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ORCIDBMC Systems Biology, Volume 6
Volume 6, 2012
- Bettina M. Länger, Cristina Pou-Barreto, Carlos González-Alcón
, Basilio Valladares, Bettina Wimmer, Néstor V. Torres:
Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies. 1 - 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:
Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control. 2 - Rotem Ben-Hamo, Sol Efroni:
Biomarker robustness reveals the PDGF network as driving disease outcome in ovarian cancer patients in multiple studies. 3 - Pinar Pir, Alex Gutteridge, Jian Wu, Bharat Rash, Douglas B. Kell, Nianshu Zhang, Stephen G. Oliver:
The genetic control of growth rate: a systems biology study in yeast. 4 - Liang-Chun Chen, Hsiang-Yuan Yeh, Cheng-Yu Yeh, Carlos Arias, Von-Wun Soo:
Identifying co-targets to fight drug resistance based on a random walk model. 5 - Jörg Linde, Peter Hortschansky, Eugen Fazius, Axel A. Brakhage, Reinhard Guthke, Hubertus Haas:
Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. 6 - Stefanie Widder, Ricard V. Solé, Javier Macía:
Evolvability of feed-forward loop architecture biases its abundance in transcription networks. 7 - Joost Boele, Brett G. Olivier, Bas Teusink:
FAME, the Flux Analysis and Modeling Environment. 8 - Jan Schellenberger, Daniel C. Zielinski, Wing Choi, Sunthosh Madireddi, Vasiliy Portnoy, David A. Scott, Jennifer L. Reed, Andrei Osterman, Bernhard Ø. Palsson:
Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. 9 - Pablo Carbonell, Davide Fichera, Shashi Bhushan Pandit, Jean-Loup Faulon:
Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. 10 - Josef Thingnes, Timothy J. Lavelle, Arne B. Gjuvsland, Stig W. Omholt, Eivind Hovig:
Towards a quantitative understanding of the MITF-PIAS3-STAT3 connection. 11 - Naveed Aslam, Harel Z. Shouval:
Regulation of cytoplasmic polyadenylation can generate a bistable switch. 12 - Thomas Maiwald, Julie Blumberg, Andreas Raue, Stefan Hengl, Marcel Schilling, Sherwin K. B. Sy, Verena Becker, Ursula Klingmüller, Jens Timmer:
In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems. 13 - Irina Surovtsova, Natalia Simus, Katrin Hübner, Sven Sahle, Ursula Kummer:
Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. 14 - Min Li, Hanhui Zhang, Jianxin Wang, Yi Pan:
A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. 15 - Sabrina Kleessen, Zoran Nikoloski:
Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. 16 - Joji M. Otaki:
Structural analysis of eyespots: dynamics of morphogenic signals that govern elemental positions in butterfly wings. 17 - Chen-Ching Lin, Ya-Jen Chen, Cho-Yi Chen, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang:
Crosstalk between transcription factors and microRNAs in human protein interaction network. 18 - Tian Xia, Jiansong Tong, Shailendra S. Rathore, Xun Gu, Julie A. Dickerson:
Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis. 19 - (Withdrawn) Predicting new molecular targets for rhein using network pharmacology. 20
- Skylar W. Marvel, Cranos M. Williams:
Set membership experimental design for biological systems. 21 - Milan van Hoek, Roeland Merks:
Redox balance is key to explaining full vs. partial switching to low-yield metabolism. 22 - Chao-Yi Dong, Kwang-Hyun Cho:
An optimally evolved connective ratio of neural networks that maximizes the occurrence of synchronized bursting behavior. 23 - Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew, Jens Nielsen:
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. 24 - Mikolaj Rybinski, Michal Lula, Pawel Banasik, Slawomir Lasota, Anna Gambin:
Tav4SB: integrating tools for analysis of kinetic models of biological systems. 25 - Barbara Szomolay, Vahid Shahrezaei:
Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles: the role of kinase-phosphatase complex formation. 26 - Arvind K. Chavali, Anna S. Blazier, Jose L. Tlaxca, Paul A. Jensen, Richard D. Pearson, Jason A. Papin:
Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. 27 - Jason E. McDermott, Deborah L. Diamond, Courtney D. Corley, Angela L. Rasmussen, Michael G. Katze, Katrina M. Waters:
Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis. 28 - Daniel C. Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M. Burke, Douglas A. Lauffenburger, Peter K. Sorger:
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. 29 - Jeffrey D. Orth, Bernhard Ø. Palsson:
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. 30 - Man-Sun Kim, Jeong-Rae Kim, Dong San Kim, Arthur D. Lander, Kwang-Hyun Cho:
Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster. 31 - Zuguang Gu, Chenyu Zhang, Jin Wang:
Gene regulation is governed by a core network in hepatocellular carcinoma. 32 - Hendrik Rohn, Anja Hartmann, Astrid Junker, Björn H. Junker, Falk Schreiber:
FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks. 33 - Dapeng Hao, Cong Ren, Chuanxing Li:
Revisiting the variation of clustering coefficient of biological networks suggests new modular structure. 34 - Nicolás Loira, Thierry Dulermo, Jean-Marc Nicaud, David James Sherman:
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. 35 - Iain Hepburn, Weiliang Chen, Stefan Wils, Erik De Schutter:
STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. 36 - Verônica A. Grieneisen, Ben Scheres, Paulien Hogeweg, Athanasius F. M. Marée:
Morphogengineering roots: comparing mechanisms of morphogen gradient formation. 37 - Ricardo de Matos Simoes, Shailesh Tripathi, Frank Emmert-Streib:
Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. 38 - Philipp Thomas, Arthur V. Straube, Ramon Grima:
The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions. 39 - Zhengzhang Chen, Kanchana Padmanabhan, Andrea M. Rocha, Yekaterina Shpanskaya, James R. Mihelcic, Kathleen Scott, Nagiza F. Samatova:
Spice: discovery of phenotype-determining component interplays. 40 - Nikolaus Sonnenschein, José Felipe Golib Dzib, Annick Lesne, Sebastian Eilebrecht, Sheerazed Boulkroun, Maria-Christina Zennaro, Arndt Benecke, Marc-Thorsten Hütt:
A network perspective on metabolic inconsistency. 41 - Michael J. McAnulty, Jiun Y. Yen, Benjamin G. Freedman, Ryan S. Senger:
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico. 42 - Scott B. Crown, Woo Ahn, Maciek R. Antoniewicz:
Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells. 43 - Davide Luciani, Gianfranco Bazzoni:
From networks of protein interactions to networks of functional dependencies. 44 - Maria Bravo, Thomas Orfeo, Kenneth G. Mann, Stephen J. Everse:
Modeling of human factor Va inactivation by activated protein C. 45 - Pedro Gonnet, Sotiris Dimopoulos, Lukas Widmer, Jörg Stelling:
A specialized ODE integrator for the efficient computation of parameter sensitivities. 46 - Rachel S. Koh, Mary J. Dunlop:
Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network. 47 - Kevin B. Wood, Philippe Cluzel:
Trade-offs between drug toxicity and benefit in the multi-antibiotic resistance system underlie optimal growth of E. coli. 48 - Seung Sohn, Tae Kim, Jay H. Lee, Sang Lee:
Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth. 49 - Ricardo J. Flores, Yiting Li, Alexander Yu, Jianhe Shen, Pulivarthi H. Rao, Serrine S. Lau, Marina Vannucci, Ching C. Lau, Tsz-Kwong Man:
A systems biology approach reveals common metastatic pathways in osteosarcoma. 50 - Paola Lecca, Daniele Morpurgo, Gianluca Fantaccini, Alessandro Casagrande, Corrado Priami:
Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics. 51 - Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yukiko Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka:
AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. 52 - Michalis K. Titsias, Antti Honkela, Neil D. Lawrence, Magnus Rattray:
Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison. 53 - Florian Martin, Ty M. Thomson, Alain Sewer, David A. Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C. Peitsch:
Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks. 54 - Benjamin D. Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P. Walker:
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. 55 - Zuguang Gu, Jialin Liu, Kunming Cao, Junfeng Zhang, Jin Wang:
Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. 56 - Nicole Radde:
Analyzing fixed points of intracellular regulation networks with interrelated feedback topology. 57 - Konstantinos Biliouris, David Babson, Claudia Schmidt-Dannert, Yiannis N. Kaznessis:
Stochastic simulations of a synthetic bacteria-yeast ecosystem. 58 - Alexander Wentzel, Per Bruheim, Anders Øverby, Øyvind M. Jakobsen, Håvard Sletta, Walid A. M. Omara, David A. Hodgson, Trond E. Ellingsen:
Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2). 59 - Ralph Patrick, Kim-Anh Lê Cao, Melissa J. Davis, Bostjan Kobe, Mikael Bodén:
Mapping the stabilome: a novel computational method for classifying metabolic protein stability. 60 - Hui Yu, Kang Tu, Yi-Jie Wang, Jun-Zhe Mao, Lu Xie, Yuan-Yuan Li, Yi-Xue Li:
Combinatorial network of transcriptional regulation and microRNA regulation in human cancer. 61 - Nizamul Morshed, Madhu Chetty, Xuan Vinh Nguyen:
Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique. 62 - Michael C. Oldham, Peter Langfelder, Steve Horvath:
Network methods for describing sample relationships in genomic datasets: application to Huntington's disease. 63 - Wenting Li, Rui Wang, Linfu Bai, Zhangming Yan, Zhirong Sun:
Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level. 64 - Yu Liu, Mehmet Koyutürk, Jill S. Barnholtz-Sloan, Mark R. Chance:
Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases. 65 - Tian Hong, Jianhua Xing, Liwu Li, John J. Tyson:
A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. 66 - Sarp A. Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A. Ercüment Çiçek, Lei Yang, Rishiraj Jadeja, Ranjan K. Dash, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu:
PathCase-SB: integrating data sources and providing tools for systems biology research. 67 - Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui:
Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis. 68 - Bruce A. Rosa, Yuhua Jiao, Sookyung Oh, Beronda L. Montgomery, Wensheng Qin, Jin Chen:
Frequency-based time-series gene expression recomposition using PRIISM. 69 - Sherry-Ann Brown, Leslie M. Loew:
Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia. 70 - Amornpan Klanchui, Chiraphan Khannapho, Atchara Phodee, Supapon Cheevadhanarak, Asawin Meechai:
iAK692: A genome-scale metabolic model of Spirulina platensis C1. 71 - Daniela Beisser, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller:
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. 72 - Dave Lee, Kieran Smallbone, Warwick B. Dunn, Ettore Murabito, Catherine Winder, Douglas B. Kell, Pedro Mendes, Neil Swainston:
Improving metabolic flux predictions using absolute gene expression data. 73 - Angelyn Lao, Vanessa Schmidt, Yvonne Schmitz, Thomas E. Willnow, Olaf Wolkenhauer:
Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease. 74 - Alejandro Fernández Villaverde, Jose A. Egea, Julio R. Banga:
A cooperative strategy for parameter estimation in large scale systems biology models. 75 - Brian Drawert, Stefan Engblom, Andreas Hellander:
URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. 76 - Brandilyn Stigler, Helen M. Chamberlin:
A regulatory network modeled from wild-type gene expression data guides functional predictions in Caenorhabditis elegans development. 77 - Rohan D. Gidvani, Peter Sudmant, Grace Li, Lance F. DaSilva, Brendan J. McConkey, Bernard P. Duncker, Brian P. Ingalls:
A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. 78 - Carlos Vilas, Eva Balsa-Canto, Maria-Sonia G. García, Julio R. Banga, Antonio A. Alonso:
Dynamic optimization of distributed biological systems using robust and efficient numerical techniques. 79 - Hee Lee, Taejeong Bae, Ji-Hyun Lee, Dae Kim, Young Oh, Yeongjun Jang, Ji-Tea Kim, Jong Jun Lee, Alessio Innocenti, Claudiu T. Supuran, Luonan Chen, Kyoohyoung Rho, Sunghoon Kim:
Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. 80 - Steffen Waldherr, Bernard Haasdonk:
Efficient parametric analysis of the chemical master equation through model order reduction. 81 - Uddipan Sarma, Indira Ghosh:
Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. 82 - Aiman Alam-Nazki, Jawahar Krishnan:
An investigation of spatial signal transduction in cellular networks. 83 - I-Chun Chou, Eberhard O. Voit:
Estimation of dynamic flux profiles from metabolic time series data. 84 - Tamás Székely, Kevin Burrage, Radek Erban, Konstantinos C. Zygalakis:
A higher-order numerical framework for stochastic simulation of chemical reaction systems. 85 - Jürgen Pahle, Joseph D. Challenger, Pedro Mendes, Alan J. McKane:
Biochemical fluctuations, optimisation and the linear noise approximation. 86 - Wei Peng, Jianxin Wang, Weiping Wang, Qing Liu, Fang-Xiang Wu, Yi Pan:
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. 87 - Kristin Tøndel, Ulf G. Indahl, Arne B. Gjuvsland, Stig W. Omholt, Harald Martens:
Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models. 88 - Neil R. Clark, Ruth Dannenfelser, Christopher M. Tan, Michael E. Komosinski, Avi Ma'ayan:
Sets2Networks: network inference from repeated observations of sets. 89 - Larry Croft, Damian Szklarczyk, Lars Juhl Jensen, Jan Gorodkin:
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. 90 - Edward Kent, Stefan Hoops, Pedro Mendes:
Condor-COPASI: high-throughput computing for biochemical networks. 91 - Jishnu Das, Haiyuan Yu:
HINT: High-quality protein interactomes and their applications in understanding human disease. 92 - Lei Zhang, Arthur D. Lander, Qing Nie:
A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts. 93 - Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang:
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database. 94 - Daniel Schmidl, Sabine Hug, Wei Li, Matthias B. Greiter, Fabian J. Theis:
Bayesian model selection validates a biokinetic model for zirconium processing in humans. 95 - Tomás Helikar, Bryan M. Kowal, Sean McClenathan, Mitchell Bruckner, Thaine W. Rowley, Alex Madrahimov, Benjamin Wicks, Manish Shrestha, Kahani Limbu, Jim A. Rogers:
The Cell Collective: Toward an open and collaborative approach to systems biology. 96 - Eduardo Tejera, João Bernardes, Irene Rebelo:
Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis. 97 - Vijay Chickarmane, Victor Olariu, Carsten Peterson:
Probing the role of stochasticity in a model of the embryonic stem cell - heterogeneous gene expression and reprogramming efficiency. 98 - Daniel Kaschek, Jens Timmer:
A variational approach to parameter estimation in ordinary differential equations. 99 - Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree, Morakot Tanticharoen, Sakarindr Bhumiratana, Asawin Meechai, Jeerayut Chaijaruwanich, Hideki Takahashi, Supapon Cheevadhanarak:
Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model. 100 - Kenneth Lo, Adrian E. Raftery, Kenneth M. Dombek, Jun Zhu, Eric E. Schadt, Roger Eugene Bumgarner, Ka Yee Yeung:
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. 101 - Tzu-Hsien Yang, Wei-Sheng Wu:
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. 102 - Christian Jungreuthmayer, Jürgen Zanghellini:
Designing optimal cell factories: integer programming couples elementary mode analysis with regulation. 103 - Marcel H. Schulz, William E. Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph:
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. 104 - Yushu 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:
Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein. 105 - Jong Myoung Park, Hye Min Park, Won Jun Kim, Hyun Uk Kim, Tae Yong Kim, Sang Yup Lee:
Flux variability scanning based on enforced objective flux for identifying gene amplification targets. 106 - Matthew S. Creamer, Edward C. Stites, Meraj Aziz, James A. Cahill, Chin Wee Tan, Michael E. Berens, Haiyong Han, Kimberly J. Bussey, Daniel D. Von Hoff, William S. Hlavacek, Richard G. Posner:
Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. 107 - Thomas Williamson, Delali A. Adiamah, Jean-Marc Schwartz, Lubomira Stateva:
Exploring the genetic control of glycolytic oscillations in Saccharomyces Cerevisiae. 108 - Marc R. Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej Dobrzynski, Jan B. Hoek, Walter Kolch, Babatunde A. Ogunnaike, Boris N. Kholodenko:
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. 109 - Joaquín Sanz, Emanuele Cozzo, Javier Borge-Holthoefer, Yamir Moreno:
Topological effects of data incompleteness of gene regulatory networks. 110 - Yonatan Savir, Nir Waysbort, Yaron E. Antebi, Tsvi Tlusty, Nir Friedman:
Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback. 111 - Mohammed Alshalalfa, Gary D. Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj:
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. 112 - Jinghang Liang, Jie Han:
Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks. 113 - Anja Karlstädt, Daniela Fliegner, Georgios Kararigas, Hugo Sanchez Ruderisch, Vera Regitz-Zagrosek, Hermann-Georg Holzhütter:
CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism. 114 - Giuseppe Facchetti, Mattia Zampieri, Claudio Altafini:
Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer. 115 - Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone:
Continuous time boolean modeling for biological signaling: application of Gillespie algorithm. 116 - Jason E. Shoemaker, Satoshi Fukuyama, Amie J. Eisfeld, Yukiko Muramoto, Shinji Watanabe, Tokiko Watanabe, Yukiko Matsuoka, Hiroaki Kitano, Yoshihiro Kawaoka:
Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs. 117 - Susanna Bazzani, Andreas Hoppe, Hermann-Georg Holzhütter:
Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism. 118 - Nishanth G. Chemmangattuvalappil, Keith Task, Ipsita Banerjee:
An integer optimization algorithm for robust identification of non-linear gene regulatory networks. 119 - Clemens Kreutz, Andreas Raue, Jens Timmer:
Likelihood based observability analysis and confidence intervals for predictions of dynamic models. 120 - Nicolae Radu Zabet:
System size reduction in stochastic simulations of the facilitated diffusion mechanism. 121 - Ji-Young Hong, Geun-Hong Kim, Jun-Woo Kim, Soon-Sung Kwon, Eisuke F. Sato, Kwang-Hyun Cho, Eun Bo Shim:
Computational modeling of apoptotic signaling pathways induced by cisplatin. 122 - Shyamesh Kumar, Dusan Kunec, Joram J. Buza, Hsin-I Chiang, Huaijun Zhou, Sugalesini Subramaniam, Ken Pendarvis, Hans H. Cheng, Shane C. Burgess:
Nuclear Factor kappa B is central to Marek's Disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo. 123 - Shingo Tsuji, Sigeo Ihara, Hiroyuki Aburatani:
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. 124 - Rainer Poltz, Michael Naumann:
Dynamics of p53 and NF-κ. 125 - Ángel Goñi-Moreno, Martyn Amos:
A reconfigurable NAND/NOR genetic logic gate. 126 - David Byrne, Alexandra Dumitriu, Daniel Segrè:
Comparative multi-goal tradeoffs in systems engineering of microbial metabolism. 127 - Leandra M. Brettner, Joanna Masel:
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. 128 - Changki Hong, Minho Lee, Dongsup Kim, Dong San Kim, Kwang-Hyun Cho, Insik Shin:
A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network. 129 - Mark Mc Auley, Darren J. Wilkinson, Janette Jones, Thomas B. L. Kirkwood:
A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. 130 - Carla Bosia, Matteo Osella, Mariama El Baroudi, Davide Corà, Michele Caselle:
