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2020

Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults

Westreich, S. T., Salcedo, J., Durbin-Johnson, B., Smilowitz, J. T., Korf, I., Mills, D. A., Barile, D. & Lemay, D. G., May 2020, In : Journal of Nutritional Biochemistry. 79, 108340.

Research output: Contribution to journalArticle

The kinesin-5 tail domain directly modulates the mechanochemical cycle of the motor domain for anti-parallel microtubule sliding

Bodrug, T., Wilson-Kubalek, E., Nithianantham, S., Thompson, A. F., Alfieri, A., Gaska, I., Major, J., Debs, G., Inagaki, S., Gutierrez, P., Gheber, L., McKenney, R., Sindelar, C., Milligan, R., Stumpff, J., Rosenfeld, S., Forth, S. T. & Al-Bassam, J., Jan 2020, In : eLife. 9, e51131.

Research output: Contribution to journalArticle

Open Access
2019

Association of lactase persistence genotypes (Rs4988235) and ethnicity with dairy intake in a healthy u.s. population

Chin, E. L., Huang, L., Bouzid, Y. Y., Kirschke, C. P., Durbin-Johnson, B., Baldiviez, L. M., Bonnel, E. L., Keim, N. L., Korf, I. F., Stephensen, C. B. & Lemay, D. G., Aug 1 2019, In : Nutrients. 11, 8, 1860.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Conserved cell types with divergent features in human versus mouse cortex

Hodge, R. D., Bakken, T. E., Miller, J. A., Smith, K. A., Barkan, E. R., Graybuck, L. T., Close, J. L., Long, B., Johansen, N., Penn, O., Yao, Z., Eggermont, J., Höllt, T., Levi, B. P., Shehata, S. I., Aevermann, B., Beller, A., Bertagnolli, D., Brouner, K., Casper, T. & 44 others, Cobbs, C., Dalley, R., Dee, N., Ding, S. L., Ellenbogen, R. G., Fong, O., Garren, E., Goldy, J., Gwinn, R. P., Hirschstein, D., Keene, C. D., Keshk, M., Ko, A. L., Lathia, K., Mahfouz, A., Maltzer, Z., McGraw, M., Nguyen, T. N., Nyhus, J., Ojemann, J. G., Oldre, A., Parry, S., Reynolds, S., Rimorin, C., Shapovalova, N. V., Somasundaram, S., Szafer, A., Thomsen, E. R., Tieu, M., Quon, G., Scheuermann, R. H., Yuste, R., Sunkin, S. M., Lelieveldt, B., Feng, D., Ng, L., Bernard, A., Hawrylycz, M., Phillips, J. W., Tasic, B., Zeng, H., Jones, A. R., Koch, C. & Lein, E. S., Sep 5 2019, In : Nature. 573, 7772, p. 61-68 8 p.

Research output: Contribution to journalArticle

39 Scopus citations

Controlling ERK Activation Dynamics in Mammary Epithelial Cells with Alternating Electric Fields through Microelectrodes

Guo, L., Li, H., Wang, Y., Li, Z., Albeck, J., Zhao, M. & Qing, Q., Oct 9 2019, In : Nano Letters. 19, 10, p. 7526-7533 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

Dimethyl fumarate dosing in humans increases frataxin expression: A potential therapy for Friedreich’s Ataxia

Jasoliya, M., Sacca, F., Sahdeo, S., Chedin, F., Pane, C., Morra, V. B., Filla, A., Pook, M. & Cortopassi, G. A., Jun 1 2019, In : PloS one. 14, 6, e0217776.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Disease-associated mutations hyperactivate KIF1A motility and anterograde axonal transport of synaptic vesicle precursors

Chiba, K., Takahashi, H., Chen, M., Obinata, H., Arai, S., Hashimoto, K., Oda, T., Mckenney, R. & Niwa, S., Sep 10 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 37, p. 18429-18434 6 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

Westreich, S. T., Ardeshir, A., Alkan, Z., Kable, M. E., Korf, I. F. & Lemay, D. G., Mar 18 2019, In : Microbiome. 7, 1, 41.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations
Open Access
4 Scopus citations

