Publications

Selected Publications

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• Sanitation enzymes: Exquisite surveillance of the noncanonical nucleotide pool to safeguard the genetic blueprint
  Broderick, K., Moutaoufik, M.T., Aly, K.A., Babu, M.*
  Seminars in Cancer Biology 2023 May 19;94:11-20. doi: 10.1016/j.semcancer.2023.05.005. Online ahead of print. (*corresponding)
  PMID:37211293
  
  
  
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• Complementary gene regulation by NRF1 and NRF2 protects against hepatic cholesterol overload
  Akl, M.G., Li, L., Baccetto, R., Phanse, S., Zhang, Q., Trites, M.J., McDonald, S., Aoki, H., Babu, M., Widenmaier, S.B.
  Cell Reports 2023 Apr 14;42(4):112399. doi: 10.1016/j.celrep.2023.112399 
  PMID:337060561
  
  
  
  
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• Insights into SACS pathological attributes in autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS)☆
  Aly, K.A., Moutaoufik, M.T., Zilocchi, M., Phanse, S., Babu, M.*
  Current Opinion Chemical Biology. 2022 Sep 17;71:102211. (*corresponding)
  PMID:36126381
  
  
  
  
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• A computational approach to rapidly design peptides that detect SARS-CoV-2 surface protein S
  Hajikarimlou, H., 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.
  NAR Genomics and Bioinformatics, Volume 4, Issue 3, September 2022, lqac058 (*corresponding)
  PMID:36004308
  
  
  
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• Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli.
  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.*
  Nature Communications 2022 Jul 14;13(1):4085 (*corresponding)
  PMID:35835781
  
  
  
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• CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system
  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., Vázquez, 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.
  Molecular Systems Biology 2022 Feb;18(2):e10629. 
  PMID:35156780
  
  
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• Adenosine A1 receptor ligands bind to α-synuclein: implications for α-synuclein misfolding and α-synucleinopathy in Parkinson's disease
  Jakova, E., Moutaoufik, M.T., Lee, J.S., Babu, M., Cayabyab.F.S.
  Translational Neurodegenertion 2022 Feb 10;11(1):9. 
  PMID:35139916
  
  
  
  
  
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• Assembly principles of the human R2TP chaperone complex reveal the presence of R2T and R2P complexes
  Seraphim, T.V., Nano, N., Cheung, Y.W.S., Aluksanasuwan, S., Colleti, C., Mao, Yu-Q., Bhandari, V., Young, G., Höll, 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.
  Structure . 2022 Jan 6;30(1):156-171.e12. 
  PMID:34492227
  
  
  
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• A Panoramic View of Proteomics and Multiomics in Precision Health
  Zilocchi, M., Wang, C., Babu, M.*, Li, J.*
  iScience, 2021 Jul 30;24(8) (*co-corresponding)
  PMID:34430814
  
  
  
  
  
  
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• The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLF
  Jessulat, M., Amin, S., Hooshyar, M., Malty, R., Moutaoufik, M.T., Zilocchi, M., Istace, Z., Phanse, S., Aoki, H., Omidi, K., Burnside, D., Samanfar, B., Aly, K.A., Golshani, A., Babu, M.*
  Nucleic Acids Research, 2021 Aug 20;49(14):8145-8160 (*corresponding)
  PMID:34244791
  
  
  
  
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• From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease
  Aly, K.A., Moutaoufik, M.T., Phanse, S., Zhang, Q., Babu M.*
  iScience 2021;24(2). (*corresponding)
  PMID:33521598
  
  
  
  
  
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• Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex
  Rizzolo, K., Yu, A. H. Y., Ologbenla, A., Kim, S., 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., & Houry, W.A.
  Nature Communications 2021;12(1):281.
  PMID:33436616
  
  
  
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• BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain
  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., Emili, A.
  Cell Systems 2020;10(4):333-350.e14.
  PMID:32325033
  
  
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• HERG channel and cancer: A mechanistic review of carcinogenic processes and therapeutic potential
  He, S., Moutaoufik, M.T., Islam, S., Persad, A., Wu, A., Aly, K.A., Fonge, H., Babu, M., Cayabyab, F.S.
  Biochimica et Biophysica Acta (BBA) - Reviews on Cancer 2020;1873(2):188355.
  PMID:32135169
  
  
  
  
  
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• Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action
  Kintses, B., Jangir, P.K., Fekete, G., Számel, M., Méhi, O., Spohn, R., Daruka, L., Martins, A., Hosseinnia, A., Gagarinova, A., Kim, S., Phanse, S., Csörgő, B., Györkei, A., Ari, E., Lázár, V., Nagy, I., Babu, M., Pál C., & Papp, B.
  Nature Communications 2019;10(1):5731.
  PMID:31844052
  
