Research Output

2018

Defect-facilitated buckling in supercoiled double-helix DNA

Brahmachari, S., Dittmore, A., Takagi, Y., Neuman, K. C. & Marko, J. F., Feb 28 2018, In : Physical Review E. 97, 2, 022416.

Research output: Contribution to journalArticle

3 Scopus citations

Design, implementation, and evaluation of a multi-disciplinary professional development program for research mentors

Brace, J. L., Baiduc, R. R., Drane, D. L., Flores, L. C., Beitel, G. J. & Lo, S. M., Aug 8 2018, In : Mentoring and Tutoring: Partnership in Learning. 26, 4, p. 377-399 23 p.

Research output: Contribution to journalArticle

1 Scopus citations

Direct membrane binding and self-interaction contribute to Mmr1 function in mitochondrial inheritance

Chen, W. T., Ping, H. A. & Lackner, L. L., Sep 15 2018, In : Molecular biology of the cell. 29, 19, p. 2346-2357 12 p.

Research output: Contribution to journalArticle

3 Scopus citations

Discovery of genomic intervals that underlie nematode responses to benzimidazoles

Zamanian, M., Cook, D. E., Zdraljevic, S., Brady, S. C., Lee, D., Lee, J. & Andersen, E. C., Mar 30 2018, In : PLoS neglected tropical diseases. 12, 3, e0006368.

Research output: Contribution to journalArticle

11 Scopus citations

Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics

Parkinson, E. I., Tryon, J. H., Goering, A. W., Ju, K. S., McClure, R. A., Kemball, J. D., Zhukovsky, S., Labeda, D. P., Thomson, R. J., Kelleher, N. L. & Metcalf, W. W., Apr 20 2018, In : ACS chemical biology. 13, 4, p. 1029-1037 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

DNA mechanics and topology

Brahmachari, S. & Marko, J. F., 2018, Advances in Experimental Medicine and Biology. Springer New York LLC, p. 11-39 29 p. (Advances in Experimental Medicine and Biology; vol. 1092).

Research output: Chapter in Book/Report/Conference proceedingChapter

Dynamic SUMO remodeling drives a series of critical events during the meiotic divisions in Caenorhabditis elegans

Davis-Roca, A. C., Divekar, N. S., Ng, R. K. & Wignall, S. M., Sep 2018, In : PLoS genetics. 14, 9, e1007626.

Research output: Contribution to journalArticle

4 Scopus citations

Effects of electrostatic interactions on ligand dissociation kinetics

Erbaş, A., De La Cruz, M. O. & Marko, J. F., Feb 16 2018, In : Physical Review E. 97, 2, 022405.

Research output: Contribution to journalArticle

6 Scopus citations

Erratum to: Shared strategies for β-lactam catabolism in the soil microbiome (Nature Chemical Biology, (2018), 14, 6, (556-564), 10.1038/s41589-018-0052-1)

Crofts, T. S., Wang, B., Spivak, A., Gianoulis, T. A., Forsberg, K. J., Gibson, M. K., Johnsky, L. A., Broomall, S. M., Rosenzweig, C. N., Skowronski, E. W., Gibbons, H. S., Sommer, M. O. A. & Dantas, G., Jan 1 2018, (Accepted/In press) In : Nature Chemical Biology.

Research output: Contribution to journalArticle

Estimating the Distribution of Protein Post-Translational Modification States by Mass Spectrometry

Compton, P. D., Kelleher, N. L. & Gunawardena, J., Aug 3 2018, In : Journal of Proteome Research. 17, 8, p. 2727-2734 8 p.

Research output: Contribution to journalArticle

5 Scopus citations

Evolutionary tuning impacts the design of bacterial tRNAs for the incorporation of unnatural amino acids by ribosomes

Uhlenbeck, O. C. & Schrader, J. M., Oct 2018, In : Current Opinion in Chemical Biology. 46, p. 138-145 8 p.

