Volume 6; Issue 1

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BMC Systems Biology
Volume 6; Issue 1

BMC Systems Biology

Volume 6; Issue 1

1

Systems analysis of the transcriptional response of human ileocecal epithelial cells toClostridium difficiletoxins and effects on cell cycle control

Kevin M D’Auria, Gina M Donato, Mary C Gray, Glynis L Kolling, Cirle A Warren, Lauren M Cave, Michael D Solga, Joanne A Lannigan, Jason A Papin, Erik L Hewlett

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 321 KB

english, 2012

2

Regulation of cytoplasmic polyadenylation can generate a bistable switch

Naveed Aslam, Harel Z Shouval

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 955 KB

english, 2012

3

Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies

Bettina M Länger, Cristina Pou-Barreto, Carlos González-Alcón, Basilio Valladares, Bettina Wimmer, Néstor V Torres

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 625 KB

english, 2012

4

Biomarker robustness reveals the PDGF network as driving disease outcome in ovarian cancer patients in multiple studies

Rotem Ben-Hamo, Sol Efroni

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 696 KB

english, 2012

5

Identifying co-targets to fight drug resistance based on a random walk model

Liang-Chun Chen, Hsiang-Yuan Yeh, Cheng-Yu Yeh, Carlos Roberto Arias, Von-Wun Soo

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 472 KB

english, 2012

6

Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach

Jörg Linde, Peter Hortschansky, Eugen Fazius, Axel A Brakhage, Reinhard Guthke, Hubertus Haas

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 348 KB

english, 2012

7

Dynamics of p53 and NF-κB regulation in response to DNA damage and identification of target proteins suitable for therapeutic intervention

Rainer Poltz, Michael Naumann

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

8

Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms

Pablo Carbonell, Davide Fichera, Shashi B Pandit, Jean-Loup Faulon

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 593 KB

english, 2012

9

Inferring transcriptional gene regulation network of starch metabolism inArabidopsis thalianaleaves using graphical Gaussian model

Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree, Morakot Tanticharoen, Sakarindr Bhumiratana, Asawin Meechai, Jeerayut Chaijaruwanich, Hideki Takahashi, Supapon Cheevadhanarak

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.13 MB

english, 2012

10

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

Kenneth Lo, Adrian E Raftery, Kenneth M Dombek, Jun Zhu, Eric E Schadt, Roger E Bumgarner, Ka Yee Yeung

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 384 KB

english, 2012

11

Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data

Tzu-Hsien Yang, Wei-Sheng Wu

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 634 KB

english, 2012

12

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Marcel H Schulz, William E Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 919 KB

english, 2012

13

Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein

Yu-Shu Liu, Pei-Wen Tsai, Yong Wang, Tan-chi Fan, Chia-Hung Hsieh, Margaret Dah-Tsyr Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan, Hao-Teng Chang

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.00 MB

english, 2012

14

Flux variability scanning based on enforced objective flux for identifying gene amplification targets

Jong Myoung Park, Hye Min Park, Won Jun Kim, Hyun Uk Kim, Tae Yong Kim, Sang Yup Lee

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.11 MB

english, 2012

15

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling

Matthew S Creamer, Edward C Stites, Meraj Aziz, James A Cahill, Chin Wee Tan, Michael E Berens, Haiyong Han, Kimberley J Bussey, Daniel D Von Hoff, William S Hlavacek, Richard G Posner

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 644 KB

english, 2012

16

Exploring the genetic control of glycolytic oscillations inSaccharomyces Cerevisiae

Thomas Williamson, Delali Adiamah, Jean-Marc Schwartz, Lubomira Stateva

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 892 KB

english, 2012

17

Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise

Marc R Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej Dobrzyński, Jan B Hoek, Walter Kolch, Babatunde A Ogunnaike, Boris N Kholodenko

