Robert Wood Johnson Medical School (RWJMS), Center for Advanced Biotechnology and Medicine

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2020

A double-stranded RNA platform is required for the interaction between a host restriction factor and the NS1 protein of influenza A virus

Chen, G., Ma, L. C., Wang, S., Woltz, R. L., Grasso, E. M., Montelione, G. T. & Krug, R. M., Jan 10 2020, In : Nucleic acids research. 48, 1, p. 304-315 12 p.

Research output: Contribution to journalArticle

Open Access

A single early-in-life antibiotic course increases susceptibility to DSS-induced colitis

Ozkul, C., Ruiz, V. E., Battaglia, T., Xu, J., Roubaud-Baudron, C., Cadwell, K., Perez-Perez, G. I. & Blaser, M. J., Jul 25 2020, In : Genome Medicine. 12, 1, 65.

Research output: Contribution to journalArticle

Open Access

Comparative dynamics of tropomyosin in vertebrates and invertebrates

James, J. K. & Nanda, V., Feb 1 2020, In : Proteins: Structure, Function and Bioinformatics. 88, 2, p. 265-273 9 p.

Research output: Contribution to journalArticle

Design of a Fe4S4 cluster into the core of a de novo four-helix bundle

Mancini, J. A., Pike, D. H., Tyryshkin, A. M., Haramaty, L., Wang, M. S., Poudel, S., Hecht, M. & Nanda, V., 2020, (Accepted/In press) In : Biotechnology and Applied Biochemistry.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Discovery and Characterization of Fluorine-Substituted Diarylpyrimidine Derivatives as Novel HIV-1 NNRTIs with Highly Improved Resistance Profiles and Low Activity for the hERG Ion Channel

Kang, D., Ruiz, F. X., Feng, D., Pilch, A., Zhao, T., Wei, F., Wang, Z., Sun, Y., Fang, Z., De Clercq, E., Pannecouque, C., Arnold, E., Liu, X. & Zhan, P., Feb 13 2020, In : Journal of medicinal chemistry. 63, 3, p. 1298-1312 15 p.

Research output: Contribution to journalArticle

4 Scopus citations

Ecological succession in the vaginal microbiota during pregnancy and birth

Rasmussen, M. A., Thorsen, J., Dominguez-Bello, M. G., Blaser, M. J., Mortensen, M. S., Brejnrod, A. D., Shah, S. A., Hjelmsø, M. H., Lehtimäki, J., Trivedi, U., Bisgaard, H., Sørensen, S. J. & Stokholm, J., Sep 1 2020, In : ISME Journal. 14, 9, p. 2325-2335 11 p.

Research output: Contribution to journalArticle

Open Access

Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data

Wang, C., Hu, J., Blaser, M. J., Li, H. & Birol, I., Jan 15 2020, In : Bioinformatics. 36, 2, p. 347-355 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

Evolutionary coupling saturation mutagenesis: Coevolution-guided identification of distant sites influencing Bacillus naganoensis pullulanase activity

Wang, X., Jing, X., Deng, Y., Nie, Y., Xu, F., Xu, Y., Zhao, Y. L., Hunt, J. F., Montelione, G. T. & Szyperski, T., Mar 1 2020, In : FEBS Letters. 594, 5, p. 799-812 14 p.

Research output: Contribution to journalArticle

4 Scopus citations

Foxn4 is a temporal identity factor conferring mid/late-early retinal competence and involved in retinal synaptogenesis

Liu, S., Liu, X., Li, S., Huang, X., Qian, H., Jin, K. & Xiang, M., Mar 3 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 9, p. 5016-5027 12 p.

Research output: Contribution to journalArticle

1 Scopus citations

High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application

Grime, G. W., Zeldin, O. B., Snell, M. E., Lowe, E. D., Hunt, J. F., Montelione, G. T., Tong, L., Snell, E. H. & Garman, E. F., Jan 8 2020, In : Journal of the American Chemical Society. 142, 1, p. 185-197 13 p.

