>, Tay, T.* Geiger-Schuller, K.R.*, Kirchgatterer, P.C., Verdine, V.K., Guo, B. Arias-Garcia, A.A., E. Allen, W. E., Singh, A., Kuksenko, O., Abudayyeh, O. O., Gootenberg, J. S., Fu, Z., Macrae, R.K., Buenrostro, J.D., Regev, A. &amp; Zhang, Z. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867422014702\" target=\"_blank\" rel=\"noopener\" title=\"A transcription factor atlas of directed differentiation.\">A transcription factor atlas of directed differentiation. <\/a><strong><em>Cell<\/em><\/strong>, 186, 209-229 (2023).<\/li>\n\n\n\n<li>Deng, Y.,\u00a0Bartosovic, M.,\u00a0<strong><u>Ma, S.<\/u><\/strong>, Zhang, D., Kukanja, P., Xiao, Y., Su, G., Liu, Y., Qin, X., Rosoklija, G.B., Dwork, A.J., Mann, J.J., Xu, M.L., Halene, S., Craft, J.E., Leong, K.W., Boldrini, M., Castelo-Branco, G. &amp; Fan, R. <a href=\"https:\/\/www.nature.com\/articles\/s41586-022-05094-1\" title=\" Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level\">Spatial profiling of chromatin accessibility in mouse and human tissues<\/a><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.06.06.447244v1\" target=\"_blank\" rel=\"noreferrer noopener\">. <\/a><strong><em>Nature<\/em><\/strong>, 609,\u00a0375\u2013383 (2022).\n<ul class=\"wp-block-list\">\n<li>Highlighted in Nature Structural &amp; Molecular Biology &#8220;<a href=\"https:\/\/www.nature.com\/articles\/s41594-022-00834-3\" target=\"_blank\" rel=\"noopener\" title=\"Chromatin found in space\">Chromatin found in space<\/a>&#8220;<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Kartha V., Duarte F., Hu Y., <strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong> Chew, J., Lareau, C., Earl, A., Burkett, Z., Kohlway, A., Lebofsky, R. &amp; Buenrostro. J. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2666979X22001082\" target=\"_blank\" rel=\"noopener\" title=\"\">Functional Inference of Gene Regulation using Single-Cell Multi-Omics.<\/a> <strong><em>Cell Genomics<\/em><\/strong>, 2,  100166 (2022).<\/li>\n\n\n\n<li>Yuan, W.,\u00a0<strong><u>Ma, S.<\/u><\/strong>, Brown, J., Kim, K., Murek, V., Trastulla, L., Meissner, A., Lodato, S., Shetty, A., Levin, J., Buenrostro, J., Ziller, M. &amp; Arlotta, P. <a href=\"https:\/\/www.nature.com\/articles\/s41593-022-01123-4#citeas\" target=\"_blank\" rel=\"noopener\" title=\"Temporally-Divergent Regulatory Mechanisms Govern Neuronal Development and Diversification in the Neocortex.\u00a0\">Temporally-Divergent Regulatory Mechanisms Govern Neuronal Development and Diversification in the Neocortex. <\/a><strong><em>Nature Neuroscience<\/em><\/strong>, 25,\u00a01049\u20131058 (2022).<\/li>\n\n\n\n<li>Concepcion, C.,\u00a0<strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, Bhutkar, A., Liu, M., DeAngelo, L.P., Kim, J.Y., Priore, I.D., Schoenfeld, A.J., Miller, M., Kartha, V.K., Westcott, P.M.K., S\u00e1nchez-Rivera, F.J., Meli, K., Gupta, M., Bronson, R.T., Riely, G.J., Rekhtman, N., Rudin, C.M., Kim, C.F., Regev, A., Buenrostro J.B. &amp; Jacks, T. <a href=\"https:\/\/cancerdiscovery.aacrjournals.org\/content\/early\/2021\/09\/24\/2159-8290.CD-21-0248\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung\"><em>Smarca4<\/em> inactivation promotes lineage-specific transformation and early metastatic features in the lung<\/a><a href=\"https:\/\/cancerdiscovery.aacrjournals.org\/content\/early\/2021\/09\/24\/2159-8290.CD-21-0248\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/cancerdiscovery.aacrjournals.org\/content\/early\/2021\/09\/24\/2159-8290.CD-21-0248\">. <\/a><strong><em>Cancer Discovery<\/em><\/strong>, 12(2), 562-585\u00a0(2021).