Babu, M. Madan - Laboratory of Molecular Biology, MRC

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Babu, M. Madan - Laboratory of Molecular Biology, MRC

PERSPECTIVES would come from the effects of water.
Title: Time to scale-up. Standfirst: The construction of modular and scalable synthetic gene networks is now a goal within
Protein Families and Regulatory Patterns in the Transcription Factors of E. coli
Madan Babu Mohan Personal Details
BioSystems 81 (2005) 125136 EXAMINE: A computational approach to reconstructing
Proof Delivery Form Journal and Article number: BST 287
nature nanotechnology | VOL 5 | SEPTEMBER 2010 | www.nature.com/naturenanotechnology 631 news & views
Transcriptional networks: reverse-engineering gene regulation on a global scale
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
BioMed Central Page 1 of 10
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
Hooking Up with Oct4 Ihor R. Lemischka1,*
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Domain Assignment to Transcription FactorsDomain Assignment to Transcription Factors 412 Proteins with
BIOINFORMATICS APPLICATIONS NOTE Vol. 26 no. 22 2010, pages 29062907
BIOINFORMATICS Inferring Gene Regulatory Networks from Time Series
Target selection and current status of structural genomics for the
41. S. Nee, Philos. Trans. R. Soc. Lond. B Biol. Sci. 355, 1607 (2000).
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only LKS stations in NH), are fully consist-ent with this assumption, particularly for the
domain is equally informative. `A-type' and `C-type' proteinprotein interaction sites have been implicated
Uncovering a Hidden Distributed Architecture Behind Scale-free Transcriptional Regulatory Networks
Genome BBiioollooggyy 2008, 99
Transcriptional control of the quorum sensing response in yeastw Arthur Wuster* and M. Madan Babu*
tinkers where the tinkering is good. For traits that require regulated gene expression, cis-regulatory DNA is the place.
Dynamic Algorithm for Inferring Qualitative Models of Gene Regulatory BIRC, School of Comp. Eng.
1 of 6 pages Madan Babu Mohan
Biological Databases and Protein Sequence Analysis M. Madan Babu, Center for Biotechnology, Anna University, Chennai 25, India
Bacterial regulatory networks are extremely flexible in evolution
10.1101/gr.1774904Access the most recent version at doi: 2004 14: 1107-1118Genome Res.
Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks
Unsupervised Knowledge Discovery in Medical Databases Using Relevance Networks
The natural history of the WRKYGCM1 zinc fingers and the relationship between transcription factors
BIOINFORMATICS Vol. 20 Suppl. 1 2004, pages i248i256
Research Focus Adaptive evolution by optimizing expression levels
Conservation and Evolution of Cis-Regulatory Systems
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles
Chemogenomics and biotechnology Arthur Wuster and M. Madan Babu
S1: List of probes (upstream regions of target genes) with in-degree 10 that map to chromosome ends
Structure and evolution of transcriptional regulatory networks M Madan Babu1,2
SUPPLEMENTARY INFORMATION S1: LIST OF 176 GENOMES USED IN THE ANALYSIS ..............................................................................S-2
Molecular Cell Mechanistic Insight into Site-Restricted
Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods
Prospects & Overviews Evolution of eukaryotic genome
19 Bishop, N. et al. (2002) Mammalian class E vps proteins recognize ubiquitin and act in the removal of endosomal protein-ubiquitin
COCEBI-789; NO. OF PAGES 8 Please cite this article in press as: De S, Babu MM. Genomic neighbourhood and the regulation of gene expression, Curr Opin Cell Biol (2010), doi:10.1016/j.ceb.2010.04.004
[Ver: A3B2-WIN8.07r/W-Standard] [3.9.20073:14pm] [18] [Page No. 1] FIRST PROOFS {OUP_FPP}nar/gkm712.3d (NAR)
