Research Output

2019

Roles for intracellular cation transporters in respiratory growth of yeast

Zhang, F., Bian, J., Chen, X., Huang, J., Smith, N., Lu, W., Xu, Y., Lee, J. & Wu, X., Oct 2019, In : Metallomics. 11, 10, p. 1667-1678 12 p.

Research output: Contribution to journalArticle

Scanning the Issue

Akyildiz, I. F., Pierobon, M., Balasubramaniam, S., Zhang, J., Chen, T., Zhong, S., Wang, J., Zhang, W., Zuo, X., Maunder, R. G., Hanzo, L., Chen, J., Liu, J., Calhoun, V. D. & Magoun, A. B., May 2019, In : Proceedings of the IEEE. 107, 5, p. 866-867 2 p., 8710358.

Research output: Contribution to journalEditorial

Secrecy capacity and secure distance for diffusion-based molecular communication systems

Mucchi, L., Martinelli, A., Jayousi, S., Caputo, S. & Pierobon, M., 2019, In : IEEE Access. 7, p. 110687-110697 11 p., 8784246.

Research output: Contribution to journalArticle

Open Access

Selenium Drives a Transcriptional Adaptive Program to Block Ferroptosis and Treat Stroke

Alim, I., Caulfield, J. T., Chen, Y., Swarup, V., Geschwind, D. H., Ivanova, E., Seravalli, J., Ai, Y., Sansing, L. H., Emma, E. J., Hondal, R. J., Mukherjee, S., Cave, J. W., Sagdullaev, B. T., Karuppagounder, S. S. & Ratan, R. R., May 16 2019, In : Cell. 177, 5, p. 1262-1279.e25

Research output: Contribution to journalArticle

39 Scopus citations

Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation

Van Den Bedem, H. & Wilson, M. A., Jul 1 2019, In : Journal of Synchrotron Radiation. 26, p. 958-966 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Similar immunological profiles between African endemic and human immunodeficiency virus type 1-associated epidemic Kaposi Sarcoma (KS) patients reveal the primary role of KS-associated herpesvirus in KS pathogenesis

Lidenge, S. J., Tso, F. Y., Ngalamika, O., Ngowi, J. R., Mortazavi, Y., Kwon, E. H., Shea, D. M., Minhas, V., Mwaiselage, J., Wood, C. & West, J. T., Apr 8 2019, In : Journal of Infectious Diseases. 219, 8, p. 1318-1328 11 p.

Research output: Contribution to journalArticle

4 Scopus citations

Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading

Yan, D., Yadav, S. R., Paterlini, A., Nicolas, W. J., Petit, J. D., Brocard, L., Belevich, I., Grison, M. S., Vaten, A., Karami, L., el-Showk, S., Lee, J. Y., Murawska, G. M., Mortimer, J., Knoblauch, M., Jokitalo, E., Markham, J. E., Bayer, E. M. & Helariutta, Y., Jun 1 2019, In : Nature Plants. 5, 6, p. 604-615 12 p.

Research output: Contribution to journalArticle

13 Scopus citations

Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants

Korasick, D. A., Končitíková, R., Kopečná, M., Hájková, E., Vigouroux, A., Moréra, S., Becker, D. F., Šebela, M., Tanner, J. J. & Kopečný, D., Feb 1 2019, In : Journal of Molecular Biology. 431, 3, p. 576-592 17 p.

Research output: Contribution to journalArticle

4 Scopus citations

Student Understanding of DNA Structure–Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models

Howell, M. E., Booth, C. S., Sikich, S. M., Helikar, T., Roston, R. L., Couch, B. A. & van Dijk, K., May 1 2019, In : Biochemistry and Molecular Biology Education. 47, 3, p. 303-317 15 p.

