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ORCIDBMC Systems Biology, Volume 4
Volume 4, 2010
- Tommaso Mazza
, Gennaro Iaccarino, Corrado Priami:
Snazer: the simulations and networks analyzer. 1 - Antoine Coulon, Olivier Gandrillon, Guillaume Beslon:
On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter. 2 - Rebecca Hamer, Pao-Yang Chen, Judith P. Armitage, Gesine Reinert, Charlotte M. Deane:
Deciphering chemotaxis pathways using cross species comparisons. 3 - Juuso A. Parkkinen, Samuel Kaski:
Searching for functional gene modules with interaction component models. 4 - Alexey M. Shibeko, Ekaterina S. Lobanova, Mikhail A. Panteleev, Fazoil I. Ataullakhanov:
Blood flow controls coagulation onset via the positive feedback of factor VII activation by factor Xa. 5 - Kieran Smallbone, Evangelos Simeonidis, Neil Swainston, Pedro Mendes:
Towards a genome-scale kinetic model of cellular metabolism. 6 - Stacey D. Finley, Linda J. Broadbelt, Vassily Hatzimanikatis:
In silico feasibility of novel biodegradation pathways for 1, 2, 4-trichlorobenzene. 7 - Jianhua Ruan, Angela K. Dean, Weixiong Zhang:
A general co-expression network-based approach to gene expression analysis: comparison and applications. 8 - Heinrich J. Huber, Maike A. Laussmann, Jochen H. M. Prehn, Markus Rehm:
Diffusion is capable of translating anisotropic apoptosis initiation into a homogeneous execution of cell death. 9 - An-Yuan Guo, Jingchun Sun, Peilin Jia, Zhongming Zhao:
A Novel microRNA and transcription factor mediated regulatory network in schizophrenia. 10 - Eva Balsa-Canto, Antonio A. Alonso, Julio R. Banga:
An iterative identification procedure for dynamic modeling of biochemical networks. 11 - Sarah-Maria Fendt, Uwe Sauer:
Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates. 12 - Andrei Yu. Zinovyev, Nadya Morozova, Nora Nonne, Emmanuel Barillot, Annick Harel-Bellan, Alexander N. Gorban:
Dynamical modeling of microRNA action on the protein translation process. 13 - Philippos Peidis, Thomas Giannakouros, Matthew E. Burow, Robert W. Williams, Robert E. Scott:
Systems genetics analyses predict a transcription role for P2P-R: Molecular confirmation that P2P-R is a transcriptional co-repressor. 14 - Guy Karlebach, Ron Shamir:
Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case. 15 - Chung-Ming Chen, Chi Lee, Cheng-Long Chuang, Chia-Chang Wang, Grace S. Shieh:
Inferring genetic interactions via a nonlinear model and an optimization algorithm. 16 - Luke Jostins, Johannes Jaeger:
Reverse engineering a gene network using an asynchronous parallel evolution strategy. 17 - Núria Domedel-Puig, Iosifina Pournara, Lorenz Wernisch:
Statistical model comparison applied to common network motifs. 18 - Tatiana T. Marquez-Lago, André Leier, Kevin Burrage:
Probability distributed time delays: integrating spatial effects into temporal models. 19 - Yu-Chao Wang, Bor-Sen Chen:
Integrated cellular network of transcription regulations and protein-protein interactions. 20 - Michael Dewar, Visakan Kadirkamanathan, Manfred Opper, Guido Sanguinetti:
Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster. 21 - Derek Gatherer:
So what do we really mean when we say that systems biology is holistic? 22 - Bart S. Hendriks, Kelly M. Seidl, Jeffrey R. Chabot:
Two additive mechanisms impair the differentiation of 'substrate-selective' p38 inhibitors from classical p38 inhibitors in vitro. 23 - Dominic P. Tolle, Nicolas Le Novère:
Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. 24 - Dominic P. Tolle, Nicolas Le Novère:
Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP. 25 - Zhen Qi, Gary W. Miller, Eberhard O. Voit:
The internal state of medium spiny neurons varies in response to different input signals. 26 - Stefan Streif, Dieter Oesterhelt, Wolfgang Marwan:
A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis. 27 - Mikael Sunnåker, Henning Schmidt, Mats Jirstrand, Gunnar Cedersund:
Zooming of states and parameters using a lumping approach including back-translation. 28 - Jong-Min Lee, Jie Zhang, Andrew I. Su, John R. Walker, Tim Wiltshire, Kihwa Kang, Ella Dragileva, Tammy Gillis, Edith T. Lopez, Marie-Josee Boily, Michel Cyr, Isaac S. Kohane, James F. Gusella, Marcy E. MacDonald, Vanessa C. Wheeler:
A novel approach to investigate tissue-specific trinucleotide repeat instability. 29 - Areejit Samal, João F. Matias Rodrigues, Jürgen Jost, Olivier C. Martin, Andreas Wagner:
Genotype networks in metabolic reaction spaces. 30 - Seth B. Roberts, Chris M. Gowen, J. Paul Brooks, Stephen S. Fong:
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. 31 - Suresh Swain, Jodie F. Wren, Stephen R. Stürzenbaum, Peter Kille, A. John Morgan, Tjalling Jager, Martijs J. Jonker, Peter K. Hankard, Claus Svendsen, Jenifer Owen, Ann Hedley, Mark L. Blaxter, David J. Spurgeon:
Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans. 32 - Yuan Xiong, Cathryn Kabacoff, Jonathan Franca-Koh, Peter N. Devreotes, Douglas N. Robinson, Pablo A. Iglesias:
Automated characterization of cell shape changes during amoeboid motility by skeletonization. 33 - Jamie Twycross, Leah R. Band, Malcolm Bennett, John R. King, Natalio Krasnogor:
Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study. 34 - Ayoun Cho, Hongseok Yun, Jin Park, Sang Lee, Sunwon Park:
Prediction of novel synthetic pathways for the production of desired chemicals. 35 - Amy M. Wiles, Mark Doderer, Jianhua Ruan, Tingting Gu, Ravi Dashnamoorthy, Barron Blackman, Alexander J. R. Bishop:
Building and analyzing protein interactome networks by cross-species comparisons. 36 - Yi Zhang, Kim A. Hatch, Joanna Bacon, Lorenz Wernisch:
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis. 37 - Bence Mélykúti, Elias August, Antonis Papachristodoulou, Hana El-Samad:
Discriminating between rival biochemical network models: three approaches to optimal experiment design. 38 - Chen Li, Masao Nagasaki, Ayumu Saito, Satoru Miyano:
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. 39 - Qiang Zhang, Sudin Bhattacharya, Douglas Kline, Robert B. Crawford, Rory B. Conolly, Russell S. Thomas, Norbert E. Kaminski, Melvin E. Andersen:
Stochastic Modeling of B Lymphocyte Terminal Differentiation and Its Suppression by Dioxin. 40 - Eleonora Piruzian, Sergey Bruskin, Alexander Ishkin, Rustam Abdeev, Sergey Moshkovskii, Stanislav Melnik, Yuri Nikolsky, Tatiana Nikolskaya:
Integrated network analysis of transcriptomic and proteomic data in psoriasis. 41 - Verena Wolf, Rushil Goel, Maria Mateescu, Thomas A. Henzinger:
Solving the chemical master equation using sliding windows. 42 - Alain Coletta, John W. Pinney, David Y. Weiss Solís, James Marsh, Steve Pettifer, Teresa K. Attwood:
Low-complexity regions within protein sequences have position-dependent roles. 43 - Nurul Mohamad, Mikael Bodén:
The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. 44 - Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha:
OptFlux: an open-source software platform for in silico metabolic engineering. 45 - Juan C. Triviño, Florencio Pazos:
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. 46 - Jin Gu, Yang Chen, Shao Li, Yanda Li:
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. 47 - Guillermo Rodrigo, Javier Carrera, Santiago F. Elena, Alfonso Jaramillo:
Robust dynamical pattern formation from a multifunctional minimal genetic circuit. 48 - Brett A. Boghigian, Hai Shi, Kyongbum Lee, Blaine A. Pfeifer:
Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design. 49 - Han Yan, Bo Zhang, Shao Li, Qianchuan Zhao:
A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway. 50 - Huiqing Liu, Angela Rose Brannon, Anupama Reddy, Gabriela Alexe, Michael Seiler, Alexandra Arreola, Jay H. Oza, Ming Yao, David Juan, Louis S. Liou, Shridar Ganesan, Arnold J. Levine, W. Kimryn Rathmell, Gyan Bhanot:
Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. 51 - Matteo Brilli, Marco Fondi, Renato Fani, Alessio Mengoni, Lorenzo Ferri, Marco Bazzicalupo, Emanuele G. Biondi:
The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis. 52 - Joonhoon Kim, Jennifer L. Reed:
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. 53 - Klaus Maier, Ute Hofmann, Matthias Reuss, Klaus Mauch:
Dynamics and Control of the Central Carbon Metabolism in Hepatoma Cells. 54 - Hidde de Jong, Caroline Ranquet, Delphine Ropers, Corinne Pinel, Johannes Geiselmann:
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. 55 - Kitiporn Plaimas, Roland Eils, Rainer König:
Identifying essential genes in bacterial metabolic networks with machine learning methods. 56 - Ming-yu Hsieh, Shujie Yang, Mary Raymond-Stinz, Jeremy S. Edwards, Bridget S. Wilson:
Spatio-temporal modeling of signaling protein recruitment to EGFR. 57 - Alexei Vazquez, Jiangxia Liu, Yi Zhou, Zoltán N. Oltvai:
Catabolic efficiency of aerobic glycolysis: The Warburg effect revisited. 58 - Aurélien Mazurie, Danail Bonchev, Benno Schwikowski, Gregory A. Buck:
Evolution of metabolic network organization. 59 - Francisco Azuaje, Yvan Devaux, Daniel R. Wagner:
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. 60 - Joachim B. Ritter, Aljoscha Wahl, Susann Freund, Yvonne Genzel, Udo Reichl:
Metabolic effects of influenza virus infection in cultured animal cells: Intra- and extracellular metabolite profiling. 61 - Elizabeth Allen, Annick Moing, Timothy M. D. Ebbels, Mickaël Maucourt, A. Deri Tomos, Dominique Rolin, Mark A. Hooks:
Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis. 62 - Sobia Raza, Neil McDerment, Paul A. Lacaze, Kevin A. Robertson, Steven Watterson, Ying Chen, Michael Chisholm, George Eleftheriadis, Stephanie Monk, Maire O'Sullivan, Arran Turnbull, Douglas Roy, Athanasios Theocharidis, Peter Ghazal, Tom C. Freeman:
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. 63 - Marc T. Facciotti, Wyming Lee Pang, Fang-Yin Lo, Kenia Whitehead, Tie Koide, Ken-ichi Masumura, Min Pan, Amardeep Kaur, David J. Larsen, David J. Reiss, Linh Hoang, Ewa Kalisiak, Trent Northen, Sunia A. Trauger, Gary Siuzdak, Nitin S. Baliga:
Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. 64 - Tom C. Freeman, Sobia Raza, Athanasios Theocharidis, Peter Ghazal:
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. 65 - Andreea Munteanu, Marco Constante, Mark Isalan, Ricard V. Solé:
Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation. 66 - Raj Chari, Bradley P. Coe, Emily A. Vucic, William W. Lockwood, Wan L. Lam:
An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. 67 - Subir K. Nandy, Paula Jouhten, Jens Nielsen:
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. 68 - Philipp Rumschinski, Steffen Borchers, Sandro Bosio, Robert Weismantel, Rolf Findeisen:
Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks. 69 - Hung Ta, Chang Yoon, Liisa Holm, Seung Han:
Inferring the physical connectivity of complex networks from their functional dynamics. 70 - Dokyun Na, Sunjae Lee, Doheon Lee:
Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. 71 - Xian-Wen Ren, Xiaobo Zhou, Ling-Yun Wu, Xiang-Sun Zhang:
An information-flow-based model with dissipation, saturation and direction for active pathway inference. 72 - Axel Krinner, Martin Hoffmann, Markus Loeffler, Dirk Drasdo, Jörg Galle:
Individual fates of mesenchymal stem cells in vitro. 73 - Zhiao Shi, Catherine K. Derow, Bing Zhang:
Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. 74 - Carla J. Davidson, Atul Narang, Michael G. Surette:
Integration of transcriptional inputs at promoters of the arabinose catabolic pathway. 75 - Ettore Mosca, Roberta Alfieri, Ivan Merelli, Federica Viti, Andrea Calabria, Luciano Milanesi:
A multilevel data integration resource for breast cancer study. 76 - Diana Fusco, Luigi Grassi, Bruno Bassetti, Michele Caselle, Marco Cosentino Lagomarsino:
Ordered structure of the transcription network inherited from the yeast whole-genome duplication. 77 - Sreenivas Chavali, Fredrik Barrenäs, Kartiek Kanduri, Mikael Benson:
Network properties of human disease genes with pleiotropic effects. 78 - Jonathan Fromentin, Damien Eveillard, Olivier F. Roux:
Hybrid modeling of biological networks: mixing temporal and qualitative biological properties. 79 - Jonathan E. Dickerson, John W. Pinney, David L. Robertson:
The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. 80 - Mi Zhang, William R. Schafer, Rainer Breitling:
A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior. 81 - Chao Wu, Fan Zhang, Xia Li, Shihua Zhang, Jiang Li, Fei Su, Kongning Li, YuQing Yan:
Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test. 82 - Giovanni Iacono, Claudio Altafini:
Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks. 83 - Hsiang Ho, Tijana Milenkovic, Vesna Memisevic, Jayavani Aruri, Natasa Przulj, Anand K. Ganesan:
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. 84 - Nadia Felli, Luciano Cianetti, Elvira Pelosi, Alessandra Carè, Chang Liu, George A. Calin, Simona Rossi, Cesare Peschle, Giovanna Marziali, Alessandro Giuliani:
