1. Cui X*, Yang H*, Cai C, Beaman C, Yang X, Liu H, Ren X, Amador Z, Jones IR, Keough KC, Zhang M, Fair T, Abnousi A, Mishra S, Ye Z, Hu M, Pollen AA, Pollard KS, Shen Y. Comparative characterization of human accelerated regions in neurons. Nature. 2025 Feb 26. doi: 10.1038/s41586-025-08622-x. Epub ahead of print. PMID: 40011774. (*These authors contributed equally.)

  2. Ren X, Zheng L, Maliskova L, Tam TW, Sun Y, Liu H, Lee J, Takagi MA, Li B, Ren B, Wang W, Shen Y. CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription. bioRxiv [Preprint]. 2024 Oct 10:2024.10.08.616922. doi: 10.1101/2024.10.08.616922. PMID: 39416108; PMCID: PMC11483005.

  3. Bonev B, Gonçalo CB, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O#, Konopka G#, Liddelow S#, Macosko E#, Bayraktar O#, Habib N#, Nowakowski TJ#. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nat Neurosci. 2024 Dec;27(12):2292-2309. doi: 10.1038/s41593-024-01806-0. Epub 2024 Dec 3. PMID: 39627587. (# Co-corresponding authors.)

  4. Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP. The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. eLife. 2024 Dec 5:2024.12.05.97577. doi: 10.7554/eLife.97577.2.sa4

  5. Catta-Preta R*, Lindtner S*, Ypsilanti A, Seban N, Price JD, Abnousi A, Su-Feher L, Wang Y, Cichewicz K, Boerma SA, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel DE, Rubenstein JLR#, Nord AS#. Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis. Developmental Cell. 2024 Oct 30. doi.org/10.1016/j.devcel.2024.10.004. (*These authors contributed equally. # Co-corresponding authors.)

  6. Feng Y, Yang X, Hou Y, Zhou Y, Leverenz JB, Eng C, Pieper AA, Goate A, Shen Y, Cheng F. Widespread transposable element dysregulation in human aging brains with Alzheimer's disease. Alzheimers Dement. 2024 Oct 2. doi: 10.1002/alz.14164. Epub ahead of print. PMID: 39356058.

  7. Pardo-Palacios FJ*, Wang D*, Reese F*, Diekhans M*, Carbonell-Sala S*, Williams B*, Loveland JE*, De María M*, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C#, Frankish A#, Au KF#, Sheynkman GM#, Mortazavi A#, Conesa A#, Brooks AN#. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nat Methods. 2024 Jul;21(7):1349-1363. doi: 10.1038/s41592-024-02298-3. Epub 2024 Jun 7. PMID: 38849569. (*These authors contributed equally. # Co-corresponding authors.)

  8. Yang J*, Chung C-I*, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X. MYC phase separation selectively modulates the transcriptome. Nature Structural & Molecular Biology. 2024 May 29; (*These authors contributed equally.)

  9. Liang XG, Hoang K, Meyerink BL, Kc P, Paraiso K, Wang L, Jones IR, Zhang Y, Katzman S, Finn TS, Tsyporin J, Qu F, Chen Z, Visel A, Kriegstein A, Shen Y, Pilaz LJ, Chen B. A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex. Proc Natl Acad Sci U S A. 2024 May 14;121(20):e2321711121. doi: 10.1073/pnas.2321711121. Epub 2024 May 7. PMID: 38713624.

  10. Yao D*, Tycko J*,#, Oh JW*, Bounds LR*, Gosai SJ*, Lataniotis L*, Mackay-Smith A, Doughty BR, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White AD, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardımcı GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JE, Bassik MC, Reilly SK#. Multicenter integrated analysis of noncoding CRISPRi screens. Nature Methods. 2024 Mar 19. doi: 10.1038/s41592-024-02216-7. (*These authors contributed equally. # Co-corresponding authors.)

  11. Chung C-I, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X. Phase separation of YAP-MAML2 differentially regulates the transcriptome. PNAS. 2024 Feb 13;121(7):e2310430121. doi: 10.1073/pnas.2310430121. Epub 2024 Feb 5. PMID: 38315854.