Research output: Contribution to journalArticle

3 Scopus citations

The effect of cysteine oxidation on DJ-1 cytoprotective function in human alveolar type II cells

Bahmed, K., Boukhenouna, S., Karim, L., Andrews, T., Lin, J., Powers, R., Wilson, M. A., Lin, C. R., Messier, E., Reisdorph, N., Powell, R. L., Tang, H. Y., Mason, R. J., Criner, G. J. & Kosmider, B., Sep 1 2019, In : Cell Death and Disease. 10, 9, 638.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

The relationship between DJ-1 and S100A8 in human primary alveolar type II cells in emphysema

Lin, C. R., Bahmed, K., Tomar, D., Marchetti, N., Criner, G. J., Bolla, S., Wilson, M. A., Madesh, M. & Kosmider, B., 2019, In : American Journal of Physiology - Lung Cellular and Molecular Physiology. 317, 6, p. L791-L804

Research output: Contribution to journalArticle

Transcriptome analysis-identified long noncoding RNA CRNDE in maintaining endothelial cell proliferation, migration, and tube formation

Moran, M., Cheng, X., Shihabudeen Haider Ali, M. S., Wase, N., Nguyen, N., Yang, W., Zhang, C., DiRusso, C. & Sun, X., Dec 1 2019, In : Scientific reports. 9, 1, 19548.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Visualizing the invisible: A guide to designing, printing, and incorporating dynamic 3D molecular models to teach structure–function relationships

Howell, M. E., Van Dijk, K., Booth, C. S., Helikar, T., Couch, B. A. & Roston, R. L., 2019, In : Journal of Microbiology and Biology Education. 19, 3, 1663.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

X-ray absorption spectroscopy of metalloproteins

Zhang, L., 2019, Methods in Molecular Biology. Humana Press Inc., p. 179-195 17 p. (Methods in Molecular Biology; vol. 1876).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations
2018

15N CEST data and traditional model-free analysis capture fast internal dynamics of DJ-1

Catazaro, J., Andrews, T., Milkovic, N. M., Lin, J., Lowe, A. J., Wilson, M. A. & Powers, R., Feb 1 2018, In : Analytical Biochemistry. 542, p. 24-28 5 p.

Research output: Contribution to journalArticle

1 Scopus citations

3-O sulfation of heparin leads to hepatotropism and longer circulatory half-life

Miller, C. M., Xu, Y., Kudrna, K. M., Hass, B. E., Kellar, B. M., Egger, A. W., Liu, J. & Harris, E. N., Jul 2018, In : Thrombosis Research. 167, p. 80-87 8 p.

Research output: Contribution to journalArticle

3 Scopus citations

ACM NANOCOM 2018: 5th ACM international conference on nanoscale computing and communication: Reykjavik, Iceland, September 5-7, 2018

Benediktsson, J. A., Dressler, F., Payne, G. F., Juntti, M., Schober, R., Tentzeris, E. M., Kokkoniemi, J., Balasingham, I., Jornet, J. M., Han, C., Feng, L., Barros, M., Perli, S., Caleffi, M., Lehtomaki, J., Vegni, A. M., Dinc, E., Cacciapuoti, A. S., Kuscu, M., Sakkaff, Z. & 6 others, Akyildiz, I. F., Balasubramaniam, S., Akan, O. B., Pierobon, M., Nakano, T. & Armada, A. G., Sep 5 2018, In : Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication, NANOCOM 2018.

Research output: Contribution to journalEditorial

Adenosine has two faces: Regionally dichotomous adenosine tone in a model of epilepsy with comorbid sleep disorders

Warren, T. J., Simeone, T. A., Smith, D. D., Grove, R., Adamec, J., Samson, K. K., Roundtree, H. M., Madhavan, D. & Simeone, K. A., Jun 2018, In : Neurobiology of Disease. 114, p. 45-52 8 p.

Research output: Contribution to journalArticle

4 Scopus citations
13 Scopus citations

A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage

Puniya, B. L., Todd, R. G., Mohammed, A., Brown, D. M., Barberis, M. & Helikar, T., Aug 2 2018, In : Frontiers in Physiology. 9, AUG, 878.

