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

Research Output 1961 2020

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Review article
2020

Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance

Xavier RUIZ, F. & Arnold, E., Apr 2020, In : Current Opinion in Structural Biology. 61, p. 113-123 11 p.

Research output: Contribution to journalReview article

RNA-Directed DNA Polymerase
HIV
Investigational Drugs
Human immunodeficiency virus 1 reverse transcriptase
Life Cycle Stages
2019
1 Citation (Scopus)

Alpha-carboxynucleoside phosphonates: Direct-acting inhibitors of viral DNA polymerases

Balzarini, J., Ford, A., Maguire, N. M., John, J., Das, K., Arnold, E., Dehaen, W. & Maguire, A., Jan 2019, In : Future Medicinal Chemistry. 11, 2, p. 137-154 18 p.

Research output: Contribution to journalReview article

Nucleic Acid Synthesis Inhibitors
Organophosphonates
Viral DNA
DNA-Directed DNA Polymerase
Nucleosides
2 Citations (Scopus)

Structural basis of response regulator function

Gao, R., Bouillet, S. & Stock, A. M., Jan 1 2019, In : Annual Review of Microbiology. 73, p. 175-197 23 p.

Research output: Contribution to journalReview article

Phosphorylation
Histidine Kinase

The role of the changing human microbiome in the asthma pandemic

Borbet, T. C., Zhang, X., Müller, A. & Blaser, M. J., Dec 2019, In : Journal of Allergy and Clinical Immunology. 144, 6, p. 1457-1466 10 p.

Research output: Contribution to journalReview article

Microbiota
Pandemics
Asthma
Helicobacter pylori
Allergens

What do archaeal and eukaryotic histidine kinases sense?

Papon, N. & Stock, A. M., Jan 1 2019, In : F1000Research. 8

Research output: Contribution to journalReview article

Open Access
Eukaryota
Histidine
Archaea
Bacteria
Phosphotransferases
2018
3 Citations (Scopus)
Kidney Calculi
Communicable Diseases
Anti-Bacterial Agents
Delivery of Health Care
16 Citations (Scopus)

Preserving microbial diversity: Microbiota from humans of all cultures are needed to ensure the health of future generations

Dominguez Bello, M. G., Knight, R., Gilbert, J. A. & Blaser, M. J., Oct 5 2018, In : Science. 362, 6410, p. 33-34 2 p.

Research output: Contribution to journalReview article

Biological Specimen Banks
Microbiota
Social Responsibility
Health
Gastrointestinal Microbiome

Using Human Induced Neural Precursor Cells to Define Early Neurodevelopmental Defects in Syndromic and Idiopathic Autism

Connacher, R. J., Dicicco-Bloom, E. & Millonig, J., Dec 1 2018, In : Current Pharmacology Reports. 4, 6, p. 422-435 14 p.

Research output: Contribution to journalReview article

Autistic Disorder
Stem cells
Induced Pluripotent Stem Cells
Defects
Throughput
2017
14 Citations (Scopus)

Hypoxia-inducible factor-1α target genes contribute to retinal neuroprotection

Cheng, L., Yu, H., Yan, N., Lai, K. & Xiang, M., Feb 27 2017, In : Frontiers in Cellular Neuroscience. 11, 20.

Research output: Contribution to journalReview article

Hypoxia-Inducible Factor 1
Genes
Retinal Vein Occlusion
Retinal Diseases
Macular Degeneration
2 Citations (Scopus)

Searching for the Pareto frontier in multi-objective protein design

Nanda, V., Belure, S. V. & Shir, O. M., Aug 1 2017, In : Biophysical Reviews. 9, 4, p. 339-344 6 p.

Research output: Contribution to journalReview article

Protein Engineering
Proteins
Computational Biology
Collagen
Economics
23 Citations (Scopus)

Toxins of prokaryotic toxin-antitoxin systems with sequence-specific endoribonuclease activity

Masuda, H. & Inouye, M., Apr 14 2017, In : Toxins. 9, 4, 140.

