M. Madan Babu's Group

Regulatory Genomics and Systems Biology

Publications

OUR PUBLICATIONS

Link to Madan’s Google Scholar page. 

2022

Umeda, M., Ma, J., Huang, B.J., Hagiwara, K., Westover, T., Abdelhamed, S., Barajas, J.M., Thomas, M.E., Walsh, M.P., Song, G., et al. (2022). Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia. Blood Cancer Discovery 3, 194–207. https://doi.org/10.1158/2643-3230.BCD-21-0160. Cite
Baer, C., Kimura, S., Rana, M.S., Kleist, A.B., Flerlage, T., Feith, D.J., Chockley, P., Walter, W., Meggendorfer, M., Olson, T.L., et al. (2022). CCL22 mutations drive natural killer cell lymphoproliferative disease by deregulating microenvironmental crosstalk. Nat Genet 54, 637–648. https://doi.org/10.1038/s41588-022-01059-2. Cite

2021

Schlick, T., Sundberg, E.J., Schroeder, S.J., and Babu, M.M. (2021). Biophysicists' outstanding response to Covid-19. Biophysical Journal 120, E1–E2. https://doi.org/10.1016/j.bpj.2021.02.020. Cite
Pan, M., Wright, W.C., Chapple, R.H., Zubair, A., Sandhu, M., Batchelder, J.E., Huddle, B.C., Low, J., Blankenship, K.B., Wang, Y., et al. (2021). The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma. Nat Commun 12, 6468. https://doi.org/10.1038/s41467-021-26640-x. Cite
Lang, B., and Babu, M.M. (2021). A community effort to bring structure to disorder. Nat Methods 18, 454–455. https://doi.org/10.1038/s41592-021-01123-5. Cite
Lam, S.D., Babu, M.M., Lees, J., and Orengo, C.A. (2021). Biological impact of mutually exclusive exon switching. PLoS Comput Biol 17, e1008708. https://doi.org/10.1371/journal.pcbi.1008708. Cite
Sveidahl Johansen, O., Ma, T., Hansen, J.B., Markussen, L.K., Schreiber, R., Reverte-Salisa, L., Dong, H., Christensen, D.P., Sun, W., Gnad, T., et al. (2021). Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis. Cell 184, 3502-3518.e33. https://doi.org/10.1016/j.cell.2021.04.037. Cite
Hauser, A.S., Kooistra, A.J., Munk, C., Heydenreich, F.M., Veprintsev, D.B., Bouvier, M., Babu, M.M., and Gloriam, D.E. (2021). GPCR activation mechanisms across classes and macro/microscales. Nat Struct Mol Biol 28, 879–888. https://doi.org/10.1038/s41594-021-00674-7. Cite
Dishman, A.F., Tyler, R.C., Fox, J.C., Kleist, A.B., Prehoda, K.E., Babu, M.M., Peterson, F.C., and Volkman, B.F. (2021). Evolution of fold switching in a metamorphic protein. Science 371, 86–90. https://doi.org/10.1126/science.abd8700. Cite

