Volume 7; Issue 1

Molecular Systems Biology

Volume 7; Issue 1

1

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

Chang, R. L., Ghamsari, L., Manichaikul, A., Hom, E. F. Y., Balaji, S., Fu, W., Shen, Y., Hao, T., Palsson, B. O., Salehi-Ashtiani, K., Papin, J. A.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 2.22 MB

english, 2014

2

Oncogenic K-Ras decouples glucose and glutamine metabolism to support cancer cell growth

Gaglio, D., Metallo, C. M., Gameiro, P. A., Hiller, K., Danna, L. S., Balestrieri, C., Alberghina, L., Stephanopoulos, G., Chiaradonna, F.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 887 KB

english, 2014

3

Glucose metabolism determines resistance of cancer cells to bioenergetic crisis after cytochrome-c release

Huber, H. J., Dussmann, H., Kilbride, S. M., Rehm, M., Prehn, J. H. M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 825 KB

english, 2014

4

Deep proteome and transcriptome mapping of a human cancer cell line

Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Paabo, S., Mann, M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 983 KB

english, 2014

5

Social interaction in synthetic and natural microbial communities

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 5.22 MB

english, 2014

6

Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

Costenoble, R., Picotti, P., Reiter, L., Stallmach, R., Heinemann, M., Sauer, U., Aebersold, R.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 730 KB

english, 2014

7

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

Haverkorn van Rijsewijk, B. R. B., Nanchen, A., Nallet, S., Kleijn, R. J., Sauer, U.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 951 KB

english, 2014

8

Microbial laboratory evolution in the era of genome-scale science

Conrad, T. M., Lewis, N. E., Palsson, B. O.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 731 KB

english, 2014

9

Structural and functional protein network analyses predict novel signaling functions for rhodopsin

Kiel, C., Vogt, A., Campagna, A., Chatr-aryamontri, A., Swiatek-de Lange, M., Beer, M., Bolz, S., Mack, A. F., Kinkl, N., Cesareni, G., Serrano, L., Ueffing, M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 4.17 MB

english, 2014

10

Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis

Klopffleisch, K., Phan, N., Augustin, K., Bayne, R. S., Booker, K. S., Botella, J. R., Carpita, N. C., Carr, T., Chen, J.-G., Cooke, T. R., Frick-Cheng, A., Friedman, E. J., Fulk, B., Hahn, M. G., Jia

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.36 MB

english, 2014

11

Algorithms in nature: the convergence of systems biology and computational thinking

Navlakha, S., Bar-Joseph, Z.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.18 MB

english, 2014

12

The essential genome of a bacterium

Christen, B., Abeliuk, E., Collier, J. M., Kalogeraki, V. S., Passarelli, B., Coller, J. A., Fero, M. J., McAdams, H. H., Shapiro, L.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.36 MB

english, 2014

13

Transcriptional activity regulates alternative cleavage and polyadenylation

Ji, Z., Luo, W., Li, W., Hoque, M., Pan, Z., Zhao, Y., Tian, B.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 3.02 MB

english, 2014

14

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

Munoz, J., Low, T. Y., Kok, Y. J., Chin, A., Frese, C. K., Ding, V., Choo, A., Heck, A. J. R.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 3.88 MB

english, 2014

15

Substrate-dependent control of MAPK phosphorylation in vivo

Kim, Y., Paroush, Z., Nairz, K., Hafen, E., Jimenez, G., Shvartsman, S. Y.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 2.16 MB

english, 2014

16

A panorama of mammalian gene expression evolution

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 101 KB

english, 2014

17

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Soding, J., Thompson, J. D., Higgins, D. G.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 448 KB

english, 2014

18

Determinants of translation efficiency and accuracy

Gingold, H., Pilpel, Y.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.85 MB

english, 2014

19

Systematic exploration of synergistic drug pairs

Cokol, M., Chua, H. N., Tasan, M., Mutlu, B., Weinstein, Z. B., Suzuki, Y., Nergiz, M. E., Costanzo, M., Baryshnikova, A., Giaever, G., Nislow, C., Myers, C. L., Andrews, B. J., Boone, C., Roth, F. P.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.52 MB

english, 2014

20

Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole

Spitzer, M., Griffiths, E., Blakely, K. M., Wildenhain, J., Ejim, L., Rossi, L., De Pascale, G., Curak, J., Brown, E., Tyers, M., Wright, G. D.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.81 MB

english, 2014

21

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

Kim, H. U., Kim, S. Y., Jeong, H., Kim, T. Y., Kim, J. J., Choy, H. E., Yi, K. Y., Rhee, J. H., Lee, S. Y.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 3.26 MB

english, 2014

22

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling

Alic, N., Andrews, T. D., Giannakou, M. E., Papatheodorou, I., Slack, C., Hoddinott, M. P., Cocheme, H. M., Schuster, E. F., Thornton, J. M., Partridge, L.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 830 KB

english, 2014

23

PREDICT: a method for inferring novel drug indications with application to personalized medicine