  12. Ren X*, Yang H*, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y. High throughput PRIME editing screens identify functional DNA variants in the human genome. Molecular Cell. 2023 Dec 21;83(24):4633-4645.e9. doi: 10.1016/j.molcel.2023.11.021. PMID: 38134886; PMCID: PMC10766087. (*These authors contributed equally.)

    		 On the cover: In this issue of Molecular Cell, Ren et al. develop PRIME, a prime-editing-mediated high-throughput genetic screen method for single-base resolution analysis of genomic sequences. Using PRIME, the authors identify essential nucleotides for enhancer activity and disease-associated functional genetic variants. The plum blossoms in a snowy winter indicate the positive hits (functional variants) identified by PRIME, while bare trees indicate genomic regions without any sequences that are considered as positive hits. The multiple plum blossoms in different positions align with PRIME's ability to simultaneously identify functional sequences across the genome.

  13. Yang X*, Jones IR*, Chen PB*, Yang H*, Ren X*, Zheng L, Li B, Li YE, Sun Q, Wen J, Beaman C, Cui X, Li Y, Wang W, Hu M, Ren B#, Shen Y#. Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons. bioRxiv. 2023 Aug 30. doi: 10.1101/2023.08.30.555359. (*These authors contributed equally. # Co-corresponding authors.)

  14. Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, Li B, Clelland CD, Luo W, Wong MY, Ren X, Cui X, Song M, Liu H, Chen C, Eng N, Ravichandran M, Sun Y, Lee D, Van Buren E, Jiang MZ, Chan CSY, Ye CJ, Perera RM, Gan L, Li Y#, Shen Y#. Functional characterization of Alzheimer’s disease genetic variants in microglia. Nature Genetics. 2023 Oct;55(10):1735-1744. doi: 10.1038/s41588-023-01506-8. Epub 2023 Sep 21. PMID: 37735198. (# Co-corresponding authors.)

  15. Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. 2023 Aug 3;83(15):2624-2640. doi: 10.1016/j.molcel.2023.06.018. Epub 2023 Jul 6. PMID: 37419111.

  16. Ren X, Takagi MA, Shen Y. Efficient bi-allelic tagging in human induced pluripotent stem cells using CRISPR. STAR Protoc. 2023 Feb 1;4(1):102084. doi: 10.1016/j.xpro.2023.102084. Epub ahead of print. PMID: 36853689; PMCID: PMC9918420.

  17. Sun W*, Wang N*, Liu H, Yu B, Jin L, Ren X, Shen Y, Wang L. Genetically encoded chemical crosslinking of RNA in vivo. Nat Chem. 2023 Jan;15(1):21-32. doi: 10.1038/s41557-022-01038-4. Epub 2022 Oct 6. PMID: 36202986; PMCID: PMC9840682. (*These authors contributed equally.)

  18. Wu D, Poddar A, Ninou E, Hwang E, Cole MA, Liu SJ, Horlbeck MA, Chen J, Replogle JM, Carosso GA, Eng NWL, Chang J, Shen Y, Weissman JS, Lim DA. Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. Cell Genom. 2022 Nov 9;2(11):100177. doi: 10.1016/j.xgen.2022.100177. Epub 2022 Sep 14. PMID: 36381608; PMCID: PMC9648144.

  19. Jones IR, Ren X, Shen Y. High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. Human Molecular Genetics. 2022, Aug 16; 31(1):47-53. doi: 10.1093/hmg/ddac193 PMID: 35972825 PMCID: PMC9585669 

  20. Ravichandran M, Hu J, Cai C, Ward NP, Venida A, Foakes C, Kuljanin M, Yang A, Hennessey CJ, Yang Y, Desousa BR, Rademaker G, Staes AAL, Cakir Z, Jain IH, Aguirre AJ, Mancias JD, Shen Y, DeNicola GM, Perera RM. Coordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer. Cancer Discov. 2022, Jun 30. 12(9):2198-2219 doi: 10.1158/2159-8290.CD-22-0044 PMID: 35771494.