Interplay between DNA sequence and negative superhelicity drives R-loop structures

Stolz, R., Sulthana, S., Hartono, S. R., Malig, M., Benham, C. J. & Chedin, F., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 13, p. 6260-6269 10 p.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

Microtubule polymerase and processive plus-end tracking functions originate from distinct features within TOG domain arrays

Cook, B. D., Chang, F., Flor-Parra, I. & Al-Bassam, J., Jun 1 2019, In : Molecular biology of the cell. 30, 12, p. 1490-1504 15 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

ScAlign: A tool for alignment, integration, and rare cell identification from scRNA-seq data

Johansen, N. & Quon, G., Aug 14 2019, In : Genome Biology. 20, 1, 166.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

ScBFA: Modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data

Li, R. & Quon, G., Sep 9 2019, In : Genome Biology. 20, 1, 193.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Tau repeat regions contain conserved histidine residues that modulate microtubule-binding in response to changes in pH

Charafeddine, R. A., Cortopassi, W. A., Lak, P., Tan, R., Mckenney, R., Jacobson, M. P., Barber, D. L. & Wittmann, T., Jan 1 2019, In : Journal of Biological Chemistry. 294, 22, p. 8779-8790 12 p.

Research output: Contribution to journalArticle

2 Scopus citations

The extruded non-template strand determines the architecture of R-loops

Carrasco-Salas, Y., Malapert, A., Sulthana, S., Molcrette, B., Chazot-Franguiadakis, L., Bernard, P., Chedin, F., Faivre-Moskalenko, C. & Vanoosthuyse, V., Jul 26 2019, In : Nucleic acids research. 47, 13, p. 6783-6795 13 p.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

The tail wags the motor

McKenney, R. J., Nov 1 2019, In : Nature Chemical Biology. 15, 11, p. 1033-1034 2 p.

Research output: Contribution to journalArticle

2018

Antagonism between the dynein and Ndc80 complexes at kinetochores controls the stability of kinetochore-microtubule attachments during mitosis

Amin, M. A., Mckenney, R. & Varma, D., Jan 1 2018, In : Journal of Biological Chemistry. 293, 16, p. 5755-5765 11 p.

Research output: Contribution to journalArticle

2 Scopus citations

A Plug-and-Play, Drug-on-Pillar Platform for Combination Drug Screening Implemented by Microfluidic Adaptive Printing

Li, J., Tan, W., Xiao, W., Carney, R., Men, Y., Li, Y., Quon, G., Ajena, Y., Lam, K. & Pan, T., Jan 1 2018, (Accepted/In press) In : Analytical Chemistry.

Research output: Contribution to journalArticle

3 Scopus citations

Cdt1 stabilizes kinetochore-microtubule attachments via an Aurora B kinase-dependent mechanism

Agarwal, S., Smith, K. P., Zhou, Y., Suzuki, A., Mckenney, R. & Varma, D., Oct 1 2018, In : The Journal of cell biology. 217, 10, p. 3446-3463 18 p.

Research output: Contribution to journalArticle

Cooperative Accumulation of Dynein-Dynactin at Microtubule Minus-Ends Drives Microtubule Network Reorganization

Tan, R., Foster, P. J., Needleman, D. J. & Mckenney, R., Jan 22 2018, In : Developmental Cell. 44, 2, p. 233-247.e4

Research output: Contribution to journalArticle

12 Scopus citations

Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility

Grotjahn, D. A., Chowdhury, S., Xu, Y., Mckenney, R., Schroer, T. A. & Lander, G. C., Mar 1 2018, In : Nature Structural and Molecular Biology. 25, 3, p. 203-207 5 p.

Research output: Contribution to journalArticle

41 Scopus citations

DNA Topoisomerase I differentially modulates R-loops across the human genome

Manzo, S. G., Hartono, S. R., Sanz, L. A., Marinello, J., De Biasi, S., Cossarizza, A., Capranico, G. & Chedin, F., Jul 30 2018, In : Genome Biology. 19, 1, 100.

