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Research at the interface between chemistry and the -omic sciences and systems biology.
Contents list for Molecular BioSystems, issue 12, 2009
Front cover
Mol. BioSyst., 2009, 5, 1373
DOI: 10.1039/b922400a
Inside front cover
Mol. BioSyst., 2009, 5, 1374
DOI: 10.1039/b922401g
Contents and Highlights in Chemical Biology
Mol. BioSyst., 2009, 5, 1375
DOI: 10.1039/B922402P
Editorial
Computational and Systems Biology
Mol. BioSyst., 2009, 5, 1391
DOI: 10.1039/b921381n
Reviews
The potential of microfluidic water-in-oil droplets in experimental biology
Yolanda Schaerli and Florian Hollfelder,
Mol. BioSyst., 2009, 5, 1392
DOI: 10.1039/b907578j
Signal initiation in biological systems: the properties and detection of transient extracellular protein interactions
Gavin J. Wright,
Mol. BioSyst., 2009, 5, 1405
DOI: 10.1039/b903580j
Enhanced HTML article available
From genes to cells to tissues—modelling the haematopoietic system
Samuel D. Foster, S. Helen Oram, Nicola K. Wilson and Berthold Göttgens,
Mol. BioSyst., 2009, 5, 1413
DOI: 10.1039/b907225j Enhanced HTML article available
ChIPing away at the genome: the new frontier travel guide
Jelena Aleksic and Steven Russell,
Mol. BioSyst., 2009, 5, 1421
DOI: 10.1039/b906179g Enhanced HTML article available
Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays
Audrey Qiuyan Fu and Boris Adryan,
Mol. BioSyst., 2009, 5, 1429
DOI: 10.1039/b906880e Enhanced HTML article available
Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes
Mohan Babu, Gabriel Musso, J. Javier Díaz-Mejía, Gareth Butland, Jack F. Greenblatt and Andrew Emili,
Mol. BioSyst., 2009, 5, 1439
DOI: 10.1039/b907407d Enhanced HTML article available
Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics
Semin Lee, Alan Brown, William Ross Pitt, Alicia Perez Higueruelo, Sungsam Gong, George Richard Bickerton, Adrian Schreyer, Duangrudee Tanramluk, Alison Baylay and Tom Leon Blundell,
Mol. BioSyst., 2009, 5, 1456
DOI: 10.1039/b906402h Enhanced HTML article available
Explorations in topology–delving underneath the surface of genetic interaction maps
Michal Breker and Maya Schuldiner,
Mol. BioSyst., 2009, 5, 1473
DOI: 10.1039/b907076c Enhanced HTML article available
The powerful law of the power law and other myths in network biology
Gipsi Lima-Mendez and Jacques van Helden,
Mol. BioSyst., 2009, 5, 1482
DOI: 10.1039/b908681a Enhanced HTML article available
Scaling relationship in the gene content of transcriptional machinery in bacteria
Ernesto Pérez-Rueda, Sarath Chandra Janga and Agustino Martínez-Antonio,
Mol. BioSyst., 2009, 5, 1494
DOI: 10.1039/b907384a Enhanced HTML article available
Systems analyses of circadian networks
Katharine E. Hubbard, Fiona C. Robertson, Neil Dalchau and Alex A. R. Webb,
Mol. BioSyst., 2009, 5, 1502
DOI: 10.1039/b907714f Enhanced HTML article available
Global signatures of protein and mRNA expression levels
Raquel de Sousa Abreu, Luiz O. Penalva, Edward M. Marcotte and Christine Vogel,
Mol. BioSyst., 2009, 5, 1512
DOI: 10.1039/b908315d Enhanced HTML article available
Theoretical models of spontaneous activity generation and propagation in the developing retina
Keith B. Godfrey and Stephen J. Eglen,
Mol. BioSyst., 2009, 5, 1527
DOI: 10.1039/b907213f Enhanced HTML article available
Structure and organization of drug-target networks: insights from genomic approaches for drug discovery
Sarath Chandra Janga and Andreas Tzakos,
Mol. BioSyst., 2009, 5, 1536
DOI: 10.1039/b908147j Enhanced HTML article available
Modelling the Drosophila embryo
Johannes Jaeger,
Mol. BioSyst., 2009, 5, 1549
DOI: 10.1039/b904722k
Logical modelling of cell cycle control in eukaryotes: a comparative study
Adrien Fauré and Denis Thieffry,
Mol. BioSyst., 2009, 5, 1569
DOI: 10.1039/b907562n Enhanced HTML article available
Nucleosome positioning—what do we really know?