Gottlieb, A., Stein, G. Y., Ruppin, E., Sharan, R.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 290 KB

english, 2014

24

The auxin signalling network translates dynamic input into robust patterning at the shoot apex

Vernoux, T., Brunoud, G., Farcot, E., Morin, V., Van den Daele, H., Legrand, J., Oliva, M., Das, P., Larrieu, A., Wells, D., Guedon, Y., Armitage, L., Picard, F., Guyomarc'h, S., Cellier, C., Parry, G

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 743 KB

english, 2014

25

Programming an in vitro DNA oscillator using a molecular networking strategy

Montagne, K., Plasson, R., Sakai, Y., Fujii, T., Rondelez, Y.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 365 KB

english, 2014

26

Towards the prediction of protein interaction partners using physical docking

Wass, M. N., Fuentes, G., Pons, C., Pazos, F., Valencia, A.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 331 KB

english, 2014

27

Network modeling of the transcriptional effects of copy number aberrations in glioblastoma

Jornsten, R., Abenius, T., Kling, T., Schmidt, L., Johansson, E., Nordling, T. E. M., Nordlander, B., Sander, C., Gennemark, P., Funa, K., Nilsson, B., Lindahl, L., Nelander, S.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 670 KB

english, 2014

28

Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli

Tsuru, S., Yasuda, N., Murakami, Y., Ushioda, J., Kashiwagi, A., Suzuki, S., Mori, K., Ying, B.-W., Yomo, T.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 392 KB

english, 2014

29

AlleleSeq: analysis of allele-specific expression and binding in a network framework

Rozowsky, J., Abyzov, A., Wang, J., Alves, P., Raha, D., Harmanci, A., Leng, J., Bjornson, R., Kong, Y., Kitabayashi, N., Bhardwaj, N., Rubin, M., Snyder, M., Gerstein, M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 290 KB

english, 2014

30

Engineering microbial biofuel tolerance and export using efflux pumps

Dunlop, M. J., Dossani, Z. Y., Szmidt, H. L., Chu, H. C., Lee, T. S., Keasling, J. D., Hadi, M. Z., Mukhopadhyay, A.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 218 KB

english, 2014

31

Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis

Aldridge, B. B., Gaudet, S., Lauffenburger, D. A., Sorger, P. K.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 625 KB

english, 2014

32

A synthetic library of RNA control modules for predictable tuning of gene expression in yeast

Babiskin, A. H., Smolke, C. D.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 259 KB

english, 2014

33

Predicting selective drug targets in cancer through metabolic networks

Folger, O., Jerby, L., Frezza, C., Gottlieb, E., Ruppin, E., Shlomi, T.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 415 KB

english, 2014

34

Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

Saeidi, N., Wong, C. K., Lo, T.-M., Nguyen, H. X., Ling, H., Leong, S. S. J., Poh, C. L., Chang, M. W.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 625 KB

english, 2014

35

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

Hebenstreit, D., Fang, M., Gu, M., Charoensawan, V., van Oudenaarden, A., Teichmann, S. A.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 353 KB

english, 2014

36

Toward an understanding of the protein interaction network of the human liver

Wang, J., Huo, K., Ma, L., Tang, L., Li, D., Huang, X., Yuan, Y., Li, C., Wang, W., Guan, W., Chen, H., Jin, C., Wei, J., Zhang, W., Yang, Y., Liu, Q., Zhou, Y., Zhang, C., Wu, Z., Xu, W., Zhang, Y.,

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.15 MB

english, 2014

37

Recycling, clustering, and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane

Kleine-Vehn, J., Wabnik, K., Martiniere, A., angowski, ukasz, Willig, K., Naramoto, S., Leitner, J., Tanaka, H., Jakobs, S., Robert, S., Luschnig, C., Govaerts, W., W Hell, S., Runions, J., Friml, J

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 606 KB

english, 2014

38

Retrieval, alignment, and clustering of computational models based on semantic annotations

