Volume 5; Issue 12

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Molecular BioSystems
Volume 5; Issue 12

Molecular BioSystems

Volume 5; Issue 12

1

ChIPing away at the genome: the new frontier travel guide

Aleksic, Jelena, Russell, Steven

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.52 MB

english, 2009

2

Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes

Babu, Mohan, Musso, Gabriel, Díaz-Mejía, J. Javier, Butland, Gareth, Greenblatt, Jack F., Emili, Andrew

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.14 MB

english, 2009

3

The potential of microfluidic water-in-oil droplets in experimental biology

Schaerli, Yolanda, Hollfelder, Florian

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.60 MB

english, 2009

4

The powerful law of the power law and other myths in network biology

Lima-Mendez, Gipsi, van Helden, Jacques

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.08 MB

english, 2009

5

Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks

Hansia, Priti, Ghosh, Amit, Vishveshwara, Saraswathi

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.94 MB

english, 2009

6

Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing

Feng, Jian, Naiman, Daniel Q., Cooper, Bret

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.27 MB

english, 2009

7

Stable G-quadruplexes are found outside nucleosome-bound regions

Wong, Han Min, Huppert, Julian Leon

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.62 MB

english, 2009

8

Predicting essential genes based on network and sequence analysis

Hwang, Yih-Chii, Lin, Chen-Ching, Chang, Jen-Yun, Mori, Hirotada, Juan, Hsueh-Fen, Huang, Hsuan-Cheng

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.67 MB

english, 2009

9

Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development

Vermeirssen, Vanessa, Joshi, Anagha, Michoel, Tom, Bonnet, Eric, Casneuf, Tine, Van de Peer, Yves

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.92 MB

english, 2009

10

Supervised learning with decision tree-based methods in computational and systems biology

Geurts, Pierre, Irrthum, Alexandre, Wehenkel, Louis

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 4.25 MB

english, 2009

11

Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition

Rangannan, Vetriselvi, Bansal, Manju

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.37 MB

english, 2009

12

Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding

Kanagarajadurai, Karuppiah, Malini, Manoharan, Bhattacharya, Aditi, Panicker, Mitradas M., Sowdhamini, Ramanathan

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.51 MB

english, 2009

13

Conformational averaging in structural biology: issues, challenges and computational solutions

Kruschel, Daniela, Zagrovic, Bojan

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.76 MB

english, 2009

14

DNA supercoiling regulates the stress-inducible expression of genes in the cyanobacterium Synechocystis

Prakash, Jogadhenu S. S., Sinetova, Maria, Zorina, Anna, Kupriyanova, Elena, Suzuki, Iwane, Murata, Norio, Los, Dmitry A.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.06 MB

english, 2009

15

Theoretical models of spontaneous activity generation and propagation in the developing retina

Godfrey, Keith B., Eglen, Stephen J.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.83 MB

english, 2009

16

Prediction of protein–protein interactions between Helicobacter pylori and a human host

Tyagi, Nidhi, Krishnadev, Oruganty, Srinivasan, Narayanaswamy

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.51 MB

english, 2009

17

Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis

Raman, Karthik, Vashisht, Rohit, Chandra, Nagasuma

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.32 MB

english, 2009

18

An integrative approach towards completing genome-scale metabolic networks

Christian, Nils, May, Patrick, Kempa, Stefan, Handorf, Thomas, Ebenhöh, Oliver

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.43 MB

english, 2009

19

Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics

Lee, Semin, Brown, Alan, Pitt, William Ross, Higueruelo, Alicia Perez, Gong, Sungsam, Bickerton, George Richard, Schreyer, Adrian, Tanramluk, Duangrudee, Baylay, Alison, Blundell, Tom Leon

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 3.40 MB

english, 2009

20

Structure and organization of drug-target networks: insights from genomic approaches for drug discovery

Janga, Sarath Chandra, Tzakos, Andreas

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.00 MB

english, 2009

21

A dependency graph approach for the analysis of differential gene expression profiles

Bernthaler, Andreas, Mühlberger, Irmgard, Fechete, Raul, Perco, Paul, Lukas, Arno, Mayer, Bernd

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.90 MB

english, 2009

22

Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

Tuncbag, Nurcan, Kar, Gozde, Gursoy, Attila, Keskin, Ozlem, Nussinov, Ruth

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.78 MB

english, 2009

23

Signal initiation in biological systems: the properties and detection of transient extracellular protein interactions

Wright, Gavin J.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.73 MB

english, 2009

24

Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins

Iyer, Lakshminarayan M., Abhiman, Saraswathi, Maxwell Burroughs, A., Aravind, L.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 5.26 MB

english, 2009

25

Energy based approach for understanding the recognition mechanism in protein–protein complexes

Michael Gromiha, M., Yokota, Kiyonobu, Fukui, Kazuhiko

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.99 MB

english, 2009

26

Inside front cover

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 430 KB

english, 2009

27

Systems analyses of circadian networks

Hubbard, Katharine E., Robertson, Fiona C., Dalchau, Neil, Webb, Alex A. R.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.05 MB

english, 2009

28

A global view of Escherichia coli Rsd protein and its interactions

Piper, Sarah E., Mitchell, Jennie E., Lee, David J., Busby, Stephen J. W.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.05 MB

english, 2009

29

Scaling relationship in the gene content of transcriptional machinery in bacteria