<\/li>\n\n\n\n<li>Choi, S., Zhang, B.,\u00a0<strong><u>Ma, S.<\/u><\/strong>, Gonzalez-Celeiro, M., Stein, D., Jin, X., Kim, S.T., Kang, Y-L, Besnard, A., Rezza, A., Grisanti, L., Buenrostro, J.D. Rendl, M., Nahrendorf, M., Sahay, A. &amp; Hsu, Y-C. <a href=\"https:\/\/www.nature.com\/articles\/s41586-021-03417-2\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.nature.com\/articles\/s41586-021-03417-2\">Corticosterone inhibits GAS6 to govern hair follicle stem-cell quiescence. <\/a><strong><em>Nature<\/em><\/strong>, 592,\u00a0428\u2013432 (2021).\n<ul class=\"wp-block-list\">\n<li>Featured in Nature \u201c<a href=\"http:\/\/doi.org\/10.1038\/d41586-021-00656-1\" title=\"http:\/\/doi.org\/10.1038\/d41586-021-00656-1\">Relax to grow more hair<\/a>\u201d<\/li>\n\n\n\n<li>Featured in Harvard News \u201c<a href=\"https:\/\/news.harvard.edu\/gazette\/story\/2021\/03\/researchers-discover-how-chronic-stress-leads-to-hair-loss\/\" target=\"_blank\" rel=\"noreferrer noopener\">How chronic stress leads to hair loss<\/a>\u201d<\/li>\n\n\n\n<li>Featured in <a href=\"https:\/\/www.sciencedaily.com\/releases\/2021\/03\/210331143023.htm\" title=\"https:\/\/www.sciencedaily.com\/releases\/2021\/03\/210331143023.htm\" target=\"_blank\" rel=\"noreferrer noopener\">ScienceDaily<\/a> and many others<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Zhang, B.,\u00a0<strong><u>Ma, S.<\/u><\/strong>, Rachmin, I., He, M., Baral, P., Choi, S., Gon\u00e7alves, W.A., Shwartz, Y., Fast, E.M., Su, Y., Zon, L.I., Regev, A., Buenrostro, J.D., Cunha, T.M., Chiu, I.M., Fisher, D.E. &amp; Hsu, Y.C. <a href=\"https:\/\/dx.doi.org\/10.1038%2Fs41586-020-1935-3\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/dx.doi.org\/10.1038%2Fs41586-020-1935-3\">Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells. <\/a><strong><em>Nature<\/em><\/strong>,\u00a0577,\u00a0676-681\u00a0(2020).\n<ul class=\"wp-block-list\">\n<li>Featured in Nature \u201c<a href=\"https:\/\/www.nature.com\/articles\/d41586-019-03949-8\" title=\"https:\/\/www.nature.com\/articles\/d41586-019-03949-8\" target=\"_blank\" rel=\"noreferrer noopener\">How the stress of fight or flight turns hair white<\/a>\u201d<\/li>\n\n\n\n<li>Featured in &gt;200 news websites<\/li>\n\n\n\n<li>Ranked 36th of the 302,805 tracked articles by online attention<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>LaFave, L., Kartha, V.*,\u00a0<strong><u>Ma, S.*<\/u><\/strong>, Meli, K., Priore, I.D., Lareau, C., Naranjo, S., Westcott, P.M.K., Duarte, F.M., Sankar, V., Chiang, Z., Brack, A., Law, T., Hauck, H., Okimoto, A., Regev, A., Buenrostro, J.D. &amp; Jacks, T. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S153561082030310X\" target=\"_blank\" rel=\"noopener\" title=\"\">Epigenomic state transitions characterize tumor progression in lung adenocarcinoma. <\/a><strong><em>Cancer Cell<\/em><\/strong>,\u00a038, 212-228, (2020). (* equal contribution)\n<ul class=\"wp-block-list\">\n<li>Featured in MIT news \u201c<a href=\"https:\/\/news.mit.edu\/2020\/tumor-epigenomic-cancer-progression-0723\" title=\"https:\/\/news.mit.edu\/2020\/tumor-epigenomic-cancer-progression-0723\" target=\"_blank\" rel=\"noreferrer noopener\">Gene-controlling