By Associate Professor Christine Louise Chaffer

Preprints

Steindl AJ; Rocha JF; Di Bassinga BT; Warren Z; Scicluna M; Córdova CMV; Gupta S; Torices L; Neumann D; Mann TJ; Gunawan I; Bhaskar D; Lock JG; Chaffer CL; Wolf G; Krishnaswamy S, 2026, scShapeBench: Discovering geometry from high dimensional scRNAseq data, http://dx.doi.org/10.48550/arxiv.2605.12662

Sun X; Rocha JF; Phelan B; Bhaskar D; Huguet G; Zhang Y; Tong A; Xu K; Fasina O; Gerstein M; Ivanova N; Chaffer CL; Wolf G; Krishnaswamy S, 2026, MIOFlow 2.0: A unified framework for inferring cellular stochastic dynamics from single cell and spatial transcriptomics data, http://dx.doi.org/10.48550/arxiv.2603.22564

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; Pe’er D, 2018, Recovering Gene Interactions from Single-Cell Data Using Data Diffusion, http://dx.doi.org/10.2139/ssrn.3155779

Venkat A; Youlten SE; San Juan BP; 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, AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity, http://dx.doi.org/10.1101/2024.05.11.593705

Silvani G; Kopecky C; Romanazzo S; Rodriguez V; Das A; Pandzic E; Lock JG; Chaffer C; Poole K; Kilian KA, Capillary constrictions prime cancer cell tumorigenicity through PIEZO1, http://dx.doi.org/10.1101/2025.07.22.666218

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

Kohane FV; Johnstone C; Neumann DP; Gunawan I; Huang T; Vafaee F; Chaffer CL; Lock JG, Epithelial–mesenchymal cell state heterogeneity predetermines differential phospho-signaling responses to EGF stimulation, http://dx.doi.org/10.1101/2025.07.05.658545

King HE; O’Connell S; Kavanagh D; Mason S; McCool C; Fernandez-Chamorro J; Chaffer C; Clark SJ; Vieira HGS; Sterne-Weiler T; Weatheritt RJ, Isoform-specific single-cell perturb-seq reveals distinct functions of alternative promoters in drug response, http://dx.doi.org/10.1101/2025.07.14.664827

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, 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

Krishnaswamy S; Tong A; Kuchroo M; Gupta S; Venkat A; Juan BS; Rangel L; Zhu B; Lock J; Chaffer C, 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

Sun X; Gupta S; Tong A; Kuchroo M; Bhaskar D; Liu C; Venkat A; San Juan BP; Rangel L; Rodriguez V; Lock JG; Chaffer CL; Krishnaswamy S, Revealing dynamic temporal trajectories and underlying regulatory networks with Cflows, http://dx.doi.org/10.1101/2023.03.28.534644

Gration B; Chai RC; Young SG; Sergio CM; Skorokhodova E; Smith JT; Castro-Martinez A; Bray A; Lin X; Yan C; Kao J; Perram J; Lai S; Lau L; Weilbaecher KN; Moore J; Pocock N; Chaffer CL; Center J; Phan TG; McCaughan G; Croucher PI, Romosozumab Safely Restores Bone Mass in Multiple Myeloma via Osteoblast Reprogramming: A Phase IIa Study, http://dx.doi.org/10.64898/2026.07.02.26357196

Amodio M; Youlten SE; Venkat A; San Juan BP; Chaffer C; Krishnaswamy S, 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 BP; Hediyeh-Zadeh S; Rangel L; Milioli HH; Rodriguez V; Bunkum A; Kohane FV; Purcell CA; Bhuva DD; Kurumlian A; Castillo L; Lim E; Gill AJ; Ganju V; Dear R; O’Toole S; Vargas AC; Hickey TE; Goldstein LD; Lock JG; Davis MJ; Chaffer CL, Targeting phenotypic plasticity prevents metastasis and the development of chemotherapy-resistant disease, http://dx.doi.org/10.1101/2022.03.21.22269988

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