Pérez-Rueda, Ernesto, Janga, Sarath Chandra, Martínez-Antonio, Agustino

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.23 MB

english, 2009

30

Front cover

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 207 KB

english, 2009

31

Logical modelling of cell cycle control in eukaryotes: a comparative study

Fauré, Adrien, Thieffry, Denis

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.07 MB

english, 2009

32

Contents and Highlights in Chemical Biology

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 5.30 MB

english, 2009

33

Prediction of conditional gene essentiality through graph theoretical analysis of genome-wide functional linkages

Manimaran, P., Hegde, Shubhada R., Mande, Shekhar C.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.13 MB

english, 2009

34

Back matter

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 754 KB

english, 2009

35

Analysis of structured and intrinsically disordered regions of transmembrane proteins

Xue, Bin, Li, Liwei, Meroueh, Samy O., Uversky, Vladimir N., Dunker, A. Keith

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.82 MB

english, 2009

36

Nucleosome positioning—what do we really know?

Travers, Andrew, Caserta, Micaela, Churcher, Mark, Hiriart, Edwige, Di Mauro, Ernesto

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.09 MB

english, 2009

37

On the basic computational structure of gene regulatory networks

Rodríguez-Caso, Carlos, Corominas-Murtra, Bernat, Solé, Ricard V.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.73 MB

english, 2009

38

Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals

Halder, Kangkan, Halder, Rashi, Chowdhury, Shantanu

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.91 MB

english, 2009

39

The ABC of reverse engineering biological signalling systems

Secrier, Maria, Toni, Tina, Stumpf, Michael P. H.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.86 MB

english, 2009

40

Dissection of USP catalytic domains reveals five common insertion points

Ye, Yu, Scheel, Hartmut, Hofmann, Kay, Komander, David

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 4.24 MB

english, 2009

41

Modelling the Drosophila embryo

Jaeger, Johannes

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.77 MB

english, 2009

42

Back cover

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 545 KB

english, 2009

43

From genes to cells to tissues—modelling the haematopoietic system

Foster, Samuel D., Oram, S. Helen, Wilson, Nicola K., Göttgens, Berthold

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.23 MB

english, 2009

44

Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations

Tartaglia, Gian Gaetano, Vendruscolo, Michele

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.66 MB

english, 2009

45

Signaling network analysis of ubiquitin-mediated proteins suggests correlations between the 26S proteasome and tumor progression

Fu, Cong, Li, Jie, Wang, Edwin

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.99 MB

english, 2009

46

A network-based method for predicting gene–nutrient interactions and its application to yeast amino-acid metabolism

Diamant, Idit, Eldar, Yonina C., Rokhlenko, Oleg, Ruppin, Eytan, Shlomi, Tomer

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.59 MB

english, 2009

47

Unraveling the potential of intrinsically disordered proteins as drug targets: application to Mycobacterium tuberculosis

Anurag, Meenakshi, Dash, Debasis

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.73 MB

english, 2009

48

Computational and Systems Biology

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 916 KB

english, 2009

49

Explorations in topology–delving underneath the surface of genetic interaction maps

Breker, Michal, Schuldiner, Maya

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.02 MB

english, 2009

50

A c-Myc regulatory subnetwork from human transposable element sequences

Wang, Jianrong, Bowen, Nathan J., Mariño-Ramírez, Leonardo, Jordan, I. King

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.19 MB

english, 2009

51

Modular logical modelling of the budding yeast cell cycle

Fauré, Adrien, Naldi, Aurélien, Lopez, Fabrice, Chaouiya, Claudine, Ciliberto, Andrea, Thieffry, Denis

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.41 MB

english, 2009

52

Signal amplification in a lattice of coupled protein kinases

Goldman, Jacki P., Levin, Matthew D., Bray, Dennis

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.10 MB

english, 2009

53

Integration of signals from the B-cell antigen receptor and the IL-4 receptor leads to a cooperative shift in the cellular response axis

Aflakian, Nooshin, Ravichandran, Srikanth, Jamal, Md. Sarwar, Jarvenpaa, Henna, Lahesmaa, Riitta, Rao, Kanury V. S.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.45 MB

english, 2009

54

Inferring the transcriptional network of Bacillus subtilis

Fadda, Abeer, Fierro, Ana Carolina, Lemmens, Karen, Monsieurs, Pieter, Engelen, Kristof, Marchal, Kathleen

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.43 MB

english, 2009

55

A metabolomic and multivariate statistical process to assess the effects of genotoxins in Saccharomycescerevisiae

Titman, Christopher M., Downs, Jessica A., Oliver, Stephen G., Carmichael, Paul L., Scott, Andrew D., Griffin, Julian L.

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.62 MB

english, 2009

56

Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays

Fu, Audrey Qiuyan, Adryan, Boris

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 1.56 MB

english, 2009