Research output: Contribution to journalArticle

24 Scopus citations

Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases

Sampattavanich, S., Steiert, B., Kramer, B. A., Gyori, B. M., Albeck, J. & Sorger, P. K., Jun 27 2018, In : Cell Systems. 6, 6, p. 664-678.e9

Research output: Contribution to journalArticle

8 Scopus citations

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species 06 Biological Sciences 0604 Genetics

Kern, C., Wang, Y., Chitwood, J., Korf, I. F., Delany, M., Cheng, H., Medrano, J. F., Van Eenennaam, A. L., Ernst, C., Ross, P. & Zhou, H., Sep 18 2018, In : BMC Genomics. 19, 1, 684.

Research output: Contribution to journalArticle

20 Scopus citations

Live-Cell Imaging and Analysis with Multiple Genetically Encoded Reporters

Pargett, M. & Albeck, J., Mar 1 2018, In : Current Protocols in Cell Biology. 78, 1, p. 4.36.1-4.36.19

Research output: Contribution to journalArticle

Magnetic Cytoskeleton Affinity Purification of Microtubule Motors Conjugated to Quantum Dots

Tjioe, M., Ryoo, H., Ishitsuka, Y., Ge, P., Bookwalter, C., Huynh, W., Mckenney, R., Trybus, K. M. & Selvin, P. R., Jul 18 2018, In : Bioconjugate Chemistry. 29, 7, p. 2278-2286 9 p.

Research output: Contribution to journalArticle

2 Scopus citations

Network Infusion to Infer Information Sources in Networks

Feizi, S., Medard, M., Quon, G., Kellis, M. & Duffy, K., Jul 6 2018, (Accepted/In press) In : IEEE Transactions on Network Science and Engineering.

Research output: Contribution to journalArticle

1 Scopus citations

Polarity of Neuronal Membrane Traffic Requires Sorting of Kinesin Motor Cargo during Entry into Dendrites by a Microtubule-Associated Septin

Karasmanis, E. P., Phan, C. T., Angelis, D., Kesisova, I. A., Hoogenraad, C. C., Mckenney, R. & Spiliotis, E. T., Jul 16 2018, In : Developmental Cell. 46, 2, p. 204-218.e7

Research output: Contribution to journalArticle

12 Scopus citations

Proceedings of the fifth international RASopathies symposium: When development and cancer intersect

Rauen, K. A., Schoyer, L., Schill, L., Stronach, B., Albeck, J., Andresen, B. S., Cavé, H., Ellis, M., Fruchtman, S. M., Gelb, B. D., Gibson, C. C., Gripp, K., Hefner, E., Huang, W. Y. C., Itkin, M., Kerr, B., Linardic, C. M., McMahon, M., Oberlander, B., Perlstein, E. & 17 others, Ratner, N., Rogers, L., Schenck, A., Shankar, S., Shvartsman, S., Stevenson, D. A., Stites, E. C., Stork, P. J. S., Sun, C., Therrien, M., Ullian, E. M., Widemann, B. C., Yeh, E., Zampino, G., Zenker, M., Timmer, W. & McCormick, F., Jan 1 2018, (Accepted/In press) In : American Journal of Medical Genetics, Part A. e40632.

Research output: Contribution to journalArticle

2 Scopus citations

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins

Yin, D., Schwarz, E. M., Thomas, C. G., Felde, R. L., Korf, I. F., Cutter, A. D., Schartner, C. M., Ralston, E. J., Meyer, B. J. & Haag, E. S., Jan 5 2018, In : Science. 359, 6371, p. 55-61 7 p.

Research output: Contribution to journalArticle

26 Scopus citations

SAMSA2: A standalone metatranscriptome analysis pipeline

Westreich, S. T., Treiber, M. L., Mills, D. A., Korf, I. F. & Lemay, D. G., May 21 2018, In : BMC Bioinformatics. 19, 1, 175.

Research output: Contribution to journalArticle

14 Scopus citations

Structural basis for disassembly of katanin heterododecamers

Nithianantham, S., McNally, F. J. & Al-Bassam, J., Jan 1 2018, In : Journal of Biological Chemistry. 293, 27, p. 10590-10605 16 p.