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 914 KB

english, 2012

18

Towards a quantitative understanding of the MITF-PIAS3-STAT3 connection

Josef Thingnes, Timothy J Lavelle, Arne B Gjuvsland, Stig W Omholt, Eivind Hovig

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 590 KB

english, 2012

19

Topological effects of data incompleteness of gene regulatory networks

Joaquin Sanz, Emanuele Cozzo, Javier Borge-Holthoefer, Yamir Moreno

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.28 MB

english, 2012

20

Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback

Yonatan Savir, Nir Waysbort, Yaron E Antebi, Tsvi Tlusty, Nir Friedman

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 807 KB

english, 2012

21

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study

Mohammed Alshalalfa, Gary D Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

22

Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks

Jinghang Liang, Jie Han

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 2.54 MB

english, 2012

23

Continuous time boolean modeling for biological signaling: application of Gillespie algorithm

Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.63 MB

english, 2012

24

Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs

Jason E Shoemaker, Satoshi Fukuyama, Amie J Eisfeld, Yukiko Muramoto, Shinji Watanabe, Tokiko Watanabe, Yukiko Matsuoka, Hiroaki Kitano, Yoshihiro Kawaoka

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 550 KB

english, 2012

25

Network-based assessment of the selectivity of metabolic drug targets inPlasmodium falciparumwith respect to human liver metabolism

Susanna Bazzani, Andreas Hoppe, Hermann-Georg Holzhütter

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 395 KB

english, 2012

26

An integer optimization algorithm for robust identification of non-linear gene regulatory networks

Nishanth Chemmangattuvalappil, Keith Task, Ipsita Banerjee

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 807 KB

english, 2012

27

Likelihood based observability analysis and confidence intervals for predictions of dynamic models

Clemens Kreutz, Andreas Raue, Jens Timmer

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 354 KB

english, 2012

28

Computational modeling of apoptotic signaling pathways induced by cisplatin

Ji-Young Hong, Geun-Hong Kim, Jun-Woo Kim, Soon-Sung Kwon, Eisuke F Sato, Kwang-Hyun Cho, Eun Bo Shim

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 834 KB

english, 2012

29

Nuclear Factor kappa B is central to Marek’s Disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo

Shyamesh Kumar, Dusan Kunec, Joram J Buza, Hsin-I Chiang, Huaijun Zhou, Sugalesini Subramaniam, Ken Pendarvis, Hans H Cheng, Shane C Burgess

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 807 KB

english, 2012

30

A reconfigurable NAND/NOR genetic logic gate

Angel Goñi-Moreno, Martyn Amos

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

31

Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

David Byrne, Alexandra Dumitriu, Daniel Segrè

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

32

Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast

Leandra M Brettner, Joanna Masel

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 706 KB

english, 2012

33

In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems

Thomas Maiwald, Julie Blumberg, Andreas Raue, Stefan Hengl, Marcel Schilling, Sherwin KB Sy, Verena Becker, Ursula Klingmüller, Jens Timmer

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 718 KB

english, 2012

34

Gene autoregulation via intronic microRNAs and its functions

Carla Bosia, Matteo Osella, Mariama El Baroudi, Davide Corà, Michele Caselle

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 847 KB

english, 2012

35

Computational codon optimization of synthetic gene for protein expression

Bevan Kai-Sheng Chung, Dong-Yup Lee

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.09 MB

english, 2012

36

Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model

Magbubah Essack, Cameron Ross MacPherson, Sebastian Schmeier, Vladimir B Bajic

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.05 MB

english, 2012

37

Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing

Bor-Sen Chen, Chih-Yuan Hsu

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 434 KB

english, 2012

38

Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics

Irina Surovtsova, Natalia Simus, Katrin Hübner, Sven Sahle, Ursula Kummer

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.67 MB

english, 2012

39

Regulation of leukotriene and 5oxoETE synthesis and the effect of 5-lipoxygenase inhibitors: a mathematical modeling approach

Tatiana A Karelina, Kirill V Zhudenkov, Oleg O Demin, Dmitry V Svetlichny, Balaji Agoram, David Fairman, Oleg V Demin

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 577 KB

english, 2012

40

A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data

Min Li, Hanhui Zhang, Jian-xin Wang, Yi Pan

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 249 KB

english, 2012

41

Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics?

