Publications

2017


  • Li, Y., Sahni, N., Pancsa, R., McGrail, D. J., Xu, J., Hua, X., Coulombe-Huntington, J., Ryan, M., Tychhon, B., Sudhakar, D., Hu, L., Tyers, M., Jiang, X., Lin, S. Y., Babu, M. M. and Yi, S. (2017).
    Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer.
    Cell reports, 21(3), 798-812. doi: 10.1016/j.celrep.2017.09.071
    PubMed PDF
  • 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.
    Nature structural & molecular biology, 24(9), 765-777. doi: 10.1038/nsmb.3441
    PubMed PDF
  • 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(7654), 317-322. doi: 10.1038/nature22070
    PubMed PDF
  • Sormanni, P., Piovesan, D., Heller, G. T., Bonomi, M., Kukic, P., Camilloni, C., Fuxreiter, M., Dosztanyi, Z., Pappu, R. V., Babu, M. M., Longhi, S., Tompa, P., Dunker, A. K., Uversky, V. N., Tosatto, S. C. and Vendruscolo, M. (2017).
    Simultaneous quantification of protein order and disorder.
    Nature chemical biology, 13(4), 339-342. doi: 10.1038/nchembio.2331
    PubMed PDF
  • Chavali, S., Gunnarsson, A. and Babu, M. M. (2017).
    Intrinsically Disordered Proteins Adaptively Reorganize Cellular Matter During Stress.
    Trends in biochemical sciences, 42(6), 410-412. doi: 10.1016/j.tibs.2017.04.007
    PubMed PDF

2016


  • Babu, M. M. (2016).
    The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease.
    Biochemical Society transactions, 44(5), 1185-1200. doi: 10.1042/BST20160172
    PubMed PDF
  • 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.
    Molecular cell, 63(4), 579-92. doi: 10.1016/j.molcel.2016.07.008
    PubMed PDF
  • Venkatakrishnan, A. J., Deupi, X., Lebon, G., Heydenreich, F. M., Flock, T., Miljus, T., Balaji, S., Bouvier, M., Veprintsev, D. B., Tate, C. G., Schertler, G. F. and Babu, M. M. (2016).
    Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region.
    Nature, (), . doi: 10.1038/nature19107
    PubMed PDF
  • 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., Babu, M. M. and Matouschek, A. (2016).
    Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome.
    The Journal of biological chemistry, 291(28), 14526-39. doi: 10.1074/jbc.M116.727578
    PubMed PDF
  • Latysheva, N. S. and Babu, M. M. (2016).
    Discovering and understanding oncogenic gene fusions through data intensive computational approaches.
    Nucleic acids research, (), . doi: 10.1093/nar/gkw282
    PubMed PDF
  • 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.
    Nature communications, 7(), 10417. doi: 10.1038/ncomms10417
    PubMed PDF

2015


  • Sun, D., Flock, T., Deupi, X., Maeda, S., Matkovic, M., Mendieta, S., Mayer, D., Dawson, R. J., Schertler, G. F., Babu, M. M. and Veprintsev, D. B. (2015).
    Probing Galphai1 protein activation at single-amino acid resolution.
    Nature structural & molecular biology, 22(9), 686-94. doi: 10.1038/nsmb.3070
    PubMed PDF
  • 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(7564), 173-9. doi: 10.1038/nature14663
    PubMed PDF
  • Gemayel, R., Chavali, S., Pougach, K., Legendre, M., Zhu, B., Boeynaems, S., van der Zande, E., Gevaert, K., Rousseau, F., Schymkowitz, J., Babu, M. M. and Verstrepen, K. J. (2015).
    Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity.
    Molecular cell, 59(4), 615-27. doi: 10.1016/j.molcel.2015.07.003
    PubMed PDF
  • 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.
    Current opinion in structural biology, 32(), viii-x. doi: 10.1016/j.sbi.2015.06.005
    PubMed PDF
  • Schrynemackers, M., Wehenkel, L., Babu, M. M. and Geurts, P. (2015).
    Classifying pairs with trees for supervised biological network inference.
    Molecular bioSystems, 11(8), 2116-25. doi: 10.1039/c5mb00174a
    PubMed PDF
  • 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 science : a publication of the Protein Society, 24(6), 909-22. doi: 10.1002/pro.2674
    PubMed PDF
  • 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 biology, 5(2), . doi: 10.1098/rsob.140221
    PubMed PDF
  • 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.
    Nature structural & molecular biology, (), . doi: 10.1038/nsmb.2958
    PubMed PDF