2004 NaturePublishing Group heterozygosity and fitness through extra-pair matings. Nature 425, 714717 (2003).
Registering -Helices and -Strands Using Backbone COH. . .O Interactions
Genome Biology 2004, 5:R92 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation
Principles of transcriptional regulation and evolution of the metabolic system in E. coli
Reconstructing the pathways of a cellular system from genome-scale signals by using matrix
Supplementary Online A time-invariant principle of genome evolution
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the
P. Li\`{o} et al. (Eds.): BIOWIRE 2007, LNCS 5151, pp. 162171, 2008. Springer-Verlag Berlin Heidelberg 2008
BIOINFORMATICS Constructing biological networks through combined literature
A time-invariant principle of genome evolution Subhajyoti De1
A C-H...O Hydrogen Bond Stabilized Polypeptide Chain Reversal Motif
JOURNAL OF BACTERIOLOGY, Apr. 2006, p. 27612773 Vol. 188, No. 8 0021-9193/06/$08.00 0 doi:10.1128/JB.188.8.27612773.2006
BIOINFORMATICS Inferring Gene Regulatory Networks From Multiple
Title: Metabolic networks, structure and dynamics Name: Guilhem Chalancon1 , Kai Kruse1 and M Madan Babu1
BioMed Central Page 1 of 12
Statistical Applications in Genetics and Molecular Biology
M. Madan Babu MRC Laboratory of Molecular Biology, Cambridge
Evolving nature of the AP2 a-appendage hub during clathrin-coated vesicle endocytosis
S5: Potential for cross-hybridization among sub-telomeric probes The sequences of inter-genic probes used in the ChIp-chip experiments were downloaded from
SUPPLEMENTARY METHODS M1: ALGORITHM TO RECONSTRUCT TRANSCRIPTIONAL NETWORKS ..................................................M-2
Exploring the Environmental Preference of Weak Interactions in ( / )8 Barrel Proteins
BIOINFORMATICS ORIGINAL PAPER Vol. 21 no. 1 2005, pages 7179
Using Bayesian Network Inference Algorithms to Recover Molecular Genetic Regulatory Networks
The many faces of the helix-turn-helix domain: Transcription regulation and beyond q
been a past history of selection on this trait. Yet, low levels of genetic variation for desiccation
Reverse engineering gene networks using singular value decomposition and robust regression
Genome-wide prediction and characterization of interactions between transcription factors
Metabolic Engineering 6 (2004) 326339 A Boolean algorithm for reconstructing the structure of
Specialist Review 99. Contextual inference of protein
Contextual inference of protein function (g403207 specialist review)
Volff J-N (ed): Gene and Protein Evolution. Genome Dyn. Basel, Karger, 2007, vol 3, pp 6680
Structure and Evolution of Transcriptional Regulatory Networks Guilhem Chalancon* and M. Madan Babu*
Crystal ball 2011emi4_236 1..26 In this feature, leading researchers in the field of environ-
Fcc Receptor I Alpha Chain (CD64) Expression in Macrophages Is Critical for the Onset of Meningitis by
Genomic neighbourhood and the regulation of gene expression Genomic neighbourhood and transcriptional regulation
Cell Stem Cell An Expanded Oct4 Interaction Network: Implications
TAT-Pathway-Dependent Lipoproteins as a Niche-Based Adaptation in Prokaryotes
The efficiency of mitochondrial electron transport chain is increased in the long-lived mrg19
Genomic analysis shows a tight link between transcription factor dynamics and regulatory
The rules of disorder or why disorder rules Jorg Gsponer*, M. Madan Babu
10.1101/gr.086165.108Access the most recent version at doi: 2009 19: 785-794 originally published online February 19, 2009Genome Res.
Transcript stability in the protein interaction network of Escherichia coli Sarath Chandra Janga* and M. Madan Babu
in the direction perpendicular to the ridge axis on the eastsideoftheridgeatdepthsbetween70and120km
www.sciencemag.org/cgi/content/full/322/5906/1365/DC1 Supporting Online Material for
COGEDE-548; NO OF PAGES 12 Please cite this article in press as: Madan Babu M, et al. Eukaryotic gene regulation in three dimensions and its impact on genome evolution, Curr Opin Genet Dev (2008), doi:10.1016/
Solitary and Repetitive Binding Motifs for the AP2 Complex -Appendage in Amphiphysin and Other
JOURNAL OF BACTERIOLOGY, Jan. 2008, p. 743746 Vol. 190, No. 2 0021-9193/08/$08.00 0 doi:10.1128/JB.01135-07
International Journal of Biological Macromolecules 41 (2007) 251259 Investigations on CH interactions in RNA binding proteins
2006LANDESBIOSCIENCE.DONOTDISTRIBUTE. www.landesbioscience.com Cell Cycle 775
The genome of the social amoeba Dictyostelium discoideum
1 Prusiner, S.B. (1982) Novel proteinaceous infectious particles cause scrapie. Science 216, 136144
Shigella apyrase ^ a novel variant of bacterial acid phosphatases? M. Madan Babua
A CH O Hydrogen Bond Stabilized Polypeptide Chain Reversal Motif at the C Terminus of Helices
REVIEW ARTICLES CURRENT SCIENCE, VOL. 80, NO. 12, 25 JUNE 20011512
Integrating Bioinformatics, Medical Sciences and Drug Discovery M. Madan Babu
Analysis of C H...O hydrogen bonds
DATE A DAtabase of TIM Barrel 2.1 Introduction......................................................................................
