Recent publications


Trites, M.J.; Stebbings, B.M.; Aoki, H.; Phanse, S; Akl, M.G.; Li, L.; Babu, M.; Widenmaier, S.B. HDL functionality is dependent on hepatocyte stress defense factors Nrf1 and Nrf2. Frontiers in Physiology 2023, 14, 1212785.

Broderick, K.; Moutaoufik, M.T.; Aly, K.A.; Babu, M. Sanitation enzymes: Exquisite surveillance of the noncanonical nucleotide pool to safeguard the genetic blueprint. Seminars in Cancer Biology 2023, 94, 11-20.

Rodionova, I.A.; Hosseinnia, A.; Kim, S.; Goodacre, N.; Zhang, L.; Zhang, Z.; Palsson, B.; Uetz, P.; Babu, M; Saier, M.H. E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding. Scientific Reports 2023, 13(1), 7345.

Akl, M.G.; Li, L.; Baccetto, R.; Phanse, S.; Zhang, Q.; Trites, M.J.; McDonald, S.; Aoki, H.; Babu, M.; Widenmaier, S.B. Complementary gene regulation by NRF1 and NRF2 protects against hepatic cholesterol overload. Cell Reports 2023, 42(4), 112399.

Hajikarimlou, M.; Hooshyar, M.; Sunba, N.; Nazemof, N.; Moutaoufik, M.T.; Phanse, S.; Said, K.B.B.; Babu, M.; Holcik, M.; Samanfar, B.; Smith, M.; Golshani, A. A Correlation between 3′-UTR of OXA1 Gene and Yeast Mitochondrial Translation. Journal of Fungi 2023, 9(4), 445.

Zilocchi, M.; Rahmatbakhsh, M.; Moutaoufik, M.T.; Broderick, K.; Gagarinova, A.; Jessulat, M.; Phanse, S.; Aoki, H.; Aly, K.A.; Babu, M. Co-fractionation-mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain. Nature Protocols 2023, 18, 3918-3973.

Dahal, S.; Clayton, K.; Cabral, T.; Cheng, R.; Jahanshahi, S.; Ahmed, C.; Koirala, A.; Villasmil Ocando, A.; Malty, R.; Been, T.; Hernandez, J.; Mangos, M.; Shen, D.; Babu, M.; Calarco, J.; Chabot, B.; Attisano, L.; Houry, W.A.; Cochrane, A. On a path toward a broad-spectrum anti-viral: inhibition of HIV-1 and coronavirus replication by SR kinase inhibitor harmine. Journal of Virology 2023, 97(10), e00396.

Hammond, N.; Snider, J.; Stagljar, I.; Mitchell, K.; Lagutin, K.; Jessulat, M.; Babu, M; Teesdale-Spittle, P.H.; Sheridan, J.P.; Sturley, S.L.; Munkacsi, A.B. Identification and characterization of protein interactions with the major Niemann-Pick type C disease protein in yeast reveals pathways of therapeutic potential. Genetics 2023, 225(1), iyad129.

Shahina, Z.; Dahms, T.E.S. A Simple and Reproducible Stereomicroscopic Method to Assess Fungal Biofilms: Application to Antifungal Susceptibility Testing. Bio-Protocols 2023, 13(13), e4713.

Shahina, Z.; Yennamalli, R.M.; Dahms, T.E.S. Key essential oil components delocalize Candida albicans Kar3p and impact microtubule structure. Microbiological Research 2023, 272, 127373.

Ndlovu, E.; Malpartida, L.; Sultana, T.; Dahms, T.E.S.; Dague, E. Host Cell Geometry and Cytoskeletal Organization Governs Candida-Host Cell Interactions at the Nanoscale. ACS Applied Materials & Interfaces 2023, 15(44), 50789-50798.

Dahms, T.E.S.; Bhat, S.V. High content cellulomics by correlative microscopy. Biophysical Journal 2023, 122(3), 549A-549A.

Klapatiuk, D.O.O.; Waugh, S.L.L.; Mukadam, A.A.A.; East, A.L.L. Limited ionicity in poor protic ionic liquids: Association Gibbs energies. Journal of Chemical Physics 2023, 158(3), 34507.

East, A.L.L.; Nguyen, C.M.; Hempelmann, R. A 2023 update on the performance of ionic-liquid proton-exchange-membrane fuel cells. Frontiers in Energy Research 2023, 11, 1031458.