  21. Yang H, Ting X, Geng YH, Xie Y, Nierenberg JL, Huo YF, Zhou YT, Huang Y, Yu YQ, Yu XY, Li ZF, Ziv E, Zhang H,Fang WG, Shen Y, Tian XX. The risk variant rs11836367 contributes to breast cancer onset and metastasis by attenuating Wnt signaling via regulating NTN4 expression. Sci Adv 2022, June 10. 8(23):eabn3509. doi: 10.1126/sciadv.abn3509 PMID: 35687692 PMCID: PMC9187238

  22. Rowland B, Huh R, Hou Z, Crowley C, Wen J, Shen Y, Hu M, Giusti-Rodríguez P, Sullivan PF, Li Y. THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. PLoS Genet. 2022 Mar 8;18(3):e1010102. doi: 10.1371/journal.pgen.1010102. PMID: 35259165; PMCID: PMC8932604.

  23. Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL. Transcriptional network orchestrating regional patterning of cortical progenitors. PNAS, 2021 Dec 21;118(51):e2024795118. doi: 10.1073/pnas.2024795118. PMID: 34921112 PMCID: PMC8713794

  24. 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. doi: 10.1038/s41586-021-03604-1. Epub 2021 Oct 6. PMID: 34616068 PMCID: PMC8494637 (*These authors contributed equally.)

  25. Ren X, Wang M, Li B, Jamieson K, Zheng L, Jones IR, Li B, Takagi MA, Lee J, Maliskova L, Tam TW, Yu M, Hu R, Lee L, Abnousi A, Li G, Li Y, Hu M, Ren B, Wang W, Shen Y. Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Sci Adv, 2021 Sep 17;7(38):eabi4360. doi: 10.1126/sciadv.abi4360. Epub 2021 Sep 15. PMID: 34524848 PMCID: PMC8443183 

  26. Yang Y*, Li G*, Qian H, Wilhelmsen KC, Shen Y, Li Y. SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection. Brief Bioinform. 2021 May 20;22(3):bbaa097. doi: 10.1093/bib/bbaa097. PMID: 32591778; PMCID: PMC8324985. (*These authors contributed equally.)

  27. Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA; University of Washington Center for Mendelian Genomics, Shen Y, Lettice LA, Silveira-Lucas EL, Petit F, Ahituv N. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nat Commun, 2021 Apr 16;12(1):2282. doi: 10.1038/s41467-021-22470-z. PMID: 33863876 PMCID: PMC805232 

  28. Wang X*, Jiang W*, Luo S, Yang X, Wang C, Wang B, Dang Y, Shen Y, Ma DK. The C. elegans homolog of human panic-disorder risk gene TMEM132D orchestrates neuronal morphogenesis through the WAVE-regulatory complex. Mol Brain, 2021 Mar 16;14(1):54. doi: 10.1186/s13041-021-00767-w. PMID: 33726789 PMCID: PMC7962252 (*These authors contributed equally.)

  29. Song M*, Pebworth MP*, Yang X*, Abnousi A, Fan C, Wen J, Rosen JD, Choudhary MNK, Cui X, Jones IR, Bergenholtz S, Eze UC, Juric I, Bingkun L, Maliskova L, Liu W, Pollen AA, Li Y, Wang T, Hu M*,#, Kriegstein AR#, Shen Y#. Cell-type-specific 3D epigenomes in the developing human cortex. Nature, 2020 Nov;587(7835):644-649. doi: 10.1038/s41586-020-2825-4. Epub 2020 Oct 14. PMID: 33057195 PMCID: PMC7704572 (*These authors contributed equally. # Co-corresponding authors.)

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  31. Gorkin D*, Barozzi I*, Zhao Y*, Zhang Y*, Huang H*, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzerv-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 2020 Jul;583(7818):744-751. doi: 10.1038/s41586-020-2093-3. Epub 2020 Jul 29. PMID: 32728240 PMCID: PMC7398618 (*These authors contributed equally.)