mechanisms play key role in cancer progression<\/a>\u201d<\/li>\n\n\n\n<li>Featured in <a href=\"https:\/\/www.sciencedaily.com\/releases\/2020\/07\/200723115857.htm\" title=\"https:\/\/www.sciencedaily.com\/releases\/2020\/07\/200723115857.htm\" target=\"_blank\" rel=\"noreferrer noopener\">ScienceDaily<\/a><\/li>\n\n\n\n<li>Featured in&nbsp;<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1535610820303627?via%3Dihub\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1535610820303627?via%3Dihub\">Cancer Cell<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Lareau, C.,\u00a0<strong><u>Ma, S.<\/u><\/strong>, Duarte F., &amp; Buenrostro J.<a href=\"https:\/\/www.nature.com\/articles\/s41467-020-14667-5\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.nature.com\/articles\/s41467-020-14667-5\">\u00a0Inference and effects of barcode multiplets in droplet-based single-cell assays<\/a>.\u00a0<strong><em>Nature Communication<\/em><\/strong><em><strong>s<\/strong><\/em>, 11, 866 (2020).<\/li>\n<\/ol>\n\n\n\n<p class=\"has-vivid-red-color has-text-color\" style=\"font-size:22px\"><strong>Patents<\/strong><\/p>\n\n\n\n<ol style=\"list-style-type:1\" class=\"wp-block-list\">\n<li>Buenrostro, J.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Regev, A., Methods and Compositions for Analyzing Nucleic Acids. <\/li>\n\n\n\n<li>Lu, C.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Methods and Devices for Analysis of Nucleic Acids from Cells.<\/li>\n\n\n\n<li><strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, Zhu, B., Yang, N. Methylation and Expression Sequencing And Methods of Use to Diagnose and Treat.<\/li>\n<\/ol>\n\n\n\n<p class=\"has-vivid-red-color has-text-color\" style=\"font-size:22px\"><strong>bioRxiv<\/strong><\/p>\n\n\n\n<ol style=\"list-style-type:1\" class=\"wp-block-list\">\n<li>Li,&nbsp;L.#,&nbsp;Tang, Z.,&nbsp;Portillo, X.,&nbsp;Arora,&nbsp;R., Yang, M., &#8230; ,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma,&nbsp;S.#<\/span><\/strong>, Church, G#. <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.11.12.623261v1\" target=\"_blank\" rel=\"noopener\" title=\"Human skin rejuvenation via mRNA\">Human skin rejuvenation via mRNA<\/a>. <strong><em>bioRxiv<\/em><\/strong> (2024) (# co-corresponding)<\/li>\n\n\n\n<li>Hu, R.*,&nbsp;Boshans, L.*,<strong>&nbsp;Zhu, B.<\/strong>,&nbsp;&#8230;,&nbsp;Buxbaum,&nbsp;J., <strong><span style=\"text-decoration: underline;\">Ma, S<\/span><\/strong><span style=\"text-decoration: underline;\"><strong>.<\/strong>#<\/span>,&nbsp;Yang, N.# <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.12.03.626438v1\" target=\"_blank\" rel=\"noopener\" title=\"\">Expanding GABAergic Neuronal Diversity in iPSC-Derived Disease Models<\/a> <strong><em>bioRxiv<\/em><\/strong> (2024) (# co-corresponding, * equal contribution)<\/li>\n\n\n\n<li><strong>Di Tullio,&nbsp;F.<\/strong>, Yang, S.-B., Yang,&nbsp;L., \u2026,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, Dong,&nbsp;Y.,&nbsp;Zhou, H.,&nbsp;Sun, T. <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2025.06.19.660551v1\" target=\"_blank\" rel=\"noopener\" title=\"Targeting ZNRF3 and RNF43 to Restore Regeneration and Reverse Metabolic Dysfunction-Associated Steatotic Liver Disease.\">Targeting ZNRF3 and RNF43 to Restore Regeneration and Reverse Metabolic Dysfunction-Associated Steatotic Liver Disease.<\/a> <strong><em>bioRxiv<\/em><\/strong> (2025).&nbsp;&nbsp;<\/li>\n\n\n\n<li>Yang, S.B., <strong>Tullio, F.D.<\/strong>, Yang, L., Cogliati, B., Schnidrig, D., Benjak, A., Roshan, S., Almeida, J.I., Li, L.,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, Tchorz, J.S., Ng, C.K., Sun, T. <a href=\"https:\/\/www.biorxiv.org\/content\/10.64898\/2025.12.06.692782v1\" target=\"_blank\" rel=\"noopener\" title=\"Liver Zonation Disruption Fuels Hepatocellular Carcinoma in Chronic Liver Disease.\">Liver Zonation Disruption Fuels Hepatocellular Carcinoma in Chronic Liver Disease.<\/a> <strong><em>bioRxiv<\/em><\/strong> (2025).<\/li>\n\n\n\n<li>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.,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, Hasson, D. &amp; Wagenblast E. A CRISPR-Based Humanized Model Reveals Cooperative Role of STAG2 Loss in Familial GATA2-Deficient MDS Progression.&nbsp;<strong><em>bioRxiv <\/em><\/strong>(2026).<\/li>\n\n\n\n<li><strong>Zhu, B.<\/strong>,&nbsp;Ghosh, A., <strong>Wang, Z.<\/strong>, <strong>Liao, Z.<\/strong>, Appiah, M., Li, J., Zhang, M., <strong>Tullio, F.D.<\/strong>, Kurowskiy, A., Fullard, J., Wagenblast, E., Walsh, M. J., Goate, A., Roussos, P., Cheung, K.L.*, Yang, N.*,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S.*<\/span><\/strong>&nbsp;<a href=\"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.01.30.702946v1\" target=\"_blank\" rel=\"noopener\" title=\"Early microglial priming in Alzheimer\u2019s disease revealed by ME-seq\">Early microglial priming in Alzheimer\u2019s disease revealed by ME-seq<\/a>.&nbsp;<strong><em>bioRxiv<\/em><\/strong> (2026).<\/li>\n\n\n\n<li>Li, Y., Neuffer, S. J., Wider, J.,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S<\/span>.<\/strong>, McCracken, L., Sanderson, T., Dong, J-F, Deng, Y.* &amp; Xiao, Y.* <a href=\"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.03.30.715462v1\" target=\"_blank\" rel=\"noopener\" title=\"OmicGlaze: spatial multi-omic mapping of traumatic brain injury\">OmicGlaze: spatial multi-omic mapping of traumatic brain injury<\/a>. <strong><em>bioRxiv<\/em><\/strong> (2026).<\/li>\n<\/ol>\n\n\n\n<p class=\"has-vivid-red-color has-text-color\" style=\"font-size:21px\"><strong>Additional Publications<\/strong><\/p>\n\n\n\n<ol style=\"list-style-type:1\" class=\"wp-block-list\">\n<li>Xiao, Y.* &amp;&nbsp;<strong>Ma, S.<\/strong>* Layering Methylome and Transcriptome in the Same Tissue Slice.&nbsp;<strong><em>Genomics, Proteomics &amp; Bioinformatics<\/em><\/strong>,<strong><em>&nbsp;<\/em><\/strong>accepted (2026).<\/li>\n\n\n\n<li>Thakore, P., Schnell, A., Zhao, M., Huang, L., Hou, Y., Christian, E., Zaghouani, S., Wang, C., Singh, V.,&nbsp;<strong>Ma, S.&nbsp;<\/strong>et al. <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.02.26.482041v1\" target=\"_blank\" rel=\"noreferrer noopener\">BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T<sub>H<\/sub>17 cells.<\/a>&nbsp;<strong><em>Nature Immunology<\/em><\/strong>, 25,&nbsp;1395\u20131410 (2024)<\/li>\n\n\n\n<li>Cheong, J.G.*, Ravishankar A.*, Sharma, S.*, Parkhurst, C.*,&nbsp;Grassmann, S., Wingert, C.K.,&nbsp;&nbsp;Laurent, P.,&nbsp;<strong><span style=\"text-decoration: underline;\">Ma, S.<\/span>&nbsp;<\/strong>et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867423007961\" target=\"_blank\" rel=\"noopener\" title=\"Epigenetic Memory of COVID-19 in Innate Immune Cells and Their Progenitors.