Schulz, M., Krause, F., Le Novere, N., Klipp, E., Liebermeister, W.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 615 KB

english, 2014

39

An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling

Sciammas, R., Li, Y., Warmflash, A., Song, Y., Dinner, A. R., Singh, H.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 567 KB

english, 2014

40

Niche adaptation by expansion and reprogramming of general transcription factors

Turkarslan, S., Reiss, D. J., Gibbins, G., Su, W. L., Pan, M., Bare, J. C., Plaisier, C. L., Baliga, N. S.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.34 MB

english, 2014

41

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., Nam, H., Feist, A. M., Palsson, B. O.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 174 KB

english, 2014

42

Human metabolic profiles are stably controlled by genetic and environmental variation

Nicholson, G., Rantalainen, M., Maher, A. D., Li, J. V., Malmodin, D., Ahmadi, K. R., Faber, J. H., Hallgrimsdottir, I. B., Barrett, A., Toft, H., Krestyaninova, M., Viksna, J., Neogi, S. G., Dumas, M

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 228 KB

english, 2014

43

Synthetic in vitro transcriptional oscillators

Kim, J., Winfree, E.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 650 KB

english, 2014

44

Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template

Bleris, L., Xie, Z., Glass, D., Adadey, A., Sontag, E., Benenson, Y.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 397 KB

english, 2014

45

Analysis of multiple compound-protein interactions reveals novel bioactive molecules

Yabuuchi, H., Niijima, S., Takematsu, H., Ida, T., Hirokawa, T., Hara, T., Ogawa, T., Minowa, Y., Tsujimoto, G., Okuno, Y.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 368 KB

english, 2014

46

The quantitative proteome of a human cell line

Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., Aebersold, R.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 248 KB

english, 2014

47

Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing

Smith, J. J., Miller, L. R., Kreisberg, R., Vazquez, L., Wan, Y., Aitchison, J. D.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 398 KB

english, 2014

48

Programming an in vitro DNA oscillator using a molecular networking strategy

Montagne, K., Plasson, R., Sakai, Y., Fujii, T., Rondelez, Y.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 158 KB

english, 2014

49

Translation's coming of age

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 120 KB

english, 2014

50

Predicting selective drug targets in cancer through metabolic networks

Folger, O., Jerby, L., Frezza, C., Gottlieb, E., Ruppin, E., Shlomi, T.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 46 KB

english, 2014

51

A regression model approach to enable cell morphology correction in high-throughput flow cytometry

Knijnenburg, T. A., Roda, O., Wan, Y., Nolan, G. P., Aitchison, J. D., Shmulevich, I.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.51 MB

english, 2014

52

Controlled vocabularies and semantics in systems biology

Courtot, M., Juty, N., Knupfer, C., Waltemath, D., Zhukova, A., Drager, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., Hoops, S., Keating, S., Kell, D. B., Kerrien, S., Lawson, J., List

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 355 KB

english, 2014

53

Antisense expression increases gene expression variability and locus interdependency

Xu, Z., Wei, W., Gagneur, J., Clauder-Munster, S., Smolik, M., Huber, W., Steinmetz, L. M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 349 KB

english, 2014

54

The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation

Caron, E., Vincent, K., Fortier, M.-H., Laverdure, J.-P., Bramoulle, A., Hardy, M.-P., Voisin, G., Roux, P. P., Lemieux, S., Thibault, P., Perreault, C.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 3.01 MB

english, 2014

55

Self-organized partitioning of dynamically localized proteins in bacterial cell division

Di Ventura, B., Sourjik, V.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 990 KB

english, 2014

56

Metabolic modeling of endosymbiont genome reduction on a temporal scale

Yizhak, K., Tuller, T., Papp, B., Ruppin, E.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 250 KB

english, 2014

57

Quantification of mRNA and protein and integration with protein turnover in a bacterium

Maier, T., Schmidt, A., Guell, M., Kuhner, S., Gavin, A.-C., Aebersold, R., Serrano, L.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 330 KB

english, 2014

58

Alternative splicing variability: exactly how similar are two identical cells?

Perriman, R. J., Ares, M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

59

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs

Wessely, F., Bartl, M., Guthke, R., Li, P., Schuster, S., Kaleta, C.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 294 KB

english, 2014

60

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

Glatter, T., Schittenhelm, R. B., Rinner, O., Roguska, K., Wepf, A., Junger, M. A., Kohler, K., Jevtov, I., Choi, H., Schmidt, A., Nesvizhskii, A. I., Stocker, H., Hafen, E., Aebersold, R., Gstaiger,

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

61

Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe

Bitton, D. A., Grallert, A., Scutt, P. J., Yates, T., Li, Y., Bradford, J. R., Hey, Y., Pepper, S. D., Hagan, I. M., Miller, C. J.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 959 KB

english, 2014

62

Cellular reprogramming by the conjoint action of ER , FOXA1, and GATA3 to a ligand-inducible growth state