Usama, W.O.; Markewich, D. J.; East, A.L.L. Regioselectivity in Wacker oxidations of internal alkenes: antiperiplanar effects? Canadian Journal of Chemistry 2023, 101(9), 579-584.

Renzaglia, K.S.; Ashton, N.W.; Suh, D.-Y. Sporogenesis in Physcomitrium patens: Intergenerational collaboration and the development of the spore wall and aperture. Frontiers in Cell and Developmental Biology 2023, 11, 1165293.

Barker, E.I.; Rabbi, F.; Brisbourne, W.A.; Aparato, V.P.M.; Valenzuela, V.E.; Renzaglia, K.S.; Suh, D.-Y. Genome-wide analysis of the GDSL esterase/lipase family genes in Physcomitrium patens and the involvement of GELP31 in spore germination. Molecular Genetics and Genomics 2023, 298(5), 1155-1172.

Widdifield, C.M.; Zakeri, F. Can simple 'molecular' corrections outperform projector augmented-wave density functional theory in the prediction of 35Cl electric field gradient tensor parameters for chlorine-containing crystalline systems? Magnetic Resonance in Chemistry 2023.



Lim, S.H.; Snider, J.; Birimberg-Schwartz, L.; Ip, W.; Serralha, J.C.; Botelho, H.M.; Lopes-Pacheco, M.; Pinto, M.C.; Moutaoufik, M.T.; Zilocchi, M.; Laselva, O.; Esmaeili, M.; Kotlyar, M.; Lyakisheva, A.; Tang, P.; Vazquez, L.L.; Akula, I.; Aboualizadeh, F.; Wong, V.; Grozavu, I.; Opacak-Bernardi, T.; Yao, Z.; Mendoza, M.; Babu, M.; Jurisica, I.; Gonska, T.; Bear, C.E.; Amaral, M.D.; Stagljar, I. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Molecular Systems Biology 2022, 18(2), e10629.

Dahal, S.; Cheng, R.; Cheung, P.K.; Been, T.; Malty, R.; Geng, M.; Manianis, S.; Shkreta, L.; Jahanshahi, S.; Toutant, J.; Chan, R.; Park, S.; Brockman, M.A.; Babu, M.; Mubareka, S.; Mossman, K.; Banerjee, A.; Gray-Owen, S.; Brown, M.; Houry, W.A.; Chabot, B.; Grierson, D.; Cochrane, A.. The Thiazole-5-Carboxamide GPS491 Inhibits HIV-1, Adenovirus, and Coronavirus Replication by Altering RNA Processing/Accumulation. Viruses-Basel 2022, 14(1), 60.

Seraphim, T.V.; Nano, N.; Cheung, Y.W.S.; Aluksanasuwan, S.; Colleti, C.; Mao, Y.-Q.; Bhandari, V.; Young, G.; Holl, L.; Phanse, S.; Gordiyenko, Y.; Southworth, D.R.; Robinson, C.V.; Thongboonkerd, V.; Gava, L.M.; Borges, J.C.; Babu, M.; Barbosa, L.R.S.; Ramos, C.H., I; Kukura, P.; Houry, W.A. Assembly principles of the human R2TP chaperone complex reveal the presence of R2T and R2P complexes. Structure 2022, 30(1), 156-171.

Hajikarimlou, M.; Hooshyar, M.; Moutaoufik, M.T.; Aly, K.A.; Azad, T.; Takallou, S.; Jagadeesan, S.; Phanse, S.; Said, K.B.; Samanfar, B.; Bell, J.C.; Dehne, F.; Babu, M.; Golshani, A. A computational approach to rapidly design peptides that detect SARS-CoV-2 surface protein S. NAR Genomics and Bioinformatics 2022, 4(3), lqac058.

Young, J.W.; Wason, I.S.; Zhao, Z.; Kim, S.; Aoki, H.; Phanse, S.; Rattray, D.G.; Foster, L.J.; Babu, M.; van Hoa, F.D. Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize, and Purify a Detergent-Sensitive Membrane Protein Assembly. Journal of Proteome Research, 2022, 21(7), 1748-1758.

Gagarinova, A.; Hosseinnia, A.; Rahmatbakhsh, M.; Istace, Z.; Phanse, S.; Moutaoufik, M.T.; Zilocchi, M.; Zhang, Q.; Aoki, H.; Jessulat, M.; Kim, S.; Aly, K.A.; Babu, M. Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli. Nature Communications 2022, 13(1), 4085.