2020

Ahmad, J., Khubaib, M., Sheikh, J.A., Pancsa, R., Kumar, S., Srinivasan, A., Babu, M.M., Hasnain, S.E., and Ehtesham, N.Z. (2020). Disorder-to-order transition in PE-PPE proteins of Mycobacterium tuberculosis augments the pro-pathogen immune response. FEBS Open Bio 10, 70–85. https://doi.org/10.1002/2211-5463.12749. Cite
Chavali, S., Singh, A.K., Santhanam, B., and Babu, M.M. (2020). Amino acid homorepeats in proteins. Nature Reviews Chemistry 4, 420–434. Cite
Jones, E.M., Lubock, N.B., Venkatakrishnan, A.J., Wang, J., Tseng, A.M., Paggi, J.M., Latorraca, N.R., Cancilla, D., Satyadi, M., Davis, J.E., et al. (2020). Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. Elife 9. https://doi.org/10.7554/eLife.54895. Cite
Li, Y., McGrail, D.J., Latysheva, N., Yi, S., Babu, M.M., and Sahni, N. (2020). Pathway perturbations in signaling networks: Linking genotype to phenotype. Semin Cell Dev Biol 99, 3–11. https://doi.org/10.1016/j.semcdb.2018.05.001. Cite
Heifetz, A., Morao, I., Babu, M.M., James, T., Southey, M.W.Y., Fedorov, D.G., Aldeghi, M., Bodkin, M.J., and Townsend-Nicholson, A. (2020). Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method. J Chem Theory Comput 16, 2814–2824. https://doi.org/10.1021/acs.jctc.9b01136. Cite
Masuho, I., Balaji, S., Muntean, B.S., Skamangas, N.K., Chavali, S., Tesmer, J.J.G., Babu, M.M., and Martemyanov, K.A. (2020). A Global Map of G Protein Signaling Regulation by RGS Proteins. Cell 183, 503-521 e19. https://doi.org/10.1016/j.cell.2020.08.052. Cite
Stancheva, V.G., Li, X.H., Hutchings, J., Gomez-Navarro, N., Santhanam, B., Babu, M.M., Zanetti, G., and Miller, E.A. (2020). Combinatorial multivalent interactions drive cooperative assembly of the COPII coat. J Cell Biol 219. https://doi.org/10.1083/jcb.202007135. Cite
Marti-Solano, M., Crilly, S.E., Malinverni, D., Munk, C., Harris, M., Pearce, A., Quon, T., Mackenzie, A.E., Wang, X., Peng, J., et al. (2020). Combinatorial expression of GPCR isoforms affects signalling and drug responses. Nature 587, 650–656. https://doi.org/10.1038/s41586-020-2888-2. Cite
Ravarani, C.N.J., Flock, T., Chavali, S., Anandapadamanaban, M., Babu, M.M., and Balaji, S. (2020). Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation. Nat Commun 11, 2384. https://doi.org/10.1038/s41467-020-16182-z. Cite
Yu, X., Nagai, J., Marti-Solano, M., Soto, J.S., Coppola, G., Babu, M.M., and Khakh, B.S. (2020). Context-Specific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable. Neuron 108, 1146-1162 e10. https://doi.org/10.1016/j.neuron.2020.09.021. Cite

2019

Latysheva, N.S., and Babu, M.M. (2019). Molecular signatures of fusion proteins in cancer. ACS Pharmacol. Transl. Sci. 2, 122–133. https://doi.org/10.1021/acsptsci.9b00019. Cite
Wright, S.C., Kozielewicz, P., Kowalski-Jahn, M., Petersen, J., Bowin, C.F., Slodkowicz, G., Marti-Solano, M., Rodriguez, D., Hot, B., Okashah, N., et al. (2019). A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection. Nat Commun 10, 667. https://doi.org/10.1038/s41467-019-08630-2. Cite
Zhou, Q., Yang, D., Wu, M., Guo, Y., Guo, W., Zhong, L., Cai, X., Dai, A., Jang, W., Shakhnovich, E.I., et al. (2019). Common activation mechanism of class A GPCRs. Elife 8. https://doi.org/10.7554/eLife.50279. Cite
Davey, N.E., Babu, M.M., Blackledge, M., Bridge, A., Capella-Gutierrez, S., Dosztanyi, Z., Drysdale, R., Edwards, R.J., Elofsson, A., Felli, I.C., et al. (2019). An intrinsically disordered proteins community for ELIXIR. F1000Res 8. https://doi.org/10.12688/f1000research.20136.1. Cite
Sanchez de Groot, N., Torrent Burgas, M., Ravarani, C.N., Trusina, A., Ventura, S., and Babu, M.M. (2019). The fitness cost and benefit of phase-separated protein deposits. Mol Syst Biol 15, e8075. https://doi.org/10.15252/msb.20178075. Cite