\">Epigenetic Memory of COVID-19 in Innate Immune Cells and Their Progenitors.<\/a>&nbsp;<strong><em>Cell<\/em><\/strong>, 186 (18), 3882-3902 (2023).<\/li>\n\n\n\n<li>Otto, J.E., Ursu, O., Wu, A.P., Winter, E.B., Cuoco, M.S. <strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, Qian, K., Michel, B.C., Buenrostro, J.D., Berger, B., Regev, A. &amp; Kadoch, C. <a href=\"https:\/\/www.cell.com\/molecular-cell\/fulltext\/S1097-2765(23)00203-4#%20\" target=\"_blank\" rel=\"noopener\" title=\"Structural and functional properties of mSWI\/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.\">Structural and functional properties of mSWI\/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.<\/a> <strong><em>Molecular Cell<\/em><\/strong>, 83, 1\u201318 (2023)<\/li>\n\n\n\n<li>Zhang, D. , Deng, Y. , Kukanja, P. , Agirre, E., Bartosovic, M., Dong, M., Ma C., <strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong> et al. <a href=\"https:\/\/www.nature.com\/articles\/s41586-023-05795-1\" target=\"_blank\" rel=\"noopener\" title=\"\">Spatial epigenome\u2013transcriptome co-profiling of mammalian tissues<\/a>. <strong><em>Nature<\/em><\/strong>, <strong>616<\/strong>,&nbsp;113\u2013122 (2023).<\/li>\n\n\n\n<li>Del Priore, I.*,&nbsp;<strong><u>Ma, S.<\/u><\/strong>*, Strecker, J., Jacks, T., LaFave, L. &amp; Buenrosto, J. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2666166721002902\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2666166721002902\">Protocol for single-cell ATAC-sequencing using combinatorial indexing.<\/a>&nbsp;<strong><em>STAR protocols<\/em><\/strong>, 100583 (2021). (* equal contribution)&nbsp;<\/li>\n\n\n\n<li><strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, Regev, A. &amp; Buenrosto, J. <a href=\"https:\/\/www.protocols.io\/view\/share-seq-v1-bmbik2ke\" target=\"_blank\" rel=\"noreferrer noopener\">SHARE-seq V1.<\/a> Protocols.io (2021).<\/li>\n\n\n\n<li>Hsieh, Y.P., Naler, L.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>&nbsp;&amp; Lu C.&nbsp;<a href=\"https:\/\/academic.oup.com\/nargab\/article\/4\/1\/lqac006\/6520109?login=true\" target=\"_blank\" rel=\"noreferrer noopener\">Cell-type-specific epigenomic variations associated with&nbsp;<em>BRCA1<\/em>&nbsp;mutation in pre-cancer human breast tissues.&nbsp;<\/a><strong><em>NAR Genomics and Bioinformatics<\/em><\/strong>, 4, lqac006 (2021).&nbsp;<\/li>\n\n\n\n<li>Biancala, 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.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>&nbsp;et al. <a href=\"https:\/\/www.nature.com\/articles\/s41592-021-01264-7\" title=\"https:\/\/www.nature.com\/articles\/s41592-021-01264-7\" target=\"_blank\" rel=\"noreferrer noopener\">Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.<\/a>&nbsp;<strong><em>Nature Methods<\/em><\/strong>, 18,&nbsp;1352\u20131362 (2021).<\/li>\n\n\n\n<li>Avagyan, S., Weber, M.C., <strong><span style=\"text-decoration: underline;\">Ma, S.<\/span><\/strong>, Prasad, M., Mannherz, W.P., Yang, S., Buenrostro, J.D., and Zon, L.I. <a href=\"https:\/\/ashpublications.org\/bloodadvances\/article\/5\/13\/2673\/475734\/Single-cell-ATAC-seq-reveals-GATA2-dependent\" title=\"https:\/\/ashpublications.org\/bloodadvances\/article\/5\/13\/2673\/475734\/Single-cell-ATAC-seq-reveals-GATA2-dependent\" target=\"_blank\" rel=\"noreferrer noopener\">Single-cell ATAC-seq reveals<em>&nbsp;GATA2<\/em>-dependent priming defect in myeloid and a maturation bottleneck in lymphoid lineages.