Research output: Contribution to journalArticle

In-cell NMR as a sensitive tool to monitor physiological condition of Escherichia coli

Sugiki, T., Yamaguchi, Y., Fujiwara, T., Inouye, M., Ito, Y. & Kojima, C., Dec 1 2020, In : Scientific reports. 10, 1, 2466.

Research output: Contribution to journalArticle

Open Access

Intratumoral injection of the seasonal flu shot converts immunologically cold tumors to hot and serves as an immunotherapy for cancer

Newman, J. H., Chesson, C. B., Herzog, N. L., Bommareddy, P. K., Aspromonte, S. M., Pepe, R., Estupinian, R., Aboelatta, M. M., Buddhadev, S., Tarabichi, S., Lee, M., Li, S., Medina, D. J., Giurini, E. F., Gupta, K. H., Guevara-Aleman, G., Rossi, M., Nowicki, C., Abed, A., Goldufsky, J. W. & 28 others, Broucek, J. R., Redondo, R. E., Rotter, D., Jhawar, S. R., Wang, S. J., Kohlhapp, F. J., Kaufman, H. L., Thomas, P. G., Gupta, V., Kuzel, T. M., Reiser, J., Paras, J., Kane, M. P., Singer, E. A., Malhotra, J., Denzin, L. K., Sant'Angelo, D. B., Rabson, A. B., Lee, L. Y., Lasfar, A., Langenfeld, J., Schenkel, J. M., Fidler, M. J., Ruiz, E. S., Marzo, A. L., Rudra, J. S., Silk, A. W. & Zloza, A., Jan 14 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 2, p. 1119-1128 10 p.

Research output: Contribution to journalArticle

Open Access
7 Scopus citations

Is hydroxychloroquine beneficial for COVID-19 patients?

Li, X., Wang, Y., Agostinis, P., Rabson, A., Melino, G., Carafoli, E., Shi, Y. & Sun, E., Jul 1 2020, In : Cell Death and Disease. 11, 7, 512.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Lysosomal protein thermal stability does not correlate with cellular half-life: Global observations and a case study of tripeptidyl-peptidase 1

Collier, A. M., Nemtsova, Y., Kuber, N., Banach-Petrosky, W., Modak, A., Sleat, D. E., Nanda, V. & Lobel, P., 2020, In : Biochemical Journal. 477, 3, p. 727-745 19 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Salivary dysbiosis and the clinical spectrum in anti-Ro positive mothers of children with neonatal lupus

Clancy, R. M., Marion, M. C., Ainsworth, H. C., Blaser, M. J., Chang, M., Howard, T. D., Izmirly, P. M., Lacher, C., Masson, M., Robins, K., Buyon, J. P. & Langefeld, C. D., Feb 2020, In : Journal of Autoimmunity. 107, 102354.

Research output: Contribution to journalArticle

1 Scopus citations

Small protein folds at the root of an ancient metabolic network

Raanan, H., Poudel, S., Pike, D. H., Nanda, V. & Falkowski, P. G., Mar 31 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 13, p. 7193-7199 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

Structural asymmetry does not indicate hemi-phosphorylation in the bacterial histidine kinase CpxA

Bouillet, S., Wu, T., Chen, S., Stock, A. M. & Gao, R., Apr 2020, In : Journal of Biological Chemistry. 295, 23

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

The outcome of TGFβ antagonism in metastatic breast cancer models in vivo reflects a complex balance between tumor-suppressive and proprogression activities of TGFβ

Yang, Y., Yang, H. H., Tang, B., Wu, A. M. L., Flanders, K. C., Moshkovich, N., Weinberg, D. S., Welsh, M. A., Weng, J., Ochoa, H. J., Hu, T. Y., Herrmann, M. A., Chen, J., Edmondson, E. F., Mark Simpson, R., Liu, F., Liu, H., Lee, M. P. & Wakefield, L. M., Feb 1 2020, In : Clinical Cancer Research. 26, 3, p. 643-656 14 p.

