Recent Publications

2016

Synchronized photoreversion of spirooxazine ring opening in thin crystals to uncover ultrafast dynamics. Siddiqui, K.M., Corthey, G., Hayes, S.A., Rossos, A., Badali, D.S., Xian, R., Murphy, R.S., Whitaker, B.J. and Miller, R.J.D. CrystEngComm 2016, 18, 7212-7216. DOI: 10.1039/c6ce01049k.

An alkylidene carbene C-H activation approach toward the enantioselective syntheses of spirolactams: Application to the synthesis of (-)-adalinine. Annadi, K. and Wee, A.G.H. J. Org. Chem. 2016, 81, 1021-1038. DOI: 10.1021/acs. joc.5b02582.

Conditional epistatic interaction maps reveal global functional rewiring of genome integrity pathways in Escherichia coli. Kumar, A., Beloglazova, N., Bundalovic-Torma, C., Phanse, S., Deineko, V., Gagarinova, A., Musso, G., Vlasblom, J., Lemak, S., Hooshyar, M., Minic, Z., Wagih, O., Mosca, R., Aloy, P., Golshani, A., Parkinson, J., Emili, A., Yakunin A.E., and Babu M.* Cell Reports 2016, 14:1-14. DOI: 10.1016/j.celrep.2015.12.060.

Laser-limited signatures of quantum coherence. Tempelaar, R., Halpin, A., Johnson, P.J.M., Cai, J., Murphy, R.S., Knoester, J., Miller, R.J.D. and Jansen, T.L.C. J. Phys. Chem. A. 2016, 120, 3042−3048. DOI: 10.1021/acs.jpca.5b10312.

Novel interactome of Saccharomyces cerevisiae myosin type II identified by a modified integrated membrane yeast two-hybrid (iMYTH) screen. Santiago, E., Akamine, P., Snider, J., Wong, V., Jessulat, M., Deineko, V., Gagarinova, A., Aoki, H., Minic, Z., Phanse, S., San Antonio, A., Cubano, L., Rymond, B.C., Babu, M., Stagljar, I., and Rodriguez-Medina, J.R. G3-Genes Genomes Genetics (Bethesda) 2016, 6(5):1469-74. DOI: 10.1534/g3.115.026609.

Photocontrol of ion permeation in lipid vesicles with (bola)amphiphilic spirooxazines. Kandasamy, Y.S., Cai, J., Ottaviano, J.G., Smith, K.A., Williams, A.N., Moore, J., Louis, K.M., Selzler, L., Beler, A., Okwuonu, T. and Murphy, R.S. Org. Biomol. Chem. 2016, 14, 296-308. DOI: 10.1039/c5ob01993a.

PpASCL, the Physcomitrella patens anther-specific chalcone synthase-like enzyme implicated in sporopollenin biosynthesis, is needed for integrity of the moss spore wall and spore viability. Daku, R.M., Rabbi, F., Buttigieg, J., Coulson, I,M., Horne, D., Martens, G., Ashton, N.W. and Suh, D.-Y. PLoS ONE 2016, 11(1). DOI: 10.1371/journal.pone.0146817

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes Phanse. S., Wan, C., Borgeson, B., Tu, F., Drew, K., Clark, G., Xiong, X., Kagan, O., Kwan, J., Bezginov, A., Chessman, K., Pal, S., Cromar, G., Papoulas, O., Ni, Z., Boutz, D.R., Stoilova, S., Havugimana, P.C., Guo, X., Malty, R.H., Sarov, M., Greenblatt, J., Babu, M., Derry, W.B., Tillier, E.R., Wallingford, J.B., Parkinson, J., Marcotte, E.M. & Emili, A. Data in Brief 2016, 6, 715-721. DOI:10.1016/j.dib.2015.11.062.

Towards a functional definition of the mitochondrial human proteome. Fasano, M., Alberio, T., Babu, M., Lundberg, E., Urbani, A. EuPA Open Proteomics 2016, 10, 24-27. DOI:10.1016/ j.euprot.2016. 01.004.

The carbocation rearrangement mechanism, clarified. Sandbeck, D.J.S., Markewich, D.J., and East, A.L.L. J. Org. Chem. 2016, 18(4), 1410-1415. DOI: 10.1021/acs.joc.5b02553.