  
  
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• ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores
  Mabanglo, M.F., Leung, E., Vahidi, S., Seraphim, T.V., Eger, B.T., Bryson, S., Bhandari, V., Zhou, J.L., Mao, Y., Rizzolo, K., Barghash, M.M., Goodreid, J.D., Phanse, S., Babu, M., Barbosa, L.R.S., Ramos, C.H.I., Batey, R.A., Kay, L.E., Pai, E.F., Houry, W.A.
  Communications Biology - Nature 2019;2:410.
  PMID:31754640
  
  
  
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• Rewiring of the Human Mitochondrial Interactome During Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis
  Moutaoufik, M.T., Malty, R., Amin, S., Zhang, Q., Phanse, S., Gagarinova, A., Zilocchi, M., Hoell, L., Minic, Z., Gagarinaova, M., Aoki, H., Stockwell, J., Jessulat, M., Goebels, F., Broderik, K., Scott, N.E., Vlasblom, J., Musso, G., Prasad, B., Lamantea, E., Garavaglia, B., Rajput, A., Murayama, K., Okazaki, Y., Foster, L.J., Bader, G.D., Cayabyab, F.S., Babu, M.*
  iScience 2019;19:1114-1132. (*corresponding)
  PMID:31536960
  
  
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• Profiling the Escherichia coli membrane interactome captured in peptidisc libraries
  Carlson, M.L., Stacey, R.G., Young, J.W., Wason, I.S.,Zhao, Z., Rattray, D.G., Scott, N., Kerr, C.H., Babu, M., Foster, L.J., Duong F.V.H.
  eLife 2019;8. pii: e46615.
  PMID:31364989
  
  
  
  
  
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• In silico engineering of synthetic binding proteins from random amino acid sequences
  Burnside, D., Schoenrock, A., Moteshareie, H., Hooshyar, M., Basra, P., Hajikarimlou, M., Dick, K., Barnes, B., Kazmirchuk, T., Jessulat, M., Pitre, S., Samanfar, B., Babu, M., Green, J.R., Wong, A., Dehne, F., Biggar, K.K., Golshani, A.
  iScience 2019;11:375-387.
  PMID:30660105
  
  
  
  
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• Acyldepsipeptide Analogs Dysregulate Human Mitochondrial ClpP Protease Activity and Cause Apoptotic Cell Death
  Wong, K. S., Mabanglo, M.F., Seraphim, T.V., Mollica, A., Mao, Y., Rizzolo, K., Leung, E., Moutaoufik, M. T., Hoell, L., Phanse, S., Goodreid, J., Barbosa, L.R.S., Ramos, C.H.I., Babu, M., Mennella, V., Batey, R.A., Schimmer, A.D., Houry, W.A.
  Cell Chemical Biology. 2018;25(8):1017-1030.e9.
  PMID:30126533
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• EPHB6 augments both development and drug sensitivity of triple-negative breast cancer tumours
  Toosi, B.M., El Zawily, A., Truitt, L., Shannon, M., Allonby, O., Babu, M., DeCoteau, J., Mousseau, D., Ali, M., Freywald, T., Gall, A.. Vizeacoumar, F. S., Kirzinger, M. W., Geyer, C.R., Anderson, D.H., Kim, T., Welm, A.L., Siegel, P., Vizeacoumar, F.J., Kusalik, A., & Freywald, A.
  Oncogene 2018;37(30):4073-4093.
  PMID:29700392
  
  
  
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• Global landscape of cell envelope protein complexes in Escherichia coli
  Babu, M.*, Bundalovic-Torma, C., Calmettes, C., Phanse, S., Zhang, Q., Jiang, Y., Minic, Z., Kim, S., Mehla, J., Gagarinova, A., Rodionova, I., Kumar, A., Guo, H., Kagan, O., Pogoutse, O., Aoki, H., Deineko, V., Caufield, J. H., Holtzapple, E., Zhang, Z., Vastermark, A., Pandya, Y., Lai, C. C., El Bakkouri, M., Hooda, Y., Shah, M., Burnside, D., Hooshyar, M., Vlasblom, J., Rajagopala, S.V., Golshani, A., Wuchty, S., Greenblatt, J.F., Saier, M., Uetz, P., F Moraes, T., Parkinson, J., Emili, A.
  Nature Biotechnology 2018;36(1):103-112. (*corresponding)
  PMID:29176613
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• A map of human mitochondrial protein interactions linked to neurodegeneration reveals new mechanisms of redox homeostasis and NF-κB signaling
  Malty, R. H., Aoki, H., A., K., Phanse, S., Amin, S., Zhang, Q., Minic, Z., Goebels, F., Musso, G., Wu, Z., Abou-tok, H., Meyer, M., V., D., Kassir, S., Sidhu, V., Jessulat, M., Scott, N. E., Xiong, X., Vlasblom, J., Prasad, B., Foster, L. J., Alberio, T., Garavaglia, B., Yu, H., Bader, G. D., Nakamura, K., Parkinson, J., and Babu, M*.
  Cell Systems 2017;5(6):564-577.e12.  (*corresponding)
  PMID:29128334
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• Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping
  Rizzolo, K., Huen, J., Kumar, A., Phanse, S., Vlasblom, J., Kakihara,Y., Zeineddine, H. A., Minic, Z., Snider, J., Wang, W., Pons, C., Seraphim, T. V., Boczek, E. E., Alberti, S., Costanzo, M., Myers, C. L., Stagljar, I., Boone, C., Babu*, M., Houry*, W. A.
  Cell Reports 2017;20(11):2735-2748. (*co-corresponding)
  PMID:28903051
  
