By Associate Professor Christine Louise Chaffer

Preprints

Venkat A; Youlten SE; Juan BPS; Purcell C; Amodio M; Burkhardt DB; Benz A; Holst J; McCool C; Mollbrink A; Lundeberg J; van Dijk D; Goldstein LD; Kummerfeld S; Krishnaswamy S; Chaffer CL, 2024, AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity, http://dx.doi.org/10.1101/2024.05.11.593705

Krishnaswamy S; Tong A; Kuchroo M; Gupta S; Venkat A; Juan BS; Rangel L; Zhu B; Lock J; Chaffer C, 2023, Revealing dynamic temporal regulatory networks driving cancer cell state plasticity with neural ODE-based optimal transport, http://dx.doi.org/10.21203/rs.3.rs-3605296/v1

Sahoo S; Ramu S; Nair MG; Pillai M; San Juan BP; Milioli HZ; Mandal S; Naidu CM; Mavatkar AD; Subramaniam H; Neogi AG; Chaffer CL; Prabhu JS; Somarelli JA; Jolly MK, 2023, Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer., http://dx.doi.org/10.1101/2023.09.30.558960

Mckinnon J; Milioli H; Purcell C; Chaffer C; Wadie B; Alexandrov T; Mitchell T; Ellis S, 2023, Enhancing Metabolite Coverage in MALDI-MSI using Laser Post-Ionisation (MALDI-2)., http://dx.doi.org/10.26434/chemrxiv-2023-sptss

Tong A; Kuchroo M; Gupta S; Venkat A; San Juan B; Rangel L; Zhu B; Lock J; Chaffer C; Krishnaswamy S, 2023, Learning transcriptional and regulatory dynamics driving cancer cell plasticity using neural ODE-based optimal transport, http://dx.doi.org/10.1101/2023.03.28.534644

Amodio M; Youlten SE; Venkat A; San Juan BP; Chaffer C; Krishnaswamy S, 2022, Single-Cell Multi-Modal GAN (scMMGAN) reveals spatial patterns in single-cell data from triple negative breast cancer, http://dx.doi.org/10.1101/2022.07.04.498732

San Juan B; Hediyeh-Zadeh S; Rangel L; Milioli H; Rodriguez V; Bunkum A; Kohane F; Purcell C; Bhuva D; Kurumlian A; Castillo L; Lim E; Gill A; Ganju V; Dear R; O’Toole S; Vargas C; Hickey T; Goldstein L; Lock J; Davis M; Chaffer C, 2022, Targeting phenotypic plasticity prevents metastasis and the development of chemotherapy-resistant disease, http://dx.doi.org/10.1101/2022.03.21.22269988

Van Dijk D; Sharma R; Nainys J; Yim K; Kathail P; Carr A; Burdziak C; Moon KR; Chaffer CL; Pattabiraman D; Bierie B; Mazutis L; Wolf G; Krishnaswamy S; Peeer D, Recovering Gene Interactions from Single-Cell Data Using Data Diffusion, http://dx.doi.org/10.2139/ssrn.3155779

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