Volume 9; Issue 1

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BMC Systems Biology
Volume 9; Issue 1

BMC Systems Biology

Volume 9; Issue 1

1

Annual acknowledgement of reviewers

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 266 KB

english, 2015

2

Positive regulation of Rho GTPase activity by RhoGDIs as a result of their direct interaction with GAPs

Ota, Takahide, Maeda, Masayo, Okamoto, Mayumi, Tatsuka, Masaaki

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.68 MB

english, 2015

3

Prediction of signaling cross-talks contributing to acquired drug resistance in breast cancer cells by Bayesian statistical modeling

Azad, AKM, Lawen, Alfons, Keith, Jonathan M

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.29 MB

english, 2015

4

Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina

Ye, Chao, Xu, Nan, Chen, Haiqin, Chen, Yong Q, Chen, Wei, Liu, Liming

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.44 MB

english, 2015

5

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

Villaverde, Alejandro F, Henriques, David, Smallbone, Kieran, Bongard, Sophia, Schmid, Joachim, Cicin-Sain, Damjan, Crombach, Anton, Saez-Rodriguez, Julio, Mauch, Klaus, Balsa-Canto, Eva, Mendes, Pedr

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 942 KB

english, 2015

6

microRNAs’ differential regulations mediate the progress of Human Papillomavirus (HPV)-induced Cervical Intraepithelial Neoplasia (CIN)

Mo, Wenjuan, Tong, Chao, Zhang, Yan, Lu, Hong

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.85 MB

english, 2015

7

Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity

Sridharan, Gautham, Ullah, Ehsan, Hassoun, Soha, Lee, Kyongbum

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 905 KB

english, 2015

8

A computational model of PKD and CERT interactions at the trans-Golgi network of mammalian cells

Weber, Patrick, Hornjik, Mariana, Olayioye, Monilola A, Hausser, Angelika, Radde, Nicole E

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.91 MB

english, 2015

9

Fluxome study of Pseudomonas fluorescens reveals major reorganisation of carbon flux through central metabolic pathways in response to inactivation of the anti-sigma factor MucA

Lien, Stina K, Niedenführ, Sebastian, Sletta, Håvard, Nöh, Katharina, Bruheim, Per

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.00 MB

english, 2015

10

Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells

Tendler, Avichai, Mayo, Avraham, Alon, Uri

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.56 MB

english, 2015

11

Mimoza: web-based semantic zooming and navigation in metabolic networks

Zhukova, Anna, Sherman, David J

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.39 MB

english, 2015

12

Time-dependent variation of pathways and networks in a 24-hour window after cerebral ischemia-reperfusion injury

Wang, Li-Ying, Liu, Jun, Li, Yuan, Li, Bing, Zhang, Ying-Ying, Jing, Zhi-Wei, Yu, Ya-Nan, Li, Hai-Xia, Guo, Shan-Shan, Zhao, Yi-Jun, Wang, Zhong, Wang, Yong-Yan

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.60 MB

english, 2015

13

Predicting internal cell fluxes at sub-optimal growth

Schultz, André, Qutub, Amina A

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.84 MB

english, 2015

14

Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks

Hasegawa, Takanori, Mori, Tomoya, Yamaguchi, Rui, Shimamura, Teppei, Miyano, Satoru, Imoto, Seiya, Akutsu, Tatsuya

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 934 KB

english, 2015

15

Spatially-resolved metabolic cooperativity within dense bacterial colonies

Cole, John A, Kohler, Lars, Hedhli, Jamila, Luthey-Schulten, Zaida

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.45 MB

english, 2015

16

Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome

Marin, Traci L, Gongol, Brendan, Martin, Marcy, King, Stephanie J, Smith, Lemar, Johnson, David A, Subramaniam, Shankar, Chien, Shu, Shyy, John

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.88 MB

english, 2015

17

Effects of promoter leakage on dynamics of gene expression

Huang, Lifang, Yuan, Zhanjiang, Liu, Peijiang, Zhou, Tianshou

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.00 MB

english, 2015

18

Robust network structure of the Sln1-Ypd1-Ssk1 three-component phospho-relay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae

Dexter, Joseph P, Xu, Ping, Gunawardena, Jeremy, McClean, Megan N

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.97 MB

english, 2015

19

Iron acquisition and oxidative stress response in aspergillus fumigatus

Brandon, Madison, Howard, Brad, Lawrence, Christopher, Laubenbacher, Reinhard

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.42 MB

english, 2015

20

Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression inEscherichia coli

K. P. Yousef, A. Streck, C. Schütte, H. Siebert, R. Hengge, M. V. Kleist

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.83 MB

english, 2015

21

CD8 + T cell response to adenovirus vaccination and subsequent suppression of tumor growth: modeling, simulation and analysis