2014


  • Hattori, H., Janky, R., Nietfeld, W., Aerts, S., Madan Babu, 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(16), 2572-86. doi: 10.4161/15384101.2015.942209
    PubMed PDF
  • Morgunov, A. S. and Babu, M. M. (2014).
    Optimizing membrane-protein biogenesis through nonoptimal-codon usage.
    Nature structural & molecular biology, 21(12), 1023-5. doi: 10.1038/nsmb.2926
    PubMed PDF
  • Venkatakrishnan, A., Flock, T., Prado, D. E., Oates, M. E., Gough, J. and Madan Babu, M. (2014).
    Structured and disordered facets of the GPCR fold.
    Current opinion in structural biology, 27C(), 129-137. doi: 10.1016/j.sbi.2014.08.002
    PubMed PDF
  • 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 reports, 8(6), 1832-44. doi: 10.1016/j.celrep.2014.07.055
    PubMed PDF
  • Weatheritt, R. J., Gibson, T. J. and Babu, M. M. (2014).
    Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems.
    Nature structural & molecular biology, (), . doi: 10.1038/nsmb.2876
    PubMed PDF
  • Tompa, P., Davey, N. E., Gibson, T. J. and Babu, M. M. (2014).
    A Million Peptide Motifs for the Molecular Biologist.
    Molecular cell, 55(2), 161-169. doi: 10.1016/j.molcel.2014.05.032
    PubMed PDF
  • 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 reports, 7(5), 1729-39. doi: 10.1016/j.celrep.2014.04.052
    PubMed PDF
  • Flock, T., Weatheritt, R. J., Latysheva, N. S. and Babu, M. M. (2014).
    Controlling entropy to tune the functions of intrinsically disordered regions.
    Current opinion in structural biology, 26C(), 62-72. doi: 10.1016/j.sbi.2014.05.007
    PubMed PDF
  • 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., Kim, P. M., Kriwacki, R. W., Oldfield, C. J., Pappu, R. V., Tompa, P., Uversky, V. N., Wright, P. E. and Babu, M. M. (2014).
    Classification of Intrinsically Disordered Regions and Proteins.
    Chemical reviews, (), . doi: 10.1021/cr400525m
    PubMed PDF
  • Mitrea, D. M., Grace, C. R., Buljan, M., Yun, M. K., Pytel, N. J., Satumba, J., Nourse, A., Park, C. G., Madan Babu, M., White, S. W. and Kriwacki, R. W. (2014).
    Structural polymorphism in the N-terminal oligomerization domain of NPM1.
    Proceedings of the National Academy of Sciences of the United States of America, (), . doi: 10.1073/pnas.1321007111
    PubMed PDF

2013


  • 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.
    Molecular cell, 51(6), 737-50. doi: 10.1016/j.molcel.2013.08.031
    PubMed PDF
  • Weatheritt, R. J. and Babu, M. M. (2013).
    Evolution. The hidden codes that shape protein evolution.
    Science, 342(6164), 1325-6. doi: 10.1126/science.1248425
    PubMed PDF
  • 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(7436), 185-94. doi: 10.1038/nature11896
    PubMed PDF
  • Marcotte, E., Boone, C., Babu, M. M. and Gavin, A. C. (2013).
    Network Biology editorial 2013.
    Molecular bioSystems, 9(7), 1557-8. doi: 10.1039/c3mb90018e
    PubMed PDF
  • Kruse, K., Sewitz, S. and Babu, M. M. (2013).
    A complex network framework for unbiased statistical analyses of DNA-DNA contact maps.
    Nucleic acids research, 41(2), 701-10. doi: 10.1093/nar/gks1096
    PubMed PDF
  • Cumberworth, A., Lamour, G., Babu, M. M. and Gsponer, J. (2013).
    Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes.
    The Biochemical journal, 454(3), 361-9. doi: 10.1042/BJ20130545
    PubMed PDF
  • 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.
    Molecular bioSystems, 9(7), 1926-30. doi: 10.1039/c3mb25475e
    PubMed PDF
  • 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.
    Current opinion in structural biology, 23(3), 443-50. doi: 10.1016/j.sbi.2013.03.006
    PubMed PDF