Research output: Contribution to journalReview article

Endoribonucleases
Antitoxins
RNA
Digestion
Ribosomes
2016
5 Citations (Scopus)

A community resource of experimental data for NMR / X-ray crystal structure pairs

Everett, J. K., Tejero, R., Murthy, S. B. K., Acton, T. B., Aramini, J. M., Baran, M. C., Benach, J., Cort, J. R., Eletsky, A., Forouhar, F., Guan, R., Kuzin, A. P., Lee, H. W., Liu, G., Mani, R., Mao, B., Mills, J. L., Montelione, A. F., Pederson, K., Powers, R. & 16 others, Ramelot, T., Rossi, P., Seetharaman, J., Snyder, D., Swapna, G. V. T., Vorobiev, S. M., Wu, Y., Xiao, R., Yang, Y., Arrowsmith, C. H., Hunt, J. F., Kennedy, M. A., Prestegard, J. H., Szyperski, T., Tong, L. & Montelione, G. T., Jan 1 2016, In : Protein Science. 25, 1, p. 30-45 16 p.

Research output: Contribution to journalReview article

Crystal structure
Nuclear magnetic resonance
X-Rays
X rays
Biomolecular Nuclear Magnetic Resonance
22 Citations (Scopus)

Rab1 in cell signaling, cancer and other diseases

Yang, X. Z., Li, X. X., Zhang, Y. J., Rodriguez-Rodriguez, L., Xiang, M., Wang, H. Y. & Zheng, X. F. S., Nov 3 2016, In : Oncogene. 35, 44, p. 5699-5704 6 p.

Research output: Contribution to journalReview article

rab1 GTP-Binding Proteins
Endoplasmic Reticulum
rab GTP-Binding Proteins
Membranes
Monomeric GTP-Binding Proteins
60 Citations (Scopus)

The intestinal microbiome and estrogen receptor-positive female breast cancer

Kwa, M., Plottel, C. S., Blaser, M. J. & Adams, S., Jan 1 2016, In : Journal of the National Cancer Institute. 108, 8, djw029.

Research output: Contribution to journalReview article

Open Access
Microbiota
Estrogen Receptors
Estrogens
Metagenome
Breast Neoplasms
2015
115 Citations (Scopus)

A unified initiative to harness Earth's microbiomes: Transition from description to causality and engineering

Alivisatos, A. P., Blaser, M. J., Brodie, E. L., Chun, M., Dangl, J. L., Donohue, T. J., Dorrestein, P. C., Gilbert, J. A., Green, J. L., Jansson, J. K., Knight, R., Maxon, M. E., McFall-Ngai, M. J., Miller, J. F., Pollard, K. S., Ruby, E. G. & Taha, S. A., Oct 30 2015, In : Science. 350, 6260, p. 507-508 2 p.

Research output: Contribution to journalReview article

44 Citations (Scopus)

Helsinki alert of biodiversity and health

Von Hertzen, L., Beutler, B., Bienenstock, J., Blaser, M., Cani, P. D., Eriksson, J., Färkkilä, M., Haahtela, T., Hanski, I., Jenmalm, M. C., Kere, J., Knip, M., Kontula, K., Koskenvuo, M., Ling, C., Mandrup-Poulsen, T., Von Mutius, E., Mäkelä, M. J., Paunio, T., Pershagen, G. & 6 others, Renz, H., Rook, G., Saarela, M., Vaarala, O., Veldhoen, M. & De Vos, W. M., May 1 2015, In : Annals of Medicine. 47, 3, p. 218-225 8 p.

Research output: Contribution to journalReview article

Biodiversity
Microbiota
Immune Tolerance
Health
Life Style
2014
19 Citations (Scopus)

Drug resistance in non-B subtype HIV-1: Impact of HIV-1 reverse transcriptase inhibitors

Singh, K., Flores, J. A., Kirby, K. A., Neogi, U., Sonnerborg, A., Hachiya, A., Das, K., Arnold, E., McArthur, C., Parniak, M. & Sarafianos, S. G., Sep 24 2014, In : Viruses. 6, 9, p. 3535-3562 28 p.

