Research Output

2020

A comparison of small bowel and fecal microbiota in children with short bowel syndrome

Piper, H. G., Coughlin, L. A., Nguyen, V., Channabasappa, N. & Koh, A. Y., May 2020, In : Journal of Pediatric Surgery. 55, 5, p. 878-882 5 p.

Research output: Contribution to journalArticle

Antisense antibacterial compounds

Pifer, R. & Greenberg, D. E., 2020, (Accepted/In press) In : Translational Research.

Research output: Contribution to journalReview article

Open Access

A sensitive yellow fever virus entry reporter identifies valosin-containing protein (VCP/P97) as an essential host factor for flavivirus uncoating

Ramanathan, H. N., Zhang, S., Douam, F., Mar, K. B., Chang, J., Yang, P. L., Schoggins, J. W., Ploss, A. & Lindenbach, B. D., Mar 1 2020, In : mBio. 11, 2, e00467-20.

Research output: Contribution to journalArticle

Open Access

Binding of Phage-Encoded FlaGrab to Motile Campylobacter jejuni Flagella Inhibits Growth, Downregulates Energy Metabolism, and Requires Specific Flagellar Glycans

Sacher, J. C., Shajahan, A., Butcher, J., Patry, R. T., Flint, A., Hendrixson, D. R., Stintzi, A., Azadi, P. & Szymanski, C. M., Mar 20 2020, In : Frontiers in Microbiology. 11, 397.

Research output: Contribution to journalArticle

Open Access

Characterization of Autoinducer-3 Structure and Biosynthesis in E. coli

Kim, C. S., Gatsios, A., Cuesta, S., Lam, Y. C., Wei, Z., Chen, H., Russell, R. M., Shine, E. E., Wang, R., Wyche, T. P., Piizzi, G., Flavell, R. A., Palm, N. W., Sperandio, V. & Crawford, J. M., Feb 26 2020, In : ACS Central Science. 6, 2, p. 197-206 10 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations
Open Access

Diet-derived galacturonic acid regulates virulence and intestinal colonization in enterohaemorrhagic Escherichia coli and Citrobacter rodentium

Jimenez, A. G., Ellermann, M., Abbott, W. & Sperandio, V., Feb 1 2020, In : Nature microbiology. 5, 2, p. 368-378 11 p.

Research output: Contribution to journalArticle

Diversification of Campylobacter jejuni Flagellar C-ring composition impacts its structure and function in motility, flagellar assembly, and cellular processes

Henderson, L. D., Matthews-Palmer, T. R. S., Gulbronson, C. J., Ribardo, D. A., Beeby, M. & Hendrixson, D. R., Jan 1 2020, In : mBio. 11, 1, e02286-19.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Dynamin regulates the dynamics and mechanical strength of the actin cytoskeleton as a multifilament actin-bundling protein

Zhang, R., Lee, D. M., Jimah, J. R., Gerassimov, N., Yang, C., Kim, S., Luvsanjav, D., Winkelman, J., Mettlen, M., Abrams, M. E., Kalia, R., Keene, P., Pandey, P., Ravaux, B., Kim, J. H., Ditlev, J. A., Zhang, G., Rosen, M. K., Frost, A., Alto, N. M. & 5 others, Gardel, M., Schmid, S. L., Svitkina, T. M., Hinshaw, J. E. & Chen, E. H., Jun 1 2020, In : Nature cell biology. 22, 6, p. 674-688 15 p.

Research output: Contribution to journalArticle

Erratum: Indole signaling at the host-microbiota-pathogen interface (mBio, (2019), 10, 3, 10.1128/mBio.01031-19)

Kumar, A. & Sperandio, V., Jan 1 2020, In : mBio. 11, 1, e03318-19.

Research output: Contribution to journalComment/debate

Open Access

Espfu-mediated actin assembly enhances enteropathogenic escherichia coli adherence and activates host cell inflammatory signaling pathways

Martins, F. H., Kumar, A., Abe, C. M., Carvalho, E., Nishiyama-Jr, M., Xing, C., Sperandio, V. & Elias, W. P., Mar 1 2020, In : mBio. 11, 2, e00617-20.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Harmonies: A hybrid approach for microbiome networks inference via exploiting sparsity

Jiang, S., Xiao, G., Koh, A. Y., Chen, Y., Yao, B., Li, Q. & Zhan, X., 2020, In : Frontiers in Genetics. 11, 445.