<\/a> <strong><em>Blood Advances<\/em><\/strong><em>,<\/em> 5, 2673-2686 (2021).<\/li>\n\n\n\n<li>Li, Q., Meissner, T., Wang, F., Du, Z.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Kshirsagar, S., Tilburgs, T., Buenrostro, J., Uesugi, M., &amp; Strominger, J. <a href=\"https:\/\/www.pnas.org\/content\/118\/9\/e2025512118\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.pnas.org\/content\/118\/9\/e2025512118\"><em>ELF3<\/em> activated by a superenhancer and an autoregulatory feedback loop is required for high-level HLA-C expression on extravillous trophoblasts.<\/a>&nbsp;<strong><em>PNAS<\/em><\/strong>,&nbsp;118, e2025512118 (2021)<\/li>\n\n\n\n<li>Sarikhani, M., Garbern, J.,&nbsp;<strong><u>Ma S.<\/u><\/strong>, et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2213671120302332\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2213671120302332\" target=\"_blank\" rel=\"noreferrer noopener\">Sustained activation of ampk enhances differentiation of human iPSC-derived cardiomyocytes via sirtuin activation.<\/a>&nbsp;<strong><em>Stem Cell Report<\/em><\/strong>,&nbsp;20, 498-514,&nbsp;(2020).<\/li>\n\n\n\n<li>Xu, H., Ding, J., Porter, C., Wallrapp, A., Tabaka, M.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>&nbsp;et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1074761319303759\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1074761319303759\" target=\"_blank\" rel=\"noreferrer noopener\">Transcriptional atlas of intestinal immune cells reveals that neuropeptide \u03b1-cgrp modulates group 2 innate lymphoid cell responses.<\/a>&nbsp;<strong><em>Immunity<\/em><\/strong>, 51, 696-708 (2019).<\/li>\n\n\n\n<li>Sarma, M., Lee, J.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Li, S. &amp; Lu, C. <a href=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2019\/LC\/C8LC00967H#!divAbstract\" title=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2019\/LC\/C8LC00967H#!divAbstract\" target=\"_blank\" rel=\"noreferrer noopener\">A diffusion-based microfluidic device for single-cell RNA-seq.<\/a>&nbsp;<strong><em>Lab on a Chip<\/em><\/strong>,&nbsp;19, 1247-1256 (2019).<\/li>\n\n\n\n<li>Murphy, T. W., Zhang, Q., Naler, L.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>&nbsp;&amp; Lu, C. <a href=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2018\/an\/c7an01346a#!divAbstract\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2018\/an\/c7an01346a#!divAbstract\">Recent advances on microfluidic technologies for single cell analysis.<\/a>&nbsp;<strong><em>Analyst<\/em><\/strong>, 143, 60-80 (2018). (review)<\/li>\n\n\n\n<li>Murphy, T. W.,&nbsp;Hsieh Y.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Zhu, Y. &amp; Lu, C.&nbsp;<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.analchem.8b01541\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.analchem.8b01541\">Microfluidic low-Input fluidized-bed enabled ChIP-seq device for automated and parallel analysis of histone modifications.<\/a>&nbsp;<strong><em>Analytical Chemistry<\/em><\/strong>, 90, 7666-7674 (2018).<\/li>\n\n\n\n<li><strong><u>Ma, S.<\/u><\/strong>, Murphy, T. W. &amp; Lu, C. <a href=\"https:\/\/aip.scitation.org\/doi\/10.1063\/1.4978426\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/aip.scitation.org\/doi\/10.1063\/1.4978426\">Microfluidics for genome-wide studies involving next generation sequencing.<\/a><strong><em>Biomicrofluidics<\/em><\/strong>,&nbsp;11, 021501 (2017). (review, Editor\u2019s Picks)<\/li>\n\n\n\n<li>Sun, C., Hsieh, Y.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Geng, S., Cao, Z., Li, L. &amp; Lu, C. <a href=\"https:\/\/www.nature.com\/articles\/srep40632\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.nature.com\/articles\/srep40632\">Immunomagnetic separation of tumor initiating cells by screening two surface markers.<\/a>&nbsp;<strong><em>Scientific Reports<\/em><\/strong>,&nbsp;7, 40632 (2017).<\/li>\n\n\n\n<li><strong><u>Ma, S.<\/u><\/strong>, Bryson, B.D., Sun, C., Fortune, S. M. &amp; Lu, C.<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.analchem.6b00381\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.analchem.6b00381\"> RNA extraction from a mycobacterium under ultrahigh electric field intensity.<\/a>&nbsp;<strong><em>Analytical Chemistry<\/em><\/strong>,&nbsp;88, 5053-5057 (2016).<\/li>\n\n\n\n<li>Sun, C., Hassanisaber, H., Yu, R.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Verbridge, S. S. &amp; Lu, C. <a href=\"https:\/\/www.nature.com\/articles\/srep29407\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.nature.com\/articles\/srep29407\">Paramagnetic structures within a microfluidic channel for enhanced immunomagnetic isolation and surface patterning of cells.<\/a>&nbsp;<strong><em>Scientific Reports<\/em><\/strong>,&nbsp;6, 29407&nbsp;(2016).<\/li>\n\n\n\n<li>Crowa, J., Achenie, L. E. K., Lu, C.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Loufakis, D. N. Cao, Z. &amp; Chang, Y. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/B9780444635778500450\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/B9780444635778500450\">Optimal design of microfluidic platforms for diffusion-based PCR for \u201cone-pot\u201d analysis of cells.<\/a>&nbsp;<strong><em>Computer Aided Chemical Engineering,&nbsp;<\/em><\/strong>37, 1199-1204 (2015).<\/li>\n\n\n\n<li><strong><u>Ma, S.<\/u><\/strong>, Schroeder, B., Sun, C., Loufakis, D. N., Cao, Z. Sriranganathan, N. &amp; Lu, C.<a href=\"https:\/\/pubs.rsc.org\/en\/Content\/ArticleLanding\/2014\/IB\/c4ib00172a#!divAbstract\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/pubs.rsc.org\/en\/Content\/ArticleLanding\/2014\/IB\/c4ib00172a#!divAbstract\"> Electroporation-based delivery of cell-penetrating peptide conjugates of peptide nucleic acids for antisense inhibition of intracellular bacteria.&nbsp;<\/a><strong><em>Integrative Biology<\/em><\/strong><em>,&nbsp;<\/em>2014, 973-978 (2014).<\/li>\n\n\n\n<li><strong><u>Ma, S.<\/u><\/strong>, Tang, Y., Liu, J. &amp; Wu, J. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0039914013009892\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0039914013009892\">Visible paper chip immunoassay for rapid determination of bacteria in water distribution system.<\/a>&nbsp;<strong><em>Talanta<\/em><\/strong>,&nbsp;120, 135-140 (2014).&nbsp;<\/li>\n\n\n\n<li><strong><u>Ma, S.<\/u><\/strong>, Loufakis, D. N., Cao Z., Chang Y., Achenie, L. EK &amp; Lu C. <a href=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2014\/LC\/C4LC00498A#!divAbstract\" target=\"_blank\" rel=\"noreferrer noopener\">Diffusion-based microfluidic PCR for \u201cone-pot\u201d analysis of cells.&nbsp;<\/a><strong><em>Lab on a Chip<\/em><\/strong>,&nbsp;14, 2905-2909 (2014).