{"id":14972,"date":"2022-08-25T11:11:01","date_gmt":"2022-08-25T15:11:01","guid":{"rendered":"http:\/\/www.bu.edu\/biology\/?post_type=profile&#038;p=14972"},"modified":"2026-04-15T11:57:30","modified_gmt":"2026-04-15T15:57:30","slug":"brian-cleary","status":"publish","type":"profile","link":"https:\/\/www.bu.edu\/biology\/people\/profiles\/brian-cleary\/","title":{"rendered":"Brian Cleary"},"content":{"rendered":"<p style=\"text-align: center; font-size: 16px;\"><a class=\"button-primary\" href=\"https:\/\/www.bu.edu\/algo-bio-lab\/\" target=\"_blank\" rel=\"noopener noreferrer\">Lab Website<\/a><a class=\"button-primary\" href=\"https:\/\/scholar.google.com\/citations?user=vXKwAL4AAAAJ&amp;hl=en&amp;oi=ao\" target=\"_blank\" rel=\"noopener noreferrer\">Google<\/a><\/p>\n<h3>Current Research<\/h3>\n<p>Our group works at the interface of the limits of algorithmic learning and the limits of biological experimentation in pursuit of the organizing principles of molecular, cellular and tissue processes.<\/p>\n<p><span>The\u00a0<\/span><a data-outlook-id=\"3930db59-75bf-4dd2-8231-87b00c7bfdde\" data-auth=\"NotApplicable\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"https:\/\/www.algobiolab.com\/\" data-linkindex=\"0\" title=\"https:\/\/www.algobiolab.com\/\" data-ogsc=\"\">AlgoBioLab<\/a><span>\u00a0combines theory, computation, and wet-lab experimentation to understand basic principles of biological organization. We study molecular and genetic organization at the level of cells and tissues; how evolution shapes organization in high dimensional, complex living systems; and how biological organization interacts with fundamental principles of statistics to determine the limits of experimentation. Most of our work is motivated by curiosity and a fondness for deep thinking, but we also do a fair amount of computational and experimental method development when it suits us.<\/span><\/p>\n<h3>Selected Publications<\/h3>\n<ul>\n<li>Cleary, B., Simonton, B., Bezney, J., Murray, E., Alam, S., Sinha, A., Habibi, E., Marshall, J., Lander, E.S., Chen, F. and Regev, A., 2021. Compressed sensing for highly efficient imaging transcriptomics. <em>Nature Biotechnology<\/em>, 39(8), pp. <a href=\"https:\/\/www.nature.com\/articles\/s41587-021-00883-x\" target=\"_blank\" rel=\"noopener noreferrer\">936-942<\/a>.<\/li>\n<li>Cleary, B., Cong, L., Cheung, A., Lander, E.S. and Regev, A., 2017. Efficient generation of transcriptomic profiles by random composite measurements. <em>Cell<\/em>, 171(6), pp. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S009286741731245X\" target=\"_blank\" rel=\"noopener noreferrer\">1424-1436<\/a>.<\/li>\n<li>Cleary, B. and Regev, A., 2020. The necessity and power of random, under-sampled experiments in biology. <em>arXiv preprint<\/em> arXiv:<a href=\"https:\/\/arxiv.org\/pdf\/2012.12961.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">2012.12961<\/a>.<\/li>\n<li>Schiebinger, G., Shu, J., Tabaka, M., Cleary, B., Subramanian, V., Solomon, A., Gould, J., Liu, S., Lin, S., Berube, P. and Lee, L., 2019. Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming. <em>Cell<\/em>, 176(4), pp. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/30712874\/\" target=\"_blank\" rel=\"noopener noreferrer\">928-943<\/a>.<\/li>\n<li>Einav, T. and Cleary, B., 2022. Extrapolating missing antibody-virus measurements across serological studies. <em>Cell Systems<\/em>, 13(7), pp. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35798005\/\" target=\"_blank\" rel=\"noopener noreferrer\">561-573<\/a>.<\/li>\n<li>Hong, D., Dey, R., Lin, X., Cleary, B. and Dobriban, E., 2022. Group testing via hypergraph factorization applied to COVID-19. <em>Nature Communications<\/em>, 13(1), pp. <a href=\"https:\/\/www.nature.com\/articles\/s41467-022-29389-z\" target=\"_blank\" rel=\"noopener noreferrer\">1-13<\/a>.<\/li>\n<li>Cleary, B., Hay, J.A., Blumenstiel, B., Harden, M., Cipicchio, M., Bezney, J., Simonton, B., Hong, D., Senghore, M., Sesay, A.K. and Gabriel, S., 2021. Using viral load and epidemic dynamics to optimize pooled testing in resource-constrained settings. <em>Science translational medicine<\/em>, 13(589), p. <a href=\"https:\/\/www.science.org\/doi\/10.1126\/scitranslmed.abf1568\" target=\"_blank\" rel=\"noopener noreferrer\">eabf1568<\/a>.<\/li>\n<li>Cleary, B., Brito, I.L., Huang, K., Gevers, D., Shea, T., Young, S. and Alm, E.J., 2015. Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. <em>Nature biotechnology<\/em>, 33(10), pp. <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4720164\/\" target=\"_blank\" rel=\"noopener noreferrer\">1053-1060<\/a>.<\/li>\n<\/ul>\n","protected":false},"author":10204,"template":"","_links":{"self":[{"href":"https:\/\/www.bu.edu\/biology\/wp-json\/wp\/v2\/profile\/14972"}],"collection":[{"href":"https:\/\/www.bu.edu\/biology\/wp-json\/wp\/v2\/profile"}],"about":[{"href":"https:\/\/www.bu.edu\/biology\/wp-json\/wp\/v2\/types\/profile"}],"author":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/biology\/wp-json\/wp\/v2\/users\/10204"}],"version-history":[{"count":11,"href":"https:\/\/www.bu.edu\/biology\/wp-json\/wp\/v2\/profile\/14972\/revisions"}],"predecessor-version":[{"id":22673,"href":"https:\/\/www.bu.edu\/biology\/wp-json\/wp\/v2\/profile\/14972\/revisions\/22673"}],"wp:attachment":[{"href":"https:\/\/www.bu.edu\/biology\/wp-json\/wp\/v2\/media?parent=14972"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}