Deng R, Cui C, Remedios LW, Bao S, Womick RM, Chiron S, Li J, Roland JT, Lau KS, Liu Q, Wilson KT, Wang Y, Coburn LA, Landman BA, Huo Y. Cross-scale Attention Guided Multi-instance Learning for Crohn’s Disease Diagnosis with Pathological Images. Multiscale Multimodal Medical Imaging, 13594:24-33, 2022.
Cui Zhou D, Jayasinghe RG, Chen S, Herndon JM, Iglesia MD, Navale P, Wendl MC, Caravan W, Sato K, Storrs E, Mo CK, Liu J, Southard-Smith AN, Wu Y, Naser Al Deen N, Baer JM, Fulton RS, Wyczalkowski MA, Liu R, Fronick CC, Fulton LA, Shinkle A, Thammavong L, Zhu H, Sun H, Wang LB, Li Y, Zuo C, McMichael JF, Davies SR, Appelbaum EL, Robbins KJ, Chasnoff SE, Yang X, Reeb AN, Oh C, Serasanambati M, Lal P, Varghese R, Mashl RJ, Ponce J, Terekhanova NV, Yao L, Wang F, Chen L, Schnaubelt M, Lu J, Schwarz JK, Puram SV, Kim AH, Song SK, Shoghi KI, Lau KS, Ju T, Chen K, Chatterjee D, Hawkins WG, Zhang H, Achilefu S, Chheda MG, Oh ST, Gillanders WE, Chen F, DeNardo DG, Fields RC, Ding L. Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer. Nature Genetics, 54(9): 1390-1405, 2022.
Simmons AJ, Lau KS. Dissociation and inDrops microfluidic encapsulation of human gut tissues for single-cell atlasing studies. STAR Protocols, 3(3):101570, 2022.
Groves SM, Ildefonso GV, McAtee CO, Ozawa PMM, Ireland AS, Stauffer PE, Wasdin PT, Huang X, Qiao Y, Lim JS, Bader J, Liu Q, Simmons AJ, Lau KS, Iams WT, Hardin DP, Saff EB, Holmes WR, Tyson DR, Lovly CM, Rathmell JC, Marth G, Sage J, Oliver TG, Weaver AM, Quaranta V. Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer. Cell Systems, 13(9):690-710, 2022.
Drewes JL, Chen J, Markham NO, Knippel RJ, Domingue JC, Tam AJ, Chan JL, Kim L, McMann M, Stevens C, Dejea CM, Tomkovich S, Michel J, White JR, Mohammad F, Campodonico VL, Heiser CN, Wu X, Wu S, Ding H, Simner P, Carroll K, Shrubsole MJ, Anders RA, Walk ST, Jobin C, Wan F, Coffey RJ, Housseau F*, Lau KS*, Sears CL*. Human colon cancer-derived Clostridioides difficile strains drive colonic tumorigenesis in mice. Cancer Discovery, 12(8):1873-1885, 2022. *Corresponding Authors
Min J, Zhang C, Bliton RJ, Caldwell B, Caplan L, Presentation KS, Park DJ, Kong SH, Lee HS, Washington MK, Kim WH, Lau KS, Magness ST, Lee HJ, Yang HK, Goldenring JR, Choi E. Dysplastic stem cell plasticity functions as a driving force for neoplastic transformation of pre-cancerous gastric mucosa. Gastroenterology, 163(4):875-890, 2022.
McKinley ET, Shao J, Ellis ST, Heiser CN, Roland JT, Macedonia MC, Vega PN, Shin S, Coffey RJ, Lau KS. MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images. Cytometry Part A, 101(6):521-528, 2022.
Brown RE, Jacobse J, Anant SA, Blunt KM, Chen B, Vega PN, Jones CT, Pilat JM, Revetta F, Gorby AH, Stengel KR, Choksi YA, Palin K, Piazuelo MB, Washington MK, Lau KS, Goettel JA, Hiebert SW, Short SP, Williams CS. MTG16 (CBFA2T3) regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. JCI Insight, 7(10):e153045, 2022.
Vega PN, Nilsson A, Kumar MP, Niitsu H, Simmons AJ, Ro J, Wang J, Chen Z, Joughin BA, Li W, McKinley ET, Liu Q, Roland JT, Washington MK, Coffey RJ, Lauffenburger DA*, Lau KS*. Cancer-associated fibroblasts and squamous epithelial cells constitute a unique microenvironment in a mouse model of inflammation-induced colon cancer. Frontiers in Oncology, 12:878920, 2022. *Corresponding Authors
Ma Z, Lytle NK, Chen B, Jyotsana N, Novak SW, Cho CJ, Caplan L, Ben-Levy O, Neininger AC, Burnette DT, Trinh VQ, Tan MCB, Patterson EA, Arrojo E Drigo R, Giraddi RR, Ramos C, Means AL, Matsumoto I, Manor U, Mills JC, Goldenring JR, Lau KS, Wahl GM, DelGiorno KE. Single-cell transcriptomics reveals a conserved metaplasia program in pancreatic injury. Gastroenterology, 162(2):604-620, 2022.
Harris CR, McKinley ET, Roland JT, Liu Q, Shrubsole MJ, Lau KS, Coffey RJ, Wrobel J, Vandekar SN. Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images. Bioinformatics, 38(6):1700–1707, 2022.