2012


  • 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.
    Molecular bioSystems, 8(3), 744-52. doi: 10.1039/c1mb05398a
    PubMed PDF
  • 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.
    Biochemical Society transactions, 40(5), 1032-7. doi: 10.1042/BST20120160
    PubMed PDF
  • Nagulapalli, M., Parigi, G., Yuan, J., Gsponer, J., Deraos, G., Bamm, V. V., Harauz, G., Matsoukas, J., de Planque, M. R., Gerothanassis, I. P., Babu, M. M., Luchinat, C. and Tzakos, A. G. (2012).
    Recognition pliability is coupled to structural heterogeneity a calmodulin intrinsically disordered binding region complex.
    Structure, 20(3), 522-33. doi: 10.1016/j.str.2012.01.021
    PubMed PDF
  • 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., Greenleaf, A. L., Selbach, M. and Pombo, A. (2012).
    Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease.
    Molecular & cellular proteomics : MCP, 11(6), M111 011767. doi: 10.1074/mcp.M111.011767
    PubMed PDF
  • 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.
    Current opinion in cell biology, 24(3), 350-8. doi: 10.1016/j.ceb.2012.03.007
    PubMed PDF
  • Gsponer, J. and Babu, M. M. (2012).
    Cellular strategies for regulating functional and nonfunctional protein aggregation.
    Cell reports, 2(5), 1425-37. doi: 10.1016/j.celrep.2012.09.036
    PubMed PDF
  • Flock, T., Venkatakrishnan, A., Vinothkumar, K. and Babu, M. M. (2012).
    Deciphering membrane protein structures from protein sequences.
    Genome biology, 13(6), 160. doi: 10.1186/gb-2012-13-6-160
    PubMed PDF
  • 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.
    Molecular cell, 47(2), 183-92. doi: 10.1016/j.molcel.2012.06.028
    PubMed PDF
  • Chandra, T., Kirschner, K., Thuret, J. Y., Pope, B. D., Ryba, T., Newman, S., Ahmed, K., Samarajiwa, S. A., Salama, R., Carroll, T., Stark, R., Janky, R., Narita, M., Xue, L., Chicas, A., Nunez, S., Janknecht, R., Hayashi-Takanaka, Y., Wilson, M. D., Marshall, A., Odom, D. T., Babu, M. M., Bazett-Jones, D. P., Tavare, S., Edwards, P. A., Lowe, S. W., Kimura, H., Gilbert, D. M. and Narita, M. (2012).
    Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation.
    Molecular cell, 47(2), 203-14. doi: 10.1016/j.molcel.2012.06.010
    PubMed PDF
  • 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 in genetics : TIG, 28(5), 221-32. doi: 10.1016/j.tig.2012.01.006
    PubMed PDF
  • Chalancon, G., Kruse, K. and Babu, M. M. (2012).
    Cell biology. Reconfiguring regulation.
    Science, 335(6072), 1050-1. doi: 10.1126/science.1219303
    PubMed PDF
  • 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.
    Molecular cell, 46(6), 871-83. doi: 10.1016/j.molcel.2012.05.039
    PubMed PDF
  • Babu, M. M., Kriwacki, R. W. and Pappu, R. V. (2012).
    Structural biology. Versatility from protein disorder.
    Science, 337(6101), 1460-1. doi: 10.1126/science.1228775
    PubMed PDF
  • Babu, M. M. (2012).
    Intrinsically disordered proteins.
    Molecular bioSystems, 8(1), 21. doi: 10.1039/c1mb90045e
    PubMed PDF