Research output: Contribution to journalArticle

Open Access

Homeostatic regulation of STING protein at the resting state by stabilizer TOLLIP

Pokatayev, V., Yang, K., Tu, X., Dobbs, N., Wu, J., Kalb, R. G. & Yan, N., Feb 1 2020, In : Nature immunology. 21, 2, p. 158-167 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

Identification of scavenger receptor B1 as the airway microfold cell receptor for mycobacterium tuberculosis

Khan, H. S., Nair, V. R., Ruhl, C. R., Alvarez-Arguedas, S., Rendiz, J. L. G., Franco, L. H., Huang, L., Shaul, P. W., Kim, J., Xie, Y., Mitchell, R. B. & Shiloh, M. U., Mar 2020, In : eLife. 9, e52551.

Research output: Contribution to journalArticle

Open Access

Interaction between the autophagy protein Beclin 1 and Na+,K+-ATPase during starvation, exercise, and ischemia

Fernández, Á. F., Liu, Y., Ginet, V., Shi, M., Nah, J., Zou, Z., Zhou, A., Posner, B. A., Xiao, G., Tanguy, M., Paradis, V., Sadoshima, J., Rautou, P. E., Puyal, J., Hu, M. C. & Levine, B., Jan 16 2020, In : JCI Insight. 5, 1, e133282.

Research output: Contribution to journalArticle

Open Access

KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs

Bacon, C. W., Challa, A., Hyder, U., Shukla, A., Borkar, A. N., Bayo, J., Liu, J., Wu, S. Y., Chiang, C. M., Kutateladze, T. G. & D'orso, I., Jan 1 2020, (Accepted/In press) In : Molecular cell.

Research output: Contribution to journalArticle

1 Scopus citations

L-Arginine sensing regulates virulence gene expression and disease progression in enteric pathogens

Menezes-Garcia, Z., Kumar, A., Zhu, W., Winter, S. E. & Sperandio, V., Jun 2 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 22, p. 12387-12393 7 p.

Research output: Contribution to journalArticle

Microbiota-independent antiviral effects of antibiotics on poliovirus and coxsackievirus: Antiviral Effects of Antibiotics on Enteric Viruses

Woods Acevedo, M. A. & Pfeiffer, J. K., Jul 2020, In : Virology. 546, p. 20-24 5 p.

Research output: Contribution to journalArticle

Mycobacterium tuberculosis lipoarabinomannan activates human neutrophils via a TLR2/1 mechanism distinct from Pam3CSK4

Hook, J. S., Cao, M., Weng, K., Kinnare, N. & Moreland, J. G., Feb 1 2020, In : Journal of Immunology. 204, 3, p. 671-681 11 p.

Research output: Contribution to journalArticle

Mycobacterium tuberculosis Sulfolipid-1 Activates Nociceptive Neurons and Induces Cough

Ruhl, C. R., Pasko, B. L., Khan, H. S., Kindt, L. M., Stamm, C. E., Franco, L. H., Hsia, C. C., Zhou, M., Davis, C. R., Qin, T., Gautron, L., Burton, M. D., Mejia, G. L., Naik, D. K., Dussor, G., Price, T. J. & Shiloh, M. U., Apr 16 2020, In : Cell. 181, 2, p. 293-305.e11

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Optimizing Breast Pocket Irrigation: The Breast Implant-Associated Anaplastic Large Cell Lymphoma (BIA-ALCL) Era

Culbertson, E. J., Felder-Scott, C., Deva, A. K., Greenberg, D. E. & Adams, W. P., May 16 2020, In : Aesthetic surgery journal. 40, 6, p. 619-625 7 p.

Research output: Contribution to journalArticle

Oxysterols provide innate immunity to bacterial infection by mobilizing cell surface accessible cholesterol

Abrams, M. E., Johnson, K. A., Perelman, S. S., Zhang, L. S., Endapally, S., Mar, K. B., Thompson, B. M., McDonald, J. G., Schoggins, J. W., Radhakrishnan, A. & Alto, N. M., Jul 1 2020, In : Nature microbiology. 5, 7, p. 929-942 14 p.

Research output: Contribution to journalArticle

2 Scopus citations

Passive immunization with an extended half-life monoclonal antibody protects Rhesus macaques against aerosolized ricin toxin

Roy, C. J., Van Slyke, G., Ehrbar, D., Bornholdt, Z. A., Brennan, M. B., Campbell, L., Chen, M., Kim, D., Mlakar, N., Whaley, K. J., Froude, J. W., Torres-Velez, F. J., Vitetta, E., Didier, P. J., Doyle-Meyers, L., Zeitlin, L. & Mantis, N. J., Dec 1 2020, In : npj Vaccines. 5, 1, 13.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Rapid dissemination and monopolization of viral populations in mice revealed using a panel of barcoded viruses

McCune, B. T., Lanahan, M. R., TenOever, B. R. & Pfeiffer, J. K., Jan 1 2020, In : Journal of virology. 94, 2, e01590-19.