Jakova, E.; Moutaoufik, M.T.; Lee, J.S.; Babu, M.; Cayabyab, F.S. Adenosine A1 receptor ligands bind to α-synuclein: implications for α-synuclein misfolding and α-synucleinopathy in Parkinson's disease. Translational Neurogeneration 2022, 11(1), 9.

Aly, K.A.; Moutaoufik, M.T.; Zilocchi, M.; Phanse, S.; Babu, M. Insights into SACS pathological attributes in autosomal recessive spastic ataxia of Charlevoix- Saguenay (ARSACS)*. Current Opinion in Chemical Biology 2022, 71, e102211.

Kumarathasan, P.; Nazemof, N.; Breznan, D.; Blais, E.; Aoki, H.; Gomes, J.; Vincent, R.; Phanse, S.; Babu, M. In vitro toxicity screening of amorphous silica nanoparticles using mitochondrial fraction exposure followed by MS-based proteomic analysis. Analyst 2022, 147(16), 3692-3708.

Shahina, Z.; Ndlovu, E.; Persaud, O.; Sultana, T.; Dahms, T.E.S. Candida albicans Reactive Oxygen Species (ROS)-Dependent Lethality and ROS-Independent Hyphal and Biofilm Inhibition by Eugenol and Citral. Microbiology Spectrum 2022, 10(6), e03183-22.

Shahina, Z.; Al Homsi, R.; Price, J.D.W.; Whiteway, M.; Sultana, T.; Dahms, T.E.S. Rosemary essential oil and its components 1,8-cineole and α-pinene induce ROS-dependent lethality and ROS-independent virulence inhibition in Candida albicans. PLOS ONE 2022, 17(11), e0277097.

Shahina, Z.; Molaeitabari, A.; Sultana, T.; Dahms, T.E.S. Cinnamon Leaf and Clove Essential Oils Are Potent Inhibitors of Candida albicans Virulence Traits. Microorganisms 2022, 10(10), 1989.

Shahina, Z.; Yennamalli, R.M.; Dahms, T.E.S. Anti-virulence activity of plant-based antifungals through microtubule inhibition. Biophysical Journal 2022, 121(3), 112-112.

Henni, A.; East, A. L. L. Comment on On the Accuracy of the Direct Method to Calculate pKa from Electronic Structure Calculations. Journal of Physical Chemistry A 2022, 126(4), 648-649.

Mukadam, A. A.; East, A. L. L. Challenges in predicting ΔrxnG in solution: The chelate effect. Journal of Chemical Physics 2022, 157(3), 34109.

Naguib, M.; Feldman, N.; Zarodkiewicz, P.; Shropshire, H.; Biamis, C.; El-Halfawy, O.M.; McCain, J.; Dezanet, C.; Decout, J.-L.; Chen, Y.; Cosa, G.; Valvano, M.A. An evolutionary conserved detoxification system for membrane lipid-derived peroxyl radicals in Gram-negative bacteria. PLOS Biology 2022, 20(5), e3001610.

Bumraiwha, H.F.K.; Sterenberg, B.T. Synthesis of 1,1'-bisphosphinoferrocenes using electrophilic addition reactions of tungsten coordinated phosphenium ions and phosphine triflates. Journal of Organometallic Chemistry 2022, 980-981, 122511.

Suh, D.-Y.; Ashton, N.W. A sporopollenin definition for the genomics age. New Phytologist 2022, 236(6), 2009-2013.

Aslam, M.; Aparato, V.P.M.; Suh, D.-Y. (2′-Oxo)alkylresorcinols restore dehydration tolerance in a knockout line of PpORS, a bryophyte-specific type III polyketide synthase in Physcomitrium (Physcomitrella) patens. Planta 2022, 255(6), 129.

Jabbour, R.; Renom-Carrasco, M.; Chan, K.W.; Voelker, L.; Berruyer, P.; Wang, Z.; Widdifield, C.M.; Lelli, M.; Gajan, D.; Coperet, C.; Thieuleux, C.; Lesage, A. Multiple Surface Site Three-Dimensional Structure Determination of a Supported Molecular Catalyst. Journal of the American Chemistry Society 2022, 144(23), 10270-10281.

Aparato, V. P. M. and Suh, D.-Y. The functions and applications of GDSL esterase/lipase proteins in agriculture: a review. JSFA Reports 2022, 2, 304-312.



