Haiqi Chen, Ph.D. Titles and Appointments Assistant Professor School Medical School Department Cecil H. and Ida Green Center for Reproductive Biology Sciences | Obstetrics and Gynecology Graduate Programs Genetics, Development and Disease Biography Haiqi Chen is an Assistant Professor at the Cecil H. and Ida Green Center for Reproductive Biology Sciences and the Department of Obstetrics and Gynecology. He received a Ph.D. in Molecular Endocrinology through a joint program between the University of Hong Kong and the Population Council at the Rockefeller University in 2017. In 2018, he began his postdoctoral training at the Broad Institute of MIT and Harvard, and later on started his own lab at the UT Southwestern Medical Center in late 2021. Haiqi is a recipient of the Lalor Foundation Fellowship in Reproductive Health and the 2024 Rising Star Award in Reproductive Biology from the Society for the Study of Reproduction. The Chen Lab studies gene regulation using the mammalian male reproductive organ as a model system.Towards this goal, two directions of the lab are: (1) developing next-generation spatial and functional genomics technologies broadly applicable to studying gene regulation/function in various biological systems in situ by combining techniques such as gene editing, high-resolution single-molecule imaging, and next-generation sequencing; (2) applying these cutting-edge technologies, along with machine learning and other data science approaches to study chromatin remodeling and tissue microenvironment, and how they impact gene regulation in the context of mammalian reproduction. Visit the Chen Lab Website. Research Interest Development of spatial and functional genomics technologies Mammalian spermatogenesis and male fertility Transgenerational inheritance of genetic and epigenetic information Publications Featured Publications Subcellular level spatial transcriptomics with PHOTON Rajachandran S, Xu Q, Cao Q, Zhang X, Chen F, Mangiameli SM, Chen H Nat Commun 2025 16 4457 Dissecting the spermatogonial stem cell niche using spatial transcriptomics. Rajachandran S, Zhang X, Cao Q, Caldeira-Brant AL, Zhang X, Song Y, Evans M, Bukulmez O, Grow EJ, Nagano M, Orwig KE, Chen H, Cell Rep 2023 Jul 42 7 112737 Dissecting mammalian reproduction with spatial transcriptomics. Zhang X, Cao Q, Rajachandran S, Grow EJ, Evans M, Chen H, Hum Reprod Update 2023 Jun Dissecting mammalian spermatogenesis using spatial transcriptomics. Chen H, Murray E, Sinha A, Laumas A, Li J, Lesman D, Nie X, Hotaling J, Guo J, Cairns BR, Macosko EZ, Cheng CY, Chen F, Cell Rep 2021 Nov 37 5 109915 Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. Chen H, Liu S, Padula S, Lesman D, Griswold K, Lin A, Zhao T, Marshall JL, Chen F, Nat Biotechnol 2020 02 38 2 165-168 Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes. Chen XD, Chen Z, Wythes G, Zhang Y, Orr BC, Sun G, Chao YK, Navarro Torres A, Thao K, Vallurupalli M, Sun J, Borji M, Tkacik E, Chen H, Bernstein BE, Chen F, Science 2024 Oct 386 6718 eadn5876 Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Mangiameli SM, Chen H, Earl AS, Dobkin JA, Lesman D, Buenrostro JD, Chen F, Nat Methods 2023 May 20 5 686-694 Cell type-specific inference of differential expression in spatial transcriptomics. Cable DM, Murray E, Shanmugam V, Zhang S, Zou LS, Diao M, Chen H, Macosko EZ, Irizarry RA, Chen F, Nat Methods 2022 Sep 19 9 1076-1087 High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways. Marshall JL, Noel T, Wang QS, Chen H, Murray E, Subramanian A, Vernon KA, Bazua-Valenti S, Liguori K, Keller K, Stickels RR, McBean B, Heneghan RM, Weins A, Macosko EZ, Chen F, Greka A, iScience 2022 Apr 25 4 104097 In vivo hypermutation and continuous evolution. Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC, Nat Rev Methods Primers 2022 2 Results 1-10 of 32 1 2 3 4 Next Last Honors & Awards The Society for the Study of Reproduction Rising Star Award (2023) The Society for the Study of Reproduction Early/Mid-career Researcher Travel Award (2020) Lalor Foundation Postdoctoral Fellowship Award (2019) Male Contraceptive Initiative Travel Award (2019) Professional Associations/Affiliations Society for the Study of Reproduction (2019)