Research output: Contribution to journalReview article

Reverse Transcriptase Inhibitors
Drug Resistance
HIV-1
HIV
Virus Diseases
111 Citations (Scopus)

The microbiome revolution

Blaser, M. J., Oct 1 2014, In : Journal of Clinical Investigation. 124, 10, p. 4162-4165 4 p.

Research output: Contribution to journalReview article

Open Access
Microbiota
Metabolic Diseases
Xenobiotics
Human Body
Immunity
2013
8 Citations (Scopus)

Foxn4: A multi-faceted transcriptional regulator of cell fates in vertebrate development

Xiang, M. & Li, S. G., Nov 1 2013, In : Science China Life Sciences. 56, 11, p. 985-993 9 p.

Research output: Contribution to journalReview article

Vertebrates
vertebrate
transcription factors
vertebrates
Tissue
82 Citations (Scopus)

HIV-1 reverse transcriptase and antiviral drug resistance. Part 1

Das, K. & Arnold, E., Apr 2013, In : Current Opinion in Virology. 3, 2, p. 111-118 8 p.

Research output: Contribution to journalReview article

Viral Drug Resistance
RNA-Directed DNA Polymerase
Anti-HIV Agents
Mutation
Reverse Transcriptase Inhibitors
55 Citations (Scopus)

HIV-1 reverse transcriptase and antiviral drug resistance. Part 2

Das, K. & Arnold, E., Apr 2013, In : Current Opinion in Virology. 3, 2, p. 119-128 10 p.

Research output: Contribution to journalReview article

Viral Drug Resistance
Drug Resistance
Pharmaceutical Preparations
Mutation
HIV-1
41 Citations (Scopus)

Intrinsic control of mammalian retinogenesis

Xiang, M., Jul 1 2013, In : Cellular and Molecular Life Sciences. 70, 14, p. 2519-2532 14 p.

Research output: Contribution to journalReview article

Intrinsic Factor
Neuroglia
Untranslated RNA
Computational Biology
Mental Competency
140 Citations (Scopus)

Pathways in microbe-induced obesity

Cox, L. M. & Blaser, M. J., Jun 4 2013, In : Cell Metabolism. 17, 6, p. 883-894 12 p.

Research output: Contribution to journalReview article

Open Access
Microbiota
Obesity
Hibernation
Gastric Bypass
Diet
17 Citations (Scopus)

Quality assessment of protein NMR structures

Rosato, A., Tejero, R. & Montelione, G. T., Oct 1 2013, In : Current Opinion in Structural Biology. 23, 5, p. 715-724 10 p.

Research output: Contribution to journalReview article

Biomolecular Nuclear Magnetic Resonance
Biota
Protein Databases
Proteins
Computational Biology
2012
307 Citations (Scopus)

How mesenchymal stem cells interact with tissue immune responses

Shi, Y., Su, J., Roberts, A. I., Shou, P., Rabson, A. & Ren, G., Mar 1 2012, In : Trends in Immunology. 33, 3, p. 136-143 8 p.

Research output: Contribution to journalReview article

Mesenchymal Stromal Cells
Adaptive Immunity
Innate Immunity
Regeneration
Wounds and Injuries
2011
167 Citations (Scopus)

Microbiome and malignancy

Plottel, C. S. & Blaser, M. J., Oct 4 2011, In : Cell Host and Microbe. 10, 4, p. 324-335 12 p.

Research output: Contribution to journalReview article

Open Access
Microbiota
Neoplasms
Microbial Interactions
Environmental Carcinogens
Viruses
293 Citations (Scopus)