2015

A comprehensive membrane interactome mapping of Sho1p reveals Fps1p as a novel key player in the regulation of the HOG pathway in S. cerevisiae. Lam, M.H.Y., Snider, J., Rehal, M., Wong, V., Aboualizadeh, F., Drecun, L., Wong, O., Jubran, B., Li, M., Ali, M., Jessulat, M., Dieneko, V., Miller, R., Lee, M.E., Park, H.O., Davidson, A., Babu, M. and Stagljar, I. Journal of Molecular Biology 2015, 427, 2088-2103. DOI: 10.1016.

Advanced Microscopy in Mycology. Editors: Czymmek, K.J. and Dahms, T.E.S. 2015, Springer, NY, USA. ISBN 978-3-319-22437-4.

Assessing the impact of western science and indigenous science educators in an online STEM course. Alkholy S.O., Gendron F., Dahms T.E.S. and Pontes-Ferreira M.* 2015, Ubiquitous Learning: An International Journal 7(3-4) 41-51.

Binuclear platinum-iridium complexes: Synthesis, reactivity and luminescence. Sterenberg, B.T., Wrigley, C.T., and Puddephatt, R.J., Dalton Transactions 2015, 44, 5555-5568. DOI: 10.1039/ c4dt03966a.

Determination of neonicotinoid insecticides and strobilurin fungicides in particle phase atmospheric samples by liquid chromatography-tandem mass spectrometry. Raina-Fulton, R. J. Agric. Food Chem., 2015, 63 (21), 5152–5162. DOI: 10.1021/acs.jafc.5b01347.

Effects of a herbicide mixture on primary and bacterial productivity in four prairie wetlands with varying salinities: An enclosure approach. Sura, S., Waiser, M.J., Tumber, V., Raina-Fulton R. and Cessna, A.J. Science of the Total Environment, 2015, 512–513, 526-539. DOI: 10.1016/j.scitotenv. 2015.01.064.

Friends or foes? Emerging insights from fungal interactions with plants. Zeilinger S., Gupta V.K., Dahms T.E.S., Silva R.N., Singh H.B., Upadhyay R.S., Gomes E.V., Tsui C.K., Nayak S.C. FEMS Microbiol Rev. 2015, 40, 182-207. DOI: 10.1093/femsre/fuv045.

Functional diversity of haloacid dehalogenase superfamily phosphatases from saccharomyces cerevisiae: Biochemical, structural, and evolutionary insights. Kuznetsova, E., Nocek2, B., Brown, G., Makarova, K, S,. Flick, R., Wolf, Y. I., Khusnutdinova, A., Evdokimova, E., Jin, K., Tan, K., Hanson, A. D., Hasnain, G., Zallot, R., de Crecy-Lagard, V., Babu, M., Savchenko, A., Joachimiak, A., Edwards, A. M., Koonin, E. V. and Yakunin, A. M. The Journal of Biological Chemistry 2015, 290, 18678-18698. DOI: 10.1074/jbc.M115.657916.

Future Directions: Advanced Mycological Microscopy. Czymmek, K.J. and Dahms, T.E.S. Advanced Microscopy in Mycology 2015, Eds. Czymmek, K.J. and Dahms, T.E.S., Springer, NY, USA, Chapter 8, 143-162.

Identification of human neuronal protein complexes reveals biochemical activities and convergent mechanisms of action in autism spectrum disorders. Li, J., Ma, Z., Shi, M., Malty, R.H., Aoki, H., Minic, Z., Phanse, S., Jin, K., Wall, D.P., Zhang, Z., Urban, A.E., Hallmayer, J., Babu, M*., Snyder, M*. Cell Systems. 2015, 1, 361-374. DOI: 10.1016/j.cels.2015. 11.002.

New trends in pesticide residue analysis in cereals, nutraceuticals, baby foods, and related processed consumer products. R. Raina-Fulton, J AOAC Int. 2015, 98(5), 1163-1170. DOI: 10.5740/jaoacint.SGE2Raina-Fulton.

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Vlasblom, J., Zuberi, K., Rodriguez, H., Arnold, R., , Gagarinova, A., Deineko, V., Kumar, A., Leung, E., Rizzolo, K., Samanfar, B., Chang, L., Phanse, S., Golshani, A., Greenblatt, J.F., Houry, W.A., Emili, A., Morris, Q., Bader, G., and Babu, M.* Bioinformatics 2015, 31(3), 306-10. DOI: 10.1093/bioinformatics/btu671.

Oxidative stress and metabolic perturbations in Escherichia coli exposed to sublethal levels of 2,4-dichlorophenoxyacetic acid. Bhat, S.V., Booth, S.C., Vantomme, E.A.N., Afroj, S., Yost, C.K. and Dahms, T.E.S. Chemosphere 2015, 135:453-461. DOI: 10.1016/j.chemosphere.2014.12.035.

