Research Output

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Review article
2020

In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display

Newton, M. S., Cabezas-Perusse, Y., Tong, C. L. & Seelig, B., Feb 21 2020, In : ACS Synthetic Biology. 9, 2, p. 181-190 10 p.

Research output: Contribution to journalReview article

2019

Algae as a green technology for heavy metals removal from various wastewater

Salama, E. S., Roh, H. S., Dev, S., Khan, M. A., Abou-Shanab, R. A. I., Chang, S. W. & Jeon, B. H., May 1 2019, In : World Journal of Microbiology and Biotechnology. 35, 5, 75.

Research output: Contribution to journalReview article

2 Scopus citations

Biological Conversion of Amino Acids to Higher Alcohols

El-Dalatony, M. M., Saha, S., Govindwar, S. P., Abou-Shanab, R. A. I. & Jeon, B. H., Aug 2019, In : Trends in biotechnology. 37, 8, p. 855-869 15 p.

Research output: Contribution to journalReview article

5 Scopus citations

Biosynthesis and chemical diversity of β-lactone natural products

Robinson, S. L., Christenson, J. K. & Wackett, L. P., Mar 2019, In : Natural Product Reports. 36, 3, p. 458-475 18 p.

Research output: Contribution to journalReview article

17 Scopus citations

Dietary factors in sulfur metabolism and pathogenesis of ulcerative colitis

Teigen, L. M., Geng, Z., Sadowsky, M. J., Vaughn, B. P., Hamilton, M. J. & Khoruts, A., Apr 2019, In : Nutrients. 11, 4, 931.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

Mechanisms of toxicity by and resistance to ferrous iron in anaerobic systems

Bennett, B. D. & Gralnick, J. A., Aug 20 2019, In : Free Radical Biology and Medicine. 140, p. 167-171 5 p.

Research output: Contribution to journalReview article

Open Access
Open Access
5 Scopus citations
2018

Aquatic Invasive Species in the Great Lakes Region: An Overview

Escobar, L. E., Mallez, S., McCartney, M., Lee, C., Zielinski, D. P., Ghosal, R., Bajer, P. G., Wagner, C., Nash, B., Tomamichel, M., Venturelli, P., Mathai, P. P., Kokotovich, A., Escobar-Dodero, J. & Phelps, N. B. D., Jan 2 2018, In : Reviews in Fisheries Science and Aquaculture. 26, 1, p. 121-138 18 p.

Research output: Contribution to journalReview article

7 Scopus citations

Enhancement of microalgal growth and biocomponent-based transformations for improved biofuel recovery: A review

Salama, E. S., Hwang, J. H., El-Dalatony, M. M., Kurade, M. B., Kabra, A. N., Abou-Shanab, R. A. I., Kim, K. H., Yang, I. S., Govindwar, S. P., Kim, S. & Jeon, B. H., Jun 2018, In : Bioresource Technology. 258, p. 365-375 11 p.

Research output: Contribution to journalReview article

11 Scopus citations

Enzyme evolution: innovation is easy, optimization is complicated

Newton, M. S., Arcus, V. L., Gerth, M. L. & Patrick, W. M., Feb 2018, In : Current Opinion in Structural Biology. 48, p. 110-116 7 p.

Research output: Contribution to journalReview article

Open Access
23 Scopus citations

Functional Genomics of Host–Microbiome Interactions in Humans

Luca, F., Kupfer, S. S., Knights, D., Khoruts, A. & Blekhman, R., Jan 2018, In : Trends in Genetics. 34, 1, p. 30-40 11 p.

Research output: Contribution to journalReview article

Open Access
20 Scopus citations

SHI7 is a self-learning pipeline for multipurpose short-read DNA quality control

Al-Ghalith, G. A., Hillmann, B., Ang, K., Shields-Cutler, R. & Knights, D., May 1 2018, In : mSystems. 3, 3, e00202-17.