Annotation of Chorismate Mutase from the Mycobacterium
M. Madan Babu MRC Laboratory of Molecular Biology, Cambridge
Supplementary Information S1: Degree Distribution of TFs in the E.coli TRN and CRN based on Operons
S2: List of 83 transcription factors that are associated with the high in-degree probes mapping to chromosomal Table S1: Transcription factors which bind to target genes that have high in-degree and located in the sub-telomeric segments. TFs in red show a
S4: List of chromatin factors that are associated with the high in-degree probes mapping to chromosomal ends
Activators, Repressors and Dual RegulatorsActivators, Repressors and Dual Regulators Domain architecture, DNA binding domain or partner domain type
Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
10.1101/gr.1327604Access the most recent version at doi: 2004 14: 451-458Genome Res.
10.1101/gr.2242604Access the most recent version at doi: 2004 14: 1362-1373Genome Res.
Please cite this article in press as: Baumbach, J. et al., CoryneRegNet 3.0--An interactive systems biology plat-form for the analysis of gene regulatory networks in corynebacteria and Escherichia coli, J. Biotechnol. (2007),
Vol. 21 no. 21 2005, pages 40074013 doi:10.1093/bioinformatics/bti648BIOINFORMATICS ORIGINAL PAPER
JOURNAL OF COMPUTATIONAL BIOLOGY Volume 12, Number 2, 2005
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach
BIOINFORMATICS Comparative Evaluation of Reverse Engineering Gene
Xpf and Not the Fanconi Anaemia Proteins or Rev3 Accounts for the Extreme Resistance to Cisplatin in
BIOINFORMATICS ORIGINAL PAPER Vol. 21 no. 7 2005, pages 9931001
COSTBI-882; NO. OF PAGES 9 Please cite this article in press as: Babu MM, et al. Intrinsically disordered proteins: regulation and disease, Curr Opin Struct Biol (2011), doi:10.1016/j.sbi.2011.03.011
Genome Biology 2004, 5:R90 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation
NCI: a server to identify non-canonical interactions in protein structures
10.1101/gr.1330003Access the most recent version at doi: 2003 13: 2423-2434; originally published online Oct 14, 2003;Genome Res.
2006LANDESBIOSCIENCE.DONOTDISTRIBUTE. [Cell Cycle 5:20, 2354-2363, 15 October 2006]; 2006 Landes Bioscience
UNCORRECTEDPROOF 1 Interplay Between Network Structures, Regulatory
Investigating transcriptional regulation: From analysis of complex networks to discovery of cis-regulatory elements
Comprehensive Analysis of Combinatorial Regulation using the Transcriptional Regulatory Network of Yeast
Genome Biology 2003, 4:R6 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
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Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction
Gene Expression Studies in Arabidopsis thaliana -a Network Perspective
Reconstruction of microbial transcriptional regulatory networks Markus J Herrga rd, Markus W Covert and Bernhard Palsson
S.2: Supplementary Material Description of Algorithms The gene regulatory network is represented as a directed graph G=(V, E) where each
Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes
BIOINFORMATICS Vol. 19 no. 15 2003, pages 19171926
Evolution of transcription factors and the gene regulatory network in Escherichia coli
Avenues and Career Options in Biotechnology M. Madan Babu, PhD
Intrinsically Disordered Proteins: Regulation and Disease Regulation of IDPs
10.1101/gr.947203Access the most recent version at doi: 2003 13: 773-780Genome Res.
Dissecting the transcription networks of a cell using computational genomics
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Computational and Systems Biology DOI: 10.1039/b921381n
Subunit-selective N-terminal domain associations organize the formation of AMPA receptor
DMEM. H1299 cells were a gift from J. Chen and were grown in RPMI. All transfections were carried out using Lipofectamine 2000 (Invitrogen), Oligofectamine (Invitrogen) or
RESEARCH Open Access Comparative genomics of the social amoebae
Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. elegans
Computational inference of transcriptional regulatory networks from expression proling and transcription
Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks