no |
title |
author |
magazine |
year |
volume |
issue |
page(s) |
type |
1 |
A combinatorial approach of Proteomics and Systems Biology in unravelling the mechanisms of acute kidney injury (AKI): involvement of NMDA receptor GRIN1 in murine AKI
|
Husi, Holger |
|
2013 |
7 |
1 |
|
article |
2 |
A comprehensive map of the influenza A virus replication cycle
|
Matsuoka, Yukiko |
|
2013 |
7 |
1 |
|
article |
3 |
A continuous-time adaptive particle filter for estimations under measurement time uncertainties with an application to a plasma-leucine mixed effects model
|
Krengel, Annette |
|
2013 |
7 |
1 |
|
article |
4 |
A kinetic model for RNA-interference of focal adhesions
|
Hoffmann, Max |
|
2013 |
7 |
1 |
|
article |
5 |
A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis
|
Erguler, Kamil |
|
2013 |
7 |
1 |
|
article |
6 |
AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response
|
Bryant, William A |
|
2013 |
7 |
1 |
|
article |
7 |
A metabolite-centric view on flux distributions in genome-scale metabolic models
|
Riemer, S Alexander |
|
2013 |
7 |
1 |
|
article |
8 |
A model of HIV drug resistance driven by heterogeneities in host immunity and adherence patterns
|
Bershteyn, Anna |
|
2013 |
7 |
1 |
|
article |
9 |
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis
|
Ghosh, Soma |
|
2013 |
7 |
1 |
|
article |
10 |
Analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli
|
Nishio, Yousuke |
|
2013 |
7 |
1 |
|
article |
11 |
An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation
|
Wang, Jianxin |
|
2013 |
7 |
1 |
|
article |
12 |
A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype
|
Pey, Jon |
|
2013 |
7 |
1 |
|
article |
13 |
Annual acknowledgement of reviewers
|
Sands, Tim |
|
2013 |
7 |
1 |
|
article |
14 |
An objective function exploiting suboptimal solutions in metabolic networks
|
Wintermute, Edwin H |
|
2013 |
7 |
1 |
|
article |
15 |
An online model composition tool for system biology models
|
Coskun, Sarp A |
|
2013 |
7 |
1 |
|
article |
16 |
A novel function prediction approach using protein overlap networks
|
Liang, Shide |
|
2013 |
7 |
1 |
|
article |
17 |
A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions
|
Kotze, Helen L |
|
2013 |
7 |
1 |
|
article |
18 |
Antibacterial mechanisms identified through structural systems pharmacology
|
Chang, Roger L |
|
2013 |
7 |
1 |
|
article |
19 |
Automated design of bacterial genome sequences
|
Carrera, Javier |
|
2013 |
7 |
1 |
|
article |
20 |
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
|
Bonnet, Eric |
|
2013 |
7 |
1 |
|
article |
21 |
Bridging the gap between gene expression and metabolic phenotype via kinetic models
|
Vital-Lopez, Francisco G |
|
2013 |
7 |
1 |
|
article |
22 |
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells
|
Zhou, Yi |
|
2013 |
7 |
1 |
|
article |
23 |
Characterization of regulatory features of housekeeping and tissue-specific regulators within tissue regulatory networks
|
Li, Pengping |
|
2013 |
7 |
1 |
|
article |
24 |
Cluster and propensity based approximation of a network
|
Ranola, John Michael |
|
2013 |
7 |
1 |
|
article |
25 |
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
|
Ebrahim, Ali |
|
2013 |
7 |
1 |
|
article |
26 |
Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies
|
Hettling, Hannes |
|
2013 |
7 |
1 |
|
article |
27 |
Computational modelling of bovine ovarian follicle development
|
Iber, Dagmar |
|
2013 |
7 |
1 |
|
article |
28 |
Computational modelling of the regulation of Insulin signalling by oxidative stress
|
Smith, Graham R |
|
2013 |
7 |
1 |
|
article |
29 |
Consensus and conflict cards for metabolic pathway databases
|
Stobbe, Miranda D |
|
2013 |
7 |
1 |
|
article |
30 |
Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning
|
Kim, Soo-Jin |
|
2013 |
7 |
1 |
|
article |
31 |
Construction and analysis of the protein-protein interaction network related to essential hypertension
|
Ran, Jihua |
|
2013 |
7 |
1 |
|
article |
32 |
Construction of the influenza A virus infection-induced cell-specific inflammatory regulatory network based on mutual information and optimization
|
Jin, Suoqin |
|
2013 |
7 |
1 |
|
article |
33 |
Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder
|
Yang, Ruoting |
|
2013 |
7 |
1 |
|
article |
34 |
Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes
|
Williams-DeVane, ClarLynda R |
|
2013 |
7 |
1 |
|
article |
35 |
Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks
|
Crespo, Isaac |
|
2013 |
7 |
1 |
|
article |
36 |
Disentangling function from topology to infer the network properties of disease genes
|
Ghersi, Dario |
|
2013 |
7 |
1 |
|