Research output: Contribution to journalArticle

7 Scopus citations

Structural basis of tubulin recruitment and assembly by microtubule polymerases with tumor overexpressed gene (TOG) domain arrays

Nithianantham, S., Cook, B. D., Beans, M., Guo, F., Chang, F. & Al-Bassam, J., Nov 13 2018, In : eLife. 7

Research output: Contribution to journalArticle

9 Scopus citations

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast

Hartono, S. R., Malapert, A., Legros, P., Bernard, P., Chedin, F. & Vanoosthuyse, V., Feb 2 2018, In : Journal of Molecular Biology. 430, 3, p. 272-284 13 p.

Research output: Contribution to journalArticle

27 Scopus citations

The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium

Kwok, E., Porter, M., Korf, I. F., Pasin, G., Bruce German, J. & Lemay, D. G., Aug 1 2018, In : PLoS One. 13, 8, e0201637.

Research output: Contribution to journalArticle

1 Scopus citations
2017

Acylcarnitines as markers of exercise-associated fuel partitioning, xenometabolism, and potential signals to muscle afferent neurons

Zhang, J., Light, A. R., Hoppel, C. L., Campbell, C., Chandler, C. J., Burnett, D. J., Souza, E. C., Casazza, G. A., Hughen, R. W., Keim, N. L., Newman, J. W., Hunter, G. R., Fernandez, J. R., Garvey, W. T., Harper, M. E., Fiehn, O. & Adams, S. H., Jan 1 2017, In : Experimental Physiology. 102, 1, p. 48-69 22 p.

Research output: Contribution to journalArticle

14 Scopus citations

Akt regulation of glycolysis mediates bioenergetic stability in epithelial cells

Hung, Y. P., Teragawa, C., Kosaisawe, N., Gillies, T. E., Pargett, M., Minguet, M., Distor, K., Rocha-Gregg, B. L., Coloff, J. L., Keibler, M. A., Stephanopoulos, G., Yellen, G., Brugge, J. S. & Albeck, J., Dec 14 2017, In : eLife. 6, e27293.

Research output: Contribution to journalArticle

7 Scopus citations

A novel amino acid and metabolomics signature in mice overexpressing muscle uncoupling protein 3

Aguer, C., Piccolo, B. D., Fiehn, O., Adams, S. H. & Harper, M. E., Feb 1 2017, In : FASEB Journal. 31, 2, p. 814-827 14 p.

Research output: Contribution to journalArticle

6 Scopus citations

A potential physiological role for bi-directional motility and motor clustering of mitotic kinesin-5 Cin8 in yeast mitosis

Shapira, O., Goldstein, A., Al-Bassam, J. & Gheber, L., Jan 1 2017, In : Journal of Cell Science. 130, 4, p. 725-734 10 p.

Research output: Contribution to journalArticle

16 Scopus citations

Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis

Zhang, X., Chiang, H. C., Wang, Y., Zhang, C., Smith, S., Zhao, X., Nair, S. J., Michalek, J., Jatoi, I., Lautner, M., Oliver, B., Wang, H., Petit, A., Soler, T., Brunet, J., Mateo, F., Angel Pujana, M., Poggi, E., Chaldekas, K., Isaacs, C. & 10 others, Peshkin, B. N., Ochoa, O., Chedin, F., Theoharis, C., Sun, L. Z., Curiel, T. J., Elledge, R., Jin, V. X., Hu, Y. & Li, R., Jun 26 2017, In : Nature Communications. 8, 15908.

Research output: Contribution to journalArticle

35 Scopus citations

Autosomal trisomy and triploidy are corrected during female meiosis in caenorhabditis elegans

Vargas, E., McNally, K., Friedman, J. A., Cortes, D. B., Wang, D. Y., Korf, I. F. & McNally, F. J., Nov 1 2017, In : Genetics. 207, 3, p. 911-922 12 p.