2011


  • Sucgang, R., Kuo, A., Tian, X., Salerno, W., Parikh, A., Feasley, C. L., Dalin, E., Tu, H., Huang, E., Barry, K., Lindquist, E., Shapiro, H., Bruce, D., Schmutz, J., Salamov, A., Fey, P., Gaudet, P., Anjard, C., Babu, M. M., Basu, S., Bushmanova, Y., van der Wel, H., Katoh-Kurasawa, M., Dinh, C., Coutinho, P. M., Saito, T., Elias, M., Schaap, P., Kay, R. R., Henrissat, B., Eichinger, L., Rivero, F., Putnam, N. H., West, C. M., Loomis, W. F., Chisholm, R. L., Shaulsky, G., Strassmann, J. E., Queller, D. C., Kuspa, A. and Grigoriev, I. V. (2011).
    Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.
    Genome biology, 12(2), R20. doi: 10.1186/gb-2011-12-2-r20
    PubMed PDF
  • 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.
    The EMBO journal, 30(5), 959-71. doi: 10.1038/emboj.2011.16
    PubMed PDF
  • 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.
    Nature communications, 2(), 526. doi: 10.1038/ncomms1536
    PubMed PDF
  • 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 : news and reviews in molecular, cellular and developmental biology, 33(8), 592-601. doi: 10.1002/bies.201100034
    PubMed PDF
  • Babu, M. M., van der Lee, R., de Groot, N. S. and Gsponer, J. (2011).
    Intrinsically disordered proteins: regulation and disease.
    Current opinion in structural biology, 21(3), 432-40. doi: 10.1016/j.sbi.2011.03.011
    PubMed PDF

2010


  • 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(22), 2906-7. doi: 10.1093/bioinformatics/btq552
    PubMed PDF
  • Wuster, A. and Babu, M. M. (2010).
    Transcriptional control of the quorum sensing response in yeast.
    Molecular bioSystems, 6(1), 134-41. doi: 10.1039/b913579k
    PubMed PDF
  • 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(11), e13922. doi: 10.1371/journal.pone.0013922
    PubMed PDF
  • Shruthi, H., Babu, M. M. and Sankaran, K. (2010).
    TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes.
    Journal of molecular evolution, 70(4), 359-70. doi: 10.1007/s00239-010-9334-2
    PubMed PDF
  • 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(4), 382-95. doi: 10.1016/j.stem.2010.03.004
    PubMed PDF
  • 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 pathogens, 6(11), e1001203. doi: 10.1371/journal.ppat.1001203
    PubMed PDF
  • Kapitzky, L., Beltrao, P., Berens, T. J., Gassner, N., Zhou, C., Wuster, A., Wu, J., Babu, M. M., Elledge, S. J., Toczyski, D., Lokey, R. S. and Krogan, N. J. (2010).
    Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action.
    Molecular systems biology, 6(), 451. doi: 10.1038/msb.2010.107
    PubMed PDF
  • De, S. and Babu, M. M. (2010).
    Genomic neighbourhood and the regulation of gene expression.
    Current opinion in cell biology, 22(3), 326-33. doi: 10.1016/j.ceb.2010.04.004
    PubMed PDF
  • De, S. and Babu, M. M. (2010).
    A time-invariant principle of genome evolution.
    Proceedings of the National Academy of Sciences of the United States of America, 107(29), 13004-9. doi: 10.1073/pnas.0914454107
    PubMed PDF
  • Chalancon, G. and Babu, M. M. (2010).
    Nanobiotechnology: Scaling up synthetic gene circuits.
    Nature nanotechnology, 5(9), 631-3. doi: 10.1038/nnano.2010.178
    PubMed PDF
  • Babu, M. M. (2010).
    Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networks.
    Biochemical Society transactions, 38(5), 1155-78. doi: 10.1042/BST0381155
    PubMed PDF

