Publications

DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling
Mao, Y., Seraphim, T.V., Wan, Y., Wu, R., Coyaud, E., Munim, M.B., Mollica, A., Laurent, E., Babu, M., Mennella, V., Raught, B., Houry, W.A.
Cell Reports . 2024 Feb 27;43(2):113713. doi: 10.1016/j.celrep.2024.113713. Epub 2024 Feb 1.
PMID: 38306274

Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain
Zilocchi, M., Rahmatbakhsh, M., Moutaoufik, M.T., Broderick, K., Gagarinova, A., Jessulat, M., Phanse, S., Aoki, H., Aly, K.A., & Babu, M.
Nature Protocols 2023 Nov 20. doi: 10.1038/s41596-023-00901-z. (*corresponding)
PMID:37985878

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

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

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

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

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

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

Adenosine A1 receptor ligands bind to alpha-synuclein: implications for alpha-synuclein misfolding and alpha-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

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 . 2021 Sep 3;S0969-2126
PMID:34492227

A Panoramic View of Proteomics and Multiomics in Precision Health
Zilocchi, M., Wang, C., Babu, M.*, Li, J.*
iScience, 2021, https://doi.org/10.1016/j.isci.2021.102925 (*co-corresponding)
PMID:34430814

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, gkab585, https://doi.org/10.1093/nar/gkab585 (*corresponding)
PMID:34244791

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), doi: https://doi.org/10.1016/j.isci.2020.102030(* corresponding)
PMID:33521598

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 volume 12, Article number: 281 (2021)
PMID:33436616

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, Volume 10, Issue 4, 22 April 2020, Pages 333-350.e14
PMID:32325033

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 Apr;1873(2)
PMID:32135169

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 Dec 16;10(1):5731
PMID:31844052

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 Nov 13;2:410
PMID:31754640

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 Sep 27;19:1114-1132(*corresponding)
PMID:31536960

Profiling the E. 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 Jul 31;8. pii: e46615
PMID:31364989

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 Jan 25;11:375-387
PMID:30660105

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 Aug 16;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 Jul;37(30):4073-4093
PMID:29700392

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 Jan;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, 1-14 (*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

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: 918
PMID:28298427

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, Jan 19;65(2):347-360
PMID:28065597

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

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

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 1 (2015) pp. 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, 339–34
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

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, 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; 2. 250 - 259.
PMID: 24373767

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

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, 565-572.
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
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, e1002377. (*co-corresponding)
PMID: 22125496

Quantifying the Escherichia 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

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

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: 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, 789-795.(*co-first author)
PMID: 18677321
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