2019

Mitchell, James, Balem, Fernanda, Tirupula, Kalyan, Man, David, Dhiman, Harpreet Kaur, Yanamala, Naveena, Ollesch, Julian, Planas-Iglesias, Joan, Jennings, Barbara J., Gerwert, Klaus, Iannaccone, Alessandro and Klein-Seetharaman, Judith (2019) Comparison of the molecular properties of retinitis pigmentosa P23H and N15S amino acid replacements in rhodopsin. PLOS ONE, 14 (5). e0214639. doi:10.1371/journal.pone.0214639

Tejpal, Shilpa, Sanghera, Narinder, Manoharan, Vijayalaxmi, Planas-Iglesias, Joan, Myler, Kate and Klein-Seetharaman, Judith (2019) Towards personalised molecular feedback for weight loss. BMC Obesity, 6 (1). 20. doi:10.1186/s40608-019-0237-5

Tan, Yi Lei, Mitchell, James, Klein-Seetharaman, Judith and Nietlispach, Daniel (2019) Characterisation of denatured states of sensory rhodopsin II by solution-state NMR. Journal of Molecular Biology, 431 (15). pp. 2790-2809. doi:10.1016/j.jmb.2019.04.039 (In Press)

2018

Mitchell, James, Yanamala, Naveena, Tan, Yi Lei, Gardner, Eric E., Tirupula, Kalyan C., Balem, Fernanda, Sheves, Mordechai, Nietlispach, Daniel and Klein‐Seetharaman, Judith (2018) Structural and Functional Consequences of the Weak Binding of Chlorin e6 to Bovine Rhodopsin. Photochemistry and Photobiology, 95 (3). pp. 787-802. doi:10.1111/php.13074

Tan, Yi Lei, Mitchell, James, Klein-Seetharaman, Judith and Nietlispach, Daniel (2018) Characterization of denatured states and reversible unfolding of sensory rhodopsin II. Journal of Molecular Biology, 430 (21). pp. 4068-4086. doi:10.1016/j.jmb.2018.07.031

Mohammadyani, Dariush, Yanamala, Naveena, Samhan-Arias, Alejandro K., Kapralov, Alexander A., Stepanov, German, Nuar, Nick, Planas-Iglesias, Joan, Sanghera, Narinder, Kagan, Valerian E. and Klein-Seetharaman, Judith (2018) Structural characterization of cardiolipin-driven activation of cytochrome c into a peroxidase and membrane perturbation. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1860 (5). pp. 1057-1068. doi:10.1016/j.bbamem.2018.01.009

2017

Maguire, John J., Tyurina, Yulia Y., Mohammadyani, Dariush, Kapralov, Aleksandr A., Anthonymuthu, Tamil S., Qu, Feng, Amoscato, Andrew A., Sparvero, Louis J., Tyurin, Vladimir A., Planas-Iglesias, Joan, He, Rong-Rong, Klein-Seetharaman, Judith, Bayır, Hülya and Kagan, Valerian E. (2017) Known unknowns of cardiolipin signaling : the best is yet to come. Biochimica and Biophysica Acta. Molecular and Cell Biology of Lipids, 1862 (1). pp. 8-24. doi:10.1016/j.bbalip.2016.08.001

2016

Woods, Kristina N., Pfeffer, Jürgen, Dutta, Arpana and Klein-Seetharaman, Judith (2016) Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors. Scientific Reports, 6 . 37290. doi:10.1038/srep37290

(2016) Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature Chemical Biology, 13 (1). pp. 81-90. doi:10.1038/nchembio.2238

Kshirsagar, Meghana, Carbonell, Jaime G., Klein-Seetharaman, Judith and Murugesan, Keerthiram (2016) Multitask matrix completion for learning protein interactions across diseases. In: Singh, Mona, (ed.) Research in Computational Molecular Biology : 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings. Lecture Notes in Computer Science, 9649 . Springer International Publishing, pp. 53-64. ISBN 9783319319575

Sanghera, Narinder, Anderson, Alexander, Nuar, Nick, Xie, Can, Mitchell, Daniel A. and Klein-Seetharaman, Judith (2016) Insulin biosensor development : a case study. International Journal of Parallel, Emergent and Distributed Systems, 32 (1). pp. 119-138. doi:10.1080/17445760.2016.1158817

2015

Mao, Gaowei, Qu, Feng, St Croix, Claudette M., Tyurina, Yulia Y., Planas-Iglesias, Joan, Jiang, Jianfei, Huang, Zhentai, Amoscato, Andrew A., Tyurin, Vladimir A., Kapralov, Alexandr A., Cheikhi, Amin, Maguire, John, Klein-Seetharaman, Judith, Bayır, Hülya and Kagan, Valerian E. (2015) Mitochondrial redox opto-lipidomics reveals mono-oxygenated cardiolipins as pro-apoptotic death signals. ACS Chemical Biology, 11 (2). pp. 530-40.

Barneda, David, Planas-Iglesias, Joan, Gaspar, Maria L., Mohammadyani, Dariush, Prasannan, Sunil, Dormann, Dirk, Han, Gil-Soo, Jesch, Stephen A., Carman, George M., Kagan, Valerian, Parker, Malcolm G., Ktistakis, Nicholas T., Klein-Seetharaman, Judith, Dixon, Ann M., Henry, Susan A. and Christian, Mark (2015) The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix. eLife, 4 . doi:10.7554/eLife.07485

(2015) Dichotomous roles for externalized cardiolipin in extracellular signaling : promotion of phagocytosis and attenuation of innate immunity. Science Signaling, 8 (395). ra95. doi:10.1126/scisignal.aaa6179

Planas-Iglesias, Joan, Dwarakanath, Himal, Mohammadyani, Dariush, Yanamala, Naveena, Kagan, Valerian E and Klein-Seetharaman, Judith (2015) Cardiolipin interactions with proteins. Biophysical Journal, 109 (6). pp. 1282-94. doi:10.1016/j.bpj.2015.07.034

Kagan, Valerian E., Tyurina, Yulia Y., Tyurin, Vladimir A., Mohammadyani, Dariush, Angeli, Jose Pedro Friedmann, Baranov, Sergei V., Klein-Seetharaman, Judith, Friedlander, Robert M., Mallampalli, Rama K., Conrad, Marcus and Bayir, Hülya (2015) Cardiolipin signaling mechanisms : collapse of asymmetry and oxidation. Antioxidants & Redox Signaling, 22 (18). pp. 1667-1680. doi:10.1089/ars.2014.6219

Kshirsagar, Meghana, Schleker, Sylvia, Carbonell, Jaime and Klein-Seetharaman, Judith (2015) Techniques for transferring host-pathogen protein interactions knowledge to new tasks. Frontiers in Microbiology, 6 . 36. doi:10.3389/fmicb.2015.00036

Schlattner, Uwe, Tokarska-Schlattner, Malgorzata, Epand, Richard M., Boissan, Mathieu, Lacombe, Marie-Lise, Klein-Seetharaman, Judith and Kagan, Valerian E. (2015) Mitochondrial NM23-H4/NDPK-D : a bifunctional nanoswitch for bioenergetics and lipid signaling. Naunyn-Schmiedeberg's Archives of Pharmacology, 388 (2). pp. 271-278. doi:10.1007/s00210-014-1047-4

Schleker, Sylvia, Kshirsagar, Meghana and Klein-Seetharaman, Judith (2015) Comparing human–Salmonella with plant–Salmonella protein–protein interaction predictions. Frontiers in Microbiology, 6 . 45. doi:10.3389/fmicb.2015.00045

Tastan, Oznur, Qi, Yanjun, Carbonell, Jaime G. and Klein-Seetharaman, Judith (2015) Refining literature curated protein interactions using expert opinions. In: Biocomputing 2015, Kohala Coast, Hawaii, USA, 4–8 Jan 2015. Published in: Proceedings of the Pacific Symposium pp. 318-329. doi:10.1142/9789814644730_0031

2014

Mohammadyani, Dariush, Tyurin, Vladimir A., O׳Brien, Matthew, Sadovsky, Yoel, Gabrilovich, Dmitry I., Klein-Seetharaman, Judith and Kagan, Valerian E. (2014) Molecular speciation and dynamics of oxidized triacylglycerols in lipid droplets : Mass spectrometry and coarse-grained simulations. Free Radical Biology and Medicine, Volume 76 . pp. 53-60. doi:10.1016/j.freeradbiomed.2014.07.042

Yanamala, N., Kapralov, A. A., Djukic, M., Peterson, J., Mao, G., Klein-Seetharaman, J., Stoyanovsky, D. A., Stursa, J., Neuzil, J. and Kagan, V. E. (2014) Structural re-arrangement and peroxidase activation of cytochrome c by anionic analogues of vitamin E, tocopherol succinate and tocopherol phosphate. Journal of Biological Chemistry, 289 (47). pp. 32488-32498. doi:10.1074/jbc.M114.601377

Dutta, Arpana, Altenbach, Christian, Mangahas, Sheryll, Yanamala, Naveena, Gardner, Eric, Hubbell, Wayne L. and Klein-Seetharaman, Judith (2014) Differential dynamics of extracellular and cytoplasmic domains in denatured states of rhodopsin. Biochemistry, 53 (46). pp. 7160-7169. doi:10.1021/bi401557e