2009


  • Zhang, X. Y., Langenick, J., Traynor, D., Babu, M. M., Kay, R. R. and Patel, K. J. (2009).
    Xpf and not the Fanconi anaemia proteins or Rev3 accounts for the extreme resistance to cisplatin in Dictyostelium discoideum.
    PLoS genetics, 5(9), e1000645. doi: 10.1371/journal.pgen.1000645
    PubMed PDF
  • Seshasayee, A. S., Fraser, G. M., Babu, M. M. and Luscombe, N. M. (2009).
    Principles of transcriptional regulation and evolution of the metabolic system in E. coli.
    Genome research, 19(1), 79-91. doi: 10.1101/gr.079715.108
    PubMed PDF
  • Pache, R. A., Babu, M. M. and Aloy, P. (2009).
    Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions.
    BMC systems biology, 3(), 74. doi: 10.1186/1752-0509-3-74
    PubMed PDF
  • Mittal, N., Roy, N., Babu, M. M. and Janga, S. C. (2009).
    Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks.
    Proceedings of the National Academy of Sciences of the United States of America, 106(48), 20300-5. doi: 10.1073/pnas.0906940106
    PubMed PDF
  • Mittal, N., Babu, M. M. and Roy, N. (2009).
    The efficiency of mitochondrial electron transport chain is increased in the long-lived mrg19 Saccharomyces cerevisiae.
    Aging cell, 8(6), 643-53. doi: 10.1111/j.1474-9726.2009.00518.x
    PubMed PDF
  • Jothi, R., Balaji, S., Wuster, A., Grochow, J. A., Gsponer, J., Przytycka, T. M., Aravind, L. and Babu, M. M. (2009).
    Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture.
    Molecular systems biology, 5(), 294. doi: 10.1038/msb.2009.52
    PubMed PDF
  • Janky, R., Helden, Jv and Babu, M. M. (2009).
    Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements.
    Methods, 48(3), 277-86. doi: 10.1016/j.ymeth.2009.04.022
    PubMed PDF
  • Janga, S. C. and Babu, M. M. (2009).
    Transcript stability in the protein interaction network of Escherichia coli.
    Molecular bioSystems, 5(2), 154-62. doi: 10.1039/b816845h
    PubMed PDF
  • Gsponer, J. and Babu, M. M. (2009).
    The rules of disorder or why disorder rules.
    Progress in biophysics and molecular biology, 99(2-3), 94-103. doi: 10.1016/j.pbiomolbio.2009.03.001
    PubMed PDF
  • De, S., Teichmann, S. A. and Babu, M. M. (2009).
    The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome.
    Genome research, 19(5), 785-94. doi: 10.1101/gr.086165.108
    PubMed PDF
  • Babu, M. M., Lang, B. and Aravind, L. (2009).
    Methods to reconstruct and compare transcriptional regulatory networks.
    Methods in molecular biology, 541(), 163-80. doi: 10.1007/978-1-59745-243-4_8
    PubMed PDF