Wang, Qing, J Klinke, David, Wang, Zhijun

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.79 MB

english, 2015

22

From ERα66 to ERα36: a generic method for validating a prognosis marker of breast tumor progression

Chamard-Jovenin, Clémence, Jung, Alain C., Chesnel, Amand, Abecassis, Joseph, Flament, Stéphane, Ledrappier, Sonia, Macabre, Christine, Boukhobza, Taha, Dumond, Hélène

Journal:

BMC Systems Biology

Year:

2015

File:

PDF, 1.04 MB

2015

23

Estimating cell diffusivity and cell proliferation rate by interpreting IncuCyte ZOOM™ assay data using the Fisher-Kolmogorov model

Johnston, Stuart T., Shah, Esha T., Chopin, Lisa K., Sean McElwain, D. L., Simpson, Matthew J.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 4.71 MB

english, 2015

24

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

Matos Simoes, Ricardo de, Dalleau, Sabine, Williamson, Kate E, Emmert-Streib, Frank

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.97 MB

english, 2015

25

Distinguishing the rates of gene activation from phenotypic variations

Chen, Ye, Lv, Cheng, Li, Fangting, Li, Tiejun

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.89 MB

english, 2015

26

Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction

Reyes-Gibby, Cielito C., Yuan, Christine, Wang, Jian, Yeung, Sai-Ching J., Shete, Sanjay

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.72 MB

english, 2015

27

Dynamics of the discovery process of protein-protein interactions from low content studies

Wang, Zichen, Clark, Neil R., Ma’ayan, Avi

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.40 MB

english, 2015

28

From ERα66 to ERα36: a generic method for validating a prognosis marker of breast tumor progression

Chamard-Jovenin, Clémence, Jung, Alain C., Chesnel, Amand, Abecassis, Joseph, Flament, Stéphane, Ledrappier, Sonia, Macabre, Christine, Boukhobza, Taha, Dumond, Hélène

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.04 MB

english, 2015

29

Systems biology surveillance decrypts pathological transcriptome remodeling

Faustino, Randolph S., Wyles, Saranya P., Groenendyk, Jody, Michalak, Marek, Terzic, Andre, Perez-Terzic, Carmen

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.76 MB

english, 2015

30

Uncovering distinct protein-network topologies in heterogeneous cell populations

Wieczorek, Jakob, Malik-Sheriff, Rahuman S, Fermin, Yessica, Grecco, Hernán E, Zamir, Eli, Ickstadt, Katja

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 905 KB

english, 2015

31

SEEK: a systems biology data and model management platform

Wolstencroft, Katherine, Owen, Stuart, Krebs, Olga, Nguyen, Quyen, Stanford, Natalie J, Golebiewski, Martin, Weidemann, Andreas, Bittkowski, Meik, An, Lihua, Shockley, David, Snoep, Jacky L., Mueller,

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.72 MB

english, 2015

32

Domain-specific model selection for structural identification of the Rab5-Rab7 dynamics in endocytosis

Tanevski, Jovan, Todorovski, Ljupčo, Kalaidzidis, Yannis, Džeroski, Sašo

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.04 MB

english, 2015

33

Increased robustness of early embryogenesis through collective decision-making by key transcription factors

Sharifi-Zarchi, Ali, Totonchi, Mehdi, Khaloughi, Keynoush, Karamzadeh, Razieh, Araúzo-Bravo, Marcos J., Baharvand, Hossein, Tusserkani, Ruzbeh, Pezeshk, Hamid, Chitsaz, Hamidreza, Sadeghi, Mehdi

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.29 MB

english, 2015

34

Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions

Hasdemir, Dicle, Hoefsloot, Huub C.J, Smilde, Age K.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.03 MB

english, 2015

35

Finding directionality and gene-disease predictions in disease associations

Garcia-Albornoz, Manuel, Nielsen, Jens

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.96 MB

english, 2015

36

Genome-scale metabolic model ofRhodococcus jostiiRHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition

Tajparast, Mohammad, Frigon, Dominic

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.33 MB

english, 2015

37

Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates

Davila-Velderrain, Jose, Villarreal, Carlos, Alvarez-Buylla, Elena R

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1013 KB

english, 2015

38

Complex regulation of Hsf1-Skn7 activities by the catalytic subunits of PKA inSaccharomyces cerevisiae: experimental and computational evidences