Kong, S. L., Li, G., Loh, S. L., Sung, W.-K., Liu, E. T.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 405 KB

english, 2014

63

Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi

Teng, S.-W., Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., Wingreen, N. S.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 485 KB

english, 2014

64

Proteomic snapshot of the EGF-induced ubiquitin network

Argenzio, E., Bange, T., Oldrini, B., Bianchi, F., Peesari, R., Mari, S., Di Fiore, P. P., Mann, M., Polo, S.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 813 KB

english, 2014

65

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

Lee, M. V., Topper, S. E., Hubler, S. L., Hose, J., Wenger, C. D., Coon, J. J., Gasch, A. P.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 407 KB

english, 2014

66

A stele-enriched gene regulatory network in the Arabidopsis root

Brady, S. M., Zhang, L., Megraw, M., Martinez, N. J., Jiang, E., Yi, C. S., Liu, W., Zeng, A., Taylor-Teeples, M., Kim, D., Ahnert, S., Ohler, U., Ware, D., Walhout, A. J. M., Benfey, P. N.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 379 KB

english, 2014

67

Synthetic conversion of a graded receptor signal into a tunable, reversible switch

Palani, S., Sarkar, C. A.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 277 KB

english, 2014

68

Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range

Bachmann, J., Raue, A., Schilling, M., Bohm, M. E., Kreutz, C., Kaschek, D., Busch, H., Gretz, N., Lehmann, W. D., Timmer, J., Klingmuller, U.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.42 MB

english, 2014

69

Stimulus-dependent dynamics of p53 in single cells

Batchelor, E., Loewer, A., Mock, C., Lahav, G.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 252 KB

english, 2014

70

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

Miller, C., Schwalb, B., Maier, K., Schulz, D., Dumcke, S., Zacher, B., Mayer, A., Sydow, J., Marcinowski, L., Dolken, L., Martin, D. E., Tresch, A., Cramer, P.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 818 KB

english, 2014

71

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli

Zeisel, A., Kostler, W. J., Molotski, N., Tsai, J. M., Krauthgamer, R., Jacob-Hirsch, J., Rechavi, G., Soen, Y., Jung, S., Yarden, Y., Domany, E.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.46 MB

english, 2014

72

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics

Mendoza-Parra, M. A., Walia, M., Sankar, M., Gronemeyer, H.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 747 KB

english, 2014

73

Economics of membrane occupancy and respiro-fermentation

Zhuang, K., Vemuri, G. N., Mahadevan, R.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 377 KB

english, 2014

74

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes

Lee, K. K., Sardiu, M. E., Swanson, S. K., Gilmore, J. M., Torok, M., Grant, P. A., Florens, L., Workman, J. L., Washburn, M. P.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 302 KB

english, 2014

75

Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions

Prabakaran, S., Everley, R. A., Landrieu, I., Wieruszeski, J.-M., Lippens, G., Steen, H., Gunawardena, J.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 429 KB

english, 2014

76

The multiple-specificity landscape of modular peptide recognition domains

Gfeller, D., Butty, F., Wierzbicka, M., Verschueren, E., Vanhee, P., Huang, H., Ernst, A., Dar, N., Stagljar, I., Serrano, L., Sidhu, S. S., Bader, G. D., Kim, P. M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.52 MB

english, 2014

77

Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques

Su, W.-L., Kleinhanz, R. R., Schadt, E. E.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 205 KB

english, 2014

78

A pharmacogenomic method for individualized prediction of drug sensitivity

Cohen, A. L., Soldi, R., Zhang, H., Gustafson, A. M., Wilcox, R., Welm, B. E., Chang, J. T., Johnson, E., Spira, A., Jeffrey, S. S., Bild, A. H.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 619 KB

english, 2014

79

Predicting selective drug targets in cancer through metabolic networks

Folger, O., Jerby, L., Frezza, C., Gottlieb, E., Ruppin, E., Shlomi, T.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 52 KB

english, 2014

80

Suppressing variation in synthetic circuits

Batchelor, E., Lahav, G.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 104 KB

english, 2014

81

A novel strategy for the comprehensive analysis of the biomolecular composition of isolated plasma membranes

Thimiri Govinda Raj, D. B., Ghesquiere, B., Tharkeshwar, A. K., Coen, K., Derua, R., Vanderschaeghe, D., Rysman, E., Bagadi, M., Baatsen, P., De Strooper, B., Waelkens, E., Borghs, G., Callewaert, N.,