2008


  • Wuster, A. and Madan Babu, M. (2008).
    Chemogenomics and biotechnology.
    Trends in biotechnology, 26(5), 252-8. doi: 10.1016/j.tibtech.2008.01.004
    PubMed PDF
  • Wuster, A. and Babu, M. M. (2008).
    Conservation and evolutionary dynamics of the agr cell-to-cell communication system across firmicutes.
    Journal of bacteriology, 190(2), 743-6. doi: 10.1128/JB.01135-07
    PubMed PDF
  • Olesen, L. E., Ford, M. G., Schmid, E. M., Vallis, Y., Babu, M. M., Li, P. H., Mills, I. G., McMahon, H. T. and Praefcke, G. J. (2008).
    Solitary and repetitive binding motifs for the AP2 complex alpha-appendage in amphiphysin and other accessory proteins.
    The Journal of biological chemistry, 283(8), 5099-109. doi: 10.1074/jbc.M708621200
    PubMed PDF
  • Janga, S. C., Collado-Vides, J. and Babu, M. M. (2008).
    Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes.
    Proceedings of the National Academy of Sciences of the United States of America, 105(41), 15761-6. doi: 10.1073/pnas.0806317105
    PubMed PDF
  • Janga, S. C. and Babu, M. M. (2008).
    Network-based approaches for linking metabolism with environment.
    Genome biology, 9(11), 239. doi: 10.1186/gb-2008-9-11-239
    PubMed PDF
  • Gsponer, J., Futschik, M. E., Teichmann, S. A. and Babu, M. M. (2008).
    Tight regulation of unstructured proteins: from transcript synthesis to protein degradation.
    Science, 322(5906), 1365-8. doi: 10.1126/science.1163581
    PubMed PDF
  • Balaji, S., Iyer, L. M., Babu, M. M. and Aravind, L. (2008).
    Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?.
    Trends in genetics : TIG, 24(7), 319-23. doi: 10.1016/j.tig.2008.04.006
    PubMed PDF
  • Babu, M. M., Janga, S. C., de Santiago, I. and Pombo, A. (2008).
    Eukaryotic gene regulation in three dimensions and its impact on genome evolution.
    Current opinion in genetics & development, 18(6), 571-82. doi: 10.1016/j.gde.2008.10.002
    PubMed PDF
  • Babu, M. M. (2008).
    Computational approaches to study transcriptional regulation.
    Biochemical Society transactions, 36(Pt 4), 758-65. doi: 10.1042/BST0360758
    PubMed PDF
  • Alpi, A. F., Pace, P. E., Babu, M. M. and Patel, K. J. (2008).
    Mechanistic insight into site-restricted monoubiquitination of FANCD2 by Ube2t, FANCL, and FANCI.
    Molecular cell, 32(6), 767-77. doi: 10.1016/j.molcel.2008.12.003
    PubMed PDF

2007


  • Madan Babu, M., Balaji, S. and Aravind, L. (2007).
    General trends in the evolution of prokaryotic transcriptional regulatory networks.
    Genome dynamics, 3(), 66-80. doi: 10.1159/000107604
    PubMed PDF
  • Lang, B., Blot, N., Bouffartigues, E., Buckle, M., Geertz, M., Gualerzi, C. O., Mavathur, R., Muskhelishvili, G., Pon, C. L., Rimsky, S., Stella, S., Babu, M. M. and Travers, A. (2007).
    High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes.
    Nucleic acids research, 35(18), 6330-7. doi: 10.1093/nar/gkm712
    PubMed PDF
  • Balaji, S., Babu, M. M. and Aravind, L. (2007).
    Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli.
    Journal of molecular biology, 372(4), 1108-22. doi: 10.1016/j.jmb.2007.06.084
    PubMed PDF
  • Anbarasu, A., Anand, S., Babu, M. M. and Sethumadhavan, R. (2007).
    Investigations on C-H…pi interactions in RNA binding proteins.
    International journal of biological macromolecules, 41(3), 251-9. doi: 10.1016/j.ijbiomac.2007.02.013
    PubMed PDF

2006


  • Nye, T. M., Berzuini, C., Gilks, W. R., Babu, M. M. and Teichmann, S. (2006).
    Predicting the strongest domain-domain contact in interacting protein pairs.
    Statistical applications in genetics and molecular biology, 5(), Article5. doi: 10.2202/1544-6115.1195
    PubMed PDF
  • Madan Babu, M., Teichmann, S. A. and Aravind, L. (2006).
    Evolutionary dynamics of prokaryotic transcriptional regulatory networks.
    Journal of molecular biology, 358(2), 614-33. doi: 10.1016/j.jmb.2006.02.019
    PubMed PDF
  • Iyer, L. M., Babu, M. M. and Aravind, L. (2006).
    The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA.
    Cell cycle, 5(7), 775-82. doi:
    PubMed PDF
  • Chakkaravarthi, S., Babu, M. M., Gromiha, M. M., Jayaraman, G. and Sethumadhavan, R. (2006).
    Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins.
    Proteins, 65(1), 75-86. doi: 10.1002/prot.21067
    PubMed PDF
  • Balaji, S., Iyer, L. M., Aravind, L. and Babu, M. M. (2006).
    Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks.
    Journal of molecular biology, 360(1), 204-12. doi: 10.1016/j.jmb.2006.04.026
    PubMed PDF
  • Balaji, S., Babu, M. M., Iyer, L. M., Luscombe, N. M. and Aravind, L. (2006).
    Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.
    Journal of molecular biology, 360(1), 213-27. doi: 10.1016/j.jmb.2006.04.029
    PubMed PDF
  • Babu, M. M., Priya, M. L., Selvan, A. T., Madera, M., Gough, J., Aravind, L. and Sankaran, K. (2006).
    A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins.
    Journal of bacteriology, 188(8), 2761-73. doi: 10.1128/JB.188.8.2761-2773.2006
    PubMed PDF
  • Babu, M. M., Iyer, L. M., Balaji, S. and Aravind, L. (2006).
    The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons.
    Nucleic acids research, 34(22), 6505-20. doi: 10.1093/nar/gkl888
    PubMed PDF
  • Babu, M. M., Balaji, S., Iyer, L. M. and Aravind, L. (2006).
    Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation.
    Cell cycle, 5(20), 2354-63. doi:
    PubMed PDF
  • Babu, M. M. and Aravind, L. (2006).
    Adaptive evolution by optimizing expression levels in different environments.
    Trends in microbiology, 14(1), 11-4. doi: 10.1016/j.tim.2005.11.005
    PubMed PDF