Pérez-Landero, Sergio, Sandoval-Motta, Santiago, Martínez-Anaya, Claudia, Yang, Runying, Folch-Mallol, Jorge Luis, Martínez, Luz María, Ventura, Larissa, Guillén-Navarro, Karina, Aldana-González, Maxi

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.72 MB

english, 2015

39

Genome-scale resources for Thermoanaerobacterium saccharolyticum

Currie, Devin H, Raman, Babu, Gowen, Christopher M, Tschaplinski, Timothy J, Land, Miriam L, Brown, Steven D, Covalla, Sean F, Klingeman, Dawn M, Yang, Zamin K, Engle, Nancy L, Johnson, Courtney M, Ro

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.28 MB

english, 2015

40

The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms

Tripathi, Sushil, Flobak, Åsmund, Chawla, Konika, Baudot, Anaïs, Bruland, Torunn, Thommesen, Liv, Kuiper, Martin, Lægreid, Astrid

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.85 MB

english, 2015

41

Regulation of ERK-MAPK signaling in human epidermis

Cursons, Joseph, Gao, Jerry, Hurley, Daniel G., Print, Cristin G., Dunbar, P. Rod, Jacobs, Marc D., Crampin, Edmund J.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.62 MB

english, 2015

42

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts

Czerwinska, Urszula, Calzone, Laurence, Barillot, Emmanuel, Zinovyev, Andrei

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.67 MB

english, 2015

43

Finding the positive feedback loops underlying multi-stationarity

Feliu, Elisenda, Wiuf, Carsten

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 891 KB

english, 2015

44

Computational modeling of sphingolipid metabolism

Wronowska, Weronika, Charzyńska, Agata, Nienałtowski, Karol, Gambin, Anna

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.08 MB

english, 2015

45

Identification of putative drug targets for human sperm-egg interaction defect using protein network approach

Sabetian, Soudabeh, Shamsir, Mohd Shahir

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.33 MB

english, 2015

46

An algorithm for the reduction of genome-scale metabolic network models to meaningful core models

Erdrich, Philipp, Steuer, Ralf, Klamt, Steffen

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 941 KB

english, 2015

47

Robust and efficient parameter estimation in dynamic models of biological systems

Gábor, Attila, Banga, Julio R.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.32 MB

english, 2015

48

Solution of the chemical master equation by radial basis functions approximation with interface tracking

Kryven, Ivan, Röblitz, Susanna, Schütte, Christof

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 4.36 MB

english, 2015

49

CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks

Kittas, Aristotelis, Barozet, Amélie, Sereshti, Jekaterina, Grabe, Niels, Tsoka, Sophia

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.30 MB

english, 2015

50

Stochastic simulation of Booleanrxnconmodels: towards quantitative analysis of large signaling networks

Mori, Tomoya, Flöttmann, Max, Krantz, Marcus, Akutsu, Tatsuya, Klipp, Edda

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.21 MB

english, 2015

51

A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems

Yin, Weiwei, Garimalla, Swetha, Moreno, Alberto, Galinski, Mary R., Styczynski, Mark P.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.78 MB

english, 2015

52

Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks

Abedpour, Nima, Kollmann, Markus

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.34 MB

english, 2015

53

Mining for novel candidate clock genes in the circadian regulatory network

Bhargava, Anuprabha, Herzel, Hanspeter, Ananthasubramaniam, Bharath

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.56 MB

english, 2015

54

Nonlinear mixed-effects modelling for single cell estimation: when, why, and how to use it

Karlsson, Markus, Janzén, David L.I., Durrieu, Lucia, Colman-Lerner, Alejandro, Kjellsson, Maria C., Cedersund, Gunnar

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.09 MB

english, 2015

55

Dysregulation of the vascular endothelial growth factor and semaphorin ligand-receptor families in prostate cancer metastasis

Bender, R. Joseph, Mac Gabhann, Feilim

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.07 MB

english, 2015

56

Flux-sum analysis identifies metabolite targets for strain improvement

Lakshmanan, Meiyappan, Kim, Tae Yong, Chung, Bevan K. S., Lee, Sang Yup, Lee, Dong-Yup