article |
37 |
Dynamic cross-regulation of antigen-specific effector and regulatory T cell subpopulations and microglia in brain autoimmunity
|
Martinez-Pasamar, Sara |
|
2013 |
7 |
1 |
|
article |
38 |
Dynamic modeling of yeast meiotic initiation
|
Ray, Debjit |
|
2013 |
7 |
1 |
|
article |
39 |
Dynamic modelling of microRNA regulation during mesenchymal stem cell differentiation
|
Weber, Michael |
|
2013 |
7 |
1 |
|
article |
40 |
Dynamics of the quorum sensing switch: stochastic and non-stationary effects
|
Weber, Marc |
|
2013 |
7 |
1 |
|
article |
41 |
Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective
|
Massucci, Francesco A |
|
2013 |
7 |
1 |
|
article |
42 |
ENNET: inferring large gene regulatory networks from expression data using gradient boosting
|
Sławek, Janusz |
|
2013 |
7 |
1 |
|
article |
43 |
EnRICH: Extraction and Ranking using Integration and Criteria Heuristics
|
Zhang, Xia |
|
2013 |
7 |
1 |
|
article |
44 |
Estimating confidence intervals in predicted responses for oscillatory biological models
|
St John, Peter C |
|
2013 |
7 |
1 |
|
article |
45 |
FiloDetect: automatic detection of filopodia from fluorescence microscopy images
|
Nilufar, Sharmin |
|
2013 |
7 |
1 |
|
article |
46 |
From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials
|
Dent, Jennifer E |
|
2013 |
7 |
1 |
|
article |
47 |
Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer
|
Li, Kening |
|
2013 |
7 |
1 |
|
article |
48 |
Function and design of the Nox1 system in vascular smooth muscle cells
|
Yin, Weiwei |
|
2013 |
7 |
1 |
|
article |
49 |
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
|
Lawler, Katherine |
|
2013 |
7 |
1 |
|
article |
50 |
Global insights into energetic and metabolic networks in Rhodobacter sphaeroides
|
Imam, Saheed |
|
2013 |
7 |
1 |
|
article |
51 |
Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis
|
Jordà, Joel |
|
2013 |
7 |
1 |
|
article |
52 |
Identification of direction in gene networks from expression and methylation
|
Simcha, David M |
|
2013 |
7 |
1 |
|
article |
53 |
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework
|
Kumar, Gaurav |
|
2013 |
7 |
1 |
|
article |
54 |
Identification of parameter correlations for parameter estimation in dynamic biological models
|
Li, Pu |
|
2013 |
7 |
1 |
|
article |
55 |
Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization
|
Guillén-Gosálbez, Gonzalo |
|
2013 |
7 |
1 |
|
article |
56 |
Identification of upstream regulators for prognostic expression signature genes in colorectal cancer
|
Bae, Taejeong |
|
2013 |
7 |
1 |
|
article |
57 |
Identification of yeast cell cycle regulated genes based on genomic features
|
Cheng, Chao |
|
2013 |
7 |
1 |
|
article |
58 |
Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism
|
Barba, Matthieu |
|
2013 |
7 |
1 |
|
article |
59 |
Impaired coupling of local and global functional feedbacks underlies abnormal synchronization and negative symptoms of schizophrenia
|
Noh, Kyungchul |
|
2013 |
7 |
1 |
|
article |
60 |
(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis
|
He, Fei |
|
2013 |
7 |
1 |
|
article |
61 |
Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0
|
Weber, Michael |
|
2013 |
7 |
1 |
|
article |
62 |
Inferring ancient metabolism using ancestral core metabolic models of enterobacteria
|
Baumler, David J |
|
2013 |
7 |
1 |
|
article |
63 |
Inferring the effective TOR-dependent network: a computational study in yeast
|
Mohammadi, Shahin |
|
2013 |
7 |
1 |
|
article |
64 |
Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology
|
Santra, Tapesh |
|
2013 |
7 |
1 |
|
article |
65 |
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways
|
Pey, Jon |
|
2013 |
7 |
1 |
|
article |
66 |
Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia
|
Bessho, Kazuhiko |
|
2013 |
7 |
1 |
|
article |
67 |
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study
|
Wang, Yu-Chao |
|
2013 |
7 |
1 |
|
article |
68 |
In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae
|
Amara, Flavio |
|
2013 |
7 |
1 |
|
article |
69 |
Joint estimation of causal effects from observational and intervention gene expression data
|
Rau, Andrea |
|
2013 |
7 |
1 |
|
article |
70 |
JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis
|
Srivastava, Prashant K |
|
2013 |
7 |
1 |
|
article |
71 |
Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways
|
Sen, Partho |
|
2013 |
7 |
1 |
|
article |
72 |
Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer’s disease
|
Mayburd, Anatoly |
|
2013 |
7 |
1 |
|
article |
73 |
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis
|
Freyre-González, Julio A |
|
2013 |
7 |
1 |
|
