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BMC Systems Biology, Volume 12
Volume 12, Number 1, December 2018
- Ian R. Vernon
, Junli Liu
Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions. 1:1-1:29 - Mohamed Shahen
Dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs. 2:1-2:13 - Zhang Wang, Seda Arat
Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets. 3:1-3:18 - Mohamed Shahen, Zihu Guo
Correction to: dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs. 21:1 - Peijia Yu, Qing Nie, Chao Tang
Nanog induced intermediate state in regulating stem cell differentiation and reprogramming. 22:1-22:13 - Erol S. Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. 25:1-25:15 - Jinmyung Jung, Mijin Kwon, Sunghwa Bae, Soorin Yim
Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy. 26:1-26:11 - James T. Yurkovich
Systems biology as an emerging paradigm in transfusion medicine. 31:1-31:9 - Helma Zecena, Daniel Tveit, Zi Wang, Ahmed Farhat, Parvita Panchal, Jing Liu, Simar J. Singh, Amandeep Sanghera, Ajay Bainiwal, Shuan Y. Teo, Frank L. Meyskens Jr, Feng Liu-Smith
Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma. 33:1-33:12 - Parvathi Haridas, Alexander P. Browning
Three-dimensional experiments and individual based simulations show that cell proliferation drives melanoma nest formation in human skin tissue. 34:1-34:15 - Bo Zhang, Hua Ye
Mathematical modelling of interacting mechanisms for hypoxia mediated cell cycle commitment for mesenchymal stromal cells. 35:1-35:18 - Fang Yang, Meng Wang, Baoyun Zhang, Wei Xiang, Ke Zhang, Mingxin Chu, Pingqing Wang:
Identification of new progestogen-associated networks in mammalian ovulation using bioinformatics. 36:1-36:12 - Elena S. Dimitrova, Leslie A. Caromile
The innate immune response to ischemic injury: a multiscale modeling perspective. 50:1-50:13 - Alessandra Ordinelli
Putative human sperm Interactome: a networks study. 52:1-52:10 - Martin Scharm
Evolution of computational models in BioModels Database and the Physiome Model Repository. 53:1-53:10 - Sang-Mok Choo
The phenotype control kernel of a biomolecular regulatory network. 49:1-49:15 - Frank Kramer
New perspectives: systems medicine in cardiovascular disease. 57:1-57:13 - Qingyang Zhang
A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test. 58:1-58:16 - Steven Woodhouse, Nir Piterman, Christoph M. Wintersteiger
SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data. 59:1-59:7 - Bertrand De Meulder
A computational framework for complex disease stratification from multiple large-scale datasets. 60:1-60:23 - Bruno Pereira, Joana Miguel, Paulo Vilaça
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. 61:1-61:12 - Claudia C. Preston, Saranya Wyles, Santiago Reyes, Emily C. Storm, Bruce W. Eckloff, Randolph Faustino
NUP155 insufficiency recalibrates a pluripotent transcriptome with network remodeling of a cardiogenic signaling module. 62:1-62:13 - Carlos Vazquez-Hernandez, Antonio Loza, Esteban Peguero-Sanchez, Lorenzo Segovia
Identification of reaction organization patterns that naturally cluster enzymatic transformations. 63:1-63:17 - Brian C. Ross, Mayla Boguslav, Holly Weeks, James C. Costello
Simulating heterogeneous populations using Boolean models. 64:1-64:11 - Marcus Thomas, Russell Schwartz
A method for efficient Bayesian optimization of self-assembly systems from scattering data. 65:1-65:17 - Xin Fang, Jonathan M. Monk
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. 66:1-66:10 - Chunhe Li
Landscape reveals critical network structures for sharpening gene expression boundaries. 67:1-67:13 - Stefano Casagranda
Principal process analysis of biological models. 68:1-68:26 - Colin P. McNally, Elhanan Borenstein:
Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss. 69:1-69:14 - Rosa D. Hernansaiz-Ballesteros
Single molecules can operate as primitive biological sensors, switches and oscillators. 70:1-70:14 - Abel Folch-Fortuny
Dynamic elementary mode modelling of non-steady state flux data. 71:1-71:15 - Robert W. Smith, Rik P. van Rosmalen
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. 72:1-72:16 - Peter D. Karp
How accurate is automated gap filling of metabolic models? 73:1-73:11 - Bin Huang
RACIPE: a computational tool for modeling gene regulatory circuits using randomization. 74:1-74:12 - Bob Strome, Ian Shenyen Hsu, Mitchell Li Cheong Man, Taraneh Zarin
Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity. 75:1-75:13 - Hooman Sedghamiz, Matthew C. Morris
High-fidelity discrete modeling of the HPA axis: a study of regulatory plasticity in biology. 76:1-76:16 - Guan-Sheng Liu, Richard Ballweg
A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice. 77:1-77:12 - Rajat Anand, Dipanka Sarmah, Samrat Chatterjee
Extracting proteins involved in disease progression using temporally connected networks. 78:1-78:13 - Håvard G. Frøysa, Shirin Fallahi, Nello Blaser
Evaluating model reduction under parameter uncertainty. 79:1-79:10 - Minoo Ashtiani
A systematic survey of centrality measures for protein-protein interaction networks. 80:1-80:17 - Michael A. Rowland, Hannah Wear, Karen H. Watanabe
Statistical relationship between metabolic decomposition and chemical uptake predicts bioconcentration factor data for diverse chemical exposures. 81:1-81:12 - Andreas Kremling
An ensemble of mathematical models showing diauxic growth behaviour. 82:1-82:16 - Kimberly C. Olney, David B. Nyer, Daniel A. Vargas, Melissa A. Wilson Sayres, Karmella A. Haynes
The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells. 83:1-83:17 - Elliot Rowe, Bernhard O. Palsson, Zachary A. King:
Escher-FBA: a web application for interactive flux balance analysis. 84:1-84:7 - Xinyue Luo, Ruijie Song, Murat Acar:
Multi-component gene network design as a survival strategy in diverse environments. 85:1-85:11 - Daniel Cook, Sirisha Achanta, Jan B. Hoek, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli
Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics. 86:1-86:29 - Adithya Sagar, Rachel LeCover
Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models. 87:1-87:15 - Theresia Conrad
Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. 88:1-88:18 - Farrah Sadre-Marandi, Thabat Dahdoul, Michael C. Reed
Sex differences in hepatic one-carbon metabolism. 89:1-89:13 - Yan-feng Cao, Shi-feng Wang, Xi Li, Yanling Zhang, Yanjiang Qiao:
The anticancer mechanism investigation of Tanshinone IIA by pharmacological clustering in protein network. 90:1-90:12 - Juan A. Martínez, Alberto Rodriguez
Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production. 102:1-102:26 - Retraction Note: detangling PPI networks to uncover functionally meaningful clusters. 113:1
- Gabriela I. Guzmán, Connor A. Olson, Ying Hefner, Patrick V. Phaneuf, Edward Catoiu, Lais B. Crepaldi, Lucas Goldschmidt Micas, Bernhard O. Palsson, Adam M. Feist
Reframing gene essentiality in terms of adaptive flexibility. 143:1-143:20 - Günter Neumann, Rebecca Wall, Ignacio Rangel, Tatiana M. Marques, Dirk Repsilber
Qualitative modelling of the interplay of inflammatory status and butyrate in the human gut: a hypotheses about robust bi-stability. 144:1-144:11 - Min Song
Mechanistic insight into activation of MAPK signaling by pro-angiogenic factors. 145:1-145:17 - Muhammad Tariq Saeed, Jamil Ahmad, Jan Baumbach
Parameter estimation of qualitative biological regulatory networks on high performance computing hardware. 146:1-146:15
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