Selected Publications:

  1. Fang R*, Halpern AR*, Rahman MM, Huang Z, Lei Z, Hell SJ, Dulac C, Zhuang X. Three-dimensional single-cell transcriptome imaging of thick tissues. eLife 10.7554/eLife.90029.1 (2023).

  2. Fang R*, Xia C*, Close JL, Zhang M, He J, Huang Z, Halpern AR, Long B, Miller JA, Lein ES, Zhuang X. Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science. 2022 Jul;377(6601):56-62.

  3. Fang R, Preissl S, Li Y, Hou X, Lucero J, Wang X, Motamedi A, Shiau AK, Zhou X, Xie F, Mukamel EA, Zhang K, Zhang Y, Behrens MM, Ecker JR, Ren B. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nat Commun. 2021 Feb 26;12(1):1337.  

  4. Preissl S*, Fang R*, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat Neurosci. 2018 Mar;21(3):432-439.

  5. Diao Y*, Fang R*, Li B*, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan KL, Ren B. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat Methods. 2017 Jun;14(6):629-635.

  6. Fang R*, Yu M*, Li G, Chee S, Liu T, Schmitt AD, Ren B. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 2016 Dec;26(12):1345-1348.

  7. Fang R*, Wang C*, Skogerbo G, Zhang Z. Functional diversity of CTCFs is encoded in their binding motifs. BMC Genomics. 2015 Aug 28;16(1):649.

    Other Publications:

  8. Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol. 2023 Jun 30;21(6):e3002133.

  9. Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, Li YE, Fang R, Baback T, Mugford J, Han CZ, Glass CK, Barr CL, Mischel PS, Bafna V, Escoubet L, Ren B, Chen CC. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. PNAS. 2023 May 16;120(20):e2210991120.

  10. Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, Zhou J, Niu SY, Castanon R, Bartlett A, Rivkin A, Wang X, Lucero J, Nery JR, Davis DA, Mash DC, Satija R, Dixon JR, Linnarsson S, Lein E, Behrens MM, Ren B, Mukamel EA, Ecker JR. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genom. 2022 Mar 9;2(3):100107.

  11. Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 2021 Oct;598(7879):103-110.

  12. Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, Han JY, Lucero J, Yan Y, Miller M, Kuan S, Gorkin D, Gaulton KJ, Shen Y, Nunn M, Mukamel EA, Behrens MM, Ecker JR, Ren B. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 2021 Oct;598(7879):129-136.

  13. Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 2021 Oct;598(7879):111-119.

  14. Yu M, Abnousi A, Zhang Y, Li G, Lee L, Chen Z, Fang R, Lagler TM, Yang Y, Wen J, Sun Q, Li Y, Ren B, Hu M. SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. Nat Methods. 2021 Sep;18(9):1056-1059.

  15. Chiou J, Zeng C, Cheng Z, Han JY, Schlichting M, Miller M, Mendez R, Huang S, Wang J, Sui Y, Deogaygay A, Okino ML, Qiu Y, Sun Y, Kudtarkar P, Fang R, Preissl S, Sander M, Gorkin DU, Gaulton KJ. Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk. Nat Genet. 2021 Apr;53(4):455-466.

  16. Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ, Sun Y, Ellisman MH, Ren B, Campbell PJ, Cleveland DW. Chromothripsis drives the evolution of gene amplification in cancer. Nature. 2021 Mar;591(7848):137-141.

  17. He Y, Hariharan M, Gorkin DU, Dickel DE, Luo C, Castanon RG, Nery JR, Lee AY, Zhao Y, Huang H, Williams BA, Trout D, Amrhein H, Fang R, Chen H, Li B, Visel A, Pennacchio LA, Ren B, Ecker JR. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature. 2020 Jul;583(7818):752-759.

  18. Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B. Joint profiling of DNA methylation and chromatin architecture in single cells. Nat Methods. 2019 Oct;16(10):991-993.

  19. Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS Comput Biol. 2019 Apr 15;15(4):e1006982.

  20. Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B. Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat Genet. 2019 Sep;51(9):1380-1388.

  21. Jiang Q, Isquith J, Zipeto MA, Diep RH, Pham J, Delos Santos N, Reynoso E, Chau J, Leu H, Lazzari E, Melese E, Ma W, Fang R, Minden M, Morris S, Ren B, Pineda G, Holm F, Jamieson C. Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation. Cancer Cell. 2019 Jan 14;35(1):81-94.e7.

  22. Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell. 2018 Jun 14;173(7):1796-1809.e17.

    Preprints:

  23. Yu M, Zemke NR, Chen Z, Juric I, Hu R, Raviram R, Abnousi A, Fang R, Zhang Y, Gorkin DU, Li Y, Zhao Y, Lee L, Schmitt AD, Qiu Y, Dickel DE, Visel A, Pennacchio LA, Hu M, Ren B. bioRxiv 2022.04.25.489471 (2022).