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BMC Systems Biology, Volume 12
Volume 12, Number 1, December 2018
- Ian R. Vernon
, Junli Liu
, Michael Goldstein, James Rowe, Jen Topping, Keith Lindsey
:
Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions. 1:1-1:29 - Mohamed Shahen
, Zihu Guo
, Akhtar Hussain Shar, Reham Ebaid, Qin Tao, Wenjuan Zhang, Ziyin Wu, Yaofei Bai, Yingxue Fu
, Chunli Zheng, He Wang, Piar Ali Shar, Jianling Liu, Zhenzhong Wang, Wei Xiao, Yonghua Wang:
Dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs. 2:1-2:13 - Zhang Wang, Seda Arat
, Michal Magid-Slav, James R. Brown
:
Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets. 3:1-3:18 - Mohamed Shahen, Zihu Guo
, Akhtar Hussain Shar, Reham Ebaid, Qin Tao, Wenjuan Zhang, Ziyin Wu, Yaofei Bai, Yingxue Fu
, Chunli Zheng, He Wang, Piar Ali Shar, Jianling Liu, Zhenzhong Wang, Wei Xiao, Yonghua Wang:
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
, Lei Zhang
:
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
, Sankha Ghatak, Bernhard O. Palsson, Jonathan M. Monk
:
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
, Doheon Lee:
Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy. 26:1-26:11 - James T. Yurkovich
, Aarash Bordbar
, Ólafur E. Sigurjónsson, Bernhard O. Palsson:
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
, Fabian V. Filipp
:
Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma. 33:1-33:12 - Parvathi Haridas, Alexander P. Browning
, Jacqui A. McGovern, D. L. Sean McElwain, Matthew J. Simpson
:
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
, Aidong Yang:
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
, Reinhard C. Laubenbacher
, Linda H. Shapiro:
The innate immune response to ischemic injury: a multiscale modeling perspective. 50:1-50:13 - Alessandra Ordinelli
, Nicola Bernabò
, Massimiliano Orsini, Mauro Mattioli, Barbara Barboni:
Putative human sperm Interactome: a networks study. 52:1-52:10 - Martin Scharm
, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani
, Ali Salehzadeh-Yazdi
, Olaf Wolkenhauer, Dagmar Waltemath
:
Evolution of computational models in BioModels Database and the Physiome Model Repository. 53:1-53:10 - Sang-Mok Choo
, Byunghyun Ban, Jae Il Joo, Kwang-Hyun Cho:
The phenotype control kernel of a biomolecular regulatory network. 49:1-49:15 - Frank Kramer
, Steffen Just, Tanja Zeller
:
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
, Berthold Göttgens
, Jasmin Fisher
:
SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data. 59:1-59:7 - Bertrand De Meulder
, Diane Lefaudeux, Aruna T. Bansal, Alexander Mazein, Amphun Chaiboonchoe, Hassan Ahmed, Irina Balaur
, Mansoor A. S. Saqi
, Johann Pellet, Stéphane Ballereau, Nathanaël Lemonnier, Kai Sun, Ioannis Pandis, Xian Yang
, Manohara Batuwitage, Kosmas Kretsos, Jonathan van Eyll
, Alun Bedding, Timothy Davison, Paul Dodson, Christopher Larminie, Anthony D. Postle, Julie Corfield, Ratko Djukanovic
, Kian Fan Chung, Ian M. Adcock
, Yike Guo, Peter J. Sterk, Alexander Manta, Anthony Rowe
, Frédéric Baribaud, Charles Auffray:
A computational framework for complex disease stratification from multiple large-scale datasets. 60:1-60:23 - Bruno Pereira, Joana Miguel, Paulo Vilaça
, Simão Soares, Isabel Rocha
, Sónia Carneiro
:
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
, Rosa-María Gutiérrez-Ríos
:
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
, Nathan Mih, Bin Du, Anand Sastry
, Erol S. Kavvas, Yara Seif, Larry Smarr, Bernhard O. Palsson:
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
, Lei Zhang, Qing Nie:
Landscape reveals critical network structures for sharpening gene expression boundaries. 67:1-67:13 - Stefano Casagranda
, Suzanne Touzeau
, Delphine Ropers
, Jean-Luc Gouzé
:
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
, Luca Cardelli, Attila Csikász-Nagy
:
Single molecules can operate as primitive biological sensors, switches and oscillators. 70:1-70:14 - Abel Folch-Fortuny
, Bas Teusink
, Huub C. J. Hoefsloot, Age K. Smilde
, Alberto Ferrer
:
Dynamic elementary mode modelling of non-steady state flux data. 71:1-71:15 - Robert W. Smith, Rik P. van Rosmalen
, Vítor A. P. Martins dos Santos
, Christian Fleck
:
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. 72:1-72:16 - Peter D. Karp
, Daniel S. Weaver, Mario Latendresse:
How accurate is automated gap filling of metabolic models? 73:1-73:11 - Bin Huang
, Dongya Jia, Jingchen Feng, Herbert Levine
, José N. Onuchic, Mingyang Lu
:
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
, Alex N. Nguyen Ba, Alan M. Moses:
Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity. 75:1-75:13 - Hooman Sedghamiz, Matthew C. Morris
, Travis J. A. Craddock
, L. Darrell Whitley, Gordon Broderick
:
High-fidelity discrete modeling of the HPA axis: a study of regulatory plasticity in biology. 76:1-76:16 - Guan-Sheng Liu, Richard Ballweg
, Alan Ashbaugh, Yin Zhang
, Joseph Facciolo, Melanie T. Cushion, Tongli Zhang
:
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
, Ali Salehzadeh-Yazdi
, Zahra Razaghi-Moghadam
, Holger Hennig, Olaf Wolkenhauer, Mehdi Mirzaie
, Mohieddin Jafari
:
A systematic survey of centrality measures for protein-protein interaction networks. 80:1-80:17 - Michael A. Rowland, Hannah Wear, Karen H. Watanabe
, Kurt A. Gust, Michael L. Mayo:
Statistical relationship between metabolic decomposition and chemical uptake predicts bioconcentration factor data for diverse chemical exposures. 81:1-81:12 - Andreas Kremling
, Johannes Geiselmann
, Delphine Ropers
, Hidde de Jong
:
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
, Christine Ann Shoemaker
, Jeffrey D. Varner
:
Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models. 87:1-87:15 - Theresia Conrad
, Olaf Kniemeyer, Sebastian Henkel, Thomas Krüger
, D. J. Mattern, Vito Valiante
, Reinhard Guthke, I. D. Jacobsen, Axel A. Brakhage, Sebastian Vlaic, Jörg Linde:
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
, H. Frederik Nijhout:
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
, Fabian Moreno
, Noemí Flores, Alvaro R. Lara
, Octavio T. Ramírez, Guillermo Gosset, Francisco Bolivar:
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
, Stacey D. Finley
:
Mechanistic insight into activation of MAPK signaling by pro-angiogenic factors. 145:1-145:17 - Muhammad Tariq Saeed, Jamil Ahmad, Jan Baumbach
, Josch Pauling, Aamir Shafi
, Rehan Zafar Paracha
, Asad Hayat, Amjad Ali
:
Parameter estimation of qualitative biological regulatory networks on high performance computing hardware. 146:1-146:15
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