Publications

Please see below for recent publications from members of our department.

• Non-negative matrix factorization and deconvolution as a dual simplex problem

  December 1, 2026

  Non-negative matrix factorization and deconvolution as a dual simplex problem

  Kleverov, D., Aladyeva, E., Serdyukov, A. & Artyomov, M. N., Dec 2026, In: Genome biology. 27, 1, 25.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Community-associated quinolone-resistant and extended-spectrum beta-lactamase-producing Escherichia coli isolates are similar to clinical infection isolates by sequence type and resistome

  February 17, 2026

  Community-associated quinolone-resistant and extended-spectrum beta-lactamase-producing Escherichia coli isolates are similar to clinical infection isolates by sequence type and resistome

  Benedict, E. E., Agee, W., Hink, T., Parrish, K. L., Reske, K. A., Peacock, K., Bosserman, R. E., Valencia, A., Saluja, A., Ovchiyan, E., Arter, O., Jolani, K., Dubberke, E. R., Dantas, G. & Kwon, J., Feb 17 2026, In: mSystems. 11, 2, p. e0159125

  Research output: Contribution to journal › Article › peer-review

  Publication

• Engineering chimeric antigen receptor CD4 T cells for Alzheimer’s disease

  February 17, 2026

  Engineering chimeric antigen receptor CD4 T cells for Alzheimer’s disease

  Boskovic, P., Shalita, R., Gao, W., Vernon, H., Deng, Y. L., Colonna, M., Majzner, R. G., Amit, I. & Kipnis, J., Feb 17 2026, In: Proceedings of the National Academy of Sciences of the United States of America. 123, 7, e2530977123.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Associations between the microbiome and immune responses to an adenovirus-based HIV-1 candidate vaccine are distinct between African and US cohorts

  February 17, 2026

  Associations between the microbiome and immune responses to an adenovirus-based HIV-1 candidate vaccine are distinct between African and US cohorts

  Li, Y., Stieh, D. J., Droit, L., Kim, A. H. J., Rodgers, R., Mihindukulasuriya, K. A., Wang, L., Pau, M. G., Yuan, O., Virgin, H. W., Barouch, D. H., Baldridge, M. T. & Handley, S. A., Feb 17 2026, In: mSystems. 11, 2, p. e0143525

  Research output: Contribution to journal › Article › peer-review

  Publication

• Intratumoral Three-Cell-Type Clusters Are a Conserved Feature of Endogenous Antitumor Immunity

  February 1, 2026

  Intratumoral Three-Cell-Type Clusters Are a Conserved Feature of Endogenous Antitumor Immunity

  Damle, S. R., Carter, J. A., Goodsell, K. E., Pineda, J. M. B., Dickerson, L. K., Jiang, X., Mudd, J. L., Walsh, T., Kenerson, H. L., Cernak, J., Chauhan, S. S. B., Beirne, E., Jana, S., Koehne, A. L., Vij, K. R., Ruzinova, M. B., Yeung, R., Akilesh, S., Collisson, E. A. & Fields, R. C. & 2 others, Crispe, I. N. & Pillarisetty, V. G., Feb 1 2026, In: Cancer immunology research. 14, 2, p. 205-218 14 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• A Case of Successful Kidney Transplant-Alone in Primary Hyperoxaluria Type 1 Using Lumasiran

  February 1, 2026

  A Case of Successful Kidney Transplant-Alone in Primary Hyperoxaluria Type 1 Using Lumasiran

  Flores, K., Merzkani, M., Abdulkhalek, S., Abuazzam, F., Java, A., Delos Santos, R., Paul, R., Gaut, J. & Alhamad, T., Feb 2026, In: Clinical Transplantation. 40, 2, e70464.

  Research output: Contribution to journal › Letter › peer-review

  Publication

• Publisher Correction: Diversity and immune dynamics of choroid plexus macrophages are shaped by distinct developmental origins (Nature Neuroscience, (2026), 10.1038/s41593-025-02158-z)

  January 1, 2026

  Publisher Correction: Diversity and immune dynamics of choroid plexus macrophages are shaped by distinct developmental origins (Nature Neuroscience, (2026), 10.1038/s41593-025-02158-z)

  Du, S., Nguyen, K. M., Ulezko Antonova, A., Fachi, J. L., Rodrigues, P. F., Verdiani, A., Molgora, M., Smirnov, I., Herz, J., Mamuladze, T., Ponce, J., Swain, A., Bugatti, M., Gilfillan, S., Cella, M., Vermi, W., Kipnis, J., Colonna, M. & Brioschi, S., 2026, (Accepted/In press) In: Nature neuroscience.

