Research Output

2020

A computational framework to explore large-scale biosynthetic diversity

Navarro-Muñoz, J. C., Selem-Mojica, N., Mullowney, M. W., Kautsar, S. A., Tryon, J. H., Parkinson, E. I., De Los Santos, E. L. C., Yeong, M., Cruz-Morales, P., Abubucker, S., Roeters, A., Lokhorst, W., Fernandez-Guerra, A., Cappelini, L. T. D., Goering, A. W., Thomson, R. J., Metcalf, W. W., Kelleher, N. L., Barona-Gomez, F. & Medema, M. H., Jan 1 2020, In : Nature Chemical Biology. 16, 1, p. 60-68 9 p.

Research output: Contribution to journalArticle

13 Scopus citations

Amplifiers co-translationally enhance CFTR biosynthesis via PCBP1-mediated regulation of CFTR mRNA

Dukovski, D., Villella, A., Bastos, C., King, R., Finley, D., Kelly, J. W., Morimoto, R. I., Hartl, F. U., Munoz, B., Lee, P. S., Zecevic, M. & Miller, J. P., Jan 1 2020, (Accepted/In press) In : Journal of Cystic Fibrosis.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

A MUC16 IgG binding activity selects for a restricted subset of IgG enriched for certain simian immunodeficiency virus epitope specificities

Schneider, J. R., Shen, X., Orlandi, C., Nyanhete, T., Sawant, S., Carias, A. M., Smith, A. D., Kelleher, N. L., Veazey, R. S., Lewis, G. K., Tomaras, G. D. & Hope, T. J., Mar 1 2020, In : Journal of virology. 94, 5, e01246-19.

Research output: Contribution to journalArticle

A Remarkable Difference That One Fluorine Atom Confers on the Mechanisms of Inactivation of Human Ornithine Aminotransferase by Two Cyclohexene Analogues of γ-Aminobutyric Acid

Zhu, W., Doubleday, P. F., Catlin, D. S., Weerawarna, P. M., Butrin, A., Shen, S., Wawrzak, Z., Kelleher, N. L., Liu, D. & Silverman, R. B., Mar 11 2020, In : Journal of the American Chemical Society. 142, 10, p. 4892-4903 12 p.

Research output: Contribution to journalArticle

A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans

Zhao, Y., Long, L., Wan, J., Biliya, S., Brady, S. C., Lee, D., Ojemakinde, A., Andersen, E. C., Vannberg, F. O., Lu, H. & McGrath, P. T., Jan 1 2020, In : PLoS genetics. 16, 2, e1008606.

Research output: Contribution to journalArticle

Open Access

Celebrating the Silver Anniversary of the North American Testis Workshop

Robaire, B., Eddy, M., Goldberg, E., Griswold, M., Heckert, L., McCarrey, J., Orgebin-Crist, M. C., Papadopoulos, V., Trasler, J., Wright, W., Yan, W. & Zirkin, B., Jan 1 2020, (Accepted/In press) In : Andrology.

Research output: Contribution to journalReview article

Open Access

Cell-nonautonomous regulation of proteostasis in aging and disease

Morimoto, R. I., Apr 2020, In : Cold Spring Harbor Perspectives in Biology. 12, 4, a034074.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Challenging Proteostasis: Role of the Chaperone Network to Control Aggregation-Prone Proteins in Human Disease

Sinnige, T., Yu, A. & Morimoto, R. I., Jan 1 2020, Advances in Experimental Medicine and Biology. Springer, p. 53-68 16 p. (Advances in Experimental Medicine and Biology; vol. 1243).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chromatin accessibility and histone acetylation in the regulation of competence in early development

Esmaeili, M., Blythe, S. A., Tobias, J. W., Zhang, K., Yang, J. & Klein, P. S., Jun 1 2020, In : Developmental Biology. 462, 1, p. 20-35 16 p.

Research output: Contribution to journalArticle

Cryo-EM structure of SWI/SNF complex bound to a nucleosome

Han, Y., Reyes, A. A., Malik, S. & He, Y., Mar 19 2020, In : Nature. 579, 7799, p. 452-455 4 p.

Research output: Contribution to journalArticle

2 Scopus citations

Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs

Chan, C. W., Badong, D., Rajan, R. & Mondragón, A., Jan 1 2020, In : RNA. 26, 3, p. 278-289 12 p.

Research output: Contribution to journalArticle

Discovery of the Biosynthetic Machinery for Stravidins, Biotin Antimetabolites

Montaser, R. & Kelleher, N. L., Jan 1 2020, (Accepted/In press) In : ACS chemical biology.

