Publications

Here is a list of some representative publications. The full list can be found on Google Scholar. #: corresponding author; *: equal contribution. Lab members are highlighted in bold.

  1. XD Chen*, Z Chen*, G Wythes, Y Zhang, BC Orr, G Sun, Y Chao, AN Torres, K Thao, M Vallurupalli, J Sun, M Borji, E Tkacik, H Chen, BE Berstein#, F Chen#. "Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes." Science; October 2024; PMID: 39388570; [pdf]

  2. S Rajachandran*, Q Xu*, Q Cao, X Zhang, F Chen, SM Magiameli, H Chen#. "Subcellular Level Spatial Transcriptomics with PHOTON." bioRxiv; September 2024; PMID: NA; [pdf]

  3. M Evans*, S Rajachandran*, X Zhang*, Y Zhang, K Saner, L Xu, KE Orwig, O Bukulmez, H Chen#. "Functional and Clinical Implications of Extrachromosomal Circular DNA in the Human Germline." bioRxiv; June 2024; PMID: NA; [pdf]

  4. S Rajachandran*, X Zhang*, Q Cao*, AL Caldeira-Brant, X Zhang, Y Song, M Evans, O Bukulmez, EJ Grow, M Nagano, KE Orwig, H Chen#. "Dissecting the Spermatogonial Stem Cell Niche Using Spatial Transcriptomics." Cell Reports; July 2023; PMID: 37393620; [pdf]

  5. X Zhang*, Q Cao*, S Rajachandran, E Grow, M Evans, H Chen#. "Dissecting mammalian reproduction with spatial transcriptomics." Human Reproduction Update; June 2023; PMID: 37353907; [pdf]

  6. SM Mangiameli, H Chen, AS Earl, JA Dobkin, D Lesman, JD Bruenrostro#, F Chen#. "Photoselective sequencing_microscopically guided genomic measurements with subcellular resolution." Nature Methods; Apr 2023; PMID: 37106232; [pdf]

  7. D Cable, E Murray, V Shanmugam, S Zhang, M Diao, H Chen, E Macosko, R Irizarry#, F Chen#. "Cell type-specific differential expression in spatial transcriptomics." Nature Methods; Sep 2022; PMID: 36050488; [pdf]

  8. RS Molina, G Rix, AA Mengiste, A Beatirz, S Daeje, HE Juan, H Chen, et al.. "In vivo hypermutation and continuous evolution." Nature Reviews Methods Primers; May 2022; PMID: 37106232; [pdf]

  9. JL Marshall*#, T Noel*, QS Wang*, H Chen*, E Murray, A Subramanian, KA Vernon, K Liguori, K Keller, RR Stickels, B McBean, RM Heneghan, A Weins, EZ Macosko, F Chen, A Greka#. "High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways." iScience; Mar 2022; PMID: 35372810; [pdf]

  10. AR Clark, J Marshall, Y Zhou, MS Montesinos, H Chen, L Nguyen, F Chen, A Greka#. "Single cell transcriptomics reveal disrupted kidney filter cell-cell interactions after early and selective podocyte injury." The American Journal of Pathology; Feb 2022; PMID: 34861215; [pdf]

  11. H Chen#, E Murray, A Sinha, A Laumas, J Li, X Nie, J Hotaling, J Guo, BR Cairns, EZ Macosko, CY Cheng, F Chen#. "Dissecting mammalian spermatogenesis using spatial transcriptomics." Cell Reports; Nov 2021; PMID: 34731600; [pdf]

  12. H Chen, S Liu, S Padula, D Lesman, K Griswold, A Lin, T Zhao, JL Marshall, F Chen#. "Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor." Nature Biotechnology; Feb 2020; PMID: 31844291; [pdf]

  13. H Chen, DD Mruk, W Lui, CKC Wong, WM Lee, CY Cheng#. "Cell polarity and planar cell polarity (PCP) in spermatogenesis." Seminars in Cell & Developmental Biology; Sep 2018; PMID: 28923514; [pdf]

  14. CL Robinson, ACN Chong, AW Ashbrook, G Jeng, J Jin, H Chen, et al. "Male germ cells support long-term propagation of Zika virus." Nature Communications; May 2018; PMID: 29844387; [pdf]

  15. H Chen, X Xiao, W Lui, WM Lee, CY Cheng#. "Vangl2 regulates spermatid planar cell polarity through microtubule (MT)-based cytoskeleton in the rat testis." Cell Death & Disease; Mar 2018; PMID: 29497043; [pdf]

  16. H Chen, DD Mruk, WM Lee, Y Cheng#. "Regulation of spermatogenesis by a local functional axis in the testis - role of the basement membrane–derived noncollagenous 1 domain peptide." The FASEB Journal; Aug 2017; PMID: 28487282; [pdf]

  17. H Chen, DD Mruk, WM Lee, CY Cheng#. "Planar cell polarity (PCP) protein Vangl2 regulates ectoplasmic specialization dynamics via its effects on actin microfilaments in the testes of male rats." Endocrinology; May 2016; PMID: 26990065; [pdf]