Research Topics
| M Madan BabuSummaryAffiliation: University of Cambridge Country: UK Publications
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Detail Information
Publications
Evolutionary dynamics of prokaryotic transcriptional regulatory networksM Madan Babu
National Center for Biotechnology Information, National Institutes of Health, MD 20894, USA
J Mol Biol 358:614-33. 2006..The methods for biological network analysis introduced here can be applied generally to study other networks, and these predictions can be used to guide specific experiments...- Computational approaches to study transcriptional regulationM Madan Babu
MRC Laboratory of Molecular Biology, Cambridge, UK
Biochem Soc Trans 36:758-65. 2008.... - Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditionsRoland A Pache
Structural and Computational Biology, Institute for Research in Biomedicine Barcelona, c Baldiri Reixac 10 12, 08028 Barcelona, Spain
BMC Syst Biol 3:74. 2009.... - Intrinsically disordered proteins: regulation and diseaseM Madan Babu
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
Curr Opin Struct Biol 21:432-40. 2011..e., molecular titration), thereby causing an imbalance in signaling pathways. We discuss the regulation of IDPs, address implications for signaling, disease and drug development, and outline directions for future research... - A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteinsM Madan Babu
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
J Bacteriol 188:2761-73. 2006..The website, along with additional information on the biosynthetic pathway, statistics on predicted lipoproteins, and related figures, is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop/... - Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulationM Madan Babu
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Cell Cycle 5:2354-63. 2006..Based on these observations, we also propose that genome-wide chromatin immunoprecipitation data might be useful to systematically uncover long-range chromatin looping effects in gene expression... - Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networksM Madan Babu
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Biochem Soc Trans 38:1155-78. 2010..Finally, I conclude by discussing open questions for future research and highlighting the implications for evolution, development, disease and applications such as genetic engineering... - General trends in the evolution of prokaryotic transcriptional regulatory networksM Madan Babu
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
Genome Dyn 3:66-80. 2007..In turn, as phylogenetic diversification proceeds, this process appears to have favored repeated convergence to scale-free-like structures, albeit with different regulatory hubs... - Structure and evolution of transcriptional regulatory networksM Madan Babu
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Curr Opin Struct Biol 14:283-91. 2004..Interactions are conserved to varying degrees among genomes. Insights from the structure and evolution of these networks can be translated into predictions and used for engineering of the regulatory networks of different organisms... - DOLOP--database of bacterial lipoproteinsM Madan Babu
Centre for Biotechnology, Anna University, Chennai 600025, India
Bioinformatics 18:641-3. 2002..mrc-lmb.cam.ac.uk/genomes/dolop along with additional information on the biosynthetic pathway, supplementary material and other related figures... - The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposonsM Madan Babu
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 34:6505-20. 2006..We also use the WRKY-GCM1 superfamily as an example to illustrate the importance of transposons in the emergence of new TFs in different lineages... - Functional determinants of transcription factors in Escherichia coli: protein families and binding sitesM Madan Babu
MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, UK
Trends Genet 19:75-9. 2003.... - Evolution of transcription factors and the gene regulatory network in Escherichia coliM Madan Babu
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Nucleic Acids Res 31:1234-44. 2003.... - Did the loss of sigma factors initiate pseudogene accumulation in M. leprae?M Madan Babu
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Trends Microbiol 11:59-61. 2003.... - Eukaryotic gene regulation in three dimensions and its impact on genome evolutionM Madan Babu
MRC Laboratory of Molecular Biology, Cambridge, UK
Curr Opin Genet Dev 18:571-82. 2008..We then address implications for human diseases and outline new directions for future research... - NCI: A server to identify non-canonical interactions in protein structuresM Madan Babu
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Nucleic Acids Res 31:3345-8. 2003..In addition, the user can view the RasMol image highlighting the interactions in the protein structure and download the RasMol script. The NCI server is available at: http://www.mrc-lmb.cam.ac.uk/genomes/nci/... - Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeastS Balaji
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda 20894, USA
J Mol Biol 360:213-27. 2006..We believe that the results presented here might provide a framework for testing the role of co-regulatory associations in eukaryotic transcriptional control... - Solitary and repetitive binding motifs for the AP2 complex alpha-appendage in amphiphysin and other accessory proteinsLene E Olesen
Laboratory of Molecular Biology, Medical Research Council, Neurobiology Division, Hills Road, Cambridge CB2 2QH, United Kingdom
J Biol Chem 283:5099-109. 2008..We describe the optimal sequence of the FXDXF motif using thermodynamic and structural data and show how sequence variation controls the affinities of these motifs for the alpha-appendage... - Gene regulatory network growth by duplicationSarah A Teichmann