article |
74 |
Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate
|
Bogdał, Marta N |
|
2013 |
7 |
1 |
|
article |
75 |
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling
|
Österlund, Tobias |
|
2013 |
7 |
1 |
|
article |
76 |
Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling
|
Borgos, Sven EF |
|
2013 |
7 |
1 |
|
article |
77 |
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study
|
Feltus, F Alex |
|
2013 |
7 |
1 |
|
article |
78 |
MC3: a steady-state model and constraint consistency checker for biochemical networks
|
Yousofshahi, Mona |
|
2013 |
7 |
1 |
|
article |
79 |
Merging concepts - coupling an agent-based model of hematopoietic stem cells with an ODE model of granulopoiesis
|
Krinner, Axel |
|
2013 |
7 |
1 |
|
article |
80 |
Mining breast cancer genes with a network based noise-tolerant approach
|
Nie, Yaling |
|
2013 |
7 |
1 |
|
article |
81 |
Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways
|
Kutumova, Elena |
|
2013 |
7 |
1 |
|
article |
82 |
Modeling heterogeneous responsiveness of intrinsic apoptosis pathway
|
Ooi, Hsu Kiang |
|
2013 |
7 |
1 |
|
article |
83 |
Modeling mutant phenotypes and oscillatory dynamics in the Saccharomyces cerevisiae cAMP-PKA pathway
|
Gonzales, Kevin |
|
2013 |
7 |
1 |
|
article |
84 |
Modeling of celiac disease immune response and the therapeutic effect of potential drugs
|
Demin, Oleg O |
|
2013 |
7 |
1 |
|
article |
85 |
Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs
|
Pokhilko, Alexandra |
|
2013 |
7 |
1 |
|
article |
86 |
Modularity and evolutionary constraints in a baculovirus gene regulatory network
|
Oliveira, Juliana Velasco |
|
2013 |
7 |
1 |
|
article |
87 |
Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits
|
Marchisio, Mario Andrea |
|
2013 |
7 |
1 |
|
article |
88 |
Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties
|
Liu, Yuanhua |
|
2013 |
7 |
1 |
|
article |
89 |
Multiple types of data are required to identify the mechanisms influencing the spatial expansion of melanoma cell colonies
|
Treloar, Katrina K |
|
2013 |
7 |
1 |
|
article |
90 |
MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples
|
Trifonov, Vladimir |
|
2013 |
7 |
1 |
|
article |
91 |
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
|
Kuperstein, Inna |
|
2013 |
7 |
1 |
|
article |
92 |
Nested sampling for parameter inference in systems biology: application to an exemplar circadian model
|
Aitken, Stuart |
|
2013 |
7 |
1 |
|
article |
93 |
Network based elucidation of drug response: from modulators to targets
|
Iorio, Francesco |
|
2013 |
7 |
1 |
|
article |
94 |
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network
|
Misra, Ashish |
|
2013 |
7 |
1 |
|
article |
95 |
New network topology approaches reveal differential correlation patterns in breast cancer
|
Bockmayr, Michael |
|
2013 |
7 |
1 |
|
article |
96 |
Noise propagation through extracellular signaling leads to fluctuations in gene expression
|
Tabbaa, Omar P |
|
2013 |
7 |
1 |
|
article |
97 |
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
|
Vafaee, Fatemeh |
|
2013 |
7 |
1 |
|
article |
98 |
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data
|
Kuo, Tien-Chueh |
|
2013 |
7 |
1 |
|
article |
99 |
Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model
|
Oguz, Cihan |
|
2013 |
7 |
1 |
|
article |
100 |
Optimization of personalized therapies for anticancer treatment
|
Vazquez, Alexei |
|
2013 |
7 |
1 |
|
article |
101 |
Path2Models: large-scale generation of computational models from biochemical pathway maps
|
Büchel, Finja |
|
2013 |
7 |
1 |
|
article |
102 |
Post-translational regulation enables robust p53 regulation
|
Shin, Yong-Jun |
|
2013 |
7 |
1 |
|
article |
103 |
Precise generation of systems biology models from KEGG pathways
|
Wrzodek, Clemens |
|
2013 |
7 |
1 |
|
article |
104 |
Probabilistic strain optimization under constraint uncertainty
|
Yousofshahi, Mona |
|
2013 |
7 |
1 |
|
article |
105 |
Promoter activity dynamics in the lag phase of Escherichia coli
|
Madar, Daniel |
|
2013 |
7 |
1 |
|
article |
106 |
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow
|
Mueller, Thomas J |
|
2013 |
7 |
1 |
|
article |
107 |
RaTrav: a tool for calculating mean first-passage times on biochemical networks
|
Torchala, Mieczyslaw |
|
2013 |
7 |
1 |
|
article |
108 |
Reaction-contingency based bipartite Boolean modelling
|
Flöttmann, Max |
|
2013 |
7 |
1 |
|
article |
109 |
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation
|
Pinna, Andrea |
|
2013 |
7 |
1 |
|
article |
110 |
Reconstruction of the experimentally supported human protein interactome: what can we learn?