Research output: Contribution to journalArticle

1 Scopus citations

Work-related adverse respiratory health outcomes at a machine manufacturing facility with a cluster of bronchiolitis, alveolar ductitis and emphysema (BADE)

Cummings, K. J., Stanton, M. L., Kreiss, K., Boylstein, R. J., Park, J. H., Cox-Ganser, J. M., Virji, M. A., Edwards, N. T., Segal, L. N., Blaser, M. J., Weissman, D. N. & Nett, R. J., Jun 1 2020, In : Occupational and Environmental Medicine. 77, 6, p. 386-392 7 p.

Research output: Contribution to journalArticle

1 Scopus citations
2019

A CUGGU/UUGGU-specific MazF homologue from Methanohalobium evestigatum

Ishida, Y., Inouye, K., Ming, O. & Inouye, M., Oct 20 2019, In : Biochemical and Biophysical Research Communications. 518, 3, p. 533-540 8 p.

Research output: Contribution to journalArticle

Analysis of brain and cerebrospinal fluid from mouse models of the three major forms of neuronal ceroid lipofuscinosis reveals changes in the lysosomal proteome

Sleat, D. E., Wiseman, J. A., El-Banna, M., Zheng, H., Zhao, C., Soherwardy, A., Moore, D. F. & Lobel, P., Jan 1 2019, In : Molecular and Cellular Proteomics. 18, 11, p. 2244-2261 18 p.

Research output: Contribution to journalArticle

1 Scopus citations

A Proteomic Screen of Neuronal Cell-Surface Molecules Reveals IgLONs as Structurally Conserved Interaction Modules at the Synapse

Ranaivoson, F. M., Turk, L. S., Ozgul, S., Kakehi, S., von Daake, S., Lopez, N., Trobiani, L., De Jaco, A., Denissova, N., Demeler, B., Özkan, E., Montelione, G. T. & Comoletti, D., Jun 4 2019, In : Structure. 27, 6, p. 893-906.e9

Research output: Contribution to journalArticle

8 Scopus citations

Aryl and Arylalkyl Substituted 3-Hydroxypyridin-2(1H)-ones: Synthesis and Evaluation as Inhibitors of Influenza A Endonuclease

Sagong, H. Y., Bauman, J. D., Nogales, A., Martínez-Sobrido, L., Arnold, E. & LaVoie, E. J., Jun 18 2019, In : ChemMedChem. 14, 12, p. 1204-1223 20 p.

Research output: Contribution to journalArticle

Building bigger beta-barrels

Nanda, V., Jan 21 2019, In : eLife. 8, e44076.

Research output: Contribution to journalArticle

Calorie restriction slows age-related microbiota changes in an Alzheimer’s disease model in female mice

Cox, L. M., Schafer, M. J., Sohn, J., Vincentini, J., Weiner, H. L., Ginsberg, S. D. & Blaser, M. J., Dec 1 2019, In : Scientific reports. 9, 1, 17904.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Catalytic linkage between caspase activity and proteostasis in Archaea

Seth-Pasricha, M., Senn, S., Sanman, L. E., Bogyo, M., Nanda, V., Bidle, K. A. & Bidle, K. D., Jan 2019, In : Environmental microbiology. 21, 1, p. 286-298 13 p.

Research output: Contribution to journalArticle

Computational simulation of adapter length-dependent lasso probe capture efficiency

Liu, J., Shukor, S., Li, S., Tamayo, A., Tosi, L., Larman, B., Nanda, V., Olson, W. K. & Parekkadan, B., May 2019, In : Biomolecules. 9, 5, 199.

Research output: Contribution to journalArticle

Open Access

Daywake, an Anti-siesta Gene Linked to a Splicing-Based Thermostat from an Adjoining Clock Gene

Yang, Y. & Edery, I., May 20 2019, In : Current Biology. 29, 10, p. 1728-1734.e4

Research output: Contribution to journalArticle

2 Scopus citations

Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile

Chen, L. A., Hourigan, S. K., Grigoryan, Z., Gao, Z., Clemente, J. C., Rideout, J. R., Chirumamilla, S., Rabidazeh, S., Saeed, S., Elson, C. O., Oliva-Hemker, M., Blaser, M. J. & Sears, C. L., Apr 1 2019, In : Journal of pediatric gastroenterology and nutrition. 68, 4, p. 502-508 7 p.