Tastan, Oznur, Dutta, Arpana, Booth, Paula and Klein-Seetharaman, Judith (2014) Retinal proteins as model systems for membrane protein folding. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Volume 1837 (Number 5). pp. 656-663. doi:10.1016/j.bbabio.2013.11.021

Tyurina, Yulia Y., Poloyac, Samuel M., Tyurin, Vladimir A., Kapralov, Alexander A., Jiang, Jianfei, Anthonymuthu, Tamil Selvan, Kapralova, Valentina I., Vikulina, Anna S., Jung, Mi-Yeon, Epperly, Michael W., Mohammadyani, Dariush, Klein-Seetharaman, Judith, Jackson, Travis C., Kochanek, Patrick M., Pitt, Bruce R., Greenberger, Joel S., Vladimirov, Yury A., Bayır, Hülya and Kagan, Valerian E. (2014) A mitochondrial pathway for biosynthesis of lipid mediators. Nature Chemistry, 6 (6). pp. 542-552. doi:10.1038/nchem.1924

Cao, W., Ramakrishnan, R., Tuyrin, V. A., Veglia, F., Condamine, T., Amoscato, A., Mohammadyani, D., Johnson, J. J., Min Zhang, L., Klein-Seetharaman, Judith, Celis, E., Kagan, V. E. and Gabrilovich, D. I. (2014) Oxidized lipids block antigen cross-presentation by dendritic cells in cancer. The Journal of Immunology, Volume 192 (Number 6). pp. 2920-2931. doi:10.4049/jimmunol.1302801

Stehle, Jochen, Silvers, Robert, Werner, Karla, Chatterjee, Deep, Gande, Santosh, Scholz, Frank, Dutta, Arpana, Wachtveitl, Josef, Klein-Seetharaman, Judith and Schwalbe, Harald (2014) Characterization of the simultaneous decay kinetics of metarhodopsin states II and III in rhodopsin by solution-state NMR spectroscopy. Angewandte Chemie International Edition, Volume 53 (Number 8). pp. 2078-2084. doi:10.1002/anie.201309581

Stehle, Jochen, Silvers, Robert, Werner, Karla, Chatterjee, Deep, Gande, Santosh, Scholz, Frank, Dutta, Arpana, Wachtveitl, Josef, Klein-Seetharaman, Judith and Schwalbe, Harald (2014) Characterization of the simultaneous decay kinetics of metarhodopsin states II and III in rhodopsin by solution-state NMR spectroscopy. Angewandte Chemie , Volume 126 (Number 8). pp. 2110-2116. doi:10.1002/ange.201309581

Boscia, Alexander L., Treece, Bradley W., Mohammadyani, Dariush, Klein-Seetharaman, Judith, Braun, Anthony R., Wassenaar, Tsjerk A., Klösgen, Beate and Tristram-Nagle, Stephanie (2014) X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes. Chemistry and Physics of Lipids, Volume 178 . pp. 1-10. doi:10.1016/j.chemphyslip.2013.12.010

Mohammadyani, Dariush, Tyurin, Vladimir A., Amoscato, Andrew A., Gabrilovich, Dmitry I., Klein-Seetharaman, Judith and Kagan, Valerian E. (2014) Computational approaches to understanding the role of oxidized tri-aclyglycerols in suppression of antigen cross-presentation in cancer. In: Biophysical Society 58th Annual Meeting, San Francisco, California, 15-19 Feb 2014. Published in: Biophysical Journal, 106 (2). 805a-806a. ISSN 0006-3495. doi:10.1016/j.bpj.2013.11.4416

2013

Kshirsagar, M., Carbonell, J. and Klein-Seetharaman, Judith (2013) Multitask learning for host-pathogen protein interactions. Bioinformatics, Volume 29 (Number 13). i217-i226. doi:10.1093/bioinformatics/btt245

Schlattner, U., Tokarska-Schlattner, M., Ramirez, S., Tyurina, Y. Y., Amoscato, A. A., Mohammadyani, D., Huang, Z., Jiang, J., Yanamala, N., Seffouh, A., Boissan, M., Epand, R. F., Epand, R. M., Klein-Seetharaman, Judith, Lacombe, M.-L. and Kagan, V. E. (2013) Dual function of mitochondrial Nm23-H4 protein in phosphotransfer and intermembrane lipid transfer : a cardiolipin-dependent switch. Journal of Biological Chemistry, 288 (1). pp. 111-121. doi:10.1074/jbc.M112.408633

2011

(2011) A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death. Nature Communications, 2 . Article: 497. doi:10.1038/ncomms1499

2010

(2010) Carbon nanotubes degraded by neutrophil myeloperoxidase induce less pulmonary inflammation. Nature Nanotechnology, 5 (5). pp. 354-359. doi:10.1038/nnano.2010.44

2008

(2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology, 9 (Suppl 1). S2. doi:10.1186/gb-2008-9-s1-s2