Research output: Contribution to journalArticle

3 Scopus citations

Biosynthesis of the microtubule-destabilizing diterpene pseudolaric acid B from golden larch involves an unusual diterpene synthase

Mafu, S., Karunanithi, P. S., Palazzo, T. A., Harrod, B. L., Rodriguez, S. M., Mollhoff, I. N., O'Brien, T. E., Tong, S., Fiehn, O., Tantillo, D. J., Bohlmann, J. & Zerbe, P., Jan 31 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 5, p. 974-979 6 p.

Research output: Contribution to journalArticle

9 Scopus citations

Critical Assessment of Small Molecule Identification 2016: automated methods

Schymanski, E. L., Ruttkies, C., Krauss, M., Brouard, C., Kind, T., Dührkop, K., Allen, F., Vaniya, A., Verdegem, D., Böcker, S., Rousu, J., Shen, H., Tsugawa, H., Sajed, T., Fiehn, O., Ghesquière, B. & Neumann, S., Mar 27 2017, In : Journal of Cheminformatics. 9, 1, 22.

Research output: Contribution to journalArticle

54 Scopus citations

Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns

Dunaway, K., Goorha, S., Matelski, L., Urraca, N., Lein, P. J., Korf, I. F., Reiter, L. T. & LaSalle, J. M., Apr 1 2017, In : Stem Cells. 35, 4, p. 981-988 8 p.

Research output: Contribution to journalArticle

8 Scopus citations

Differential effects of the dynein-regulatory factor Lissencephaly-1 on processive dynein-dynactin motility

Gutierrez, P. A., Ackermann, B. E., Vershinin, M. & Mckenney, R., Jan 1 2017, In : Journal of Biological Chemistry. 292, 29, p. 12245-12255 11 p.

Research output: Contribution to journalArticle

20 Scopus citations

Discovery of synthesis and secretion of polyol esters of fatty acids by four basidiomycetous yeast species in the order Sporidiobolales

Garay, L. A., Sitepu, I. R., Cajka, T., Fiehn, O., Cathcart, E., Fry, R. W., Kanti, A., Joko Nugroho, A., Faulina, S. A., Stephanandra, S., German, J. B. & Boundy-Mills, K. L., Mar 13 2017, (Accepted/In press) In : Journal of Industrial Microbiology and Biotechnology. p. 1-14 14 p.

Research output: Contribution to journalArticle

10 Scopus citations

Dmrt1 is necessary for male sexual development in zebrafish

Webster, K. A., Schach, U., Ordaz, A., Steinfeld, J. S., Draper, B. W. & Siegfried, K. R., Feb 1 2017, In : Developmental Biology. 422, 1, p. 33-46 14 p.

Research output: Contribution to journalArticle

60 Scopus citations

Dual inhibition of key proliferation signaling pathways in triple-negative breast cancer cells by a novel derivative of Taiwanin A

Kuo, Y. H., Chiang, E. P. I., Chao, C. Y., Rodriguez, R. L., Chou, P. Y., Tsai, S. Y., Pai, M. H. & Tang, F. Y., Mar 1 2017, In : Molecular Cancer Therapeutics. 16, 3, p. 480-493 14 p.

Research output: Contribution to journalArticle

6 Scopus citations

Early PQQ supplementation has persistent long-term protective effects on developmental programming of hepatic lipotoxicity and inflammation in obese mice

Jonscher, K. R., Stewart, M. S., Alfonso-Garcia, A., DeFelice, B. C., Wang, X. X., Luo, Y., Levi, M., Heerwagen, M. J. R., Janssen, R. C., De La Houssaye, B. A., Wiitala, E., Florey, G., Jonscher, R. L., Potma, E. O., Fiehn, O. & Friedman, J. E., Apr 1 2017, In : FASEB Journal. 31, 4, p. 1434-1448 15 p.

Research output: Contribution to journalArticle

17 Scopus citations

Effect of steroidal saponins from Agave on the polysaccharide cell wall composition of Saccharomyces cerevisiae and Kluyveromyces marxianus

Alcázar, M., Kind, T., Gschaedler, A., Silveria, M., Arrizon, J., Fiehn, O., Vallejo, A., Higuera, I. & Lugo, E., Apr 1 2017, In : LWT - Food Science and Technology. 77, p. e1

Research output: Contribution to journalArticle

8 Scopus citations