Research output: Contribution to journalArticle

1 Scopus citations

De novo design of symmetric ferredoxins that shuttle electrons in vivo

Mutter, A. C., Tyryshkin, A. M., Campbell, I. J., Poudel, S., Bennett, G. N., Silberg, J. J., Nanda, V. & Falkowski, P. G., 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 29, p. 14557-14562 6 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

De novo protein design by citizen scientists

Koepnick, B., Flatten, J., Husain, T., Ford, A., Silva, D. A., Bick, M. J., Bauer, A., Liu, G., Ishida, Y., Boykov, A., Estep, R. D., Kleinfelter, S., Nørgård-Solano, T., Wei, L., Players, F., Montelione, G. T., DiMaio, F., Popović, Z., Khatib, F., Cooper, S. & 1 others, Baker, D., Jun 20 2019, In : Nature. 570, 7761, p. 390-394 5 p.

Research output: Contribution to journalArticle

12 Scopus citations

Development of a Humanized Murine Model for the Study of Oxalobacter formigenes Intestinal Colonization

Pebenito, A. M., Liu, M., Nazzal, L. & Blaser, M. J., Oct 22 2019, In : Journal of Infectious Diseases. 220, 11, p. 1848-1858 11 p.

Research output: Contribution to journalArticle

2 Scopus citations

Drug-like Fragments Inhibit agr-Mediated Virulence Expression in Staphylococcus aureus

Bezar, I. F., Mashruwala, A. A., Boyd, J. M. & Stock, A. M., Dec 1 2019, In : Scientific reports. 9, 1, 6786.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Epidermal growth factor receptor signaling suppresses αvβ6 integrin and promotes periodontal inflammation and bone loss

Bi, J., Koivisto, L., Dai, J., Zhuang, D., Jiang, G., Larjava, M., Shen, Y., Bi, L., Liu, F., Haapasalo, M., Häkkinen, L. & Larjava, H., Dec 5 2019, In : Journal of cell science. 133, 5

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Epistasis and entrenchment of drug resistance in HIV-1 subtype B

Biswas, A., Haldane, A., Arnold, E. & Levy, R. M., Oct 2019, In : eLife. 8, e50524.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Fecal microbiome characteristics and the resistome associated with acquisition of multidrug-resistant organisms among elderly subjects

Araos, R., Battaglia, T., Ugalde, J. A., Rojas-Herrera, M., Blaser, M. J. & D’agata, E. M. C., Sep 1 2019, In : Frontiers in Microbiology. 10, SEP, 2260.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Berman, H. M., Adams, P. D., Bonvin, A. A., Burley, S. K., Carragher, B., Chiu, W., DiMaio, F., Ferrin, T. E., Gabanyi, M. J., Goddard, T. D., Griffin, P. R., Haas, J., Hanke, C. A., Hoch, J. C., Hummer, G., Kurisu, G., Lawson, C. L., Leitner, A., Markley, J. L., Meiler, J. & 18 others, Montelione, G. T., Phillips, G. N., Prisner, T., Rappsilber, J., Schriemer, D. C., Schwede, T., Seidel, C. A. M., Strutzenberg, T. S., Svergun, D. I., Tajkhorshid, E., Trewhella, J., Vallat, B., Velankar, S., Vuister, G. W., Webb, B., Westbrook, J. D., White, K. L. & Sali, A., Dec 3 2019, In : Structure. 27, 12, p. 1745-1759 15 p.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Genome-wide screening for identification of novel toxin-antitoxin systems in Staphylococcus aureus

Kato, F., Yoshizumi, S., Yamaguchi, Y. & Inouye, M., 2019, In : Applied and environmental microbiology. 85, 20, e00915-19.