Research output: Contribution to journalArticle

6 Scopus citations

Applying molecular communication theory to estimate information loss in cell signal transduction: An approach based on cancer transcriptomics

Sakkaff, Z., Immaneni, A. & Pierobon, M., Sep 5 2018, Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication, NANOCOM 2018. Association for Computing Machinery, Inc, (Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication, NANOCOM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

A TLR/AKT/FoxO3 immune tolerance-like pathway disrupts the repair capacity of oligodendrocyte progenitors

Srivastava, T., Diba, P., Dean, J. M., Banine, F., Shaver, D., Hagen, M., Gong, X., Su, W., Emery, B., Marks, D. L., Harris, E. N., Baggenstoss, B., Weigel, P. H., Sherman, L. S. & Back, S. A., May 1 2018, In : Journal of Clinical Investigation. 128, 5, p. 2025-2041 17 p.

Research output: Contribution to journalArticle

12 Scopus citations

Brain is a potential sanctuary for subtype C HIV-1 irrespective of ART treatment outcome

Tso, F. Y., Kang, G., Kwon, E. H., Julius, P., Li, Q., West, J. T. & Wood, C., Jul 2018, In : PloS one. 13, 7, e0201325.

Research output: Contribution to journalArticle

8 Scopus citations

CancerDiscover: An integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data

Mohammed, A., Biegert, G., Adamec, J. & Helikar, T., 2018, In : Oncotarget. 9, 2, p. 2565-2573 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

Characterization of a recurrent missense mutation in the forkhead DNA-binding domain of FOXP1

Johnson, T. B., Mechels, K., Anderson, R. E., Cain, J. T., Sturdevant, D. A., Braddock, S., Pinz, H., Wilson, M. A., Landsverk, M., Roux, K. J. & Weimer, J. M., Dec 1 2018, In : Scientific reports. 8, 1, 16161.

Research output: Contribution to journalArticle

CHCA-1 is a copper-regulated CTR1 homolog required for normal development, copper accumulation, and copper-sensing behavior in Caenorhabditis elegans

Yuan, S., Sharma, A. K., Richart, A., Lee, J. & Kim, B. E., Jul 13 2018, In : Journal of Biological Chemistry. 293, 28, p. 10911-10925 15 p.

Research output: Contribution to journalArticle

2 Scopus citations

Combining Mass Spectrometry and NMR Improves Metabolite Detection and Annotation

Bhinderwala, F., Wase, N., Dirusso, C. & Powers, R., Nov 2 2018, In : Journal of proteome research. 17, 11, p. 4017-4022 6 p.

Research output: Contribution to journalArticle

5 Scopus citations

Computational Models for Trapping Ebola Virus Using Engineered Bacteria

Martins, D. P., Barros, M. T., Pierobon, M., Kandhavelu, M., Lio, P. & Balasubramaniam, S., Nov 1 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 6, p. 2017-2027 11 p., 8359015.

Research output: Contribution to journalArticle

2 Scopus citations

Concentrations of purine metabolites are elevated in fluids from adults and infants and in livers from mice fed diets depleted of bovine milk exosomes and their RNA cargos

Aguilar-Lozano, A., Baier, S., Grove, R., Shu, J., Giraud, D., Leiferman, A., Mercer, K. E., Cui, J., Badger, T. M., Adamec, J., Andres, A. & Zempleni, J., 2018, In : Journal of Nutrition. 148, 12, p. 1886-1894 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Coordinated regulation of transcription by CcpA and the Staphylococcus aureus twocomponent system HptRS

Reed, J. M., Olson, S., Brees, D. F., Griffin, C. E., Grove, R. A., Davis, P. J., Kachman, S. D., Adamec, J. & Somerville, G. A., Dec 2018, In : PloS one. 13, 12, e0207161.