Andrew Travers, Micaela Caserta, Mark Churcher, Edwige Hiriart and Ernesto Di Mauro,
Mol. BioSyst., 2009, 5, 1582
DOI: 10.1039/b907227f
Supervised learning with decision tree-based methods in computational and systems biology
Pierre Geurts, Alexandre Irrthum and Louis Wehenkel,
Mol. BioSyst., 2009, 5, 1593
DOI: 10.1039/b907946g
Conformational averaging in structural biology: issues, challenges and computational solutions
Daniela Kruschel and Bojan Zagrovic,
Mol. BioSyst., 2009, 5, 1606
DOI: 10.1039/b917186j
Papers
On the basic computational structure of gene regulatory networks
Carlos Rodríguez-Caso, Bernat Corominas-Murtra and Ricard V. Solé,
Mol. BioSyst., 2009, 5, 1617
DOI: 10.1039/b904960f Enhanced HTML article available
Prediction of protein–protein interactions between Helicobacter pylori and a human host
Nidhi Tyagi, Oruganty Krishnadev and Narayanaswamy Srinivasan,
Mol. BioSyst., 2009, 5, 1630
DOI: 10.1039/b906543c Enhanced HTML article available
Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins
Lakshminarayan M. Iyer, Saraswathi Abhiman, A. Maxwell Burroughs and L. Aravind,
Mol. BioSyst., 2009, 5, 1636
DOI: 10.1039/b917682a
Integration of signals from the B-cell antigen receptor and the IL-4 receptor leads to a cooperative shift in the cellular response axis
Nooshin Aflakian, Srikanth Ravichandran, Md. Sarwar Jamal, Henna Jarvenpaa, Riitta Lahesmaa and Kanury V. S. Rao,
Mol. BioSyst., 2009, 5, 1661
DOI: 10.1039/b901992h Enhanced HTML article available
Predicting essential genes based on network and sequence analysis
Yih-Chii Hwang, Chen-Ching Lin, Jen-Yun Chang, Hirotada Mori, Hsueh-Fen Juan and Hsuan-Cheng Huang,
Mol. BioSyst., 2009, 5, 1672
DOI: 10.1039/b900611g Enhanced HTML article available
Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing
Jian Feng, Daniel Q. Naiman and Bret Cooper,
Mol. BioSyst., 2009, 5, 1679
DOI: 10.1039/b903031j Enhanced HTML article available
Analysis of structured and intrinsically disordered regions of transmembrane proteins
Bin Xue, Liwei Li, Samy O. Meroueh, Vladimir N. Uversky and A. Keith Dunker,
Mol. BioSyst., 2009, 5, 1688
DOI: 10.1039/b905913j Enhanced HTML article available
Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals
Kangkan Halder, Rashi Halder and Shantanu Chowdhury,
Mol. BioSyst., 2009, 5, 1703
DOI: 10.1039/b905132e Enhanced HTML article available
Stable G-quadruplexes are found outside nucleosome-bound regions
Han Min Wong and Julian Leon Huppert,
Mol. BioSyst., 2009, 5, 1713
DOI: 10.1039/b905848f Enhanced HTML article available
A dependency graph approach for the analysis of differential gene expression profiles
Andreas Bernthaler, Irmgard Mühlberger, Raul Fechete, Paul Perco, Arno Lukas and Bernd Mayer,
Mol. BioSyst., 2009, 5, 1720
DOI: 10.1039/b903109j Enhanced HTML article available
A network-based method for predicting gene–nutrient interactions and its application to yeast amino-acid metabolism
Idit Diamant, Yonina C. Eldar, Oleg Rokhlenko, Eytan Ruppin and Tomer Shlomi,
Mol. BioSyst., 2009, 5, 1732
DOI: 10.1039/b823287n Enhanced HTML article available
Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis
Karthik Raman, Rohit Vashisht and Nagasuma Chandra,
Mol. BioSyst., 2009, 5, 1740
DOI: 10.1039/b905817f Enhanced HTML article available
Unraveling the potential of intrinsically disordered proteins as drug targets: application to Mycobacterium tuberculosis
Meenakshi Anurag and Debasis Dash,
Mol. BioSyst., 2009, 5, 1752
DOI: 10.1039/b905518p Enhanced HTML article available
Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition
Vetriselvi Rangannan and Manju Bansal,
Mol. BioSyst., 2009, 5, 1758
DOI: 10.1039/b906535k Enhanced HTML article available
Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example
Nurcan Tuncbag, Gozde Kar, Attila Gursoy, Ozlem Keskin and Ruth Nussinov,
Mol. BioSyst., 2009, 5, 1770
DOI: 10.1039/b905661k Enhanced HTML article available
Energy based approach for understanding the recognition mechanism in protein–protein complexes