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., Gilbert, J. A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., Vaughan, R., Hunter, C., Park, J., Morrison, N., Rocca-Serra, P., Sterk, P., Arumugam, M., Bailey, M., Baumgartner, L., Birren, B. W. & 78 others, Blaser, M. J., Bonazzi, V., Booth, T., Bork, P., Bushman, F. D., Buttigieg, P. L., Chain, P. S. G., Charlson, E., Costello, E. K., Huot-Creasy, H., Dawyndt, P., Desantis, T., Fierer, N., Fuhrman, J. A., Gallery, R. E., Gevers, D., Gibbs, R. A., Gil, I. S., Gonzalez, A., Gordon, J. I., Guralnick, R., Hankeln, W., Highlander, S., Hugenholtz, P., Jansson, J., Kau, A. L., Kelley, S. T., Kennedy, J., Knights, D., Koren, O., Kuczynski, J., Kyrpides, N., Larsen, R., Lauber, C. L., Legg, T., Ley, R. E., Lozupone, C. A., Ludwig, W., Lyons, D., Maguire, E., Methé, B. A., Meyer, F., Muegge, B., Nakielny, S., Nelson, K. E., Nemergut, D., Neufeld, J. D., Newbold, L. K., Oliver, A. E., Pace, N. R., Palanisamy, G., Peplies, J., Petrosino, J., Proctor, L., Pruesse, E., Quast, C., Raes, J., Ratnasingham, S., Ravel, J., Relman, D. A., Assunta-Sansone, S., Schloss, P. D., Schriml, L., Sinha, R., Smith, M. I., Sodergren, E., Spor, A., Stombaugh, J., Tiedje, J. M., Ward, D. V., Weinstock, G. M., Wendel, D., White, O., Whiteley, A., Wilke, A., Wortman, J. R., Yatsunenko, T. & Glöckner, F. O., May 1 2011, In : Nature biotechnology. 29, 5, p. 415-420 6 p.

Research output: Contribution to journalReview article

Genes
Specifications
Checklist
DNA Sequence Analysis
Ecosystems
217 Citations (Scopus)

Regulation of growth and death in Escherichia coli by toxin-antitoxin systems

Yamaguchi, Y. & Inouye, M., Nov 1 2011, In : Nature Reviews Microbiology. 9, 11, p. 779-790 12 p.

Research output: Contribution to journalReview article

Antitoxins
Escherichia coli
Growth
Cell Physiological Phenomena
Multiple Drug Resistance
13 Citations (Scopus)

The effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone redox species between the photochemical reaction center and the ubiquinol-cytochrome c 2 oxidoreductase

Woronowicz, K., Sha, D., Frese, R. N., Sturgis, J. N., Nanda, V. & Niederman, R., Aug 1 2011, In : Metallomics. 3, 8, p. 765-774 10 p.

Research output: Contribution to journalReview article

Photosynthetic membranes
Photochemical reactions
Cytochromes c
Oxidation-Reduction
Oxidoreductases
2010
11 Citations (Scopus)

Advances in protein NMR provided by the NIGMS Protein Structure Initiative: Impact on drug discovery

Montelione, G. & Szyperski, T., May 1 2010, In : Current Opinion in Drug Discovery and Development. 13, 3, p. 335-349 15 p.

Research output: Contribution to journalReview article

National Institute of General Medical Sciences (U.S.)
Drug Discovery
Drug Design
Genomics
Proteins
59 Citations (Scopus)

A microscale protein NMR sample screening pipeline

Rossi, P., Swapna, G. V. T., Huang, Y. J., Aramini, J. M., Anklin, C., Conover, K., Hamilton, K., Xiao, R., Acton, T. B., Ertekin, A., Everett, J. K. & Montelione, G. T., Jan 1 2010, In : Journal of biomolecular NMR. 46, 1, p. 11-22 12 p.

Research output: Contribution to journalReview article

Screening
Pipelines
Nuclear magnetic resonance
Genomics
Proteins
163 Citations (Scopus)

Designing artificial enzymes by intuition and computation

Nanda, V. & Koder, R. L., Jan 1 2010, In : Nature Chemistry. 2, 1, p. 15-24 10 p.

Research output: Contribution to journalReview article

Enzymes
Computational methods
Proteins
Catalysts
Catalyst selectivity
106 Citations (Scopus)

Molecular strategies for phosphorylation-mediated regulation of response regulator activity

Gao, R. & Stock, A., Apr 1 2010, In : Current Opinion in Microbiology. 13, 2, p. 160-167 8 p.

Research output: Contribution to journalReview article

Phosphorylation
Proteins
Dimerization
222 Citations (Scopus)

Structures of influenza A proteins and insights into antiviral drug targets

Das, K., Aramini, J. M., Ma, L. C., Krug, R. M. & Arnold, E., May 1 2010, In : Nature Structural and Molecular Biology. 17, 5, p. 530-538 9 p.