Research output: Contribution to journalReview article

Open Access
17 Scopus citations

Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications

Le Bastard, Q., Al-Ghalith, G. A., Grégoire, M., Chapelet, G., Javaudin, F., Dailly, E., Batard, E., Knights, D. & Montassier, E., Feb 1 2018, In : Alimentary Pharmacology and Therapeutics. 47, 3, p. 332-345 14 p.

Research output: Contribution to journalReview article

Open Access
48 Scopus citations

The gut microbiome of nonhuman primates: Lessons in ecology and evolution

Clayton, J. B., Gomez, A., Amato, K., Knights, D., Travis, D. A., Blekhman, R., Knight, R., Leigh, S., Stumpf, R., Wolf, T., Glander, K. E., Cabana, F. & Johnson, T. J., Jun 2018, In : American journal of primatology. 80, 6, e22867.

Research output: Contribution to journalReview article

21 Scopus citations
2017

Advances in the use of genetically modified plant biomass for biodiesel generation

Wan, S., Truong-Trieu, V. M. T., Ward, T., Whalen, J. K. & Altosaar, I., Jan 1 2017, In : Biofuels, Bioproducts and Biorefining. 11, 4, p. 749-764 16 p.

Research output: Contribution to journalReview article

5 Scopus citations

Environmental Escherichia coli: ecology and public health implications—a review

Jang, J., Hur, H. G., Sadowsky, M. J., Byappanahalli, M. N., Yan, T. & Ishii, S., Sep 2017, In : Journal of Applied Microbiology. 123, 3, p. 570-581 12 p.

Research output: Contribution to journalReview article

Open Access
62 Scopus citations

Experimental evolution and proximate mechanisms in biology

Yi, X., Dec 2017, In : Synthetic and Systems Biotechnology. 2, 4, p. 253-258 6 p.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

Infant fungal communities: Current knowledge and research opportunities

Ward, T. L., Knights, D. & Gale, C. A., Feb 13 2017, In : BMC medicine. 15, 1, 30.

Research output: Contribution to journalReview article

Open Access
14 Scopus citations

Interaction of gut microbiota with bile acid metabolism and its influence on disease states

Staley, C., Weingarden, A. R., Khoruts, A. & Sadowsky, M. J., Jan 1 2017, In : Applied Microbiology and Biotechnology. 101, 1, p. 47-64 18 p.

Research output: Contribution to journalReview article

Open Access
84 Scopus citations

Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review

Shamseldin, A., Abdelkhalek, A. & Sadowsky, M. J., Feb 1 2017, In : Symbiosis. 71, 2, p. 91-109 19 p.

Research output: Contribution to journalReview article

13 Scopus citations

Recent progress in microalgal biomass production coupled with wastewater treatment for biofuel generation

Salama, E. S., Kurade, M. B., Abou-Shanab, R. A. I., El-Dalatony, M. M., Yang, I. S., Min, B. & Jeon, B. H., Jan 1 2017, In : Renewable and Sustainable Energy Reviews. 79, p. 1189-1211 23 p.

Research output: Contribution to journalReview article

120 Scopus citations
11 Scopus citations
2016

A revised classification of the Icteridae (Aves) based on DNA sequence data

Remsen, J. V., Powell, A. F. L. A., Schodde, R., Barker, F. K. & Lanyon, S. M., Mar 22 2016, In : Zootaxa. 4093, 2, p. 285-292 8 p.

Research output: Contribution to journalReview article

6 Scopus citations
2015

Antibiotics, pediatric dysbiosis, and disease

Vangay, P., Ward, T., Gerber, J. S. & Knights, D., May 13 2015, In : Cell Host and Microbe. 17, 5, p. 553-564 12 p.

Research output: Contribution to journalReview article

178 Scopus citations

Bygiene: The new paradigm of bidirectional hygiene

Al-Ghalith, G. A. & Knights, D., Dec 2015, In : Yale Journal of Biology and Medicine. 88, 4, p. 359-365 7 p.