Research output: Contribution to journalReview article

4 Scopus citations

Expanding Covalent Attachment Sites of Nonnative Chromophores to Encompass the C-Terminal Hydrophilic Domain in Biohybrid Light-Harvesting Architectures

Hood, D., Sahin, T., Parkes-Loach, P. S., Jiao, J., Harris, M. A., Dilbeck, P., Niedzwiedzki, D. M., Kirmaier, C., Loach, P. A., Bocian, D. F., Lindsey, J. S. & Holten, D., Mar 1 2018, In : ChemPhotoChem. 2, 3, p. 300-313 14 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles

Hahnel, S. R., Zdraljevic, S., Rodriguez, B. C., Zhao, Y., McGrath, P. T. & Andersen, E. C., Oct 2018, In : PLoS pathogens. 14, 10, e1007226.

Research output: Contribution to journalArticle

10 Scopus citations

FGF mediated mapk and pi3k/akt signals make distinct contributions to pluripotency and the establishment of neural crest

Geary, L. & Labonne, C., Jan 19 2018, In : eLife. 7, e33845.

Research output: Contribution to journalArticle

9 Scopus citations

From micelles to bicelles: Effect of the membrane on particulate methane monooxygenase activity

Ro, S. Y., Ross, M. O., Deng, Y. W., Batelu, S., Lawton, T. J., Hurley, J. D., Stemmler, T. L., Hoffman, B. M. & Rosenzweig, A. C., Jan 1 2018, In : Journal of Biological Chemistry. 293, 27, p. 10457-10465 9 p.

Research output: Contribution to journalArticle

14 Scopus citations

Histone deacetylase activity has an essential role in establishing and maintaining the vertebrate neural crest

Rao, A. & LaBonne, C., Aug 2018, In : Development (Cambridge). 145, 15, dev163386.

Research output: Contribution to journalArticle

9 Scopus citations

Histone H2A.Z Suppression of Interferon-Stimulated Transcription and Antiviral Immunity Is Modulated by GCN5 and BRD2

Au-Yeung, N. & Horvath, C. M., Aug 31 2018, In : iScience. 6, p. 68-82 15 p.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

How many human proteoforms are there?

Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., Costello, C. E., Cravatt, B. F., Fenselau, C., Garcia, B. A., Ge, Y., Gunawardena, J., Hendrickson, R. C., Hergenrother, P. J., Huber, C. G., Ivanov, A. R., Jensen, O. N., Jewett, M. C., Kelleher, N. L., Kiessling, L. L. & 33 others, Krogan, N. J., Larsen, M. R., Loo, J. A., Ogorzalek Loo, R. R., Lundberg, E., Maccoss, M. J., Mallick, P., Mootha, V. K., Mrksich, M., Muir, T. W., Patrie, S. M., Pesavento, J. J., Pitteri, S. J., Rodriguez, H., Saghatelian, A., Sandoval, W., Schlüter, H., Sechi, S., Slavoff, S. A., Smith, L. M., Snyder, M. P., Thomas, P. M., Uhlén, M., Van Eyk, J. E., Vidal, M., Walt, D. R., White, F. M., Williams, E. R., Wohlschlager, T., Wysocki, V. H., Yates, N. A., Young, N. L. & Zhang, B., Feb 14 2018, In : Nature Chemical Biology. 14, 3, p. 206-214 9 p.

Research output: Contribution to journalReview article

132 Scopus citations
8 Scopus citations

Identification of the First Diketomorpholine Biosynthetic Pathway Using FAC-MS Technology

Robey, M. T., Ye, R., Bok, J. W., Clevenger, K. D., Islam, M. N., Chen, C., Gupta, R., Swyers, M., Wu, E., Gao, P., Thomas, P. M., Wu, C. C., Keller, N. P. & Kelleher, N. L., May 18 2018, In : ACS chemical biology. 13, 5, p. 1142-1147 6 p.