Research output: Contribution to journalReview article

Influenza A virus
Human Influenza
Antiviral Agents
Proteins
RNA Replicase
2009
422 Citations (Scopus)

Biological insights from structures of two-component proteins

Gao, R. & Stock, A., Oct 1 2009, In : Annual Review of Microbiology. 63, p. 133-154 22 p.

Research output: Contribution to journalReview article

Proteins
Signal Transduction
Phosphorylation
Bacteria
Histidine Kinase
89 Citations (Scopus)

Chapter 12 mRNA Interferases, Sequence-Specific Endoribonucleases from the Toxin-Antitoxin Systems

Yamaguchi, Y. & Inouye, M., Dec 1 2009, In : Progress in Molecular Biology and Translational Science. 85, C, p. 467-500 34 p.

Research output: Contribution to journalReview article

Endoribonucleases
Antitoxins
Messenger RNA
Cell Death
Mycobacterium tuberculosis
334 Citations (Scopus)

Coadaptation of Helicobacter pylori and humans: Ancient history, modern implications

Atherton, J. C. & Blaser, M. J., Sep 1 2009, In : Journal of Clinical Investigation. 119, 9, p. 2475-2487 13 p.

Research output: Contribution to journalReview article

Open Access
Ancient History
Helicobacter pylori
Adenocarcinoma
Bacteria
Genetic Recombination
141 Citations (Scopus)

Proteomics of the lysosome

Lübke, T., Lobel, P. & Sleat, D. E., Apr 1 2009, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1793, 4, p. 625-635 11 p.

Research output: Contribution to journalReview article

Lysosomes
Proteomics
Proteins
Lysosomal Storage Diseases
Medical Genetics
295 Citations (Scopus)

Structure and Function of HIV-1 Reverse Transcriptase: Molecular Mechanisms of Polymerization and Inhibition

Sarafianos, S. G., Marchand, B., Das, K., Himmel, D. M., Parniak, M. A., Hughes, S. H. & Arnold, E., Jan 23 2009, In : Journal of molecular biology. 385, 3, p. 693-713 21 p.

Research output: Contribution to journalReview article

Polymerization
HIV-1
RNA-Directed DNA Polymerase
Pharmaceutical Preparations
Anti-HIV Agents
81 Citations (Scopus)

Structures of RNA polymerase-antibiotic complexes

Ho, M. X., Hudson, B. P., Das, K., Arnold, E. & Ebright, R. H., Dec 1 2009, In : Current Opinion in Structural Biology. 19, 6, p. 715-723 9 p.

Research output: Contribution to journalReview article

DNA-Directed RNA Polymerases
Anti-Bacterial Agents
Rifamycins
Bacterial RNA
DNA
17 Citations (Scopus)

Unique opportunities for NMR methods in structural genomics

Montelione, G., Arrowsmith, C., Girvin, M. E., Kennedy, M. A., Markley, J. L., Powers, R., Prestegard, J. H. & Szyperski, T., Apr 1 2009, In : Journal of Structural and Functional Genomics. 10, 2, p. 101-106 6 p.

Research output: Contribution to journalReview article

Genomics
Nuclear magnetic resonance
Proteins
Buffaloes
Education
2008
74 Citations (Scopus)

Disappearing microbiota: Helicobacter pylori protection against esophageal adenocarcinoma

Blaser, M. J., Oct 1 2008, In : Cancer Prevention Research. 1, 5, p. 308-311 4 p.