Research output: Contribution to journalReview article

6 Scopus citations

Coffee provides a natural multitarget pharmacopeia against the hallmarks of cancer

Gaascht, F., Dicato, M. & Diederich, M., Nov 1 2015, In : Genes and Nutrition. p. 1-17 17 p.

Research output: Contribution to journalReview article

29 Scopus citations

Development of Fecal Microbiota Transplantation Suitable for Mainstream Medicine

Khoruts, A., Sadowsky, M. J. & Hamilton, M. J., Jan 1 2015, In : Clinical Gastroenterology and Hepatology. 13, 2, p. 246-250 5 p.

Research output: Contribution to journalReview article

25 Scopus citations

How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: The Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes

Rauwerdink, A. & Kazlauskas, R. J., Oct 2 2015, In : ACS Catalysis. 5, 10, p. 6153-6176 24 p.

Research output: Contribution to journalReview article

69 Scopus citations

Leishmania cell wall as a potent target for antiparasitic drugs. A focus on the glycoconjugates

Cabezas, Y., Legentil, L., Robert-Gangneux, F., Daligault, F., Belaz, S., Nugier-Chauvin, C., Tranchimand, S., Tellier, C., Gangneux, J. P. & Ferrières, V., Aug 21 2015, In : Organic and Biomolecular Chemistry. 13, 31, p. 8393-8404 12 p.

Research output: Contribution to journalReview article

17 Scopus citations

Rapid bursts and slow declines: On the possible evolutionary trajectories of enzymes

Newton, M. S., Arcus, V. L. & Patrick, W. M., Jun 6 2015, In : Journal of the Royal Society Interface. 12, 107, 20150036.

Research output: Contribution to journalReview article

17 Scopus citations

The Influence of Bariatric Surgery on Serum Bile Acids in Humans and Potential Metabolic and Hormonal Implications: a Systematic Review

Johnson, A. J., Teigen, L. M., Jahansouz, C., Earthman, C. P. & Sibley, S. D., Dec 1 2015, In : Current obesity reports. 4, 4, p. 441-450 10 p.

Research output: Contribution to journalReview article

17 Scopus citations
2014

Aptamers as drug delivery vehicles

Kruspe, S., Mittelberger, F., Szameit, K. & Hahn, U., Jan 1 2014, In : ChemMedChem. 9, 9, p. 1998-2011 14 p.

Research output: Contribution to journalReview article

36 Scopus citations

Designer microbes for biosynthesis

Quin, M. B. & Schmidt-Dannert, C., Oct 2014, In : Current opinion in biotechnology. 29, 1, p. 55-61 7 p.

Research output: Contribution to journalReview article

16 Scopus citations

Multi-omics analysis of inflammatory bowel disease

Huang, H., Vangay, P., McKinlay, C. E. & Knights, D., Dec 1 2014, In : Immunology Letters. 162, 2, p. 62-68 7 p.

Research output: Contribution to journalReview article

19 Scopus citations

Staphylococcal superantigens interact with multiple host receptors to cause serious diseases

Stach, C. S., Herrera, A. & Schlievert, P. M., Aug 2014, In : Immunologic Research. 59, 1-3, p. 177-181 5 p.

Research output: Contribution to journalReview article

33 Scopus citations

Traversing the fungal terpenome

Quin, M. B., Flynn, C. M. & Schmidt-Dannert, C., Oct 1 2014, In : Natural Product Reports. 31, 10, p. 1449-1473 25 p.

Research output: Contribution to journalReview article

103 Scopus citations

Vitamin D status following bariatric surgery: Implications and recommendations

Johnson, A. J., Beckman, L. M. & Earthman, C. P., Dec 20 2014, In : Nutrition in Clinical Practice. 29, 6, p. 751-758 8 p.

