Representative Publications

Ozyoruk, K.B., Can, S., Darbaz, B. et al. A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded. Nat. Biomed. Eng 6, 1407–1419 (2022).

Chen, C., Lu, M.Y., Williamson, D.F.K. et al. Fast and scalable search of whole-slide images via self-supervised deep learning. Nat. Biomed. Eng 6, 1420–1434 (2022).

Maringanti VS, Bucci V, Gerber GK. MDITRE: scalable and interpretable machine learning for predicting host status from temporal microbiome dynamics. mSystems. 2022 Sep 7:e0013222. doi: 10.1128/msystems.00132-22. PMID: 36069455; PMCID: PMC9600536.

Chen RJ, Lu MY, Williamson DFK, Chen TY, Lipkova J, Noor Z, Shaban M, Shady M, Williams M, Joo B, Mahmood F. Pan-cancer integrative histology-genomic analysis via multimodal deep learning. Cancer Cell. 2022 Aug 08; 40(8):865-878.e6. PMID: 35944502.

Dawkins JJ, Allegretti JR, Gibson TE, McClure E, Delaney M, Bry L, Gerber GK. Gut metabolites predict Clostridioides difficile recurrence. Microbiome. 2022 06 09; 10(1):87. PMID: 35681218; PMCID: PMC9178838.

Lipkova J, Chen TY, Lu MY, Chen RJ, Shady M, Williams M, Wang J, Noor Z, Mitchell RN, Turan M, Coskun G, Yilmaz F, Demir D, Nart D, Basak K, Turhan N, Ozkara S, Banz Y, Odening KE, Mahmood F. Deep learning-enabled assessment of cardiac allograft rejection from endomyocardial biopsies. Nat Med. 2022 03; 28(3):575-582. PMID: 35314822; PMCID: PMC9353336.

Lu MY, Sater HA, Mahmood F. Multiplex computational pathology for treatment response predication. Cancer Cell. 2021 08 09; 39(8):1053-1055. PMID: 34375608.

Lu MY, Chen TY, Williamson DFK, Zhao M, Shady M, Lipkova J, Mahmood F. AI-based pathology predicts origins for cancers of unknown primary. Nature. 2021 06; 594(7861):106-110. PMID: 33953404.

Creswell R, Tan J, Leff JW, Brooks B, Mahowald MA, Thieroff-Ekerdt R, Gerber GK. High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans. Genome Med. 2020 07 03; 12(1):59. PMID: 32620143.

Bogart E, Creswell R, Gerber GK. MITRE: inferring features from microbiota time-series data linked to host status. Genome Biol. 2019 09 02; 20(1):186. PMID: 31477162; PMCID: PMC6721208.

Abdel-Gadir A, Stephen-Victor E, Gerber GK, Noval Rivas M, Wang S, Harb H, Wang L, Li N, Crestani E, Spielman S, Secor W, Biehl H, DiBenedetto N, Dong X, Umetsu DT, Bry L, Rachid R, Chatila TA. Microbiota therapy acts via a regulatory T cell MyD88/ROR-gamma pathway to suppress food allergy. Nat Med. 2019 07; 25(7):1164-1174. PMID: 31235962.

Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver PA, Gerber GK. Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. Cell Host Microbe. 2019 Jun 12; 25(6):803-814.e5. PMID: 31175044; PMCID: PMC6579560.