M. Michael Gromiha, Kiyonobu Yokota and Kazuhiko Fukui,
Mol. BioSyst., 2009, 5, 1779
DOI: 10.1039/b904161n Enhanced HTML article available
Modular logical modelling of the budding yeast cell cycle
Adrien Fauré, Aurélien Naldi, Fabrice Lopez, Claudine Chaouiya, Andrea Ciliberto and Denis Thieffry,
Mol. BioSyst., 2009, 5, 1787
DOI: 10.1039/b910101m Enhanced HTML article available
Dissection of USP catalytic domains reveals five common insertion points
Yu Ye, Hartmut Scheel, Kay Hofmann and David Komander,
Mol. BioSyst., 2009, 5, 1797
DOI: 10.1039/b907669g Enhanced HTML article available
Signaling network analysis of ubiquitin-mediated proteins suggests correlations between the 26S proteasome and tumor progression
Cong Fu, Jie Li and Edwin Wang,
Mol. BioSyst., 2009, 5, 1809
DOI: 10.1039/b905382d Enhanced HTML article available
Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development
Vanessa Vermeirssen, Anagha Joshi, Tom Michoel, Eric Bonnet, Tine Casneuf and Yves Van de Peer,
Mol. BioSyst., 2009, 5, 1817
DOI: 10.1039/b908108a Enhanced HTML article available
A c-Myc regulatory subnetwork from human transposable element sequences
Jianrong Wang, Nathan J. Bowen, Leonardo Mariño-Ramírez and I. King Jordan,
Mol. BioSyst., 2009, 5, 1831
DOI: 10.1039/b908494k Enhanced HTML article available
Inferring the transcriptional network of Bacillus subtilis
Abeer Fadda, Ana Carolina Fierro, Karen Lemmens, Pieter Monsieurs, Kristof Engelen and Kathleen Marchal,
Mol. BioSyst., 2009, 5, 1840
DOI: 10.1039/b907310h Enhanced HTML article available
Signal amplification in a lattice of coupled protein kinases
Jacki P. Goldman, Matthew D. Levin and Dennis Bray,
Mol. BioSyst., 2009, 5, 1853
DOI: 10.1039/b903397a Enhanced HTML article available
Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks
Priti Hansia, Amit Ghosh and Saraswathi Vishveshwara,
Mol. BioSyst., 2009, 5, 1860
DOI: 10.1039/b903807h Enhanced HTML article available
Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations
Gian Gaetano Tartaglia and Michele Vendruscolo,
Mol. BioSyst., 2009, 5, 1873
DOI: 10.1039/b913099n Enhanced HTML article available
Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding
Karuppiah Kanagarajadurai, Manoharan Malini, Aditi Bhattacharya, Mitradas M. Panicker and Ramanathan Sowdhamini,
Mol. BioSyst., 2009, 5, 1877
DOI: 10.1039/b906391a Enhanced HTML article available
An integrative approach towards completing genome-scale metabolic networks
Nils Christian, Patrick May, Stefan Kempa, Thomas Handorf and Oliver Ebenhöh,
Mol. BioSyst., 2009, 5, 1889
DOI: 10.1039/b915913b Enhanced HTML article available
DNA supercoiling regulates the stress-inducible expression of genes in the cyanobacterium Synechocystis
Jogadhenu S. S. Prakash, Maria Sinetova, Anna Zorina, Elena Kupriyanova, Iwane Suzuki, Norio Murata and Dmitry A. Los,
Mol. BioSyst., 2009, 5, 1904
DOI: 10.1039/b903022k Enhanced HTML article available
A metabolomic and multivariate statistical process to assess the effects of genotoxins in Saccharomycescerevisiae
Christopher M. Titman, Jessica A. Downs, Stephen G. Oliver, Paul L. Carmichael, Andrew D. Scott and Julian L. Griffin,
Mol. BioSyst., 2009, 5, 1913
DOI: 10.1039/b907754e Enhanced HTML article available
The ABC of reverse engineering biological signalling systems
Maria Secrier, Tina Toni and Michael P. H. Stumpf,
Mol. BioSyst., 2009, 5, 1925
DOI: 10.1039/b908951a
Prediction of conditional gene essentiality through graph theoretical analysis of genome-wide functional linkages
P. Manimaran, Shubhada R. Hegde and Shekhar C. Mande,
Mol. BioSyst., 2009, 5, 1936
DOI: 10.1039/b905264j Enhanced HTML article available
A global view of Escherichia coli Rsd protein and its interactions
Sarah E. Piper, Jennie E. Mitchell, David J. Lee and Stephen J. W. Busby,
Mol. BioSyst., 2009, 5, 1943
DOI: 10.1039/b904955j Enhanced HTML article available
Back matter
Mol. BioSyst., 2009, 5, 1948
DOI: 10.1039/B922403N
Back cover
Mol. BioSyst., 2009, 5, 1951
DOI: 10.1039/b922404c
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