Hematopoietic differentiation: a coordinated dynamical process towards attractor stable states. 85 - Michal Dabrowski, Norbert Dojer, Malgorzata Zawadzka, Jakub Mieczkowski, Bozena Kaminska:
Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems. 86 - Nicola Bernabò, Mauro Mattioli, Barbara Barboni:
The spermatozoa caught in the net: the biological networks to study the male gametes post-ejaculatory life. 87 - Ozgur E. Akman, David A. Rand, Paul E. Brown, Andrew J. Millar:
Robustness from flexibility in the fungal circadian clock. 88 - Jason E. Shoemaker, Kalyan Gayen, Natàlia Garcia-Reyero, Edward J. Perkins, Daniel L. Villeneuve, Li Liu, Francis J. Doyle:
Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk. 89 - Chengxiang Qiu, Juan Wang, Pengying Yao, Edwin Wang, Qinghua Cui:
microRNA evolution in a human transcription factor and microRNA regulatory network. 90 - Ryo Hashimoto, Kazuko Hirose, Taku Sato, Nobuhiro Fukushima, Nobuaki Miura, Shin-Ichiro Nishimura:
Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank. 91 - Chen Li, Marco Donizelli, Nicolas Rodriguez, Harish Dharuri, Lukas Endler, Vijayalakshmi Chelliah, Lu Li, Enuo He, Arnaud Henry, Melanie I. Stefan, Jacky L. Snoep, Michael Hucka, Nicolas Le Novère, Camille Laibe:
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. 92 - William J. Bosl, Rong Li:
The role of noise and positive feedback in the onset of autosomal dominant diseases. 93 - Alexander Hunziker, Mogens H. Jensen, Sandeep Krishna:
Stress-specific response of the p53-Mdm2 feedback loop. 94 - Balaji Veeramani, Joel S. Bader:
Predicting functional associations from metabolism using bi-partite network algorithms. 95 - David van Dijk, Gökhan Ertaylan, Charles A. B. Boucher, Peter M. A. Sloot:
Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. 96 - Hong Yu, Jialiang Huang, Nan Qiao, Christopher D. Green, Jing-Dong J. Han:
Evaluating diabetes and hypertension disease causality using mouse phenotypes. 97 - Victoria V. Mironova, Nadezda A. Omelyanchuk, Guy Yosiphon, Stanislav I. Fadeev, Nikolay A. Kolchanov, Eric Mjolsness, Vitali A. Likhoshvai:
A plausible mechanism for auxin patterning along the developing root. 98 - Yuanfeng Wang, Scott Christley, Eric Mjolsness, Xiaohui Xie:
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. 99 - Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, Charlotte M. Deane:
The function of communities in protein interaction networks at multiple scales. 100 - Simon van Mourik, Aalt D. J. van Dijk, Maarten de Gee, Richard G. H. Immink, Kerstin Kaufmann, Gerco C. Angenent, Roeland C. H. J. van Ham, Jaap Molenaar:
Continuous-time modeling of cell fate determination in Arabidopsis flowers. 101 - Elisabetta Marras, Antonella Travaglione, Gautam Chaurasia, Matthias E. Futschik, Enrico Capobianco:
Inferring modules from human protein interactome classes. 102 - Thanh-Phuong Nguyen, Ferenc Jordán:
A quantitative approach to study indirect effects among disease proteins in the human protein interaction network. 103 - Andrew E. Teschendorff, Simone Severini:
Increased entropy of signal transduction in the cancer metastasis phenotype. 104 - Abhay K. Singh, Thanura R. Elvitigala, Jeffrey C. Cameron, Bijoy K. Ghosh, Maitrayee Bhattacharyya-Pakrasi, Himadri B. Pakrasi:
Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium. 105 - Andrea C. Pfeifer, Daniel Kaschek, Julie Bachmann, Ursula Klingmüller, Jens Timmer:
Model-based extension of high-throughput to high-content data. 106 - Scott Christley, Briana Lee, Xing Dai, Qing Nie:
Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. 107 - Steffen Waldherr, Jingbo Wu, Frank Allgöwer:
Bridging time scales in cellular decision making with a stochastic bistable switch. 108 - Nail M. Gizzatkulov, Igor Goryanin, Eugeny A. Metelkin, Ekaterina A. Mogilevskaya, Kirill Peskov, Oleg V. Demin:
DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. 109 - Pau Rué, Jordi Villà-Freixa, Kevin Burrage:
Simulation methods with extended stability for stiff biochemical Kinetics. 110 - Mariana Obertello, Gabriel Krouk, Manpreet S. Katari, Suzan J. Runko, Gloria M. Coruzzi:
Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis. 111