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 665 KB

english, 2014

82

Protein localization as a principal feature of the etiology and comorbidity of genetic diseases

Park, S., Yang, J.-S., Shin, Y.-E., Park, J., Jang, S. K., Kim, S.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 447 KB

english, 2014

83

Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico

Moriya, H., Chino, A., Kapuy, O., Csikasz-Nagy, A., Novak, B.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 741 KB

english, 2014

84

Environmental and genetic perturbations reveal different networks of metabolic regulation

Greenberg, A. J., Hackett, S. R., Harshman, L. G., Clark, A. G.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 683 KB

english, 2014

85

Quantitative analysis of transient and sustained transforming growth factor- signaling dynamics

Zi, Z., Feng, Z., Chapnick, D. A., Dahl, M., Deng, D., Klipp, E., Moustakas, A., Liu, X.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 654 KB

english, 2014

86

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

Raes, J., Letunic, I., Yamada, T., Jensen, L. J., Bork, P.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 213 KB

english, 2014

87

Rewiring makes the difference

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

88

Proteome-wide systems analysis of a cellulosic biofuel-producing microbe

Tolonen, A. C., Haas, W., Chilaka, A. C., Aach, J., Gygi, S. P., Church, G. M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.07 MB

english, 2014

89

Strong negative feedback from Erk to Raf confers robustness to MAPK signalling

Fritsche-Guenther, R., Witzel, F., Sieber, A., Herr, R., Schmidt, N., Braun, S., Brummer, T., Sers, C., Bluthgen, N.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 282 KB

english, 2014

90

Temporal competition between differentiation programs determines cell fate choice

Kuchina, A., Espinar, L., Cagatay, T., Balbin, A. O., Zhang, F., Alvarado, A., Garcia-Ojalvo, J., Suel, G. M.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 331 KB

english, 2014

91

Queueing up for enzymatic processing: correlated signaling through coupled degradation

Cookson, N. A., Mather, W. H., Danino, T., Mondragon-Palomino, O., Williams, R. J., Tsimring, L. S., Hasty, J.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 339 KB

english, 2014

92

Transcriptional control of metabolic fluxes

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

93

The self-assessment trap: can we all be better than average?

Norel, R., Rice, J. J., Stolovitzky, G.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 82 KB

english, 2014

94

5-Hydroxymethylcytosine: a new kid on the epigenetic block?

Matarese, F., Carrillo-de Santa Pau, E., Stunnenberg, H. G.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 346 KB

english, 2014

95

Inferring regulatory mechanisms from patterns of evolutionary divergence

Tirosh, I., Barkai, N.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 459 KB

english, 2014

96

Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation

Kratochvill, F., Machacek, C., Vogl, C., Ebner, F., Sedlyarov, V., Gruber, A. R., Hartweger, H., Vielnascher, R., Karaghiosoff, M., Rulicke, T., Muller, M., Hofacker, I., Lang, R., Kovarik, P.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 344 KB

english, 2014

97

RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42

Misselwitz, B., Dilling, S., Vonaesch, P., Sacher, R., Snijder, B., Schlumberger, M., Rout, S., Stark, M., von Mering, C., Pelkmans, L., Hardt, W.-D.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 686 KB

english, 2014

98

Origin of bistability underlying mammalian cell cycle entry

Yao, G., Tan, C., West, M., Nevins, J. R., You, L.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 285 KB

english, 2014

99

Carbohydrate-active enzymes exemplify entropic principles in metabolism

Kartal, O., Mahlow, S., Skupin, A., Ebenhoh, O.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 323 KB

english, 2014

100

Fleeting hormone cues get stabilized for plant organogenesis

Sauer, M., Friml, J.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 111 KB

english, 2014

101

Winner takes all in a race for cell fate

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 68 KB

english, 2014

102

Adapt locally and act globally: strategy to maintain high chemoreceptor sensitivity in complex environments

Lan, G., Schulmeister, S., Sourjik, V., Tu, Y.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 648 KB

english, 2014

103

Cell-to-cell variability of alternative RNA splicing

Waks, Z., Klein, A. M., Silver, P. A.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 352 KB

english, 2014

104

Phosphorylation network rewiring by gene duplication

Freschi, L., Courcelles, M., Thibault, P., Michnick, S. W., Landry, C. R.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 201 KB

english, 2014

105

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

Zhang, J., Vaga, S., Chumnanpuen, P., Kumar, R., Vemuri, G. N., Aebersold, R., Nielsen, J.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 217 KB

english, 2014

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