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Nat Genet 36:492-6. 2004..In addition, we conclude that evolution has been incremental, rather than making entire regulatory circuits or motifs by duplication with inheritance of interactions... - Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networksS Balaji
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
J Mol Biol 360:204-12. 2006..Thus, an "over-engineered" backup system in the form of distributed architecture is likely to be a major determinant of the "evolvability" of the gene expression in organisms faced with environmental diversity... - Tight regulation of unstructured proteins: from transcript synthesis to protein degradationJörg Gsponer
Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Science 322:1365-8. 2008..Fidelity in signaling may require that most IUPs be available in appropriate amounts and not present longer than needed... - Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domainsS Balaji
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 33:3994-4006. 2005.... - Statistical analysis of domains in interacting protein pairsTom M W Nye
Medical Research Council Biostatistics Unit, Cambridge, UK
Bioinformatics 21:993-1001. 2005..This predictive scheme is tested against protein complexes in the Protein Quaternary Structure (PQS) database, and is used to predict domain-domain contacts within 705 interacting protein pairs taken from our pooled data set... - Transcriptional control of the quorum sensing response in yeastArthur Wuster
MRC Laboratory of Molecular Biology, Cambridge, UK
Mol Biosyst 6:134-41. 2010..cerevisiae quorum sensing and may facilitate the engineering of regulatory circuits for applications such as the expression of heterologous proteins via aromatic alcohols... - Conservation of gene co-regulation in prokaryotes and eukaryotesSarah A Teichmann
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Trends Biotechnol 20:407-10; discussion 410. 2002..Our analysis reveals that the number of conserved co-regulated genes is small in eukaryotes, as has been shown previously in prokaryotes, indicating that there are extensive variations in the gene regulatory network across organisms... - Methods to reconstruct and compare transcriptional regulatory networksM Madan Babu
MRC Laboratory of Molecular Biology, Cambridge, UK
Methods Mol Biol 541:163-80. 2009..In this chapter, we will focus in detail on the first approach and describe methods to reconstruct and analyze the transcriptional regulatory networks of uncharacterized organisms by using a known regulatory network as a template... - Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coliS Balaji
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
J Mol Biol 372:1108-22. 2007.... - Transcript stability in the protein interaction network of Escherichia coliSarath Chandra Janga
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK CB2 0QH
Mol Biosyst 5:154-62. 2009..Our results provide a direct link between mRNA stability and centrality of a protein in PPI network indicating the importance of post-transcriptional mechanisms on nascent RNAs in the cell... - The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNALakshminarayan M Iyer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Cell Cycle 5:775-82. 2006.... - Transcriptional regulation constrains the organization of genes on eukaryotic chromosomesSarath Chandra Janga
Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 0QH, United Kingdom
Proc Natl Acad Sci U S A 105:15761-6. 2008.... - High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomesBenjamin Lang
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Nucleic Acids Res 35:6330-7. 2007.... - The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptomeSubhajyoti De
MRC Laboratory of Molecular Biology, Cambridge, UK
Genome Res 19:785-94. 2009..We propose that, in addition to other molecular mechanisms, change in genomic neighborhood is an important factor that drives transcriptome evolution... - Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?S Balaji
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
Trends Genet 24:319-23. 2008..Through a detailed analysis of the latter, we predict components of the system responding to protein-aggregation stress... - Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elementsRekin s Janky
Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, United Kingdom
Methods 48:277-86. 2009..Here we review some of the available computational methodologies for studying transcriptional regulatory networks as well as their interpretation... - Spial: analysis of subtype-specific features in multiple sequence alignments of proteinsArthur Wuster
Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK
Bioinformatics 26:2906-7. 2010..AVAILABILITY: http://www.mrc-lmb.cam.ac.uk/genomes/spial/; supplementary information is available at http://www.mrc-lmb.cam.ac.uk/genomes/spial/help.html... - 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 architectureSreenivas Chavali
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK
Bioessays 33:592-601. 2011..The knowledge of unique genomic features and splicing mechanisms in O. dioica may be exploited for synthetic biology applications, such as generation of orthogonal splicing systems... - A time-invariant principle of genome evolutionSubhajyoti De
Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
Proc Natl Acad Sci U S A 107:13004-9. 2010..We discuss implications for genome evolution, GWAS, disease genomics, and gene therapy and emphasize the need to investigate both types of mutations within a single framework... - Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegansKatherine P Weber
Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