Bhat, S. V., Price, J. D. W. and Dahms, T. E. S. AFM-based correlative microscopy illuminates human pathogens. Frontiers in Cellular and Infection Microbiology 2021, 11, 655501. doi: 10.3389/fcimb.2021.655501

El-Baz, A. M., Mosbah, R. A., Goda, R. M., Mansour, B., Sultana, T., Dahms, T. E. S. and El-Ganiny A. M. Back to Nature: Combating Candida albicans Biofilm, Phospholipase and Hemolysin Using Plant Essential Oils. Antibiotics 2021, 10(1), 81. doi: 10.3390/antibiotics10010081.

Mehla, J., Liechti, G., Morgenstein, R. M., Caufield, J. H., Hosseinnia, A., Gagarinova, A., Phanse, S., Goodacre, N., Brockett, M., Sakhawalkar, N., Babu, M., Xiao, R., Montelione, G. T., Vorobiev, S., Blaauwen, T. D., Hunt, J. F. and Uetz, P. ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis. J Biol Chem 2021, 100700.

Martinez-Matias, N., Chorna, N., Gonzalez-Crespo, S., Villanueva, L., Montes-Rodriguez, I., Melendez-Aponte, L. M., Roche-Lima, A., Carrasquillo-Carrion, K., Santiago-Cartagena, E., Rymond, B. C., Babu, M., Stagljar, I. and Rodriguez-Medina, J. R. Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis. Sci Rep 2021, 11 (1), 7411.

Aly, K. A., Moutaoufik, M. T., Phanse, S., Zhang, Q. and Babu, M., From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. iScience 2021, 24 (2), 102030.

Rizzolo, K., Yu, A. Y. H., Ologbenla, A., Kim, S. R., Zhu, H., Ishimori, K., Thibault, G., Leung, E., Zhang, Y. W., Teng, M., Haniszewski, M., Miah, N., Phanse, S., Minic, Z., Lee, S., Caballero, J. D., Babu, M., Tsai, F. T. F., Saio, T. and Houry, W. A. Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex. Nat Commun 2021, 12 (1), 281.



Rabbi, F., Renzaglia, K.S., Ashton, N.W., Suh, D.-Y. Reactive oxygen species are required for spore wall formation in Physcomitrella patens. Botany 2020, 98, 575–587.

Jun, D., Idem, U. and Dahms, T. E. S. Altered Envelope Structure and Nanomechanical Properties of a C-Terminal Protease A-Deficient Rhizobium leguminosarum. Microorganisms 2020, 8(9), 1421. doi: 10.3390/microorganisms8091421.

Sharma, K., Sultana, T., Dahms, T. E. S. and Dillon, J.-A. R. CcpN: a moonlighting protein regulating catabolite repression of gluconeogenic genes inBacillus subtilis also affects cell length and interacts with DivIVA. Canadian Journal of Microbiology 2020, 66(12), 723-732. doi: 10.1139/cjm-2020-0022.

Sharma, K., Sultana, T., Liao, M., Dahms, T. E. S. and Dillon, J.-A. R. EF1025, a hypothetical protein from Enterococcus faecalis, interacts with DivIVA and affects cell length and cell shape. Frontiers in Microbiology 2020, 11, 83.

Patel, D. H. and East, A. L. L. Semicontinuum (cluster-continuum) modeling of acid-catalyzed aqueous reactions: alkene hydration. J. Phys. Chem. A 2020, 124, 9088-9104.

Klapatiuk, D. O., Johnson, K. E. and East, A. L. L. Limited ionicity in protic ionic liquids: organic acid/trialkylamine mixtures. ECS Trans. 2020, 98(10), 149-159.

Patel, D. H., Marx, D. and East, A. L. L. Improving yield and rate of acid-catalyzed deconstruction of lignin by mechanochemical activation. Chem. Phys. Chem. 2020, 21, 2660-2666.

Mukadam, A. A.; Aravindakshan, N. P. and East, A. L. L. Comment on ‘Local, solvation pressures and conformational changes in ethylenediamine aqueous solutions probed using Raman spectroscopy’ by M. Caceres, A. Lobato, N. J. Mendoza, L. J. Bonales and V. G. Baonza, Phys. Chem. Chem. Phys., 2016, 18, 26192. Phys. Chem. Chem. Phys. 2020, 22, 7119-7125.

Hooshyar, M., Jessulat, M., Burnside, D., Kluew, A., Babu, M and Golshani, A. Deletion of yeast TPK1 reduces the efficiency of non-homologous end joining DNA repair. Biochem Biophys Res Commun 2020, 533 (4), 899-904.