2018

Ahmad, J., Farhana, A., Pancsa, R., Arora, S.K., Srinivasan, A., Tyagi, A.K., Babu, M.M., Ehtesham, N.Z., and Hasnain, S.E. (2018). Contrasting Function of Structured N-Terminal and Unstructured C-Terminal Segments of Mycobacterium tuberculosis PPE37 Protein. MBio 9. https://doi.org/10.1128/mBio.01712-17. Cite
Hauser, A.S., Chavali, S., Masuho, I., Jahn, L.J., Martemyanov, K.A., Gloriam, D.E., and Babu, M.M. (2018). Pharmacogenomics of GPCR Drug Targets. Cell 172, 41-54 e19. https://doi.org/10.1016/j.cell.2017.11.033. Cite
Kayikci, M., Venkatakrishnan, A.J., Scott-Brown, J., Ravarani, C.N.J., Flock, T., and Babu, M.M. (2018). Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas. Nat Struct Mol Biol 25, 185–194. https://doi.org/10.1038/s41594-017-0019-z. Cite
Li, X.H., Chavali, P.L., and Babu, M.M. (2018). Capturing dynamic protein interactions. Science 359, 1105–1106. https://doi.org/10.1126/science.aat0576. Cite
Masuho, I., Chavali, S., Muntean, B.S., Skamangas, N.K., Simonyan, K., Patil, D.N., Kramer, G.M., Ozelius, L., Babu, M.M., and Martemyanov, K.A. (2018). Molecular Deconvolution Platform to Establish Disease Mechanisms by Surveying GPCR Signaling. Cell Rep 24, 557-568 e5. https://doi.org/10.1016/j.celrep.2018.06.080. Cite
Ravarani, C.N., Erkina, T.Y., De Baets, G., Dudman, D.C., Erkine, A.M., and Babu, M.M. (2018). High-throughput discovery of functional disordered regions: investigation of transactivation domains. Mol Syst Biol 14, e8190. https://doi.org/10.15252/msb.20188190. Cite
Li, X.H., and Babu, M.M. (2018). Human Diseases from Gain-of-Function Mutations in Disordered Protein Regions. Cell 175. https://doi.org/10.1016/j.cell.2018.08.059. Cite
Li, X.H., Chavali, P.L., Pancsa, R., Chavali, S., and Babu, M.M. (2018). Function and Regulation of Phase-Separated Biological Condensates. Biochemistry 57, 2452–2461. https://doi.org/10.1021/acs.biochem.7b01228. Cite
Natan, E., Endoh, T., Haim-Vilmovsky, L., Flock, T., Chalancon, G., Hopper, J.T.S., Kintses, B., Horvath, P., Daruka, L., Fekete, G., et al. (2018). Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins. Nat Struct Mol Biol 25, 279–288. https://doi.org/10.1038/s41594-018-0029-5. Cite
Wootten, D., Christopoulos, A., Marti-Solano, M., Babu, M.M., and Sexton, P.M. (2018). Mechanisms of signalling and biased agonism in G protein-coupled receptors. Nat Rev Mol Cell Biol 19, 638–653. https://doi.org/10.1038/s41580-018-0049-3. Cite
Sente, A., Peer, R., Srivastava, A., Baidya, M., Lesk, A.M., Balaji, S., Shukla, A.K., Babu, M.M., and Flock, T. (2018). Molecular mechanism of modulating arrestin conformation by GPCR phosphorylation. Nat Struct Mol Biol 25, 538–545. https://doi.org/10.1038/s41594-018-0071-3. Cite
Slodkowicz, G., and Babu, M.M. (2018). From prioritisation to understanding: mechanistic predictions of variant effects. Mol Syst Biol 14, e8741. https://doi.org/10.15252/msb.20188741. Cite
Torrent, M., Chalancon, G., Sanchez de Groot, N., Wuster, A., and Babu, M.M. (2018). Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Science Signaling 11, eaat6409. https://doi.org/10.1126/scisignal.aat6409. Cite