2005


  • Nye, T. M., Berzuini, C., Gilks, W. R., Babu, M. M. and Teichmann, S. A. (2005).
    Statistical analysis of domains in interacting protein pairs.
    Bioinformatics, 21(7), 993-1001. doi: 10.1093/bioinformatics/bti086
    PubMed PDF
  • Eichinger, L., Pachebat, J. A., Glockner, G., Rajandream, M. A., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., Tunggal, B., Kummerfeld, S., Madera, M., Konfortov, B. A., Rivero, F., Bankier, A. T., Lehmann, R., Hamlin, N., Davies, R., Gaudet, P., Fey, P., Pilcher, K., Chen, G., Saunders, D., Sodergren, E., Davis, P., Kerhornou, A., Nie, X., Hall, N., Anjard, C., Hemphill, L., Bason, N., Farbrother, P., Desany, B., Just, E., Morio, T., Rost, R., Churcher, C., Cooper, J., Haydock, S., van Driessche, N., Cronin, A., Goodhead, I., Muzny, D., Mourier, T., Pain, A., Lu, M., Harper, D., Lindsay, R., Hauser, H., James, K., Quiles, M., Madan Babu, M., Saito, T., Buchrieser, C., Wardroper, A., Felder, M., Thangavelu, M., Johnson, D., Knights, A., Loulseged, H., Mungall, K., Oliver, K., Price, C., Quail, M. A., Urushihara, H., Hernandez, J., Rabbinowitsch, E., Steffen, D., Sanders, M., Ma, J., Kohara, Y., Sharp, S., Simmonds, M., Spiegler, S., Tivey, A., Sugano, S., White, B., Walker, D., Woodward, J., Winckler, T., Tanaka, Y., Shaulsky, G., Schleicher, M., Weinstock, G., Rosenthal, A., Cox, E. C., Chisholm, R. L., Gibbs, R., Loomis, W. F., Platzer, M., Kay, R. R., Williams, J., Dear, P. H., Noegel, A. A., Barrell, B. and Kuspa, A. (2005).
    The genome of the social amoeba Dictyostelium discoideum.
    Nature, 435(7038), 43-57. doi: 10.1038/nature03481
    PubMed PDF
  • Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., Della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C., Schonbach, C., Sekiguchi, K., Semple, C. A., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S. L., Tang, S., Taylor, M. S., Tegner, J., Teichmann, S. A., Ueda, H. R., van Nimwegen, E., Verardo, R., Wei, C. L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S. M., Teasdale, R. D., Liu, E. T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J. S., Hume, D. A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J., Hayashizaki, Y., Consortium, Fantom, Group, Riken Genome Exploration Research and Genome Science, Group (2005).
    The transcriptional landscape of the mammalian genome.
    Science, 309(5740), 1559-63. doi: 10.1126/science.1112014
    PubMed PDF
  • Balaji, S., Babu, M. M., Iyer, L. M. and Aravind, L. (2005).
    Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.
    Nucleic acids research, 33(13), 3994-4006. doi: 10.1093/nar/gki709
    PubMed PDF
  • Aravind, L., Anantharaman, V., Balaji, S., Babu, M. M. and Iyer, L. M. (2005).
    The many faces of the helix-turn-helix domain: transcription regulation and beyond.
    FEMS microbiology reviews, 29(2), 231-62. doi: 10.1016/j.femsre.2004.12.008
    PubMed PDF