Research output: Contribution to journalArticle

12 Scopus citations

IFN--inducible antiviral responses require ULK1-mediated activation of MLK3 and ERK5

Saleiro, D., Blyth, G. T., Kosciuczuk, E. M., Ozark, P. A., Majchrzak-Kita, B., Arslan, A. D., Fischietti, M., Reddy, N. K., Horvath, C. M., Davis, R. J., Fish, E. N. & Platanias, L. C., Nov 20 2018, In : Science Signaling. 11, 557, aap9921.

Research output: Contribution to journalArticle

1 Scopus citations

Interrogation of Benzomalvin Biosynthesis Using Fungal Artificial Chromosomes with Metabolomic Scoring (FAC-MS): Discovery of a Benzodiazepine Synthase Activity

Clevenger, K. D., Ye, R., Bok, J. W., Thomas, P. M., Islam, M. N., Miley, G. P., Robey, M. T., Chen, C., Yang, K., Swyers, M., Wu, E., Gao, P., Wu, C. C., Keller, N. P. & Kelleher, N. L., Jun 12 2018, In : Biochemistry. 57, 23, p. 3237-3243 7 p.

Research output: Contribution to journalArticle

10 Scopus citations

Large-scale investigation of the reasons why potentially important genes are ignored

Stoeger, T., Gerlach, M., Morimoto, R. I. & Nunes Amaral, L. A., Sep 2018, In : PLoS biology. 16, 9, e2006643.

Research output: Contribution to journalArticle

47 Scopus citations

Management of primary ovarian insufficiency symptoms in survivors of childhood and adolescent cancer

Gargus, E., Deans, R., Anazodo, A. & Woodruff, T. K., Sep 1 2018, In : JNCCN Journal of the National Comprehensive Cancer Network. 16, 9, p. 1137-1149 13 p.

Research output: Contribution to journalReview article

4 Scopus citations

Mechanism of N2 Reduction Catalyzed by Fe-Nitrogenase Involves Reductive Elimination of H2

Harris, D. F., Lukoyanov, D. A., Shaw, S., Compton, P., Tokmina-Lukaszewska, M., Bothner, B., Kelleher, N., Dean, D. R., Hoffman, B. M. & Seefeldt, L. C., Feb 6 2018, In : Biochemistry. 57, 5, p. 701-710 10 p.

Research output: Contribution to journalArticle

21 Scopus citations

Metformin Targets Mitochondrial Electron Transport to Reduce Air-Pollution-Induced Thrombosis

Soberanes, S., Misharin, A. V., Jairaman, A., Morales-Nebreda, L., McQuattie-Pimentel, A. C., Cho, T., Hamanaka, R. B., Meliton, A. Y., Reyfman, P. A., Walter, J. M., Chen, C-I., Chi, M., Chiu, S., Gonzalez-Gonzalez, F. J., Antalek, M., Abdala-Valencia, H., Chiarella, S. E., Sun, K. A., Woods, P. S., Ghio, A. J. & 12 others, Jain, M., Perlman, H., Ridge, K. M., Morimoto, R. I., Sznajder, J. I., Balch, W. E., Bhorade, S. M., Bharat, A., Prakriya, M., Chandel, N. S., Mutlu, G. M. & Budinger, G. R. S., Oct 11 2018, In : Cell Metabolism.

Research output: Contribution to journalArticle

14 Scopus citations

Methanobactins: Maintaining copper homeostasis in methanotrophs and beyond

Kenney, G. E. & Rosenzweig, A. C., Jan 1 2018, In : Journal of Biological Chemistry. 293, 13, p. 4606-4615 10 p.

Research output: Contribution to journalReview article

17 Scopus citations

Microevolution in response to transient heme-iron restriction enhances intracellular bacterial community development and persistence

Hardison, R. L., Harrison, A., Wallace, R. M., Heimlich, D. R., O’Bryan, M. E., Sebra, R. P., Pinkett, H. W., Justice, S. S. & Mason, K. M., Oct 2018, In : PLoS pathogens. 14, 10, e1007355.