Research output: Contribution to journalArticle

2 Scopus citations

Development of iFOX-hunting as a functional genomic tool and demonstration of its use to identify early senescence-related genes in the polyploid Brassica napus

Ling, J., Li, R., Nwafor, C. C., Cheng, J., Li, M., Xu, Q., Wu, J., Gan, L., Yang, Q., Liu, C., Chen, M., Zhou, Y., Cahoon, E. B. & Zhang, C., Feb 1 2018, In : Plant Biotechnology Journal. 16, 2, p. 591-602 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

Dietary omega-3 and omega-6 polyunsaturated fatty acids modulate hepatic pathology

Khadge, S., Sharp, J. G., Thiele, G. M., McGuire, T. R., Klassen, L. W., Duryee, M. J., Britton, H. C., Dafferner, A. J., Beck, J., Black, P. N., DiRusso, C. C. & Talmadge, J. E., Feb 2018, In : Journal of Nutritional Biochemistry. 52, p. 92-102 11 p.

Research output: Contribution to journalArticle

13 Scopus citations

Discontinuous fatty acid elongation yields hydroxylated seed oil with improved function

Li, X., Teitgen, A. M., Shirani, A., Ling, J., Busta, L., Cahoon, R. E., Zhang, W., Li, Z., Chapman, K. D., Berman, D., Zhang, C., Minto, R. E. & Cahoon, E. B., Sep 1 2018, In : Nature Plants. 4, 9, p. 711-720 10 p.

Research output: Contribution to journalArticle

12 Scopus citations
19 Scopus citations

Endosomal Escape of Antisense Oligonucleotides Internalized by Stabilin Receptors Is Regulated by Rab5C and EEA1 during Endosomal Maturation

Miller, C. M., Wan, W. B., Seth, P. P. & Harris, E. N., Apr 2018, In : Nucleic Acid Therapeutics. 28, 2, p. 86-96 11 p.

Research output: Contribution to journalArticle

11 Scopus citations

Erratum: IgE stimulates human and mouse arterial cell apoptosis and cytokine expression and promotes atherogenesis in Apoe-/- mice (Journal of Clinical Investigation (2018) 128:11 (5184) DOI: 10.1172/JCI124107)

Wang, J., Cheng, X., Xiang, M. X., Alanne-Kinnunen, M., Wang, J. A., Chen, H., He, A., Sun, X., Lin, Y., Tang, T. T., Tu, X., Sjöberg, S., Sukhova, G. K., Liao, Y. H., Conrad, D. H., Yu, L., Kawakami, T., Kovanen, P. T., Libby, P. & Shi, G. P., Nov 1 2018, In : Journal of Clinical Investigation. 128, 11, p. 5184 1 p.

Research output: Contribution to journalComment/debate

Open Access

Estimating Information Exchange Performance of Engineered Cell-to-cell Molecular Communications: A Computational Approach

Harper, C., Pierobon, M. & Magarini, M., Oct 8 2018, INFOCOM 2018 - IEEE Conference on Computer Communications. Institute of Electrical and Electronics Engineers Inc., p. 729-737 9 p. 8485834. (Proceedings - IEEE INFOCOM; vol. 2018-April).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations

Estimating the Molecular Information Through Cell Signal Transduction Pathways

Sakkaff, Z., Immaneni, A. & Pierobon, M., Aug 24 2018, 2018 IEEE 19th International Workshop on Signal Processing Advances in Wireless Communications, SPAWC 2018. Institute of Electrical and Electronics Engineers Inc., 8445884. (IEEE Workshop on Signal Processing Advances in Wireless Communications, SPAWC; vol. 2018-June).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Functional and Structural Analysis of Phenazine O -Methyltransferase LaPhzM from Lysobacter antibioticus OH13 and One-Pot Enzymatic Synthesis of the Antibiotic Myxin

Jiang, J., Guiza Beltran, D., Schacht, A., Wright, S., Zhang, L. & Du, L., Apr 20 2018, In : ACS chemical biology. 13, 4, p. 1003-1012 10 p.

Research output: Contribution to journalArticle

5 Scopus citations

Global epidemiology of human herpesvirus 8 in men who have sex with men: A systematic review and meta-analysis

Liu, Z., Fang, Q., Zuo, J., Chen, Y., Minhas, V., Wood, C. & Zhang, T., Mar 2018, In : Journal of Medical Virology. 90, 3, p. 582-591 10 p.