Luisa Ana B Cruz, Marit Hebly, Giang-Huong Duong, Sebastian A Wahl, Jack T Pronk, Joseph J Heijnen, Pascale Daran-Lapujade, Walter M van Gulik

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.13 MB

english, 2012

42

Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach

Shengjun Fan, Qiang Geng, Zhenyu Pan, Xin Li, Lu Tie, Yan Pan, Xuejun Li

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 754 KB

english, 2012

43

Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences

Shibin Mathew, Maria Jaramillo, Xinan Zhang, Li Ang Zhang, Alejandro Soto-Gutiérrez, Ipsita Banerjee

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 443 KB

english, 2012

44

Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations

Sabrina Kleessen, Zoran Nikoloski

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 405 KB

english, 2012

45

Structural analysis of eyespots: dynamics of morphogenic signals that govern elemental positions in butterfly wings

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 952 KB

english, 2012

46

Crosstalk between transcription factors and microRNAs in human protein interaction network

Chen-Ching Lin, Ya-Jen Chen, Cho-Yi Chen, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.38 MB

english, 2012

47

Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis

Tian Xia, Jiansong Tong, Shailendra S Rathore, Xun Gu, Julie A Dickerson

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 544 KB

english, 2012

48

Predicting new molecular targets for rhein using network pharmacology

Aihua Zhang, Hui Sun, Bo Yang, Xijun Wang

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 947 KB

english, 2012

49

Set membership experimental design for biological systems

Skylar W Marvel, Cranos M Williams

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 630 KB

english, 2012

50

Redox balance is key to explaining fullvs. partial switching to low-yield metabolism

Milan JA van Hoek, Roeland MH Merks

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 341 KB

english, 2012

51

An optimally evolved connective ratio of neural networks that maximizes the occurrence of synchronized bursting behavior

Chao-Yi Dong, Kwang-Hyun Cho

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 465 KB

english, 2012

52

Genome-scale metabolic reconstructions ofPichia stipitisandPichia pastorisandin silicoevaluation of their potentials

Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew, Jens Nielsen

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.54 MB

english, 2012

53

Tav4SB: integrating tools for analysis of kinetic models of biological systems

Mikołaj Rybiński, Michał Lula, Paweł Banasik, Sławomir Lasota, Anna Gambin

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 858 KB

english, 2012

54

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease

Arvind K Chavali, Anna S Blazier, Jose L Tlaxca, Paul A Jensen, Richard D Pearson, Jason A Papin

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 964 KB

english, 2012

55

Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis

Jason E McDermott, Deborah L Diamond, Courtney Corley, Angela L Rasmussen, Michael G Katze, Katrina M Waters

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 544 KB

english, 2012

56

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

Daniel C Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M Burke, Douglas A Lauffenburger, Peter K Sorger

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.03 MB

english, 2012

57

Gap-filling analysis of theiJO1366Escherichia colimetabolic network reconstruction for discovery of metabolic functions

Jeffrey D Orth, BernhardØ Palsson

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 285 KB

english, 2012

58

Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks inDrosophila melanogaster

Man-Sun Kim, Jeong-Rae Kim, Dongsan Kim, Arthur D Lander, Kwang-Hyun Cho

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 492 KB

english, 2012

59

Gene regulation is governed by a core network in hepatocellular carcinoma

Zuguang Gu, Chenyu Zhang, Jin Wang

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 964 KB

english, 2012

60

FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

Hendrik Rohn, Anja Hartmann, Astrid Junker, Björn H Junker, Falk Schreiber

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 700 KB

english, 2012

61

Revisiting the variation of clustering coefficient of biological networks suggests new modular structure

Dapeng Hao, Cong Ren, Chuanxing Li

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 933 KB

english, 2012

62

A genome-scale metabolic model of the lipid-accumulating yeastYarrowia lipolytica