Panorama of ancient metazoan macromolecular complexes. Wan, C., Borgeson, B., Phanse, S., Tu, F., Drew, K., Clark, G., Xiong, X., Kagan, O., Kwan, J.,Bezginov, A., Chessman, K., Pal, S., Cromar, G., Papoulas, O., Ni, Z., Boutz, D. R., Stoilova, S., Havugimana, P. C., Guo, X., Malty, R. H., Sarov, M., Greenblatt, J., Babu, M., Derry, W. B., Tillier, E. R., Wallingford, J. B., Parkinson, J., Marcotte, E. M. & Emili, A. Nature 2015, 525, 339-344. DOI:10.1038/nature14877.

Photocontrol of ion permeation in lipid vesicles with amphiphilic dithienylethenes. Kandasamy, Y.S., Cai, J., Beler, A., Sang, M.-S.J., Andrews, P.D. and Murphy, R.S. Org. Biomol. Chem. 2015, 13, 2652-2663. DOI: 10.1039/c4ob02382j.

Prokaryotic Systems Biology. Editors: Krogan, N. J., and Babu, M. Advances in Experimental Medicine and Biology 2015, Springer Publishing, New York.

Quantitative and systems-based approaches for deciphering bacterial membrane interactome and gene function. Deineko, V., Kumar, A., Vlasblom, J., Babu, M*. Advances in Experimental Medicine and Biology 2015; 883, 135-54. DOI: 10.1007/978-3-319-23603-2.

Rab5 family guanine nucleotide exchange factors bind retromer and promote its recruitment to endosomes. Bean, D.M.B., Davey, M., Snider, J., Jessulat, M., Dieneko, V., Tinney, M., Staglijar, I., Babu, M., Conibear, E. Mol. Biol. Cell. 2015, 26(6), 1119-28. DOI: 10.1091/mbc.E14-08-1281.

Rhizobium leguminosarum bv. viciae 3841 adapts to 2,4-dichlorophenoxyacetic acid with “auxin-like” morphological changes, cell envelope remodeling and upregulation of central metabolic pathways. Bhat S.V., Booth S.C., McGrath S.G.K. and Dahms T.E.S. PLoS ONE, 2015, 10:4, 1-21. DOI:10.1371/ journal.pone.0123813.

Semicontinuum solvation modeling improves predictions of carbamate stability in the CO2 + aqueous amine reaction. Sumon, K.Z., Bains, C.H., Markewich, D.J., Henni, A., and East, A.L.L. J. Phys. Chem. B. 2015, 119, 12256-12264. DOI: 10.1021/acs.jpcb.5b06076.

Sequential electrophilic P–C bond formation in metal-coordinated chlorophosphines. Jayaraman A., Jacob, T.V., Bisskey, J., Sterenberg, B.T., Dalton Transactions 2015, 44, 8788-8791. DOI: 10.1039/ c5dt01281c.

Spindle checkpoint factors Bub1 and Bub2 promote DNA double strand break repair by non-homologous end joining. Jessulat, M., Malty, R., Nguyen-Tran, D., Deineko, V., Aoki, H., Vlasblom, J., Omidi, K., Jin, K., Minic, Z., Hooshyar, M., Burnside, D., Samanfar, B., Phanse, S., Freywald, T., Prasad, B., Zhang, Z., Vizeacoumar, F., Krogan, N., Freywald, A., Golshani, A., and Babu, M. Molecular and Cellular Biology 2015, 35:14, 2448-463. DOI:10.1128/MCB.00007-15.

Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships. Jin, K., Musso, G., Vlasblom, J., Jessulat, M., Deineko, V., Negroni, J., Mosca, R., Malty, R., Nguyen-Tran, D-H., Aoki, H., Minic, Z., Freywald, T., Phanse, S., Xiang, Q., Freywald, A., Aloy, P., Zhang, Z and Babu, M. Journal of Proteome Research 2015, 14(2), 1220-37. DOI: 10.1021/pr501148.

Stereoselective syntheses of (+)-2-epi-deoxoprosopinine, (‒)-deoxoproso-phylline, (+)-cis-195A, and 2,5-di-epi-cis-195A from a common chiral non-racemic building block. Annadi, K. and Wee, A.G.H. J. Org. Chem. 2015, 80, 5236-5251, DOI: 10.1021/acs.joc.5b00621.