  
  
  
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• Systematic protein–protein interaction mapping for clinically relevant human GPCRs
  Sokolina, K., Kittanakom, S., Snider, J., Kotlyar, M., Maurice, P., Gandía, J., Benleulmi-Chaachoua, A., Tadagaki, K., Oishi, A., Wong, V., Malty, R.H., Deineko, V., Aoki, H., Amin, S., Yao, Z., Morató, X., Otasek, D., Kobayashi, H., Menendez, J., Auerbach, D., Angers, S., Pržulj, N., Bouvier, M., Babu, M., Ciruela, F., Jockers, R., Jurisica, I., Stagljar, I.
  Molecular Systems Biology 2017;13(3):918.
  PMID:28298427
  
  
  
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• A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome
  Yao, Z., Darowski, K., St-Denis, N., Wong, V., Offensperger, F., Villedieu, A., Amin, S., Malty, R., Aoki, H., Guo, H., Xu, Y., Iorio, C., Kotlyar, M., Emili, A., Jurisica, I., Neel, B.G., Babu, M., Gingras, A., Stagljar I.
  Molecular Cell 2017;65(2):347-360.
  PMID:28065597
  
  
  
  
  
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• Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery
  Gagarinova, A., Stewart, G., Samanfar, B., Phanse, S., White, C.A., Aoki, H., Deineko, V., Beloglazova, N., Yakunin, A.F., Golshani, A., Brown, E.D., Babu, M., Emili, A.
  Cell Reports 2016;17(3):904-916.
  PMID:27732863
  
  
  
  
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• 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(3):648-61. (*corresponding)
  PMID:26774489
  
  
  
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• 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(5):361-374. (*co-corresponding)
  PMID:26949739
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• 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(7569):339-44.
  PMID: 26344197
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• Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli
  Babu, M*, Arnold, A., Bundalovic-Torma, C., Gagarinova, A., Wong, K.S., Kumar, A., Stewart, G., Samanfar, B., Aoki, H., Wagih, O., Vlasblom, J., Phanse, S., Lad, K., Yu, AYH, Graham, C., Jin, K., Brown, E., Golshani, A., Kim, P., Moreno-Hagelsieb, G., Greenblatt, J., Houry, W.A., Parkinson, J. and Emili, A.
  PLoS Genetics 2014;10(2):e1004120. (*corresponding)
  PMID: 24586182
  
  
  
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• Binary Protein-protein Interaction Landscape of Escherichia coli
  Rajagopala, S.V*., Sikorski, P., Kumar, A., Mosca, R., Vlasblom, J., Arnold, R., Franca-Koh, J., Pakala, S.B., Phanse, S., Ceol, A., Häuser, R., Siszler, G., Wuchty, S., Emili, A., Babu, M*., Aloy, P., Pieper, R. and Uetz, P.
  Nature Biotechnology 2014;32(3):285-290. (*co-corresponding)
  PMID: 24561554
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• NleH defines a new family of bacterial effector kinases
  Grishin, A.M., Cherney, M., Anderson, D.H., Phanse, S., Babu, M. and Cygler, M.
  Structure 2014;22(2):250-9.
  PMID: 24373767
  
  
  
  
  
  
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• A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities
  Vizeacoumar, F. J., Arnold, R., Vizeacoumar, F. S., Chandrashekhar, M., Buzina, A., Young, J. T. F., Kwan, J.H.M., Sayad, A., Mero, P., Lawo, S., Tanaka, H., Brown, K. R., Baryshnikova, A., Mak, A. B., Fedyshyn, Y., Wang, Y., Brito, G. C., Kasimer, D., Makhnevych, T., Ketela, T., Datti, A., Babu, M., Emili, A., Pelletier L, Wrana J, Wainberg Z, Kim P. M., Rottapel R, O'Brien C. A., Andrews B, Boone C, Moffat J.
  Molecular Systems Biology 2013;9:696.
  PMID: 24104479
  
