By Associate Professor Emily Sau Wai Wong

Preprints

Petrova V; Niu M; Vierbuchen T; Wong ES, 2025, ASPEN: Robust detection of allelic dynamics in single cell RNA-seq., http://dx.doi.org/10.1101/2025.04.16.649227

Zhuang X; Wang Q; Joost S; Ferrena A; Humphreys DT; Li Z; Blum M; Bastl K; Ding S; Landais Y; Zhan Y; Zhao Y; Chaligne R; Lee J-H; Carrasco SE; Bhanot UK; Koche RP; Bott MJ; Katajisto P; Soto-Feliciano YM; Pisanic T; Thomas T; Zheng D; Wong ES; Tammela T, 2024, Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis., http://dx.doi.org/10.1101/2024.06.23.600305

DaSilva LF; Senan S; Patel ZM; Janardhan Reddy A; Gabbita S; Nussbaum Z; Valdez Córdova CM; Wenteler A; Weber N; Tunjic TM; Ahmad Khan T; Li Z; Smith C; Bejan M; Karmel Louis L; Cornejo P; Connell W; Wong ES; Meuleman W; Pinello L, 2024, DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements., http://dx.doi.org/10.1101/2024.02.01.578352

Cornejo-Páramo P; Zhang X; Louis L; Yang Y-H; Li Z; Humphreys D; Wong E, 2024, A Bag-Of-Motif Model Captures Cell States at Distal Regulatory Sequences, http://dx.doi.org/10.1101/2024.01.03.574012

Medina-Cano D; Islam M; Petrova V; Dixit S; Balic Z; Yang M; Stadtfeld M; Wong E; Vierbuchen T, 2024, A MOUSE ORGANOID PLATFORM FOR MODELING CEREBRAL CORTEX DEVELOPMENT AND CIS-REGULATORY EVOLUTION IN VITRO, http://dx.doi.org/10.1101/2024.09.30.615887

Subramanian S; Subramanian S; Thoms JAI; Huang Y; Cornejo P; Koch F; Jacquelin S; Shen S; Song E; Joshi S; Brownlee C; Woll P; Fajardo DC; Beck D; Curtis D; Yehson K; Antonenas V; Brien TO; Trickett A; Powell J; Lewis I; Pitson S; Gandhi M; Lane S; Vafaee F; Wong E; Göttgens B; Rokny HA; Wong JWH; Pimanda J, 2023, Cell Type-Specific Regulation by a Heptad of Transcription Factors in Human Hematopoietic Stem and Progenitor Cells, http://dx.doi.org/10.1101/2023.04.18.537282

Cornejo-Páramo P; Petrova V; Zhang X; Young R; Wong E, 2022, Emergence of new enhancers at late DNA replicating regions, http://dx.doi.org/10.1101/2022.12.22.521323

Marjaneh MM; Kirk E; Patrick R; Alankerage D; Humphreys D; Del Monte-Nieto G; Cornejo-Paramo P; Janbandhu V; Doan T; Dunwoodie S; Wong E; Moran C; Martin ICA; Thomson P; Harvey R, 2022, Quantitative trait and transcriptome analysis of genetic complexity underpinning cardiac interatrial septation in mice using an advanced intercross line, http://dx.doi.org/10.1101/2022.10.31.514499

Cornejo-Páramo P; Roper K; Degnan S; Degnan B; Wong E, 2021, Distal regulation, silencers and a shared combinatorial syntax are hallmarks of animal embryogenesis, http://dx.doi.org/10.1101/2021.09.08.459542

Achinger-Kawecka J; Stirzaker C; Portman N; Campbell E; Chia K-M; Du Q; Laven-Law G; Nair S; Yong A; Wilkinson A; Clifton S; Milioli H; Alexandrou S; Caldon E; Song J; Khoury A; Meyer B; Gee JMW; Schmitt A; Wong E; Hickey T; Lim E; Clark S, 2021, Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer, http://dx.doi.org/10.1101/2021.06.21.449340

Floc’hlay S; Wong E; Zhao B; Viales R; Thomas-Chollier M; Thieffry D; Garfield D; Furlong EEM, 2020, Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs, http://dx.doi.org/10.1101/2020.05.21.107961

Wong E; Tan SZ; Garside V; Vanwalleghem G; Gaiti F; Scott E; McGlinn E; Francois M; Degnan B, 2019, Early origin and deep conservation of enhancers in animals, http://dx.doi.org/10.1101/633651

Friedman C; Nguyen Q; Lukowski S; Chiu HS; Helfer A; Miklas J; Suo SS; Jackie Han J-D; Osteil P; Peng G; Jing N; Baillie G; Senabouth A; Christ A; Bruxner T; Murry C; Wong E; Ding J; Wang Y; Hudson J; Ruohola-Baker H; Bar-Joseph Z; Tam P; Powell J; Palpant N, 2017, Analysis of cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription, http://dx.doi.org/10.1101/229294

Wong E; Chenoweth S; Blows M; Powell J, 2017, Evidence for stabilizing selection at pleiotropic loci for human complex traits, http://dx.doi.org/10.1101/126888

Friedman CE; Nguyen Q; Lukowski SW; Helfer A; Chiu HS; Voges HK; Suo Suo S; Jackie Han J-D; Osteil P; Peng G; Jing N; Baillie GJ; Senabouth A; Christ AN; Bruxner TJ; Murry CE; Wong ES; Ding J; Wang Y; Hudson J; Bar-Joseph Z; Tam PPL; Powell JE; Palpant NJ, Cardiac Directed Differentiation Using Small Molecule WNT Modulation at Single-Cell Resolution, http://dx.doi.org/10.2139/ssrn.3155757

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