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  33. Huh R, Yang Y, Jiang Y, Shen Y, Li Y.  SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble. Nucleic Acids Research, 2020 Jan 10;48(1):86-95. doi: 10.1093/nar/gkz959. PMID: 31777938 PMCID: PMC6943136 

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  35. Alexander J, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD.  Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLIFE, 2019 May 24:8:e41769. doi: 10.7554/eLife.41769. PMID: 31124784 PMCID: PMC6534382

  36. Zhan L, Krabbe G, Du F, Jones I, Reichert MC, Telpoukhovskaia M, Kodama L, Wang C, Cho S, Sayed F, Li Y, Le D, Zhou Y, Shen Y, West B, Gan L. Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain. PLos Biol, 2019 Feb 8;17(2):e3000134. doi: 10.1371/journal.pbio.3000134. eCollection 2019 Feb. PMID: 30735499 PMCID: PMC6383943

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  39. 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 K, Ren B.  A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nature Method, 2017 Jun;14(6):629-635. doi: 10.1038/nmeth.4264. Epub 2017 Apr 17. PMID: 28417999; PMCID: PMC5490986.

  40. He Y, Gorkin D, Dickel D, Nery J, Castanon R, Lee AY, Shen Y, Visel A, Pennacchio L, Ren B, Ecker J.  Improved regulatory element prediction based on tissue-specific local epigenomic signatures. PNAS, 2017 Feb 28;114(9):E1633-E1640. doi: 10.1073/pnas.1618353114. Epub 2017 Feb 13. PMID: 28193886 PMCID: PMC5338528

  41. Diao Y*, Li B, Young I, Lee AY, Meng Z, Maliskova L, Guan K, Shen Y*,#, Ren B#. A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening. Genome Research, 2016 Mar;26(3):397-405. doi: 10.1101/gr.197152.115. Epub 2016 Jan 26. PMID: 26813977; PMCID: PMC4772021. (*These authors contributed equally. # Co-corresponding authors.)

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  45. Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics. 2013 Oct;45(10):1198-206. doi: 10.1038/ng.2746. Epub 2013 Sep 1. PMID: 23995138; PMCID: PMC4095776.

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  48. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.  Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012 Apr 11;485(7398):376-80. doi: 10.1038/nature11082. PMID: 22495300; PMCID: PMC3356448.

  49. Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C. Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012 Jun 8;149(6):1368-80. doi: 10.1016/j.cell.2012.04.027. Epub 2012 May 17. PMID: 22608086; PMCID: PMC3589129.. 

  50. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS#, Reiter JF#.  Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet. 2012;8(3):e1002576. doi: 10.1371/journal.pgen.1002576. Epub 2012 Mar 15. PMID: 22438827; PMCID: PMC3305387. (# Co-corresponding authors.)

  51. Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G. Functional Modules Distinguish Human Induced Pluripotent Stem Cells from Embryonic Stem Cells. Stem Cells Dev. 2011 Nov;20(11):1937-50. doi: 10.1089/scd.2010.0574. Epub 2011 Jun 20. PMID: 21542696; PMCID: PMC3202894.

  52. Shen Y, Fouse SD, and Fan G. Genome-wide DNA methylation profiling: the mDIP- Chip technology. Methods Mol Biol. 2009;568:203-16. doi: 10.1007/978-1-59745-280-9_13. PMID: 19582429.

  53. Shen Y, Matsuno Y, Fouse S, Rao N, Root S, Xu RH, Pellegrini M, Riggs A, and Fan G. X-inactivation in female human embryonic stem cells is in a non-random pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4709-14. doi: 10.1073/pnas.0712018105. Epub 2008 Mar 13. PMID: 18339804; PMCID: PMC2290804.

  54. Fouse S, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, and Fan G. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, Polycomb binding and histone H3 lys4/lys27 trimethylation. Cell Stem Cell. 2008 Feb 7;2(2):160-9. doi: 10.1016/j.stem.2007.12.011. PMID: 18371437; PMCID: PMC3070208.

  55. Shen Y, Chow J, Wang Z, Fan G. Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Human Molecular Genetics. 2006 Sep 1;15(17):2623-35. doi: 10.1093/hmg/ddl188. Epub 2006 Jul 26. PMID: 16870691.

  56. Fan G#, Martinowich K, Chin MH, He F, Fouse SD, Hutnick L, Hattori D, Ge W, Shen Y, Wu H, ten Hoeve J, Shuai K, Sun YE#. DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development. 2005 Aug;132(15):3345-56. doi: 10.1242/dev.01912. PMID: 16014513. (# Co-corresponding authors.)