Gene autoregulation via intronic microRNAs and its functions. 131 - Isaac Crespo, Kirsten Roomp, Wiktor Jurkowski, Hiroaki Kitano, Antonio del Sol:
Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease. 132 - Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel J. V. Gonçalves, Melody K. Morris, Martijn P. van Iersel, Douglas A. Lauffenburger, Julio Saez-Rodriguez:
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. 133 - Bevan Chung, Dong-Yup Lee:
Computational codon optimization of synthetic gene for protein expression. 134 - Magbubah Essack, Cameron MacPherson, Sebastian Schmeier, Vladimir B. Bajic:
Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model. 135 - Bor-Sen Chen, Chih-Yuan Hsu:
Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing. 136 - André Fujita, Patricia Severino, Kaname Kojima, João Ricardo Sato, Alexandre Galvão Patriota, Satoru Miyano:
Functional clustering of time series gene expression data by Granger causality. 137 - Galina Lebedeva, Azusa Yamaguchi, Simon P. Langdon, Kenneth Macleod, David J. Harrison:
A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen. 138 - Hendrik Rohn, Astrid Junker, Anja Hartmann, Eva Grafahrend-Belau, Hendrik Treutler, Matthias Klapperstück, Tobias Czauderna, Christian Klukas, Falk Schreiber:
VANTED v2: a framework for systems biology applications. 139 - Elad Noor, Nathan E. Lewis, Ron Milo:
A proof for loop-law constraints in stoichiometric metabolic networks. 140 - Tatiana A. Karelina, Kirill V. Zhudenkov, Oleg O. Demin, Dmitry V. Svetlichny, Balaji Agoram, David Fairman, Oleg V. Demin:
Regulation of leukotriene and 5oxoETE synthesis and the effect of 5-lipoxygenase inhibitors: a mathematical modeling approach. 141 - Gengjie Jia, Gregory Stephanopoulos, Rudiyanto Gunawan:
Incremental parameter estimation of kinetic metabolic network models. 142 - Hye-Won Kang:
A multiscale approximation in a heat shock response model of E. coli. 143 - Michal Kolár, Jörn Meier, Ville Mustonen, Michael Lässig, Johannes Berg:
GraphAlignment: Bayesian pairwise alignment of biological networks. 144 - Anne-Claire Haury, Fantine Mordelet, Paola Vera-Licona, Jean-Philippe Vert:
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. 145 - Mariano Beguerisse-Díaz, Mercedes C. Hernández-Gómez, Alessandro M. Lizzul, Mauricio Barahona, Radhika Desikan:
Compound stress response in stomatal closure: a mathematical model of ABA and ethylene interaction in guard cells. 146 - Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja, Eugenia Marbach, Jörg Linde, Anke Meyer-Baese, Sebastian Zellmer, Reinhard Guthke, Rolf Gebhardt:
The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes. 147 - Nadine Töpfer, Szymon Jozefczuk, Zoran Nikoloski:
Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. 148 - Andreas Kremling, Katharina Pflüger-Grau, Max Chavarría, Jacek Puchalka, Vítor A. P. Martins dos Santos, Victor de Lorenzo:
Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida. 149 - Ali Navid, Eivind Almaas:
Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach. 150 - Ana Luisa B. Cruz, Marit Hebly, Giang-Huong Duong, Sebastian A. Wahl, Jack T. Pronk, Joseph J. Heijnen, Pascale A. S. Daran-Lapujade, Walter M. van Gulik:
Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics? 151 - ShengJun Fan, Qiang Geng, Zhen-Yu Pan, Xin Li, Lu Tie, Yan Pan, Xuejun Li:
Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach. 152 - Yuliang Wang, James A. Eddy, Nathan D. Price:
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. 153 - Shibin Mathew, Maria Jaramillo, Xinan Zhang, Li Zhang, Alejandro Soto-Gutiérrez, Ipsita Banerjee:
Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences. 154 - Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee:
Metabolic Flux-Based Modularity using Shortest Retroactive distances. 155
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