2017

Chavali, S., Chavali, P.L., Chalancon, G., de Groot, N.S., Gemayel, R., Latysheva, N.S., Ing-Simmons, E., Verstrepen, K.J., Balaji, S., and Babu, M.M. (2017). Constraints and consequences of the emergence of amino acid repeats in eukaryotic proteins. Nat Struct Mol Biol 24, 765–777. https://doi.org/10.1038/nsmb.3441. Cite
Chavali, S., Gunnarsson, A., and Babu, M.M. (2017). Intrinsically Disordered Proteins Adaptively Reorganize Cellular Matter During Stress. Trends Biochem Sci 42, 410–412. https://doi.org/10.1016/j.tibs.2017.04.007. Cite
Flock, T., Hauser, A.S., Lund, N., Gloriam, D.E., Balaji, S., and Babu, M.M. (2017). Selectivity determinants of GPCR-G-protein binding. Nature 545, 317–322. https://doi.org/10.1038/nature22070. Cite
Li, Y., Sahni, N., Pancsa, R., McGrail, D.J., Xu, J., Hua, X., Coulombe-Huntington, J., Ryan, M., Tychhon, B., Sudhakar, D., et al. (2017). Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer. Cell Rep 21, 798–812. https://doi.org/10.1016/j.celrep.2017.09.071. Cite
Sormanni, P., Piovesan, D., Heller, G.T., Bonomi, M., Kukic, P., Camilloni, C., Fuxreiter, M., Dosztanyi, Z., Pappu, R.V., Babu, M.M., et al. (2017). Simultaneous quantification of protein order and disorder. Nat Chem Biol 13, 339–342. https://doi.org/10.1038/nchembio.2331. Cite

2016

Ravarani, C.N., Chalancon, G., Breker, M., de Groot, N.S., and Babu, M.M. (2016). Affinity and competition for TBP are molecular determinants of gene expression noise. Nat Commun 7, 10417. https://doi.org/10.1038/ncomms10417. Cite
Babu, M.M. (2016). The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease. Biochem Soc Trans 44, 1185–1200. https://doi.org/10.1042/BST20160172. Cite
Latysheva, N.S., and Babu, M.M. (2016). Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res 44, 4487–4503. https://doi.org/10.1093/nar/gkw282. Cite
Latysheva, N.S., Oates, M.E., Maddox, L., Flock, T., Gough, J., Buljan, M., Weatheritt, R.J., and Babu, M.M. (2016). Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer. Mol Cell 63, 579–592. https://doi.org/10.1016/j.molcel.2016.07.008. Cite
Venkatakrishnan, A.J.*, Deupi, X., Lebon, G., Heydenreich, F.M., Flock, T., Miljus, T., Balaji, S., Bouvier, M., Veprintsev, D.B., Tate, C.G., et al. (2016). Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region. Nature 536, 484–487. https://doi.org/10.1038/nature19107. Cite
Yu, H., Singh Gautam, A.K., Wilmington, S.R., Wylie, D., Martinez-Fonts, K., Kago, G., Warburton, M., Chavali, S., Inobe, T., Finkelstein, I.J., et al. (2016). Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome. J Biol Chem 291, 14526–14539. https://doi.org/10.1074/jbc.M116.727578. Cite

2015

Flock, T., Ravarani, C.N., Sun, D., Venkatakrishnan, A.J., Kayikci, M., Tate, C.G., Veprintsev, D.B., and Babu, M.M. (2015). Universal allosteric mechanism for Galpha activation by GPCRs. Nature 524, 173–179. https://doi.org/10.1038/nature14663. Cite
Sanchez de Groot, N., Gomes, R.A., Villar-Pique, A., Babu, M.M., Coelho, A.V., and Ventura, S. (2015). Proteome response at the edge of protein aggregation. Open Biol 5, 140221. https://doi.org/10.1098/rsob.140221. Cite
Sun, D., Flock, T., Deupi, X., Maeda, S., Matkovic, M., Mendieta, S., Mayer, D., Dawson, R.J., Schertler, G.F., Babu, M.M., et al. (2015). Probing Galphai1 protein activation at single-amino acid resolution. Nat Struct Mol Biol 22, 686–694. https://doi.org/10.1038/nsmb.3070. Cite
Fishbain, S., Inobe, T., Israeli, E., Chavali, S., Yu, H., Kago, G., Babu, M.M., and Matouschek, A. (2015). Sequence composition of disordered regions fine-tunes protein half-life. Nat Struct Mol Biol 22, 214–221. https://doi.org/10.1038/nsmb.2958. Cite
Gemayel, R., Chavali, S., Pougach, K., Legendre, M., Zhu, B., Boeynaems, S., van der Zande, E., Gevaert, K., Rousseau, F., Schymkowitz, J., et al. (2015). Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity. Mol Cell 59, 615–627. https://doi.org/10.1016/j.molcel.2015.07.003. Cite
Latysheva, N.S., Flock, T., Weatheritt, R.J., Chavali, S., and Babu, M.M. (2015). How do disordered regions achieve comparable functions to structured domains? Protein Sci 24, 909–922. https://doi.org/10.1002/pro.2674. Cite
Panchenko, A.R., and Babu, M.M. (2015). Editorial overview: Linking protein sequence and structural changes to function in the era of next-generation sequencing. Curr Opin Struct Biol 32, viii–x. https://doi.org/10.1016/j.sbi.2015.06.005. Cite
Schrynemackers, M., Wehenkel, L., Babu, M.M., and Geurts, P. (2015). Classifying pairs with trees for supervised biological network inference. Mol Biosyst 11, 2116–2125. https://doi.org/10.1039/c5mb00174a. Cite