Research output: Contribution to journalArticle

Reduced anti-inflammatory gut microbiota are associated with depression and anhedonia

Mason, B. L., Li, Q., Minhajuddin, A., Czysz, A. H., Coughlin, L. A., Hussain, S. K., Koh, A. Y. & Trivedi, M. H., Apr 1 2020, In : Journal of affective disorders. 266, p. 394-401 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

Salmonella finds a way: Metabolic versatility of Salmonella enterica serovar Typhimurium in diverse host environments

Taylor, S. J. & Winter, S. E., Jun 1 2020, In : PLoS pathogens. 16, 6, p. e1008540

Research output: Contribution to journalArticle

Open Access

The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

Xavier, J. B., Young, V. B., Skufca, J., Ginty, F., Testerman, T., Pearson, A. T., Macklin, P., Mitchell, A., Shmulevich, I., Xie, L., Caporaso, J. G., Crandall, K. A., Simone, N. L., Godoy-Vitorino, F., Griffin, T. J., Whiteson, K. L., Gustafson, H. H., Slade, D. J., Schmidt, T. M., Walther-Antonio, M. R. S. & 10 others, Korem, T., Webb-Robertson, B. J. M., Styczynski, M. P., Johnson, W. E., Jobin, C., Ridlon, J. M., Koh, A. Y., Yu, M., Kelly, L. & Wargo, J. A., Mar 2020, In : Trends in Cancer. 6, 3, p. 192-204 13 p.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

The Genetics and Epigenetics of 22q11.2 Deletion Syndrome

Du, Q., De La Morena, M. T. & van Oers, N. S. C., Feb 6 2020, In : Frontiers in Genetics. 10, 1365.

Research output: Contribution to journalReview article

Open Access
1 Scopus citations

The gut microbiome and thromboembolism

Hasan, R. A., Koh, A. Y. & Zia, A., May 2020, In : Thrombosis research. 189, p. 77-87 11 p.

Research output: Contribution to journalReview article

1 Scopus citations

The Impact of Lactobacillus Probiotics on the Gut Microbiota in Children With Short Bowel Syndrome

Piper, H. G., Coughlin, L. A., Hussain, S., Nguyen, V., Channabasappa, N. & Koh, A. Y., Jul 2020, In : Journal of Surgical Research. 251, p. 112-118 7 p.

Research output: Contribution to journalArticle

1 Scopus citations

The lon-1 protease is required by borrelia burgdorferi to infect the mammalian host

Thompson, C., Mason, C., Parrilla, S. & Ouyang, Z., Jun 1 2020, In : Infection and immunity. 88, 6, e00951.

Research output: Contribution to journalArticle

The tripartite interaction of phosphate, autophagy, and αKlotho in health maintenance

Shi, M., Maique, J., Shaffer, J., Davidson, T., Sebti, S., Fernández, Á. F., Zou, Z., Yan, S., Levine, B., Moe, O. W. & Hu, M. C., Feb 1 2020, In : FASEB Journal. 34, 2, p. 3129-3150 22 p.

Research output: Contribution to journalArticle

Open Access

TLR9 and beclin 1 crosstalk regulates muscle AMPK activation in exercise

Liu, Y., Nguyen, P. T., Wang, X., Zhao, Y., Meacham, C. E., Zou, Z., Bordieanu, B., Johanns, M., Vertommen, D., Wijshake, T., May, H., Xiao, G., Shoji-Kawata, S., Rider, M. H., Morrison, S. J., Mishra, P. & Levine, B., Feb 27 2020, In : Nature. 578, 7796, p. 605-609 5 p.

Research output: Contribution to journalArticle

2 Scopus citations

Transcriptional profiling identifies caspase-1 as a T cell–intrinsic regulator of Th17 differentiation

Gao, Y., Deason, K., Jain, A., Irizarry-Caro, R. A., Dozmorov, I., Coughlin, L. A., Rauch, I., Evers, B. M., Koh, A. Y., Wakeland, E. K. & Pasare, C., Jan 1 2020, In : Journal of Experimental Medicine. 217, 4, e20190476.

Research output: Contribution to journalArticle

1 Scopus citations

Upregulation of Rubicon promotes autosis during myocardial ischemia/reperfusion injury

Nah, J., Zhai, P., Huang, C. Y., Fernández, Á. F., Mareedu, S., Levine, B. & Sadoshima, J., Jun 1 2020, In : Journal of Clinical Investigation. 130, 6, p. 2978-2991 14 p.