Research output: Contribution to journalArticle

6 Scopus citations

GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDTRANSFERASE1 (GINT1) is a GlcNAc-containing glycosylinositol phosphorylceramide glycosyltransferase

Ishikawa, T., Fang, L., Rennie, E. A., Sechet, J., Yan, J., Jing, B., Moore, W., Cahoon, E. B., Scheller, H. V., Kawai-Yamada, M. & Mortimer, J. C., Jun 2018, In : Plant physiology. 177, 3, p. 938-952 15 p.

Research output: Contribution to journalArticle

7 Scopus citations

Identification of biologically essential nodes via determinative power in logical models of cellular processes

Pentzien, T., Puniya, B. L., Helikar, T. & Matache, M. T., Aug 31 2018, In : Frontiers in Physiology. 9, AUG, 1185.

Research output: Contribution to journalArticle

2 Scopus citations

Identification of bottlenecks in the accumulation of cyclic fatty acids in camelina seed oil

Yu, X. H., Cahoon, R. E., Horn, P. J., Shi, H., Prakash, R. R., Cai, Y., Hearney, M., Chapman, K. D., Cahoon, E. B., Schwender, J. & Shanklin, J., Apr 2018, In : Plant Biotechnology Journal. 16, 4, p. 926-938 13 p.

Research output: Contribution to journalArticle

9 Scopus citations

Identification of genes encoding enzymes catalyzing the early steps of carrot polyacetylene biosynthesis

Busta, L., Yim, W. C., Labrant, E. W., Wang, P., Grimes, L., Malyszka, K., Cushman, J. C., Santos, P., Kosma, D. K. & Cahoon, E. B., Dec 1 2018, In : Plant physiology. 178, 4, p. 1507-1521 15 p.

Research output: Contribution to journalArticle

5 Scopus citations

Immune regulation and anti-cancer activity by lipid inflammatory mediators

Khadge, S., Sharp, J. G., McGuire, T. R., Thiele, G. M., Black, P., DiRusso, C., Cook, L., Klassen, L. W. & Talmadge, J. E., Dec 2018, In : International Immunopharmacology. 65, p. 580-592 13 p.

Research output: Contribution to journalReview article

5 Scopus citations

Induction of oil accumulation by heat stress is metabolically distinct from N stress in the green microalgae Coccomyxa subellipsoidea C169

Allen, J. W., Tevatia, R., Demirel, Y., DiRusso, C. C. & Black, P. N., Sep 2018, In : PloS one. 13, 9, e0204505.

Research output: Contribution to journalArticle

4 Scopus citations

Innovations in improving lipid production: Algal chemical genetics

Wase, N., Black, P. & DiRusso, C., Jul 2018, In : Progress in Lipid Research. 71, p. 101-123 23 p.

Research output: Contribution to journalReview article

7 Scopus citations

Integration of biology, ecology and engineering for sustainable algal-based biofuel and bioproduct biorefinery

Allen, J., Unlu, S., Demirel, Y., Black, P. & Riekhof, W., 2018, In : Bioresources and Bioprocessing. 5, 1, 47.

Research output: Contribution to journalReview article

Open Access
7 Scopus citations

Intraperitoneal nanotherapy for metastatic ovarian cancer based on siRNA-mediated suppression of DJ-1 protein combined with a low dose of cisplatin

Schumann, C., Chan, S., Millar, J. A., Bortnyak, Y., Carey, K., Fedchyk, A., Wong, L., Korzun, T., Moses, A. S., Lorenz, A., Shea, D., Taratula, O., Khalimonchuk, O. & Taratula, O., Jun 2018, In : Nanomedicine: Nanotechnology, Biology, and Medicine. 14, 4, p. 1395-1405 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Lipid composition and emulsifying properties of Camelina sativa seed lecithin

Belayneh, H. D., Wehling, R. L., Cahoon, E. & Ciftci, O. N., Mar 1 2018, In : Food Chemistry. 242, p. 139-146 8 p.

Research output: Contribution to journalArticle

7 Scopus citations