Nicolas Loira, Thierry Dulermo, Jean-Marc Nicaud, David James Sherman

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 267 KB

english, 2012

63

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

Iain Hepburn, Weiliang Chen, Stefan Wils, Erik De Schutter

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 729 KB

english, 2012

64

Morphogengineering roots: comparing mechanisms of morphogen gradient formation

Verônica A Grieneisen, Ben Scheres, Paulien Hogeweg, Athanasius F M Marée

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 2.05 MB

english, 2012

65

Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

Ricardo de Matos Simoes, Shailesh Tripathi, Frank Emmert-Streib

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 2.07 MB

english, 2012

66

The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions

Philipp Thomas, Arthur V Straube, Ramon Grima

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 725 KB

english, 2012

67

The genetic control of growth rate: a systems biology study in yeast

Pınar Pir, Alex Gutteridge, Jian Wu, Bharat Rash, Douglas B Kell, Nianshu Zhang, Stephen G Oliver

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 821 KB

english, 2012

68

Spice: discovery of phenotype-determining component interplays

Zhengzhang Chen, Kanchana Padmanabhan, Andrea M Rocha, Yekaterina Shpanskaya, James R Mihelcic, Kathleen Scott, Nagiza F Samatova

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 3.92 MB

english, 2012

69

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolismin silico

Michael J McAnulty, Jiun Y Yen, Benjamin G Freedman, Ryan S Senger

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 821 KB

english, 2012

70

Rational design of13C-labeling experiments for metabolic flux analysis in mammalian cells

Scott B Crown, Woo Suk Ahn, Maciek R Antoniewicz

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 391 KB

english, 2012

71

From networks of protein interactions to networks of functional dependencies

Davide Luciani, Gianfranco Bazzoni

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 996 KB

english, 2012

72

Modeling of human factor Va inactivation by activated protein C

Maria Cristina Bravo, Thomas Orfeo, Kenneth G Mann, Stephen J Everse

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 3.66 MB

english, 2012

73

A specialized ODE integrator for the efficient computation of parameter sensitivities

Pedro Gonnet, Sotiris Dimopoulos, Lukas Widmer, Jörg Stelling

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 575 KB

english, 2012

74

Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network

Rachel S Koh, Mary J Dunlop

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 248 KB

english, 2012

75

Trade-offs between drug toxicity and benefit in the multi-antibiotic resistance system underlie optimal growth of E. coli

Kevin B Wood, Philippe Cluzel

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 881 KB

english, 2012

76

Genome-scale metabolic model of the fission yeastSchizosaccharomyces pombeand the reconciliation ofin silico/in vivomutant growth

Seung Bum Sohn, Tae Yong Kim, Jay H Lee, Sang Yup Lee

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 585 KB

english, 2012

77

A systems biology approach reveals common metastatic pathways in osteosarcoma

Ricardo J Flores, Yiting Li, Alexander Yu, Jianhe Shen, Pulivarthi H Rao, Serrine S Lau, Marina Vannucci, Ching C Lau, Tsz-Kwong Man

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 751 KB

english, 2012

78

Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics

Paola Lecca, Daniele Morpurgo, Gianluca Fantaccini, Alessandro Casagrande, Corrado Priami

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

79

AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease

Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yukiko Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.11 MB

english, 2012

80

Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison

Michalis K Titsias, Antti Honkela, Neil D Lawrence, Magnus Rattray

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 417 KB

english, 2012

81

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

Florian Martin, Ty M Thomson, Alain Sewer, David A Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C Peitsch

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 571 KB

english, 2012

82

Yeast 5 – an expanded reconstruction of theSaccharomyces cerevisiaemetabolic network

Benjamin D Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P Walker

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 268 KB

english, 2012

83

Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes

Zuguang Gu, Jialin Liu, Kunming Cao, Junfeng Zhang, Jin Wang

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.70 MB

english, 2012

84

Analyzing fixed points of intracellular regulation networks with interrelated feedback topology

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 655 KB

english, 2012

85

Stochastic simulations of a synthetic bacteria-yeast ecosystem

Konstantinos Biliouris, David Babson, Claudia Schmidt-Dannert, Yiannis N Kaznessis

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.31 MB

english, 2012

86

Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching inStreptomyces coelicolorA3(2)