PLoS ONE 5:e13922. 2010..Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication... - Network-based approaches for linking metabolism with environmentSarath Chandra Janga
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Genome Biol 9:239. 2008..Progress in the reconstruction of genome-wide metabolic maps has led to the development of network-based computational approaches for linking an organism with its biochemical habitat... - Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networksNitish Mittal
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
Proc Natl Acad Sci U S A 106:20300-5. 2009..Future studies uncovering the posttranscriptional networks in higher eukaryotes can help our understanding of the link between different levels of regulation and their role in pathological conditions... - Predicting the strongest domain-domain contact in interacting protein pairsTom M W Nye
Medical Research Council Biostatistics Unit
Stat Appl Genet Mol Biol 5:Article5. 2006.... - The rules of disorder or why disorder rulesJörg Gsponer
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
Prog Biophys Mol Biol 99:94-103. 2009..In addition, we discuss how such properties, individually and in combination, facilitate combinatorial regulation and re-use of the same component in multiple biological processes... - Xpf and not the Fanconi anaemia proteins or Rev3 accounts for the extreme resistance to cisplatin in Dictyostelium discoideumXiao Yin Zhang
Medical Research Council, Laboratory for Molecular Biology, Cambridge, United Kingdom
PLoS Genet 5:e1000645. 2009..Other DNA damage-resistant organisms and chemoresistant cancer cells might adopt a similar strategy to develop resistance to DNA crosslinking agents... - Conservation and evolutionary dynamics of the agr cell-to-cell communication system across firmicutesArthur Wuster
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
J Bacteriol 190:743-6. 2008..This suggests that the regulatory network controlled by agr is dynamic and evolves rapidly... - Adaptive evolution by optimizing expression levels in different environmentsM Madan Babu
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Trends Microbiol 14:11-4. 2006..These studies clarify how adaptation could occur by the alteration of gene expression... - Genomic neighbourhood and the regulation of gene expressionSubhajyoti De
MRC Laboratory of Molecular Biology, Cambridge, UK
Curr Opin Cell Biol 22:326-33. 2010..Understanding the role of genomic neighbourhood on gene regulation has fundamental implications for evolution, development, disease and genetic engineering... - Evolving nature of the AP2 alpha-appendage hub during clathrin-coated vesicle endocytosisGerrit J K Praefcke
Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
EMBO J 23:4371-83. 2004..In the final coated vesicle, most appendage binding partners are absent and thus the functional status of the appendage domain as an interaction hub is temporal and transitory giving directionality to vesicle assembly... - Mechanistic insight into site-restricted monoubiquitination of FANCD2 by Ube2t, FANCL, and FANCIArno F Alpi
Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Mol Cell 32:767-77. 2008..This work therefore establishes a system that provides mechanistic insight into the functions of FANCL and FANCI in the catalysis of FANCD2 monoubiquitination... - Subunit-selective N-terminal domain associations organize the formation of AMPA receptor heteromersMaxim Rossmann
Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
EMBO J 30:959-71. 2011..Our findings reveal that distinct NTD properties set the stage for the biogenesis of functionally diverse pools of homo- and heteromeric AMPAR tetramers... - Shigella apyrase--a novel variant of bacterial acid phosphatases?M Madan Babu
Centre for Biotechnology, Anna University, 600 025, Chennai, India
FEBS Lett 512:8-12. 2002..It revealed interesting structure-function relationships and probable roles relevant to pathogenesis... - Registering alpha-helices and beta-strands using backbone C-H...O interactionsS Kumar Singh
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
Proteins 51:167-71. 2003..Modeling studies revealed ready accommodation of serine residues along the helix face that contacts the strand. The theoretically generated folds correspond to "open" polypeptide structures... - GenCompass: a universal system for analysing gene expression for any genomeNicholas M Luscombe
Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520 8114, USA
Trends Biotechnol 22:552-5. 2004..First, it requires prior knowledge of the DNA sequence encoded in the organism of interest, and second, chips must be designed specifically for each genome, greatly increasing the initial cost incurred in manufacturing the arrays... - Genomic analysis of regulatory network dynamics reveals large topological changesNicholas M Luscombe
Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
Nature 431:308-12. 2004..We anticipate that many of the concepts presented here--particularly the large-scale topological changes and hub transience--will apply to other biological networks, including complex sub-systems in higher eukaryotes... - Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteinsS Chakkaravarthi
School of Biotechnology and Chemical Engineering, Vellore Institute of Technology, Vellore, India
Proteins 65:75-86. 2006.... - Investigations on C-H...pi interactions in RNA binding proteinsAnand Anbarasu
School of Bio Technology, Chemical and Bio Medical Engineering, VIT University, Vellore 632014, India
Int J Biol Macromol 41:251-9. 2007..Seven percent of the theoretically predicted stabilizing residues were also involved in C-Hcdots, three dots, centeredpi interactions and hence these residues may also contribute additional stability to RNA binding proteins...