2014

Flock, T., Weatheritt, R.J., Latysheva, N.S., and Babu, M.M. (2014). Controlling entropy to tune the functions of intrinsically disordered regions. Curr Opin Struct Biol 26, 62–72. https://doi.org/10.1016/j.sbi.2014.05.007. Cite
Hagai, T., Azia, A., Babu, M.M., and Andino, R. (2014). Use of host-like peptide motifs in viral proteins is a prevalent strategy in host-virus interactions. Cell Rep 7, 1729–1739. https://doi.org/10.1016/j.celrep.2014.04.052. Cite
van der Lee, R., Lang, B., Kruse, K., Gsponer, J., Sanchez de Groot, N., Huynen, M.A., Matouschek, A., Fuxreiter, M., and Babu, M.M. (2014). Intrinsically disordered segments affect protein half-life in the cell and during evolution. Cell Rep 8, 1832–1844. https://doi.org/10.1016/j.celrep.2014.07.055. Cite
Hattori, H., Janky, R., Nietfeld, W., Aerts, S., Babu, M.M., and Venkitaraman, A.R. (2014). p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response. Cell Cycle 13, 2572–2586. https://doi.org/10.4161/15384101.2015.942209. Cite
Mitrea, D.M., Grace, C.R., Buljan, M., Yun, M.K., Pytel, N.J., Satumba, J., Nourse, A., Park, C.G., Babu, M.M., White, S.W., et al. (2014). Structural polymorphism in the N-terminal oligomerization domain of NPM1. Proc Natl Acad Sci U S A 111, 4466–4471. https://doi.org/10.1073/pnas.1321007111. Cite
Morgunov, A.S., and Babu, M.M. (2014). Optimizing membrane-protein biogenesis through nonoptimal-codon usage. Nat Struct Mol Biol 21, 1023–1025. https://doi.org/10.1038/nsmb.2926. Cite
Tompa, P., Davey, N.E., Gibson, T.J., and Babu, M.M. (2014). A million peptide motifs for the molecular biologist. Mol Cell 55, 161–169. https://doi.org/10.1016/j.molcel.2014.05.032. Cite
van der Lee, R., Buljan, M., Lang, B., Weatheritt, R.J., Daughdrill, G.W., Dunker, A.K., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D.T., et al. (2014). Classification of intrinsically disordered regions and proteins. Chem Rev 114, 6589–6631. https://doi.org/10.1021/cr400525m. Cite
Venkatakrishnan, A.J., Flock, T., Prado, D.E., Oates, M.E., Gough, J., and Babu, M.M. (2014). Structured and disordered facets of the GPCR fold. Curr Opin Struct Biol 27, 129–137. https://doi.org/10.1016/j.sbi.2014.08.002. Cite
Weatheritt, R.J., Gibson, T.J., and Babu, M.M. (2014). Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems. Nat Struct Mol Biol 21, 833–839. https://doi.org/10.1038/nsmb.2876. Cite