Zilocchi, M., Broderick, K., Phanse, S., Aly, K. A. and Babu, M. Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. Comput Struct Biotechnol J 2020, 18, 2535-2546.

Hajikarimlou, M., Hunt, K., Kirby, G., Takallou, S., Jagadeesan, S. K., Omidi, K., Hooshyar, M., Burnside, D., Moteshareie, H., Babu, M., Smith, M., Holcik, M., Samanfar, B. and Golshani, A. Lithium Chloride Sensitivity in Yeast and Regulation of Translation. Int J Mol Sci 2020, 21 (16).

Hajikarimlou, M., Moteshareie, H., Omidi, K., Hooshyar, M., Shaikho, S., Kazmirchuk, T., Burnside, D., Takallou, S., Zare, N., Jagadeesan, S. K., Puchacz, N., Babu, M., Smith, M., Holcik, M., Samanfar, B. and Golshani, A. Sensitivity of yeast to lithium chloride connects the activity of YTA6 and YPR096C to translation of structured mRNAs. PLoS One 2020, 15 (7), e0235033.

Velez-Segarra, V., Gonzalez-Crespo, S., Santiago-Cartagena, E., Vazquez-Quinones, L. E., Martinez-Matias, N., Otero, Y., Zayas, J. J., Siaca, R., Del Rosario, J., Mejias, I., Aponte, J. J., Collazo, N. C., Lasso, F. J., Snider, J., Jessulat, M., Aoki, H., Rymond, B. C., Babu, M., Stagljar, I. and Rodriguez-Medina, J. R. Protein Interactions of the Mechanosensory Proteins Wsc2 and Wsc3 for Stress Resistance in Saccharomyces cerevisiae. G3 (Bethesda) 2020, 10 (9), 3121-3135.

Zilocchi, M., Colugnat, I., Lualdi, M., Meduri, M., Marini, F., Corasolla Carregari, V., Moutaoufik, M. T., Phanse, S., Pieroni, L., Babu, M., Garavaglia, B., Fasano, M. and Alberio, T. Exploring the Impact of PARK2 Mutations on the Total and Mitochondrial Proteome of Human Skin Fibroblasts. Front Cell Dev Biol 2020, 8, 423.

Pourhaghighi, R., Ash, P. E. A., Phanse, S., Goebels, F., Hu, L. Z. M., Chen, S., Zhang, Y., Wierbowski, S. D., Boudeau, S., Moutaoufik, M. T., Malty, R. H., Malolepsza, E., Tsafou, K., Nathan, A., Cromar, G., Guo, H., Abdullatif, A. A., Apicco, D. J., Becker, L. A., Gitler, A. D., Pulst, S. M., Youssef, A., Hekman, R., Havugimana, P. C., White, C. A., Blum, B. C., Ratti, A., Bryant, C. D., Parkinson, J., Lage, K., Babu, M., Yu, H., Bader, G. D., Wolozin, B. and Emili, A. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst 2020, 10 (4), 333-350 e14.

He, S., Moutaoufik, M. T., Islam, S., Persad, A., Wu, A., Aly, K. A., Fonge, H., Babu, M. and Cayabyab, F. S. HERG channel and cancer: A mechanistic review of carcinogenic processes and therapeutic potential. Biochim Biophys Acta Rev Cancer 2020, 1873 (2), 188355.

Zilocchi, M., Moutaoufik, M. T., Jessulat, M., Phanse, S., Aly, K. A. and Babu, M., Misconnecting the dots: altered mitochondrial protein-protein interactions and their role in neurodegenerative disorders. Expert Rev Proteomics 2020, 17 (2), 119-136.

El-Halfawy, O. M., Czarny, T. L., Flannagan, R. S., Day, J., Jr, J. C. B., Kuiack, R. C., Salim, A., Eckert, P., Epand, R. M., McGavin, M. J., Organ, M. G., Heinrichs, D. E. and Brown, E. D. Discovery of an antivirulence compound that reverses β-lactam resistance in MRSA. Nature Chemical Biology 2020, 16(2), 143-149.

Farha, M. A., El-Halfawy, O. M., Gale, R. T., MacNair, C. R., Carfrae, L. A., Zhang, X., Jentsch, N. G., Magolan, J. and Brown, E. D. Uncovering the hidden antibiotic potential of Cannabis. ACS Infect Dis 2020, 6(3), 338-346.


Past Publications