Alexander Wentzel, Per Bruheim, Anders Øverby, Øyvind M Jakobsen, Håvard Sletta, Walid A M Omara, David A Hodgson, Trond E Ellingsen

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 707 KB

english, 2012

87

Mapping the stabilome: a novel computational method for classifying metabolic protein stability

Ralph Patrick, Kim-Anh Lê Cao, Melissa Davis, Bostjan Kobe, Mikael Bodén

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 410 KB

english, 2012

88

Combinatorial network of transcriptional regulation and microRNA regulation in human cancer

Hui Yu, Kang Tu, Yi-Jie Wang, Jun-Zhe Mao, Lu Xie, Yuan-Yuan Li, Yi-Xue Li

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 306 KB

english, 2012

89

Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique

Nizamul Morshed, Madhu Chetty, Nguyen Xuan Vinh

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 828 KB

english, 2012

90

Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease

Michael C Oldham, Peter Langfelder, Steve Horvath

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.06 MB

english, 2012

91

Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level

Wenting Li, Rui Wang, Linfu Bai, Zhangming Yan, Zhirong Sun

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 795 KB

english, 2012

92

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases

Yu Liu, Mehmet Koyutürk, Jill S Barnholtz-Sloan, Mark R Chance

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 770 KB

english, 2012

93

A simple theoretical framework for understanding heterogeneous differentiation of CD4+T cells

Tian Hong, Jianhua Xing, Liwu Li, John J Tyson

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.28 MB

english, 2012

94

PathCase-SB: integrating data sources and providing tools for systems biology research

Sarp A Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A Ercument Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K Dash, Nicola Lai, Gultekin Ozsoyoglu, Zehra Meral Ozsoyoglu

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

95

Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis

Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 478 KB

english, 2012

96

Frequency-based time-series gene expression recomposition using PRIISM

Bruce A Rosa, Yuhua Jiao, Sookyung Oh, Beronda L Montgomery, Wensheng Qin, Jin Chen

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 699 KB

english, 2012

97

Evolvability of feed-forward loop architecture biases its abundance in transcription networks

Stefanie Widder, Ricard Solé, Javier Macía

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 654 KB

english, 2012

98

Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated withataxia

Sherry-Ann Brown, Leslie M Loew

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.04 MB

english, 2012

99

iAK692: A genome-scalemetabolic model of Spirulina platensis C1

Amornpan Klanchui, Chiraphan Khannapho, Atchara Phodee, Supapon Cheevadhanarak, Asawin Meechai

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 955 KB

english, 2012

100

Integrated pathway modules using time-course metabolic profiles and EST data fromMilnesium tardigradum

Daniela Beisser, Markus A Grohme, Joachim Kopka, Marcus Frohme, Ralph O Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W Klau, Marcus Dittrich, Tobias Müller

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 960 KB

english, 2012

101

Improving metabolic flux predictions using absolute gene expression data

Dave Lee, Kieran Smallbone, Warwick B Dunn, Ettore Murabito, Catherine L Winder, Douglas B Kell, Pedro Mendes, Neil Swainston

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 260 KB

english, 2012

102

Multi-compartmental modeling of SORLA’s influence on amyloidogenic processing in Alzheimer’s disease

Angelyn Lao, Vanessa Schmidt, Yvonne Schmitz, Thomas E Willnow, Olaf Wolkenhauer

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.13 MB

english, 2012

103

A cooperative strategy for parameter estimation in large scale systems biology models

Alejandro F Villaverde, Jose A Egea, Julio R Banga

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 740 KB

english, 2012

104

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

Brian Drawert, Stefan Engblom, Andreas Hellander

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.21 MB

english, 2012

105

A regulatory network modeled from wild-type gene expression data guides functional predictions inCaenorhabditis elegansdevelopment

Brandilyn Stigler, Helen M Chamberlin

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 894 KB

english, 2012

106

A quantitative model of the initiation of DNA replication inSaccharomyces cerevisiaepredicts the effects of system perturbations

Rohan D Gidvani, Peter Sudmant, Grace Li, Lance F DaSilva, Brendan J McConkey, Bernard P Duncker, Brian P Ingalls