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 983 KB

english, 2015

57

Optimization of lipid production with a genome-scale model ofYarrowia lipolytica

Kavšček, Martin, Bhutada, Govindprasad, Madl, Tobias, Natter, Klaus

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 883 KB

english, 2015

58

Systematic synergy modeling: understanding drug synergy from a systems biology perspective

Chen, Di, Liu, Xi, Yang, Yiping, Yang, Hongjun, Lu, Peng

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1012 KB

english, 2015

59

A multi-omic analysis of human naïve CD4+ T cells

Mitchell, Christopher J., Getnet, Derese, Kim, Min-Sik, Manda, Srikanth S., Kumar, Praveen, Huang, Tai-Chung, Pinto, Sneha M., Nirujogi, Raja Sekhar, Iwasaki, Mio, Shaw, Patrick G., Wu, Xinyan, Zhong,

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.74 MB

english, 2015

60

Differential variability and correlation of gene expression identifies key genes involved in neuronal differentiation

Ando, Tatsuya, Kato, Ryuji, Honda, Hiroyuki

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.85 MB

english, 2015

61

Bacterial social interactions drive the emergence of differential spatial colony structures

Blanchard, Andrew E., Lu, Ting

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.52 MB

english, 2015

62

The organization of domains in proteins obeys Menzerath-Altmann’s law of language

Shahzad, Khuram, Mittenthal, Jay E., Caetano-Anollés, Gustavo

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.41 MB

english, 2015

63

Erratum to: ppiPre: predicting protein-protein interactions by combining heterogeneous features

Deng, Yue, Gao, Lin, Wang, Bingbo

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 320 KB

english, 2015

64

A correction method for systematic error in1H-NMR time-course data validated through stochastic cell culture simulation

Sokolenko, Stanislav, Aucoin, Marc G.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.29 MB

english, 2015

65

Inferring microbial interaction network from microbiome data using RMN algorithm

Tsai, Kun-Nan, Lin, Shu-Hsi, Liu, Wei-Chung, Wang, Daryi

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.21 MB

english, 2015

66

The wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy indrosophila melanogaster

Fear, Justin M., Arbeitman, Michelle N., Salomon, Matthew P., Dalton, Justin E., Tower, John, Nuzhdin, Sergey V., McIntyre, Lauren M.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.21 MB

english, 2015

67

Incorporating prior knowledge improves detection of differences in bacterial growth rate

Rickett, Lydia M, Pullen, Nick, Hartley, Matthew, Zipfel, Cyril, Kamoun, Sophien, Baranyi, József, Morris, Richard J.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 721 KB

english, 2015

68

Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics

Nienałtowski, Karol, Włodarczyk, Michał, Lipniacki, Tomasz, Komorowski, Michał

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 678 KB

english, 2015

69

Exploring causal networks underlying fat deposition and muscularity in pigs through the integration of phenotypic, genotypic and transcriptomic data

Peñagaricano, Francisco, Valente, Bruno D., Steibel, Juan P., Bates, Ronald O., Ernst, Catherine W., Khatib, Hasan, Rosa, Guilherme JM

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.64 MB

english, 2015

70

Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential

Cava, Claudia, Bertoli, Gloria, Castiglioni, Isabella

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.80 MB

english, 2015

71

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

Dräger, Andreas, Zielinski, Daniel C, Keller, Roland, Rall, Matthias, Eichner, Johannes, Palsson, Bernhard O, Zell, Andreas

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.13 MB

english, 2015

72

Impact of kinetic isotope effects in isotopic studies of metabolic systems

Millard, Pierre, Portais, Jean-Charles, Mendes, Pedro

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.70 MB

english, 2015

73

Towards in vivo estimation of reaction kinetics using high-throughput metabolomics data: a maximum likelihood approach

Zhang, Weiruo, Kolte, Ritesh, Dill, David L

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 637 KB

english, 2015

74

Mathematical analysis of the regulation of competing methyltransferases

Reed, Michael C., Gamble, Mary V., Hall, Megan N., Nijhout, H. Frederik

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.40 MB

english, 2015

75

Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology

Bianconi, Fortunato, Baldelli, Elisa, Luovini, Vienna, Petricoin, Emanuel F., Crinò, Lucio, Valigi, Paolo

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.69 MB

english, 2015

76

Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes

Cook, Daniel, Ogunnaike, Babatunde A., Vadigepalli, Rajanikanth

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.88 MB

english, 2015

77

In silicoevaluation and exploration of antibiotic tuberculosis treatment regimens