  
  
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• Mapping the functional yeast ABC transporter interactome
  Snider, J., Hanif, A. Lee, M. E., Jin, K., Yu, Q. R., Graham, C., Chuk, M., Damjanovic, D., Wierzbicka, M., Tang, P., Balderes, D., Wong, V., Jessulat, M., Darowski, K. D., San Luis, B., Shevelev, I., Sturley, S. L., Boone, C., Greenblatt, J. F., Zhang, Z., Paumi, C. M., Babu, M., Park, H., Michaelis S., & Stagljar, I.
  Nature Chemical Biology 2013;9(9):565-72.
  PMID: 23831759
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• Interaction landscape of membrane protein complexes in Saccharomyces Cerevisiae
  Babu, M., Vlasblom, J., Pu, S., Guo, X., Graham, C., Vizeacoumar, F.J., Bean, B.D.M., Phanse, S., Fong, V., Davey, M., Snider, J., Hnatshak, O., Bajaj, N., Chandran, S., Punna, T., Christopolous, C., Wong, V., Zhong, G., Li, J., Stagljar, I., Conibear, E., Wodak, S.J.W., Emili, A. and Greenblatt, J.F.
  Nature 2012;489:585-9.
  PMID: 22940862
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• A census of human soluble protein complexes
  Havugimana, P.C., Hart, G.T., Nepusz, T., Yang, H., Turinsky, A.L., Li, Z., Wang, P.I., Boutz, D.R., Fong, V., Phanse, S., Babu, M., Craig, S.A., Hu, P., Wan, C., Vlasblom, J., Dar, V., Bezginov, A., Clark, G.W., Wu, G.C., Wodak, S.J., Tillier, E.R.M., Paccanaro, A., Marcotte, E.M., Emili, A.
  Cell 2012;150:1068-1081.
  PMID: 22939629
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• Genetic interaction maps in Escherichia coli reveal condition-dependent functional crosstalk among cell envelope biogenesis pathways
  Babu, M*., Díaz-Mejía, J.J., Vlasblom, J., Gagarinova, A., Phanse, S., Graham, C., Arnold, R., Yousif, F., Ding, H., Xiong, X., Nazarians-Armavil, A., Alamgir, Md., Ali, M., Pogoutse, O., Pe′er, A., Parkinson, J., Golshani, A., Whitfield, C., Wodak, S.J., Moreno-Hagelsieb, G., Greenblatt, J.F. and Emili, A.*
  PLoS Genetics 2011;7(11):e1002377.  (*co-corresponding)
  PMID: 22125496
  
  
  
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• Quantifying the E. coli proteome and transcriptome in a single cell with single-molecule sensitivity
  Taniguchi, Y., Choi, P.J., Li, G-W., Chen, H., Babu, M., Hearn, J., Emili, A. and Xie, X.S.
  Science 2010;329:533-538.
  PMID: 20671182
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• Structure of a SLC26 anion transporter STAS domain in complex with acyl carrier protein: implications for E. coli YchM in fatty acid metabolism
  Babu, M., Greenblatt, J., Emili, A., Strynadka, N. C.J., Reithmeier, A.F. and Moraes, T.F.
  Structure 2010;18,:1450-1462.
  PMID: 21070944
  
  
  
  
  
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• Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins
  Hu, P.*, Janga, S.C.*, Babu, M.*, Diaz-Mejia, J.J.*, Butland, G.*, Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., Chandran, S., Christopoulos, C., Nazarians-Armavi,l A., Nasseri, N. K., Musso, G., Ali, M., Nazemof, N., Eroukova, V., Golshani, A., Paccanaro, A., Greenblatt, J. F., Moreno-Hagelsieb, G., Emili, A.
  PLoS Biology 2009;7(4):e96. (*co-first author)
  PMID: 19402753
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• eSGA: E. coli synthetic genetic array analysis
  Butland, G.*, Babu, M.*, Diaz-Mejia, J.J., Bohdana, F., Phanse, S., Gold, B., Yang, W., Li, J., Gagarinova, A. G., Pogoutse, O., Mori, H., Wanner, B. L., Lo, H., Wasniewski, J., Christopolous, C., Ali, M., Venn, P., Safavi-Naini, A., Sourour, N., Caron, S., Choi, J. Y., Laigle, L., Nazarians-Armavil, A., Deshpande, A., Joe, S., Datsenko, K. A., Yamamoto, N., Andrews, B. J., Boone, C., Ding, H., Sheikh, B., Moreno-Hagelseib, G., Greenblatt, J. F., Emili, A.
  Nature Methods 2008;5:89-795.(*co-first author)
  PMID: 18677321
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