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.12 MB

english, 2012

107

Dynamic optimization of distributed biological systems using robust and efficient numerical techniques

Carlos Vilas, Eva Balsa-Canto, Maria-Sonia G García, Julio R Banga, Antonio A Alonso

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 477 KB

english, 2012

108

FAME, the Flux Analysis and Modeling Environment

Joost Boele, Brett G Olivier, Bas Teusink

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 218 KB

english, 2012

109

Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug

Hee Sook Lee, Taejeong Bae, Ji-Hyun Lee, Dae Gyu Kim, Young Sun Oh, Yeongjun Jang, Ji-Tea Kim, Jong-Jun Lee, Alessio Innocenti, Claudiu T Supuran, Luonan Chen, Kyoohyoung Rho, Sunghoon Kim

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 776 KB

english, 2012

110

Efficient parametric analysis of the chemical master equation through model order reduction

Steffen Waldherr, Bernard Haasdonk

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 630 KB

english, 2012

111

Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade

Uddipan Sarma, Indira Ghosh

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.01 MB

english, 2012

112

An investigation of spatial signal transduction in cellular networks

Aiman Alam-Nazki, J Krishnan

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.10 MB

english, 2012

113

Estimation of dynamic flux profiles from metabolic time series data

I-Chun Chou, Eberhard O Voit

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.19 MB

english, 2012

114

A higher-order numerical framework for stochastic simulation of chemical reaction systems

Tamás Székely Jr, Kevin Burrage, Radek Erban, Konstantinos C Zygalakis

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 492 KB

english, 2012

115

Biochemical fluctuations, optimisation and the linear noise approximation

Jürgen Pahle, Joseph D Challenger, Pedro Mendes, Alan J McKane

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 429 KB

english, 2012

116

Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks

Wei Peng, Jianxin Wang, Weiping Wang, Qing Liu, Fang-Xiang Wu, Yi Pan

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.39 MB

english, 2012

117

Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models

Kristin Tøndel, Ulf G Indahl, Arne B Gjuvsland, Stig W Omholt, Harald Martens

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.17 MB

english, 2012

118

Sets2Networks: network inference from repeated observations of sets

Neil R Clark, Ruth Dannenfelser, Christopher M Tan, Michael E Komosinski, Avi Ma’ayan

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 2.40 MB

english, 2012

119

Predicting outcomes of steady-state13C isotope tracing experiments using Monte Carlo sampling

Jan Schellenberger, Daniel C Zielinski, Wing Choi, Sunthosh Madireddi, Vasiliy Portnoy, David A Scott, Jennifer L Reed, Andrei L Osterman, Bernhard ∅ Palsson

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.00 MB

english, 2012

120

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

Larry Croft, Damian Szklarczyk, Lars Juhl Jensen, Jan Gorodkin

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 222 KB

english, 2012

121

Condor-COPASI: high-throughput computing for biochemical networks

Edward Kent, Stefan Hoops, Pedro Mendes

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.35 MB

english, 2012

122

HINT: High-quality protein interactomes and their applications in understanding human disease

Jishnu Das, Haiyuan Yu

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 2.10 MB

english, 2012

123

A reaction–diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts

Lei Zhang, Arthur D Lander, Qing Nie

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.21 MB

english, 2012

124

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

Xueyang Feng, You Xu, Yixin Chen, Yinjie J Tang

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 588 KB

english, 2012

125

Bayesian model selection validates a biokinetic model for zirconium processing in humans

Daniel Schmidl, Sabine Hug, Wei Bo Li, Matthias B Greiter, Fabian J Theis

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 452 KB

english, 2012

126

The Cell Collective: Toward an open and collaborative approach to systems biology

Tomáš Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Alex Madrahimov, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A Rogers

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 696 KB

english, 2012

127

Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis

Eduardo Tejera, João Bernardes, Irene Rebelo

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 433 KB

english, 2012

128

Probing the role of stochasticity in a model of the embryonic stem cell – heterogeneous gene expression and reprogramming efficiency