Research output: Contribution to journalArticle

2 Scopus citations

Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course

Ventura, R. E., Iizumi, T., Battaglia, T., Liu, M., Perez-Perez, G. I., Herbert, J. & Blaser, M. J., Dec 1 2019, In : Scientific reports. 9, 1, 16396.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Helicobacter pylori lipids can form ordered membrane domains (rafts)

Huang, Z., Zhang, X. S., Blaser, M. J. & London, E., Nov 1 2019, In : Biochimica et Biophysica Acta - Biomembranes. 1861, 11, 183050.

Research output: Contribution to journalArticle

Identification of MazF Homologue in Legionella pneumophila Which Cleaves RNA at the AACU Sequence

Shaku, M., Park, J. H., Inouye, M. & Yamaguchi, Y., Jul 1 2019, In : Journal of molecular microbiology and biotechnology. 28, 6, p. 269-280 12 p.

Research output: Contribution to journalArticle

2 Scopus citations

Immunization against poly-N-acetylglucosamine reduces neutrophil activation and GVHD while sparing microbial diversity

Hülsdünker, J., Thomas, O. S., Haring, E., Unger, S., Núñez, N. G., Tugues, S., Gao, Z., Duquesne, S., Cywes-Bentley, C., Oyardi, O., Kirschnek, S., Schmitt-Graeff, A., Pabst, O., Koenecke, C., Duyster, J., Apostolova, P., Blaser, M. J., Becher, B., Pier, G. B., Häcker, G. & 1 others, Zeiser, R., Oct 8 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 41, p. 20700-20706 7 p.

Research output: Contribution to journalArticle

Open Access

Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity

Shen, N., Caixàs, A., Ahlers, M., Patel, K., Gao, Z., Dutia, R., Blaser, M. J., Clemente, J. C. & Laferrère, B., Aug 2019, In : Surgery for Obesity and Related Diseases. 15, 8, p. 1367-1373 7 p.

Research output: Contribution to journalArticle

10 Scopus citations

Longitudinal comparison of bacterial diversity and antibiotic resistance genes in New York City sewage

Joseph, S. M., Battaglia, T., Maritz, J. M., Carlton, J. M. & Blaser, M. J., 2019, In : mSystems. 4, 4, e00327-19.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Long-term effects of early-life antibiotic exposure on resistance to subsequent bacterial infection

Roubaud-Baudron, C., Ruiz, V. E., Swan, A. M., Vallance, B. A., Ozkul, C., Pei, Z., Li, J., Battaglia, T. W., Perez-Perez, G. I. & Blaser, M. J., Nov 1 2019, In : mBio. 10, 6, e02820-19.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Michael G. Rossmann (1930-2019)

Wu, H. & Arnold, E., Aug 1 2019, In : Nature structural & molecular biology. 26, 8, p. 660-662 3 p.

Research output: Contribution to journalArticle

Open Access
Open Access

PET-RAFT and SAXS: High Throughput Tools to Study Compactness and Flexibility of Single-Chain Polymer Nanoparticles

Upadhya, R., Murthy, N. S., Hoop, C. L., Kosuri, S., Nanda, V., Kohn, J., Baum, J. & Gormley, A. J., Nov 12 2019, In : Macromolecules. 52, 21, p. 8295-8304 10 p.

Research output: Contribution to journalArticle

2 Scopus citations

Protein structure prediction assisted with sparse NMR data in CASP13

Sala, D., Huang, Y. J., Cole, C. A., Snyder, D. A., Liu, G., Ishida, Y., Swapna, G. V. T., Brock, K. P., Sander, C., Fidelis, K., Kryshtafovych, A., Inouye, M., Tejero, R., Valafar, H., Rosato, A. & Montelione, G. T., Dec 1 2019, In : Proteins: Structure, Function and Bioinformatics. 87, 12, p. 1315-1332 18 p.

Research output: Contribution to journalArticle