|
Klapa, Maria I |
|
2013 |
7 |
1 |
|
article |
111 |
Rosen’s (M,R) system in process algebra
|
Gatherer, Derek |
|
2013 |
7 |
1 |
|
article |
112 |
Rule–based regulatory and metabolic model for Quorum sensing in P. aeruginosa
|
Schaadt, Nadine S |
|
2013 |
7 |
1 |
|
article |
113 |
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
|
Chaouiya, Claudine |
|
2013 |
7 |
1 |
|
article |
114 |
Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation
|
Hock, Sabrina |
|
2013 |
7 |
1 |
|
article |
115 |
Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells
|
Cho, Hyunju |
|
2013 |
7 |
1 |
|
article |
116 |
SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks
|
Fazekas, Dávid |
|
2013 |
7 |
1 |
|
article |
117 |
Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT
|
Liebal, Ulf W |
|
2013 |
7 |
1 |
|
article |
118 |
Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems
|
Rodriguez-Fernandez, Maria |
|
2013 |
7 |
1 |
|
article |
119 |
Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast
|
Yvert, Gaël |
|
2013 |
7 |
1 |
|
article |
120 |
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti
|
Ponce-de-León, Miguel |
|
2013 |
7 |
1 |
|
article |
121 |
Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice
|
Tchitchek, Nicolas |
|
2013 |
7 |
1 |
|
article |
122 |
Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration
|
Saithong, Treenut |
|
2013 |
7 |
1 |
|
article |
123 |
Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis
|
Greenfest-Allen, Emily |
|
2013 |
7 |
1 |
|
article |
124 |
Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κB signaling networks
|
Joo, Jaewook |
|
2013 |
7 |
1 |
|
article |
125 |
Stochastic flux analysis of chemical reaction networks
|
Kahramanoğulları, Ozan |
|
2013 |
7 |
1 |
|
article |
126 |
Structure, function, and behaviour of computational models in systems biology
|
Knüpfer, Christian |
|
2013 |
7 |
1 |
|
article |
127 |
Summarizing cellular responses as biological process networks
|
Lasher, Christopher D |
|
2013 |
7 |
1 |
|
article |
128 |
sybil – Efficient constraint-based modelling in R
|
Gelius-Dietrich, Gabriel |
|
2013 |
7 |
1 |
|
article |
129 |
Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries
|
Lee, Yi-Ying |
|
2013 |
7 |
1 |
|
article |
130 |
Systems analysis reveals a transcriptional reversal of the mesenchymal phenotype induced by SNAIL-inhibitor GN-25
|
Azmi, Asfar S |
|
2013 |
7 |
1 |
|
article |
131 |
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma
|
Pradhan, Meeta P |
|
2013 |
7 |
1 |
|
article |
132 |
The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models
|
Palsson, Sirus |
|
2013 |
7 |
1 |
|
article |
133 |
The last generation of bacterial growth in limiting nutrient
|
Bren, Anat |
|
2013 |
7 |
1 |
|
article |
134 |
The systems biology simulation core algorithm
|
Keller, Roland |
|
2013 |
7 |
1 |
|
article |
135 |
Topology of molecular interaction networks
|
Winterbach, Wynand |
|
2013 |
7 |
1 |
|
article |
136 |
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress
|
Wang, Qinghua |
|
2013 |
7 |
1 |
|
article |
137 |
Transcriptome meta-analysis reveals a central role for sex steroids in the degeneration of hippocampal neurons in Alzheimer’s disease
|
Winkler, Jessica M |
|
2013 |
7 |
1 |
|
article |
138 |
Transdifferentiation of pancreatic cells by loss of contact-mediated signaling
|
Back, Walter de |
|
2013 |
7 |
1 |
|
article |
139 |
Transient oscillatory dynamics of interferon beta signaling in macrophages
|
Pertsovskaya, Inna |
|
2013 |
7 |
1 |
|
article |
140 |
Translation of SBGN maps: Process Description to Activity Flow
|
Vogt, Torsten |
|
2013 |
7 |
1 |
|
article |
141 |
Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics
|
Salerno, Luca |
|
2013 |
7 |
1 |
|
article |
142 |
Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes
|
Shi, Hongbo |
|
2013 |
7 |
1 |
|
article |