Pienaar, Elsje, Dartois, Véronique, Linderman, Jennifer J., Kirschner, Denise E.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.61 MB

english, 2015

78

A global sensitivity analysis approach for morphogenesis models

Boas, Sonja E. M., Navarro Jimenez, Maria I., Merks, Roeland M. H., Blom, Joke G.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.60 MB

english, 2015

79

Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data

Intosalmi, Jukka, Ahlfors, Helena, Rautio, Sini, Mannerstöm, Henrik, Chen, Zhi Jane, Lahesmaa, Riitta, Stockinger, Brigitta, Lähdesmäki, Harri

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 857 KB

english, 2015

80

Deciphering the signaling mechanisms of the plant cell wall degradation machinery inAspergillus oryzae

Udatha, D.B.R.K. Gupta, Topakas, Evangelos, Salazar, Margarita, Olsson, Lisbeth, Andersen, Mikael R., Panagiotou, Gianni

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.69 MB

english, 2015

81

Bayesian modeling suggests that IL-12 (p40), IL-13 and MCP-1 drive murine cytokine networksin vivo

Field, Sarah L., Dasgupta, Tathagata, Cummings, Michele, Savage, Richard S., Adebayo, Julius, McSara, Hema, Gunawardena, Jeremy, Orsi, Nicolas M.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.99 MB

english, 2015

82

Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice

Abshagen, Kerstin, König, Matthias, Hoppe, Andreas, Müller, Isabell, Ebert, Matthias, Weng, Honglei, Holzhütter, Herrmann-Georg, Zanger, Ulrich M., Bode, Johannes, Vollmar, Brigitte, Thomas, Maria, Do

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.29 MB

english, 2015

83

Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis

Boas, Sonja E. M., Merks, Roeland M. H.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.88 MB

english, 2015

84

Reconstruction of gene networks using prior knowledge

Ghanbari, Mahsa, Lasserre, Julia, Vingron, Martin

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 626 KB

english, 2015

85

A simple method for identifying parameter correlations in partially observed linear dynamic models

Li, Pu, Vu, Quoc Dong

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.04 MB

english, 2015

86

Cellular automaton-based model for radiation-induced bystander effects

Hattori, Yuya, Yokoya, Akinari, Watanabe, Ritsuko

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 6.79 MB

english, 2015

87

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations

Palmisano, Alida, Hoops, Stefan, Watson, Layne T., Jones, Thomas C., Tyson, John J., Shaffer, Clifford A.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 3.63 MB

english, 2015

88

FlexFlux: combining metabolic flux and regulatory network analyses

Marmiesse, Lucas, Peyraud, Rémi, Cottret, Ludovic

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.82 MB

english, 2015

89

PROXIMAL: a method for Prediction of Xenobiotic Metabolism

Yousofshahi, Mona, Manteiga, Sara, Wu, Charmian, Lee, Kyongbum, Hassoun, Soha

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.28 MB

english, 2015

90

Scope and limitations of yeast as a model organism for studying human tissue-specific pathways

Mohammadi, Shahin, Saberidokht, Baharak, Subramaniam, Shankar, Grama, Ananth

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 5.55 MB

english, 2015

91

A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells

Song, Ruijie, Peng, Weilin, Liu, Ping, Acar, Murat

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.58 MB

english, 2015

92

A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication

Kolar, Katja, Wischhusen, Hanna M., Müller, Konrad, Karlsson, Maria, Weber, Wilfried, Zurbriggen, Matias D.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.83 MB

english, 2015

93

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy

Strasser, Michael K., Feigelman, Justin, Theis, Fabian J., Marr, Carsten

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.41 MB

english, 2015

94

Analysis of a spatial gene expression database for sea anemoneNematostella vectensisduring early development

Botman, Daniel, Jansson, Fredrik, Röttinger, Eric, Martindale, Mark Q., de Jong, Johann, Kaandorp, Jaap A.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.37 MB

english, 2015

95

Tracing regulatory routes in metabolism using generalised supply-demand analysis

Christensen, Carl D., Hofmeyr, Jan-Hendrik S., Rohwer, Johann M.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.23 MB

english, 2015

96

Metabolic modeling predicts metabolite changes inMycobacterium tuberculosis

Garay, Christopher D., Dreyfuss, Jonathan M., Galagan, James E.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

97

The relationship between stochastic and deterministic quasi-steady state approximations

Kim, Jae Kyoung, Josić, Krešimir, Bennett, Matthew R.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.26 MB

english, 2015

98

Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators

Padi, Megha, Quackenbush, John

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 2.34 MB

english, 2015

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