\n<ul class=\"wp-block-list\">\n<li>Selected as hot article<\/li>\n\n\n\n<li>&nbsp;Selected as cover<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Loufakis, D.N., Cao, Z.,&nbsp;<strong><u>Ma, S.<\/u>,<\/strong>&nbsp;Mittelman, D. &amp; Lu, C. <a href=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2014\/SC\/C4SC00319E#!divAbstract\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2014\/SC\/C4SC00319E#!divAbstract\">Focusing of mammalian cells under an ultrahigh pH gradient created by unidirectional electropulsation in a confined microchamber.&nbsp;<\/a><strong><em>Chemical Science<\/em><\/strong>,&nbsp;5, 3331-3337 (2014).<\/li>\n\n\n\n<li>Sun, C., Ouyang M., Cao, Z.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Alqublan, H., Sriranganathan, N., Wang, Y. &amp; Lu, C. <a href=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2014\/cc\/c4cc04730c#!divAbstract\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2014\/cc\/c4cc04730c#!divAbstract\">Electroporation-delivered fluorescent protein biosensors for probing molecular activities in cells without genetic encoding.<\/a>&nbsp;<strong><em>Chemical Communications<\/em><\/strong>,&nbsp;50, 11536-11539 (2014).&nbsp;<\/li>\n\n\n\n<li>Tan, J., Zhao W., Yu J.,&nbsp;<strong><u>Ma, S.<\/u><\/strong>, Sailor, M. J. &amp; Wu, J. <a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/adhm.201200161\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/adhm.201200161\">Capture, enrichment, and mass spectrometric detection of low\u2010molecular\u2010weight biomarkers with nanoporous silicon microparticles.<\/a>&nbsp;<strong><em>Advanced Healthcare Materials<\/em><\/strong>,&nbsp;1, 742-750 (2012).<\/li>\n\n\n\n<li>Liu, Z., Wu, Q., Song, X. &amp;&nbsp;<strong><u>Ma, S.<\/u><\/strong>&nbsp;<a href=\"https:\/\/tow.cnki.net\/kcms\/detail\/detail.aspx?filename=HXJZ200905024&amp;dbcode=CRJT_CJFD&amp;dbname=CJFD2009&amp;v=\" target=\"_blank\" rel=\"noreferrer noopener\" title=\"https:\/\/tow.cnki.net\/kcms\/detail\/detail.aspx?filename=HXJZ200905024&amp;dbcode=CRJT_CJFD&amp;dbname=CJFD2009&amp;v=\">Solid high-proton conductors based on heteropoly acids.<\/a>&nbsp;<strong><em>Progress in Chemistry<\/em><\/strong>,&nbsp;21, 982-989 (2009).<\/li>\n<\/ol>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>[Google Scholar] Selected Publications Patents bioRxiv Additional Publications<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"template-full-width-page.php","meta":{"_eb_attr":"","om_disable_all_campaigns":false,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"class_list":["post-4","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/saimalab.com\/index.php\/wp-json\/wp\/v2\/pages\/4","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/saimalab.com\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/saimalab.com\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/saimalab.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/saimalab.com\/index.php\/wp-json\/wp\/v2\/comments?post=4"}],"version-history":[{"count":137,"href":"https:\/\/saimalab.com\/index.php\/wp-json\/wp\/v2\/pages\/4\/revisions"}],"predecessor-version":[{"id":1805,"href":"https:\/\/saimalab.com\/index.php\/wp-json\/wp\/v2\/pages\/4\/revisions\/1805"}],"wp:attachment":[{"href":"https:\/\/saimalab.com\/index.php\/wp-json\/wp\/v2\/media?parent=4"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}