Research output: Contribution to journalReview article

Open Access
Microbiota
Biodiversity
Disease Susceptibility
Helicobacter Infections
Esophageal Neoplasms
10 Citations (Scopus)

PCTA: A new player in TGF-β signaling

Liu, F., Nov 14 2008, In : Science signaling. 1, 46, p. pe49

Research output: Contribution to journalReview article

Transforming Growth Factors
Association reactions
Growth Factor Receptors
Phosphorylation
Chemical activation
515 Citations (Scopus)

Protein production and purification

Gräslund, S., Nordlund, P., Weigelt, J., Hallberg, B. M., Bray, J., Gileadi, O., Knapp, S., Oppermann, U., Arrowsmith, C., Hui, R., Ming, J., dhe-Paganon, S., Park, H. W., Savchenko, A., Yee, A., Edwards, A., Vincentelli, R., Cambillau, C., Kim, R., Kim, S. H. & 64 others, Rao, Z., Shi, Y., Terwilliger, T. C., Kim, C. Y., Hung, L. W., Waldo, G. S., Peleg, Y., Albeck, S., Unger, T., Dym, O., Prilusky, J., Sussman, J. L., Stevens, R. C., Lesley, S. A., Wilson, I. A., Joachimiak, A., Collart, F., Dementieva, I., Donnelly, M. I., Eschenfeldt, W. H., Kim, Y., Stols, L., Wu, R., Zhou, M., Burley, S. K., Emtage, J. S., Sauder, J. M., Thompson, D., Bain, K., Luz, J., Gheyi, T., Zhang, F., Atwell, S., Almo, S. C., Bonanno, J. B., Fiser, A., Swaminathan, S., Studier, F. W., Chance, M. R., Sali, A., Acton, T. B., Xiao, R., Zhao, L., Ma, L. C., Hunt, J. F., Tong, L., Cunningham, K., Inouye, M., Anderson, S., Janjua, H., Shastry, R., Ho, C. K., Wang, D., Wang, H., Jiang, M., Montelione, G. T., Stuart, D. I., Owens, R. J., Daenke, S., Schütz, A., Heinemann, U., Yokoyama, S., Büssow, K. & Gunsalus, K. C., Feb 1 2008, In : Nature Methods. 5, 2, p. 135-146 12 p.

Research output: Contribution to journalReview article

Recombinant Proteins
Purification
Decision making
Research Personnel
Consensus
62 Citations (Scopus)

The intramolecular chaperone-mediated protein folding

Chen, Y. J. & Inouye, M., Dec 1 2008, In : Current Opinion in Structural Biology. 18, 6, p. 765-770 6 p.

Research output: Contribution to journalReview article

Protein Folding
Proteins
Peptide Hydrolases
27 Citations (Scopus)

Understanding microbe-induced cancers

Blaser, M. J., Jun 1 2008, In : Cancer Prevention Research. 1, 1, p. 15-20 6 p.

Research output: Contribution to journalReview article

Open Access
Neoplasms
Carcinogenesis
Microbial Interactions
Therapeutics
2007
195 Citations (Scopus)

Bacterial response regulators: versatile regulatory strategies from common domains

Gao, R., Mack, T. R. & Stock, A., May 1 2007, In : Trends in Biochemical Sciences. 32, 5, p. 225-234 10 p.

Research output: Contribution to journalReview article

Cues
Phosphorylation
Genome
Proteins
Genes
19 Citations (Scopus)

Lysosomal proteomics and disease

Sleat, D. E., Jadot, M. & Lobel, P., Sep 1 2007, In : Proteomics - Clinical Applications. 1, 9, p. 1134-1146 13 p.

Research output: Contribution to journalReview article

Proteomics
Organelles
Lysosomes
Macromolecular Substances
Inborn Genetic Diseases
1 Citation (Scopus)

The Raz mTaz of human mesenchymal stem cells

Banerjee, D., Glod, J. & Rabson, A., Oct 1 2007, In : Stem Cells and Development. 16, 5, p. 691-693 3 p.

Research output: Contribution to journalReview article

Helper-Inducer T-Lymphocytes
Multiple Myeloma
Mesenchymal Stromal Cells
Dendritic Cells
Tumor Necrosis Factor-alpha
2006
312 Citations (Scopus)

Current insights into the regulation of programmed cell death by NF-κB

Dutta, J., Fan, Y., Gupta, N., Fan, G. & Gelinas, C., Oct 30 2006, In : Oncogene. 25, 51, p. 6800-6816 17 p.

Research output: Contribution to journalReview article

Cell Death
Necrosis
Apoptosis
Neoplasms
Oncogenes