Research output: Contribution to journalArticle

Effects of telomerase overexpression in the model organism Caenorhabditis elegans

Bayat, M., Tanny, R. E., Wang, Y., Herden, C., Daniel, J., Andersen, E. C., Liebau, E. & Waschk, D. E. J., Mar 30 2020, In : Gene. 732, 144367.

Research output: Contribution to journalArticle

Elucidating Proteoform Dynamics Underlying the Senescence Associated Secretory Phenotype

Doubleday, P. F., Fornelli, L. & Kelleher, N. L., Feb 7 2020, In : Journal of Proteome Research. 19, 2, p. 938-948 11 p.

Research output: Contribution to journalArticle

Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology

Abrisch, R. G., Gumbin, S. C., Wisniewski, B. T., Lackner, L. L. & Voeltz, G. K., Apr 6 2020, In : The Journal of cell biology. 219, 4

Research output: Contribution to journalArticle

Open Access

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila

Bernasek, S. M., Peláez, N., Carthew, R. W., Bagheri, N. & Amaral, L. A. N., Jan 1 2020, In : PLoS computational biology. 16, 3, e1007406.

Research output: Contribution to journalArticle

Open Access

Identification of Plasmodium falciparum proteoforms from liver stage models

Winer, B., Edgel, K. A., Zou, X., Sellau, J., Hadiwidjojo, S., Garver, L. S., McDonough, C. E., Kelleher, N. L., Thomas, P. M., Villasante, E., Ploss, A. & Gerbasi, V. R., Jan 7 2020, In : Malaria journal. 19, 1, 10.

Research output: Contribution to journalArticle

Open Access

Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry

Kafader, J. O., Durbin, K. R., Melani, R. D., Des Soye, B. J., Schachner, L. F., Senko, M. W., Compton, P. D. & Kelleher, N. L., Mar 6 2020, In : Journal of Proteome Research. 19, 3, p. 1346-1350 5 p.

Research output: Contribution to journalArticle

Mechanism-Based Design of 3-Amino-4-Halocyclopentenecarboxylic Acids as Inactivators of GABA Aminotransferase

Shen, S., Doubleday, P. F., Weerawarna, P. M., Zhu, W., Kelleher, N. L. & Silverman, R. B., Jan 1 2020, (Accepted/In press) In : ACS Medicinal Chemistry Letters.

Research output: Contribution to journalArticle

MicroRNA miR-7 Regulates Secretion of Insulin-Like Peptides

Agbu, P., Cassidy, J. J., Braverman, J., Jacobson, A. & Carthew, R. W., Feb 1 2020, In : Endocrinology (United States). 161, 2, bqz040.

Research output: Contribution to journalArticle

Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes

Kafader, J. O., Melani, R. D., Durbin, K. R., Ikwuagwu, B., Early, B. P., Fellers, R. T., Beu, S. C., Zabrouskov, V., Makarov, A. A., Maze, J. T., Shinholt, D. L., Yip, P. F., Tullman-Ercek, D., Senko, M. W., Compton, P. D. & Kelleher, N. L., Apr 1 2020, In : Nature Methods. 17, 4, p. 391-394 4 p.

Research output: Contribution to journalArticle

Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response

Béguelin, W., Teater, M., Meydan, C., Hoehn, K. B., Phillip, J. M., Soshnev, A. A., Venturutti, L., Rivas, M. A., Calvo-Fernández, M. T., Gutierrez, J., Camarillo, J. M., Takata, K., Tarte, K., Kelleher, N. L., Steidl, C., Mason, C. E., Elemento, O., Allis, C. D., Kleinstein, S. H. & Melnick, A. M., May 11 2020, In : Cancer Cell. 37, 5, p. 655-673.e11

Research output: Contribution to journalArticle

1 Scopus citations

Native vs Denatured: An in Depth Investigation of Charge State and Isotope Distributions

Kafader, J. O., Melani, R. D., Schachner, L. F., Ives, A. N., Patrie, S. M., Kelleher, N. L. & Compton, P. D., Mar 4 2020, In : Journal of the American Society for Mass Spectrometry. 31, 3, p. 574-581 8 p.

Research output: Contribution to journalArticle

NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle

Kosciuk, T., Price, I. R., Zhang, X., Zhu, C., Johnson, K. N., Zhang, S., Halaby, S. L., Komaniecki, G. P., Yang, M., DeHart, C. J., Thomas, P. M., Kelleher, N. L., Christopher Fromme, J. & Lin, H., Dec 1 2020, In : Nature communications. 11, 1, 1067.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Novel Interface for High-Throughput Analysis of Biotherapeutics by Electrospray Mass Spectrometry

Park, H. M., Winton, V. J., Drader, J. J., Manalili Wheeler, S., Lazar, G. A., Kelleher, N. L., Liu, Y., Tran, J. C. & Compton, P. D., Jan 21 2020, In : Analytical Chemistry. 92, 2, p. 2186-2193 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

Ordered patterning of the sensory system is susceptible to stochastic features of gene expression

Giri, R., Papadopoulos, D. K., Posadas, D. M., Potluri, H. K., Tomancak, P., Mani, M. & Carthew, R. W., Feb 2020, In : eLife. 9, e53638.