Research output: Contribution to journalArticle

Open Access

VaMPR: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning

Kim, J., Greenberg, D. E., Pifer, R., Jiang, S., Xiao, G., Shelburne, S. A., Koh, A., Xie, Y. & Zhan, X., Jan 1 2020, In : PLoS Computational Biology. 16, 1, e1007511.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Whole-genome sequencing of Staphylococcus epidermidis bloodstream isolates from a prospective clinical trial reveals that complicated bacteraemia is caused by a limited number of closely related sequence types

Shelburne, S. A., Dib, R. W., Endres, B. T., Reitzel, R., Li, X., Kalia, A., Sahasrabhojane, P., Chaftari, A. M., Hachem, R., Vargas-Cruz, N. S., Jiang, Y., Garey, K., Fowler, V. G., Holland, T. L., Gu, J., Miller, W., Sakurai, A., Arias, C. A., Aitken, S. L., Greenberg, D. E. & 3 others, Kim, J., Flores, A. R. & Raad, I., May 2020, In : Clinical Microbiology and Infection. 26, 5, p. 646.e1-646.e8

Research output: Contribution to journalArticle

Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis

Zhu, W., Winter, M. G., Spiga, L., Hughes, E. R., Chanin, R., Mulgaonkar, A., Pennington, J., Maas, M., Behrendt, C. L., Kim, J., Sun, X., Beiting, D. P., Hooper, L. V. & Winter, S. E., Mar 11 2020, In : Cell Host and Microbe. 27, 3, p. 376-388.e8

Research output: Contribution to journalArticle

2019

A bioactive mammalian disaccharide associated with autoimmunity activates STING-TBK1-dependent immune response

Fermaintt, C. S., Sano, K., Liu, Z., Ishii, N., Seino, J., Dobbs, N., Suzuki, T., Fu, Y. X., Lehrman, M. A., Matsuo, I. & Yan, N., Dec 1 2019, In : Nature communications. 10, 1, 2377.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

A chaperone for the stator units of a bacterial flagellum

Ribardo, D. A., Kelley, B. R., Johnson, J. G. & Hendrixson, D. R., Jan 1 2019, In : mBio. 10, 4, e01732-19.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

AcrAB-TolC Inhibition by Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers Restores Antibiotic Activity in Vitro and in Vivo

Sturge, C. R., Felder-Scott, C. F., Pifer, R., Pybus, C., Jain, R., Geller, B. L. & Greenberg, D. E., Jan 1 2019, In : ACS Infectious Diseases.

Research output: Contribution to journalArticle

2 Scopus citations

Alveolar Macrophage Chemokine Secretion Mediates Neutrophilic Lung Injury in Nox2-Deficient Mice

Potera, R. M., Cao, M., Jordan, L. F., Hogg, R. T., Hook, J. S. & Moreland, J. G., Feb 15 2019, In : Inflammation. 42, 1, p. 185-198 14 p.

Research output: Contribution to journalArticle

2 Scopus citations

A NIK–SIX signalling axis controls inflammation by targeted silencing of non-canonical NF-κB

Liu, Z., Mar, K. B., Hanners, N. W., Perelman, S. S., Kanchwala, M., Xing, C., Schoggins, J. W. & Alto, N. M., Jan 1 2019, In : Nature.

Research output: Contribution to journalLetter

5 Scopus citations

A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape

Hubel, P., Urban, C., Bergant, V., Schneider, W. M., Knauer, B., Stukalov, A., Scaturro, P., Mann, A., Brunotte, L., Hoffmann, H. H., Schoggins, J. W., Schwemmle, M., Mann, M., Rice, C. M. & Pichlmair, A., Apr 1 2019, In : Nature immunology. 20, 4, p. 493-502 10 p.

Research output: Contribution to journalArticle

13 Scopus citations

Bacterial stabilization of a panel of picornaviruses

Aguilera, E. R., Nguyen, Y., Sasaki, J. & Pfeiffer, J. K., Mar 1 2019, In : mSphere. 4, 2, e00183-19.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

Biological Functions of Autophagy Genes: A Disease Perspective

Levine, B. & Kroemer, G., Jan 10 2019, In : Cell. 176, 1-2, p. 11-42 32 p.

Research output: Contribution to journalReview article

204 Scopus citations

Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin

He, Z., Gharaibeh, R. Z., Newsome, R. C., Pope, J. L., Dougherty, M. W., Tomkovich, S., Pons, B., Mirey, G., Vignard, J., Hendrixson, D. R. & Jobin, C., Feb 1 2019, In : Gut. 68, 2, p. 289-300 12 p.

Research output: Contribution to journalArticle

29 Scopus citations

Cancer Immune Checkpoint Inhibitor Therapy and the Gut Microbiota

Frankel, A. E., Deshmukh, S., Reddy, A., Lightcap, J., Hayes, M., McClellan, S., Singh, S., Rabideau, B., Glover, T. G., Roberts, B. & Koh, A., Apr 1 2019, In : Integrative Cancer Therapies. 18

Research output: Contribution to journalReview article

Open Access
5 Scopus citations