2013

Buljan, M., Chalancon, G., Dunker, A.K., Bateman, A., Balaji, S., Fuxreiter, M., and Babu, M.M. (2013). Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr Opin Struct Biol 23, 443–450. https://doi.org/10.1016/j.sbi.2013.03.006. Cite
Babu, M.M. (2013). Bacterial Gene Regulation and Transcriptional Networks (Caister Academic Press). Cite
Campiteli, M.G., Comin, C.H., Costa Lda, F., Babu, M.M., and Cesar, R.M. (2013). A methodology to infer gene networks from spatial patterns of expression–an application to fluorescence in situ hybridization images. Mol Biosyst 9, 1926–1930. https://doi.org/10.1039/c3mb25475e. Cite
Chalancon, G., Kruse, K., and Babu, M.M. (2013). Metabolic Networks, Structure and Dynamics. In Encyclopedia of Systems Biology, W. Dubitzky, O. Wolkenhauer, K.-H. Cho, and H. Yokota, eds. (New York, NY: Springer New York), pp. 1263–1267. Cite
Kruse, K., Chalancon, G., and Babu, M.M. (2013). Metabolic Networks, Applications. In Encyclopedia of Systems Biology, W. Dubitzky, O. Wolkenhauer, K.-H. Cho, and H. Yokota, eds. (New York, NY: Springer New York), pp. 1252–1254. Cite
Venkatakrishnan, A.J., Deupi, X., Lebon, G., Tate, C.G., Schertler, G.F., and Babu, M.M. (2013). Molecular signatures of G-protein-coupled receptors. Nature 494, 185–194. https://doi.org/10.1038/nature11896. Cite
Chalancon, G., Kruse, K., and Babu, M.M. (2013). Metabolic Networks, Reconstruction. In Encyclopedia of Systems Biology, W. Dubitzky, O. Wolkenhauer, K.-H. Cho, and H. Yokota, eds. (New York, NY: Springer New York), pp. 1259–1263. Cite
Chalancon, G., Kruse, K., and Babu, M.M. (2013). Clustering Coefficient. In Encyclopedia of Systems Biology, W. Dubitzky, O. Wolkenhauer, K.-H. Cho, and H. Yokota, eds. (New York, NY: Springer New York), pp. 422–424. Cite
Cumberworth, A., Lamour, G., Babu, M.M., and Gsponer, J. (2013). Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes. Biochem J 454, 361–369. https://doi.org/10.1042/BJ20130545. Cite
Dunker, A.K., Babu, M.M., Barbar, E., Blackledge, M., Bondos, S.E., Dosztanyi, Z., Dyson, H.J., Forman-Kay, J., Fuxreiter, M., Gsponer, J., et al. (2013). What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered. Intrinsically Disord Proteins 1, e24157. https://doi.org/10.4161/idp.24157. Cite
Kruse, K., Sewitz, S., and Babu, M.M. (2013). A complex network framework for unbiased statistical analyses of DNA-DNA contact maps. Nucleic Acids Res 41, 701–710. https://doi.org/10.1093/nar/gks1096. Cite
Marcotte, E., Boone, C., Babu, M.M., and Gavin, A.C. (2013). Network Biology editorial 2013. Mol Biosyst 9, 1557–1558. https://doi.org/10.1039/c3mb90018e. Cite
Wickramasinghe, V.O., Savill, J.M., Chavali, S., Jonsdottir, A.B., Rajendra, E., Gruner, T., Laskey, R.A., Babu, M.M., and Venkitaraman, A.R. (2013). Human inositol polyphosphate multikinase regulates transcript-selective nuclear mRNA export to preserve genome integrity. Mol Cell 51, 737–750. https://doi.org/10.1016/j.molcel.2013.08.031. Cite
Weatheritt, R.J., and Babu, M.M. (2013). Evolution. The hidden codes that shape protein evolution. Science 342, 1325–1326. https://doi.org/10.1126/science.1248425. Cite

