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Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition.

Liu Y, Carbonetto P, Willwerscheid J, Oakes SA, Macleod KF, Stephens M

Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition. Nat Genet. 2025 Jan; 57(1):263-273.

PMID: 39747597

Inflammation-Induced Claudin-2 Upregulation Limits Pancreatitis Progression by Enhancing Tight Junction-Controlled Pancreatic Ductal Transport.

Kesaraju S, Li Y, Xing J, Tracy M, Wannemo K, Holder A, Zhao P, Khan MA, Kainov J, Rana N, Sidahmed M, Hyoju S, Smith L, Matthews J, Tay S, Khalili-Araghi F, Rana M, Oakes SA, Shen L, Weber CR

Inflammation-Induced Claudin-2 Upregulation Limits Pancreatitis Progression by Enhancing Tight Junction-Controlled Pancreatic Ductal Transport. bioRxiv. 2024 Nov 13.

PMID: 39605652

Direct inhibition of tumor hypoxia response with synthetic transcriptional repressors.

Qiao Z, Nguyen LC, Yang D, Dann C, Thomas DM, Henn M, Valdespino A, Swenson CS, Oakes SA, Rosner MR, Moellering RE

Direct inhibition of tumor hypoxia response with synthetic transcriptional repressors. Nat Chem Biol. 2025 Feb; 21(2):247-255.

PMID: 39215099

Inhibition of the eukaryotic initiation factor-2a kinase PERK decreases risk of autoimmune diabetes in mice.

Muralidharan C, Huang F, Enriquez JR, Wang JE, Nelson JB, Nargis T, May SC, Chakraborty A, Figatner KT, Navitskaya S, Anderson CM, Calvo V, Surguladze D, Mulvihill MJ, Yi X, Sarkar S, Oakes SA, Webb-Robertson BM, Sims EK, Staschke KA, Eizirik DL, Nakayasu ES, Stokes ME, Tersey SA, Mirmira RG

Inhibition of the eukaryotic initiation factor-2a kinase PERK decreases risk of autoimmune diabetes in mice. J Clin Invest. 2024 Jun 18; 134(16).

PMID: 38889047

Inhibition of the Eukaryotic Initiation Factor-2-a Kinase PERK Decreases Risk of Autoimmune Diabetes in Mice.

Muralidharan C, Huang F, Enriquez JR, Wang JE, Nelson JB, Nargis T, May SC, Chakraborty A, Figatner KT, Navitskaya S, Anderson CM, Calvo V, Surguladze D, Mulvihill MJ, Yi X, Sarkar S, Oakes SA, Webb-Robertson BM, Sims EK, Staschke KA, Eizirik DL, Nakayasu ES, Stokes ME, Tersey SA, Mirmira RG

Inhibition of the Eukaryotic Initiation Factor-2-a Kinase PERK Decreases Risk of Autoimmune Diabetes in Mice. bioRxiv. 2024 Jun 03.

PMID: 38895427

Unfolding emergency calls stress granules to the ER.

Pincus D, Oakes SA

Unfolding emergency calls stress granules to the ER. Nat Cell Biol. 2024 Jun; 26(6):845-846.

PMID: 38822214

Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition.

Liu Y, Carbonetto P, Willwerscheid J, Oakes SA, Macleod KF, Stephens M

Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition. bioRxiv. 2024 May 26.

PMID: 37645713

The Integrated Stress Response in Pancreatic Development, Tissue Homeostasis, and Cancer.

Malnassy G, Ziolkowski L, Macleod KF, Oakes SA

The Integrated Stress Response in Pancreatic Development, Tissue Homeostasis, and Cancer. Gastroenterology. 2024 Dec; 167(7):1292-1306.

PMID: 38768690

Stress and human health in diabetes: A report from the 19th Chicago Biomedical Consortium symposium.

Mirmira RG, Kulkarni RN, Xu P, Drossos T, Varady K, Knutson KL, Reutrakul S, Martyn-Nemeth P, Sargis RM, Wallia A, Tuchman AM, Weissberg-Benchell J, Danielson KK, Oakes SA, Thomas CC, Layden BT, May SC, Burbea Hoffmann M, Gatta E, Solway J, Philipson LH

Stress and human health in diabetes: A report from the 19th Chicago Biomedical Consortium symposium. J Clin Transl Sci. 2023; 7(1):e263.

PMID: 38229904

DISSECTING TUMOR TRANSCRIPTIONAL HETEROGENEITY FROM SINGLE-CELL RNA-SEQ DATA BY GENERALIZED BINARY COVARIANCE DECOMPOSITION.

Liu Y, Carbonetto P, Willwerscheid J, Oakes SA, Macleod KF, Stephens M

DISSECTING TUMOR TRANSCRIPTIONAL HETEROGENEITY FROM SINGLE-CELL RNA-SEQ DATA BY GENERALIZED BINARY COVARIANCE DECOMPOSITION. bioRxiv. 2023 Aug 17.

PMID: 37645713