Research output: Contribution to journalReview article

20 Scopus citations
2013

Anticancer bioactivity of compounds from medicinal plants used in European medieval traditions

Teiten, M. H., Gaascht, F., Dicato, M. & Diederich, M., 2013, In : Biochemical Pharmacology. p. 1239-1247 9 p.

Research output: Contribution to journalReview article

43 Scopus citations

Energy, ecology and the distribution of microbial life

Macalady, J. L., Hamilton, T. L., Grettenberger, C. L., Jones, D. S., Tsao, L. E. & Burgos, W. D., Jul 19 2013, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 368, 1622

Research output: Contribution to journalReview article

11 Scopus citations

Human milk metagenome: A functional capacity analysis

Ward, T. L., Hosid, S., Ioshikhes, I. & Altosaar, I., May 28 2013, In : BMC microbiology. 13, 1, 116.

Research output: Contribution to journalReview article

95 Scopus citations
2012

Aurones: interesting natural and synthetic compounds with emerging biological potential.

Zwergel, C., Gaascht, F., Valente, S., Diederich, M., Bagrel, D. & Kirsch, G., 2012, In : Natural Product Communications. 7, 3, p. 389-94 6 p.

Research output: Contribution to journalReview article

35 Scopus citations

Gene technology in agriculture, environment and biopharming: Beyond Bt-Rice and building better breeding budgets for crops

Zaidi, M. A., El Bilali, J., Koziol, A. G., Ward, T. L., Styles, G., Greenham, T. J., Faiella, W. M., Son, H. H., Wan, S., Taga, I. & Altosaar, I., Oct 2012, In : Journal of Plant Biochemistry and Biotechnology. 21, p. S2-S9

Research output: Contribution to journalReview article

2 Scopus citations

Human gut microbiome viewed across age and geography

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., Knight, R. & 1 others, Gordon, J. I., Jun 14 2012, In : Nature. 486, 7402, p. 222-227 6 p.

Research output: Contribution to journalReview article

3063 Scopus citations

Shuttling happens: Soluble flavin mediators of extracellular electron transfer in Shewanella

Brutinel, E. D. & Gralnick, J. A., Jan 1 2012, In : Applied Microbiology and Biotechnology. 93, 1, p. 41-48 8 p.

Research output: Contribution to journalReview article

168 Scopus citations

Strategy and tactics of disarming GHG at the source: N 2O reductase crops

Wan, S., Ward, T. L. & Altosaar, I., Aug 1 2012, In : Trends in biotechnology. 30, 8, p. 410-415 6 p.

Research output: Contribution to journalReview article

11 Scopus citations

Targeting the Wingless Signaling Pathway with Natural Compounds as Chemopreventive or Chemotherapeutic Agents

Teiten, M-H., Gaascht, F., Dicato, M. & Diederich, M., 2012, In : Current Pharmaceutical Biotechnology. 13, p. 245-254 10 p.

Research output: Contribution to journalReview article

29 Scopus citations
2011

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation

Zaneveld, J. R. R., Parfrey, L. W., Van Treuren, W., Lozupone, C., Clemente, J. C., Knights, D., Stombaugh, J., Kuczynski, J. & Knight, R., Oct 1 2011, In : Trends in Microbiology. 19, 10, p. 472-482 11 p.

Research output: Contribution to journalReview article

19 Scopus citations

Engineering of biocatalysts: From evolution to creation

Quin, M. B. & Schmidt-Dannert, C., Sep 2 2011, In : ACS Catalysis. 1, 9, p. 1017-1021 5 p.

Research output: Contribution to journalReview article

61 Scopus citations

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

306 Scopus citations

Saccharomyces cerivisiae as a model system for kidney disease: What can yeast tell us about renal function?

Kolb, A. R., Buck, T. M. & Brodsky, J. L., Jul 1 2011, In : American Journal of Physiology - Renal Physiology. 301, 1, p. F1-F11

Research output: Contribution to journalReview article

10 Scopus citations