2012

Buljan, M., Chalancon, G., Eustermann, S., Wagner, G.P., Fuxreiter, M., Bateman, A., and Babu, M.M. (2012). Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 46, 871–883. https://doi.org/10.1016/j.molcel.2012.05.039. Cite
Chalancon, G., Kruse, K., and Babu, M.M. (2012). Cell biology. Reconfiguring regulation. Science 335, 1050–1051. https://doi.org/10.1126/science.1219303. Cite
Babu, M.M. (2012). Intrinsically disordered proteins. Mol Biosyst 8, 21. https://doi.org/10.1039/c1mb90045e. Cite
Babu, M.M., Kriwacki, R.W., and Pappu, R.V. (2012). Structural biology. Versatility from protein disorder. Science 337, 1460–1461. https://doi.org/10.1126/science.1228775. Cite
Chalancon, G., Ravarani, C.N., Balaji, S., Martinez-Arias, A., Aravind, L., Jothi, R., and Babu, M.M. (2012). Interplay between gene expression noise and regulatory network architecture. Trends Genet 28, 221–232. https://doi.org/10.1016/j.tig.2012.01.006. Cite
Chandra, T., Kirschner, K., Thuret, J.Y., Pope, B.D., Ryba, T., Newman, S., Ahmed, K., Samarajiwa, S.A., Salama, R., Carroll, T., et al. (2012). Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell 47, 203–214. https://doi.org/10.1016/j.molcel.2012.06.010. Cite
Flock, T., Venkatakrishnan, A.J., Vinothkumar, K.R., and Babu, M.M. (2012). Deciphering membrane protein structures from protein sequences. Genome Biol 13, 160. https://doi.org/10.1186/gb-2012-13-6-160. Cite
Hebenstreit, D., Deonarine, A., Babu, M.M., and Teichmann, S.A. (2012). Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells. Curr Opin Cell Biol 24, 350–358. https://doi.org/10.1016/j.ceb.2012.03.007. Cite
Nagulapalli, M., Parigi, G., Yuan, J., Gsponer, J., Deraos, G., Bamm, V.V., Harauz, G., Matsoukas, J., de Planque, M.R., Gerothanassis, I.P., et al. (2012). Recognition pliability is coupled to structural heterogeneity: a calmodulin intrinsically disordered binding region complex. Structure 20, 522–533. https://doi.org/10.1016/j.str.2012.01.021. Cite
Charoensawan, V., Janga, S.C., Bulyk, M.L., Babu, M.M., and Teichmann, S.A. (2012). DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes. Mol Cell 47, 183–192. https://doi.org/10.1016/j.molcel.2012.06.028. Cite
Gsponer, J., and Babu, M.M. (2012). Cellular strategies for regulating functional and nonfunctional protein aggregation. Cell Rep 2, 1425–1437. https://doi.org/10.1016/j.celrep.2012.09.036. Cite
Moller, A., Xie, S.Q., Hosp, F., Lang, B., Phatnani, H.P., James, S., Ramirez, F., Collin, G.B., Naggert, J.K., Babu, M.M., et al. (2012). Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease. Mol Cell Proteomics 11, M111 011767. https://doi.org/10.1074/mcp.M111.011767. Cite
Sanchez de Groot, N., Torrent, M., Villar-Pique, A., Lang, B., Ventura, S., Gsponer, J., and Babu, M.M. (2012). Evolutionary selection for protein aggregation. Biochem Soc Trans 40, 1032–1037. https://doi.org/10.1042/BST20120160. Cite
Trott, J., Hayashi, K., Surani, A., Babu, M.M., and Martinez-Arias, A. (2012). Dissecting ensemble networks in ES cell populations reveals micro-heterogeneity underlying pluripotency. Mol Biosyst 8, 744–752. https://doi.org/10.1039/c1mb05398a. Cite

2011

Babu, M.M., van der Lee, R., de Groot, N.S., and Gsponer, J. (2011). Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 21, 432–440. https://doi.org/10.1016/j.sbi.2011.03.011. Cite
Chalancon, G., and Babu, M.M. (2011). Structure and Evolution of Transcriptional Regulatory Networks. In Bacterial Stress Responses, G. Storz, and R. Hengge, eds. (Washington, DC: ASM Press), pp. 3–16. Cite
Chavali, S., Morais, D.A., Gough, J., and Babu, M.M. (2011). Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture. Bioessays 33, 592–601. https://doi.org/10.1002/bies.201100034. Cite
Escudero, L.M., Costa Lda, F., Kicheva, A., Briscoe, J., Freeman, M., and Babu, M.M. (2011). Epithelial organisation revealed by a network of cellular contacts. Nat Commun 2, 526. https://doi.org/10.1038/ncomms1536. Cite
Rossmann, M., Sukumaran, M., Penn, A.C., Veprintsev, D.B., Babu, M.M., and Greger, I.H. (2011). Subunit-selective N-terminal domain associations organize the formation of AMPA receptor heteromers. EMBO J 30, 959–971. https://doi.org/10.1038/emboj.2011.16. Cite
Seshasayee, A.S., and Babu, M.M. (2011). Unanticipated intra‐ and inter‐kingdom cross‐talk involving small molecules. Environmental Microbiology Reports 3, 1–26. Cite
Sucgang, R., Kuo, A., Tian, X., Salerno, W., Parikh, A., Feasley, C.L., Dalin, E., Tu, H., Huang, E., Barry, K., et al. (2011). Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol 12, R20. https://doi.org/10.1186/gb-2011-12-2-r20. Cite

2010

Babu, M.M. (2010). Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networks. Biochem Soc Trans 38, 1155–1178. https://doi.org/10.1042/BST0381155. Cite
De, S., and Babu, M.M. (2010). A time-invariant principle of genome evolution. Proc Natl Acad Sci U S A 107, 13004–13009. https://doi.org/10.1073/pnas.0914454107. Cite
Chalancon, G., and Babu, M.M. (2010). Nanobiotechnology: Scaling up synthetic gene circuits. Nat Nanotechnol 5, 631–633. https://doi.org/10.1038/nnano.2010.178. Cite
De, S., and Babu, M.M. (2010). Genomic neighbourhood and the regulation of gene expression. Curr Opin Cell Biol 22, 326–333. https://doi.org/10.1016/j.ceb.2010.04.004. Cite
Janga, S.C., and Babu, M.M. (2010). Transcriptional regulatory networks. In Networks in Cell Biology, F. Rao, G. Caldarelli, M. Buchanan, M. Vendruscolo, and P. De Los Rios, eds. (Cambridge: Cambridge University Press), pp. 14–35. Cite
Kapitzky, L., Beltrao, P., Berens, T.J., Gassner, N., Zhou, C., Wuster, A., Wu, J., Babu, M.M., Elledge, S.J., Toczyski, D., et al. (2010). Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. Mol Syst Biol 6, 451. https://doi.org/10.1038/msb.2010.107. Cite
Mittal, R., Sukumaran, S.K., Selvaraj, S.K., Wooster, D.G., Babu, M.M., Schreiber, A.D., Verbeek, J.S., and Prasadarao, N.V. (2010). Fcgamma receptor I alpha chain (CD64) expression in macrophages is critical for the onset of meningitis by Escherichia coli K1. PLoS Pathog 6, e1001203. https://doi.org/10.1371/journal.ppat.1001203. Cite
Pardo, M., Lang, B., Yu, L., Prosser, H., Bradley, A., Babu, M.M., and Choudhary, J. (2010). An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell 6, 382–395. https://doi.org/10.1016/j.stem.2010.03.004. Cite
Shruthi, H., Babu, M.M., and Sankaran, K. (2010). TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes. J Mol Evol 70, 359–370. https://doi.org/10.1007/s00239-010-9334-2. Cite
Wuster, A., and Babu, M.M. (2010). Transcriptional control of the quorum sensing response in yeast. Mol Biosyst 6, 134–141. https://doi.org/10.1039/b913579k. Cite
Wuster, A., Venkatakrishnan, A.J., Schertler, G.F., and Babu, M.M. (2010). Spial: analysis of subtype-specific features in multiple sequence alignments of proteins. Bioinformatics 26, 2906–2907. https://doi.org/10.1093/bioinformatics/btq552. Cite
Weber, K.P., De, S., Kozarewa, I., Turner, D.J., Babu, M.M., and de Bono, M. (2010). Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS One 5, e13922. https://doi.org/10.1371/journal.pone.0013922. Cite

2009 and earlier

St. Jude Children’s Research Hospital

  • Department of Structural Biology
  • Center for Data Driven Discovery
  • 262 Danny Thomas Pl Memphis, 38105
  • Phone: +1 901-595-1049
  • angie.williams@stjude.org

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