Research output: Contribution to journalArticle

7 Scopus citations

Mitochondrial anchors: Positioning mitochondria and more

Kraft, L. M. & Lackner, L. L., May 27 2018, In : Biochemical and Biophysical Research Communications. 500, 1, p. 2-8 7 p.

Research output: Contribution to journalArticle

7 Scopus citations

Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence

Turcan, S., Makarov, V., Taranda, J., Wang, Y., Fabius, A. W. M., Wu, W., Zheng, Y., El-Amine, N., Haddock, S., Nanjangud, G., Lekaye, H. C., Brennan, C., Cross, J., Huse, J. T., Kelleher, N. L., Osten, P., Thompson, C. B. & Chan, T. A., Jan 1 2018, In : Nature Genetics. 50, 1, p. 62-72 11 p.

Research output: Contribution to journalArticle

49 Scopus citations

Natural products from thioester reductase containing biosynthetic pathways

Mullowney, M., McClure, R. A., Robey, M. T., Kelleher, N. L. & Thomson, R. J., Sep 1 2018, In : Natural product reports. 35, 9, p. 847-878 32 p.

Research output: Contribution to journalReview article

11 Scopus citations

Notch signaling regulates differentiation and steroidogenesis in female mouse ovarian granulosa cells

Prasasya, R. D. & Mayo, K. E., Jan 1 2018, In : Endocrinology. 159, 1, p. 184-198 15 p.

Research output: Contribution to journalArticle

7 Scopus citations

Nuclear pore complex in genome organization and gene expression in yeast

Randise-Hinchliff, C. & Brickner, J. H., Jan 1 2018, Nuclear Pore Complexes in Genome Organization, Function and Maintenance. Springer International Publishing, p. 87-109 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

Ovarian tissue cryopreservation in young females through the Oncofertility Consortium's National Physicians Cooperative

Armstrong, A. G., Kimler, B. F., Smith, B. M., Woodruff, T. K., Pavone, M. E. & Duncan, F. E., Feb 2018, In : Future Oncology. 14, 4, p. 363-378 16 p.

Research output: Contribution to journalArticle

10 Scopus citations

Positional information specifies the site of organ regeneration and not tissue maintenance in planarians

Hill, E. M. & Petersen, C. P., Mar 16 2018, In : eLife. 7, e33680.

Research output: Contribution to journalArticle

8 Scopus citations

Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk

Ntai, I., Fornelli, L., DeHart, C. J., Hutton, J. E., Doubleday, P. F., LeDuc, R. D., van Nispen, A. J., Fellers, R. T., Whiteley, G., Boja, E. S., Rodriguez, H. & Kelleher, N. L., Apr 17 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 16, p. 4140-4145 6 p.

Research output: Contribution to journalArticle

21 Scopus citations

Problems of classification in the family Paramyxoviridae

Rima, B., Collins, P., Easton, A., Fouchier, R., Kurath, G., Lamb, R. A., Lee, B., Maisner, A., Rota, P. & Wang, L. F., May 1 2018, In : Archives of Virology. 163, 5, p. 1395-1404 10 p.

Research output: Contribution to journalArticle

11 Scopus citations

ProForma: A Standard Proteoform Notation

Leduc, R. D., Schwämmle, V., Shortreed, M. R., Cesnik, A. J., Solntsev, S. K., Shaw, J. B., Martin, M. J., Vizcaino, J. A., Alpi, E., Danis, P., Kelleher, N. L., Smith, L. M., Ge, Y., Agar, J. N., Chamot-Rooke, J., Loo, J. A., Pasa-Tolic, L. & Tsybin, Y. O., Mar 2 2018, In : Journal of Proteome Research. 17, 3, p. 1321-1325 5 p.

Research output: Contribution to journalArticle

17 Scopus citations

Proteoforms as the next proteomics currency: Identifying precise molecular forms of proteins can improve our understanding of function

Smith, L. M. & Kelleher, N. L., Mar 9 2018, In : Science. 359, 6380, p. 1106-1107 2 p.

Research output: Contribution to journalArticle

41 Scopus citations

Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase

Cao, L., Caldararu, O., Rosenzweig, A. C. & Ryde, U., Jan 2 2018, In : Angewandte Chemie - International Edition. 57, 1, p. 162-166 5 p.

Research output: Contribution to journalArticle

55 Scopus citations

Recent Advances in the Genetic Manipulation of Methylosinus trichosporium OB3b

Ro, S. Y. & Rosenzweig, A. C., Jan 1 2018, Methods in Enzymology. Academic Press Inc, p. 335-349 15 p. (Methods in Enzymology; vol. 605).

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Scopus citations

Reply to “Far away from the lamppost”

Stoeger, T., Gerlach, M., Morimoto, R. I. & Amaral, L. A. N., Dec 2018, In : PLoS biology. 16, 12, e3000075.

Research output: Contribution to journalArticle

Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins

Park, Y. J., Kenney, G. E., Schachner, L. F., Kelleher, N. L. & Rosenzweig, A. C., Jun 26 2018, In : Biochemistry. 57, 25, p. 3515-3523 9 p.

Research output: Contribution to journalArticle

5 Scopus citations

Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment

Pattison, J. M., Melo, S. P., Piekos, S. N., Torkelson, J. L., Bashkirova, E., Mumbach, M. R., Rajasingh, C., Zhen, H. H., Li, L., Liaw, E., Alber, D., Rubin, A. J., Shankar, G., Bao, X., Chang, H. Y., Khavari, P. A. & Oro, A. E., Dec 1 2018, In : Nature Genetics. 50, 12, p. 1658-1665 8 p.

Research output: Contribution to journalLetter

12 Scopus citations

Retrievable hydrogels for ovarian follicle transplantation and oocyte collection

Rios, P. D., Kniazeva, E., Lee, H. C., Xiao, S., Oakes, R. S., Saito, E., Jeruss, J. S., Shikanov, A., Woodruff, T. K. & Shea, L. D., Aug 2018, In : Biotechnology and Bioengineering. 115, 8, p. 2075-2086 12 p.

Research output: Contribution to journalArticle

8 Scopus citations

RNA sensor LGP2 inhibits TRAF ubiquitin ligase to negatively regulate innate immune signaling

Parisien, J. P., Lenoir, J. J., Mandhana, R., Rodriguez, K. R., Qian, K., Bruns, A. M. & Horvath, C. M., Jun 2018, In : EMBO Reports. 19, 6, e45176.

Research output: Contribution to journalArticle

15 Scopus citations

Selective substrate uptake: The role of ATP-binding cassette (ABC) importers in pathogenesis

Tanaka, K. J., Song, S., Mason, K. & Pinkett, H. W., Apr 2018, In : Biochimica et Biophysica Acta - Biomembranes. 1860, 4, p. 868-877 10 p.

Research output: Contribution to journalReview article

32 Scopus citations

Sendai Virus Infection Induces Expression of Novel RNAs in Human Cells

Mandhana, R. & Horvath, C. M., Dec 1 2018, In : Scientific reports. 8, 1, 16815.

Research output: Contribution to journalArticle

Separate roles for chromatin and lamins in nuclear mechanics

Stephens, A. D., Banigan, E. J. & Marko, J. F., Dec 26 2018, In : Nucleus. 9, 1, p. 119-124 6 p.

Research output: Contribution to journalArticle

11 Scopus citations

Shared genomic regions underlie natural variation in diverse toxin responses

Evans, K. S., Brady, S. C., Bloom, J. S., Tanny, R. E., Cook, D. E., Giuliani, S. E., Hippleheuser, S. W., Zamanian, M. & Andersen, E. C., Dec 2018, In : Genetics. 210, 4, p. 1509-1525 17 p.

Research output: Contribution to journalArticle

5 Scopus citations