  Research output: Contribution to journal › Comment/debate

  Publication

• High depth targeted next-generation sequencing in vascular malformations

  January 1, 2026

  High depth targeted next-generation sequencing in vascular malformations

  Pakhathirathien, P., Wongkittichote, P., Wittayakornrerk, S., Treesit, T., Feinggumloon, S., Pichipichatkul, K., Bua-Ngam, C., Sarovath, A., Thanachatchairattana, P., Dumrongwongsiri, S., Bowling, K. M., Corliss, M. M., Cao, Y., Tim-Aroon, T., Khongkraparn, A., Noojaroen, S. & Wattanasirichaigoon, D., 2026, In: Human molecular genetics. 35, 1, ddaf169.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Strategies for identifying NUP98 rearrangements in adult myeloid neoplasms

  August 14, 2025

  Strategies for identifying NUP98 rearrangements in adult myeloid neoplasms

  Yuen, L. D., Hasserjian, R. P., Fathi, A. T., Luskin, M. R., Winer, E. S., Cin, P. D., Kim, A. S., Lindsley, R. C., Tsai, H. K. & Nardi, V., Aug 14 2025, In: Haematologica. 111, 2, p. 518-534 17 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Feasibility and potential impact of a local proficiency testing program in Accra, Ghana

  June 1, 2025

  Feasibility and potential impact of a local proficiency testing program in Accra, Ghana

  Ahmad, Y., Sarpong, K. A. N., Bansah, L. Y., Adafia, R., Asare, F. & Amukele, T. K., Jun 1 2025, In: American journal of clinical pathology. 163, 6, p. 847-853 7 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Targeting hepatocyte-specific SLC2A8 blocks hepatic steatosis and dissociates TCA cycle flux inhibition from glutamine anaplerosis

  January 1, 2025

  Targeting hepatocyte-specific SLC2A8 blocks hepatic steatosis and dissociates TCA cycle flux inhibition from glutamine anaplerosis

  Adams, J. A., Zhang, Y., Sun, J., Tilston-Lunel, A., Higgins, C. B., Heitmeier, M., Ballentine, S., Tycksen, E., Dolle, R. E., Hruz, P. W. & DeBosch, B. J., 2025, In: Hepatology Communications. 9, 10

  Research output: Contribution to journal › Article › peer-review

  Publication

• Remote support of an external quality assessment program in 10 laboratories in Bhutan, Uganda, and Malawi pathologists overseas experience between 2009 and 2017

  July 1, 2024

  Remote support of an external quality assessment program in 10 laboratories in Bhutan, Uganda, and Malawi pathologists overseas experience between 2009 and 2017

  Harb, R., Tuggey, R., Ladenson, J. & Amukele, T., Jul 1 2024, In: American journal of clinical pathology. 162, 1, p. 7-11 5 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Characterizing the role of informal payments in the delivery of pathology and clinical laboratory services

  June 1, 2024

  Characterizing the role of informal payments in the delivery of pathology and clinical laboratory services

  Glynn, E. H., Amukele, T., Soge, O., Baird, G. & Vian, T., Jun 1 2024, In: American journal of clinical pathology. 161, 6, p. 561-569 9 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid

  December 1, 2023

  Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid

  Pruss, K. M., Chen, H., Liu, Y., Van Treuren, W., Higginbottom, S. K., Jarman, J. B., Fischer, C. R., Mak, J., Wong, B., Cowan, T. M., Fischbach, M. A., Sonnenburg, J. L. & Dodd, D., Dec 2023, In: Nature communications. 14, 1, 512.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Pathologists Overseas: A volunteer-based model for building sustainable, high-quality pathology and laboratory medicine services in low- and middle-income countries

  August 30, 2022

  Pathologists Overseas: A volunteer-based model for building sustainable, high-quality pathology and laboratory medicine services in low- and middle-income countries

  Glynn, E. H., Nelson, A. M., Tesfazghi, M., Harb, R. & Amukele, T., Aug 30 2022, In: Frontiers in Medicine. 9, 977840.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization

  January 1, 2022

  Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization

  Pruss, K. M., Enam, F., Battaglioli, E., DeFeo, M., Diaz, O. R., Higginbottom, S. K., Fischer, C. R., Hryckowian, A. J., Van Treuren, W., Dodd, D., Kashyap, P. & Sonnenburg, J. L., Jan 2022, In: Nature Metabolism. 4, 1, p. 19-28 10 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• A rapid, point-of-care red blood cell agglutination assay detecting antibodies against SARS-CoV-2

  May 14, 2021

  A rapid, point-of-care red blood cell agglutination assay detecting antibodies against SARS-CoV-2

  Kruse, R. L., Huang, Y., Smetana, H., Gehrie, E. A., Amukele, T. K., Tobian, A. A. R., Mostafa, H. H. & Wang, Z. Z., May 14 2021, In: Biochemical and Biophysical Research Communications. 553, p. 165-171 7 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• C. difficile exploits a host metabolite produced during toxin-mediated disease

  May 13, 2021

  C. difficile exploits a host metabolite produced during toxin-mediated disease

  Pruss, K. M. & Sonnenburg, J. L., May 13 2021, In: Nature. 593, 7858, p. 261-265 5 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations

  February 1, 2021

  Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations

  Pruss, K. M., Marcobal, A., Southwick, A. M., Dahan, D., Smits, S. A., Ferreyra, J. A., Higginbottom, S. K., Sonnenburg, E. D., Kashyap, P. C., Choudhury, B., Bode, L. & Sonnenburg, J. L., Feb 2021, In: ISME Journal. 15, 2, p. 577-591 15 p.

  Research output: Contribution to journal › Article › peer-review

  Publication

• The economics of medical drones

  January 1, 2020

  The economics of medical drones

  Amukele, T., Jan 2020, In: The Lancet Global Health. 8, 1, p. e22

  Research output: Contribution to journal › Comment/debate

  Publication