Research output: Contribution to journalArticle

Open Access

Physics and Biology (of Chromosomes)

Marko, J. F., Jan 17 2020, In : Journal of Molecular Biology. 432, 2, p. 621-631 11 p.

Research output: Contribution to journalArticle

Rapid Dynamics of Signal-Dependent Transcriptional Repression by Capicua

Keenan, S. E., Blythe, S. A., Marmion, R. A., Djabrayan, N. J. V., Wieschaus, E. F. & Shvartsman, S. Y., Mar 23 2020, In : Developmental Cell. 52, 6, p. 794-801.e4

Research output: Contribution to journalArticle

Repurposing Papaverine as an Antiviral Agent against Influenza Viruses and Paramyxoviruses

Aggarwal, M., Leser, G. P. & Lamb, R. A., Feb 28 2020, In : Journal of virology. 94, 6

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

STRIPAK Limits Stem Cell Differentiation of a WNT Signaling Center to Control Planarian Axis Scaling

Schad, E. G. & Petersen, C. P., Jan 20 2020, In : Current Biology. 30, 2, p. 254-263.e2

Research output: Contribution to journalArticle

Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation

Abdella, R., Aggarwal, M., Okura, T., Lamb, R. A. & He, Y., Mar 3 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 9, p. 4931-4941 11 p.

Research output: Contribution to journalArticle

2 Scopus citations

Tec-1 kinase negatively regulates regenerative neurogenesis in planarians

Karge, A., Bonar, N. A., Wood, S. & Petersen, C. P., Jan 2020, In : eLife. 9, e47293.

Research output: Contribution to journalArticle

Open Access

The effector mechanism of siRNA spherical nucleic acids

Yamankurt, G., Stawicki, R. J., Posadas, D. M., Nguyen, J. Q., Carthew, R. W. & Mirkin, C. A., Jan 21 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 3, p. 1312-1320 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

The multifunctional nature of mitochondrial contact site proteins

Harper, C. S., White, A. J. & Lackner, L. L., Aug 2020, In : Current Opinion in Cell Biology. 65, p. 58-65 8 p.

Research output: Contribution to journalReview article

Thorough performance evaluation of 213 nm ultraviolet photodissociation for top-down proteomics

Fornelli, L., Srzentić, K., Toby, T. K., Doubleday, P. F., Huguet, R., Mullen, C., Melani, R. D., Seckler, H. D. S., DeHart, C. J., Weisbrod, C. R., Durbin, K. R., Greer, J. B., Early, B. P., Fellers, R. T., Zabrouskov, V., Thomas, P. M., Compton, P. D. & Kelleher, N. L., Jan 1 2020, In : Molecular and Cellular Proteomics. 19, 2, p. 405-420 16 p.

Research output: Contribution to journalArticle

Open Access

Voltage Rollercoaster Filtering of Low-Mass Contaminants During Native Protein Analysis

McGee, J. P., Melani, R. D., Goodwin, M., McAlister, G., Huguet, R., Senko, M. W., Compton, P. D. & Kelleher, N. L., Mar 4 2020, In : Journal of the American Society for Mass Spectrometry. 31, 3, p. 763-767 5 p.

Research output: Contribution to journalArticle

1 Scopus citations

Zygotic pioneer factor activity of odd-paired/zic is necessary for late function of the drosophila segmentation network

Soluri, I. V., Zumerling, L. M., Parra, O. A. P., Clark, E. G. & Blythe, S. A., Apr 2020, In : eLife. 9, e53916.

Research output: Contribution to journalArticle

Open Access
2019

Accurate estimation of context-dependent false discovery rates in top-down proteomics

LeDuc, R. D., Fellers, R. T., Early, B. P., Greer, J. B., Shams, D. P., Thomas, P. M. & Kelleher, N. L., Jan 1 2019, In : Molecular and Cellular Proteomics. 18, 4, p. 796-805 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

A cell separation checkpoint that enforces the proper order of late cytokinetic events

Brace, J. L., Doerfler, M. D. & Weiss, E. L., Jan 1 2019, In : Journal of Cell Biology. 218, 1, p. 150-170 21 p.

Research output: Contribution to journalArticle

2 Scopus citations

A comprehensive pipeline for translational top-down proteomics from a single blood draw

Toby, T. K., Fornelli, L., Srzentić, K., DeHart, C. J., Levitsky, J., Friedewald, J. & Kelleher, N. L., Jan 1 2019, In : Nature Protocols. 14, 1, p. 119-152 34 p.

Research output: Contribution to journalArticle

8 Scopus citations

A conserved mechanism for mitochondria-dependent dynein anchoring

Kraft, L. M. & Lackner, L. L., Jan 1 2019, In : Molecular biology of the cell. 30, 5, p. 691-702 12 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Activation of Notch Signaling by Oocytes and Jag1 in Mouse Ovarian Granulosa Cells

Hubbard, N., Prasasya, R. D. & Mayo, K. E., Dec 1 2019, In : Endocrinology. 160, 12, p. 2863-2876 14 p.

Research output: Contribution to journalArticle

A five-level classification system for proteoform identifications

Smith, L. M., Thomas, P. M., Shortreed, M. R., Schaffer, L. V., Fellers, R. T., LeDuc, R. D., Tucholski, T., Ge, Y., Agar, J. N., Anderson, L. C., Chamot-Rooke, J., Gault, J., Loo, J. A., Paša-Tolić, L., Robinson, C. V., Schlüter, H., Tsybin, Y. O., Vilaseca, M., Vizcaíno, J. A., Danis, P. O. & 1 others, Kelleher, N. L., Oct 1 2019, In : Nature Methods. 16, 10, p. 939-940 2 p.

Research output: Contribution to journalLetter

4 Scopus citations
1 Scopus citations

A metastable subproteome underlies inclusion formation in muscle proteinopathies

Ciryam, P., Antalek, M., Cid, F., Tartaglia, G. G., Dobson, C. M., Guettsches, A. K., Eggers, B., Vorgerd, M., Marcus, K., Kley, R. A., Morimoto, R. I., Vendruscolo, M. & Weihl, C. C., Dec 3 2019, In : Acta Neuropathologica Communications. 7, 1, 197.

Research output: Contribution to journalArticle

Open Access

A mutation in histone H2B represents a new class of oncogenic driver

Bennett, R. L., Bele, A., Small, E. C., Will, C. M., Nabet, B., Oyer, J. A., Huang, X., Ghosh, R. P., Grzybowski, A. T., Yu, T., Zhang, Q., Riva, A., Lele, T. P., Schatz, G. C., Kelleher, N. L., Ruthenburg, A. J., Liphardt, J. & Licht, J. D., Oct 2019, In : Cancer discovery. 9, 10, p. 1438-1451 14 p.

Research output: Contribution to journalArticle

2 Scopus citations

An activating mutation of the NSD2 histone methyltransferase drives oncogenic reprogramming in acute lymphocytic leukemia

Swaroop, A., Oyer, J. A., Will, C. M., Huang, X., Yu, W., Troche, C., Bulic, M., Durham, B. H., Wen, Q. J., Crispino, J. D., MacKerell, A. D., Bennett, R. L., Kelleher, N. L. & Licht, J. D., Jan 31 2019, In : Oncogene. 38, 5, p. 671-686 16 p.

Research output: Contribution to journalArticle

5 Scopus citations

An escape-room inspired game for genetics review

Brady, S. C. & Andersen, E. C., Jan 1 2019, (Accepted/In press) In : Journal of Biological Education.

Research output: Contribution to journalArticle

An excreted small molecule promotes C. elegans reproductive development and aging

Ludewig, A. H., Artyukhin, A. B., Aprison, E. Z., Rodrigues, P. R., Pulido, D. C., Burkhardt, R. N., Panda, O., Zhang, Y. K., Gudibanda, P., Ruvinsky, I. & Schroeder, F. C., Aug 1 2019, In : Nature Chemical Biology. 15, 8, p. 838-845 8 p.

Research output: Contribution to journalArticle

3 Scopus citations

A novel crosslinking protocol stabilizes amyloid β oligomers capable of inducing Alzheimer's-associated pathologies

Cline, E. N., Das, A., Bicca, M. A., Mohammad, S. N., Schachner, L. F., Kamel, J. M., DiNunno, N., Weng, A., Paschall, J. D., Bu, R. L., Khan, F. M., Rollins, M. G., Ives, A. N., Shekhawat, G., Nunes-Tavares, N., de Mello, F. G., Compton, P. D., Kelleher, N. L. & Klein, W. L., Mar 2019, In : Journal of neurochemistry. 148, 6, p. 822-836 15 p.

Research output: Contribution to journalArticle

3 Scopus citations