2004


  • Teichmann, S. A. and Babu, M. M. (2004).
    Gene regulatory network growth by duplication.
    Nature genetics, 36(5), 492-6. doi: 10.1038/ng1340
    PubMed PDF
  • Praefcke, G. J., Ford, M. G., Schmid, E. M., Olesen, L. E., Gallop, J. L., Peak-Chew, S. Y., Vallis, Y., Babu, M. M., Mills, I. G. and McMahon, H. T. (2004).
    Evolving nature of the AP2 alpha-appendage hub during clathrin-coated vesicle endocytosis.
    The EMBO journal, 23(22), 4371-83. doi: 10.1038/sj.emboj.7600445
    PubMed PDF
  • Luscombe, N. M., Babu, M. M., Yu, H., Snyder, M., Teichmann, S. A. and Gerstein, M. (2004).
    Genomic analysis of regulatory network dynamics reveals large topological changes.
    Nature, 431(7006), 308-12. doi: 10.1038/nature02782
    PubMed PDF
  • Luscombe, N. M. and Babu, M. M. (2004).
    GenCompass: a universal system for analysing gene expression for any genome.
    Trends in biotechnology, 22(11), 552-5. doi: 10.1016/j.tibtech.2004.08.013
    PubMed PDF
  • Babu, M. M., Luscombe, N. M., Aravind, L., Gerstein, M. and Teichmann, S. A. (2004).
    Structure and evolution of transcriptional regulatory networks.
    Current opinion in structural biology, 14(3), 283-91. doi: 10.1016/j.sbi.2004.05.004
    PubMed PDF

2003


  • Singh, S. K., Babu, M. M. and Balaram, P. (2003).
    Registering alpha-helices and beta-strands using backbone C-H…O interactions.
    Proteins, 51(2), 167-71. doi: 10.1002/prot.10245
    PubMed PDF
  • Madan Babu, M. and Teichmann, S. A. (2003).
    Functional determinants of transcription factors in Escherichia coli: protein families and binding sites.
    Trends in genetics : TIG, 19(2), 75-9. doi: 10.1016/S0168-9525(02)00039-2
    PubMed PDF
  • Madan Babu, M. and Teichmann, S. A. (2003).
    Evolution of transcription factors and the gene regulatory network in Escherichia coli.
    Nucleic acids research, 31(4), 1234-44. doi:
    PubMed PDF
  • Madan Babu, M. (2003).
    Did the loss of sigma factors initiate pseudogene accumulation in M. leprae?.
    Trends in microbiology, 11(2), 59-61. doi:
    PubMed PDF
  • Babu, M. M. (2003).
    NCI: A server to identify non-canonical interactions in protein structures.
    Nucleic acids research, 31(13), 3345-8. doi:
    PubMed PDF

2002


  • Teichmann, S. A. and Babu, M. M. (2002).
    Conservation of gene co-regulation in prokaryotes and eukaryotes.
    Trends in biotechnology, 20(10), 407-10; discussion 410. doi:
    PubMed PDF
  • Madan Babu, M. and Sankaran, K. (2002).
    DOLOP–database of bacterial lipoproteins.
    Bioinformatics, 18(4), 641-3. doi:
    PubMed PDF
  • Madan Babu, M., Kumar Singh, S. and Balaram, P. (2002).
    A C-H triplebond O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins.
    Journal of molecular biology, 322(4), 871-80. doi:
    PubMed PDF
  • Babu, M. M., Kamalakkannan, S., Subrahmanyam, Y. V. and Sankaran, K. (2002).
    Shigella apyrase–a novel variant of bacterial acid phosphatases?.
    FEBS letters, 512(1-3), 8-12. doi:
    PubMed PDF