Vijay Chickarmane, Victor Olariu, Carsten Peterson

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 475 KB

english, 2012

129

A variational approach to parameter estimation in ordinary differential equations

Daniel Kaschek, Jens Timmer

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 853 KB

english, 2012

130

Metabolic Flux-Based Modularity using Shortest Retroactive distances

Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 841 KB

english, 2012

131

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

Yuliang Wang, James A Eddy, Nathan D Price

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.64 MB

english, 2012

132

Genome-level transcription data ofYersinia pestisanalyzed with a New metabolic constraint-based approach

Ali Navid, Eivind Almaas

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 2.98 MB

english, 2012

133

Modeling and analysis of flux distributions in the two branches of the phosphotransferase system inPseudomonas putida

Andreas Kremling, Katharina Pflüger-Grau, Max Chavarría…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 268 KB

english, 2012

134

Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation inEscherichia coli

Nadine Töpfer, Szymon Jozefczuk, Zoran Nikoloski

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.13 MB

english, 2012

135

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption toin vitrocultivation of murine hepatocytes

Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1015 KB

english, 2012

136

Compound stress response in stomatal closure: a mathematical model of ABA and ethylene interaction in guard cells

Mariano Beguerisse-Dıaz, Mercedes C Hernández-Gómez…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 529 KB

english, 2012

137

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

Anne-Claire Haury, Fantine Mordelet, Paola Vera-Licona…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 800 KB

english, 2012

138

GraphAlignment: Bayesian pairwise alignment of biological networks

Michal Kolář, Jörn Meier, Ville Mustonen, Michael Lässig…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 362 KB

english, 2012

139

A multiscale approximation in a heat shock response model of E. coli

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.23 MB

english, 2012

140

Incremental parameter estimation of kinetic metabolic network models

Gengjie Jia, Gregory Stephanopoulos, Rudiyanto Gunawan

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 512 KB

english, 2012

141

A proof for loop-law constraints in stoichiometric metabolic networks

Elad Noor, Nathan E Lewis, Ron Milo

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 204 KB

english, 2012

142

VANTED v2: a framework for systems biology applications

Hendrik Rohn, Astrid Junker, Anja Hartmann, Eva Grafahrend-Belau…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 603 KB

english, 2012

143

A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen

Galina Lebedeva, Azusa Yamaguchi, Simon P Langdon, Kenneth Macleod…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.51 MB

english, 2012

144

Functional clustering of time series gene expression data by Granger causality

André Fujita, Patricia Severino, Kaname Kojima, João Ricardo Sato…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 353 KB

english, 2012

145

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 898 KB

english, 2012

146

Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease

Isaac Crespo, Kirsten Roomp, Wiktor Jurkowski, Hiroaki Kitano…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 722 KB

english, 2012

147

A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation

Mark T Mc Auley, Darren J Wilkinson, Janette JL Jones…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 939 KB

english, 2012

148

A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network

Changki Hong, Minho Lee, Dongsup Kim, Dongsan Kim, Kwang-Hyun Cho…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 438 KB

english, 2012

149

A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network

Shingo Tsuji, Sigeo Ihara, Hiroyuki Aburatani

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 841 KB

english, 2012

150

System size reduction in stochastic simulations of the facilitated diffusion mechanism

Nicolae Radu Zabet

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 467 KB

english, 2012

151

CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism

Anja Karlstädt, Daniela Fliegner, Georgios Kararigas…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.05 MB

english, 2012

152

Designing optimal cell factories: integer programming couples elementary mode analysis with regulation

Christian Jungreuthmayer, Jürgen Zanghellini

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 515 KB

english, 2012

153

A network perspective on metabolic inconsistency

Nikolaus Sonnenschein, José Felipe Golib Dzib, Annick Lesne…

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 737 KB

english, 2012

154

Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles: the role of kinase-phosphatase complex formation

Barbara Szomolay, Vahid Shahrezaei

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.55 MB

english, 2012

155

Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer

Facchetti, Giuseppe, Zampieri, Mattia, Altafini, Claudio

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 774 KB

english, 2012

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