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ORCIDBMC Systems Biology, Volume 11
Volume 11, Number 1, December 2017
- Patricia Aquino
, Brent Honda, Suma Jaini, Anna Lyubetskaya, Krutika Hosur, Joanna G. Chiu, Iriny Ekladious, Dongjian Hu, Lin Jin, Marianna K. Sayeg, Arion Stettner, Julia Wang, Brandon G. Wong, Winnie S. Wong, Stephen L. Alexander, Cong Ba, Seth I. Bensussen, David B. Bernstein, Dana Braff, Susie Cha, Daniel I. Cheng, Jang-Hwan Cho, Kenny Chou, James Chuang, Daniel E. Gastler, Daniel J. Grasso, John S. Greifenberger, Chen Guo, Anna K. Hawes, Divya V. Israni, Saloni R. Jain, Jessica Kim, Junyu Lei, Hao Li, David Li, Qian Li, Christopher P. Mancuso, Ning Mao, Salwa F. Masud, Cari L. Meisel, Jing Mi, Christine S. Nykyforchyn, Minhee Park, Hannah M. Peterson, Alfred K. Ramirez, Daniel S. Reynolds, Nae Gyune Rim, Jared C. Saffie, Hang Su, Wendell R. Su, Yaqing Su, Meng Sun, Meghan M. Thommes, Tao Tu, Nitinun Varongchayakul, Tyler E. Wagner, Benjamin H. Weinberg, Rouhui Yang, Anastasia Yaroslavsky, Christine Yoon, Yanyu Zhao, Alicia J. Zollinger, Anne M. Stringer, John W. Foster, Joseph Wade, Sahadaven Raman, Natasha Broude, Wilson W. Wong, James E. Galagan:
Coordinated regulation of acid resistance in Escherichia coli. 1:1-1:15 - David M. Bassen, Michael Vilkhovoy, Mason Minot, Jonathan T. Butcher, Jeffrey D. Varner:
JuPOETs: a constrained multiobjective optimization approach to estimate biochemical model ensembles in the Julia programming language. 10:1-10:11 - Antje Jensch, Caterina Thomaseth, Nicole Radde:
Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines. 11:1-11:15 - Jian Yang, Tinghong Yang, Duzhi Wu, Limei Lin, Fan Yang, Jing Zhao:
The integration of weighted human gene association networks based on link prediction. 12:1-12:17 - Tatsuaki Tsuruyama:
Kinetic stability analysis of protein assembly on the center manifold around the critical point. 13:1-13:9 - Brian K. Chu, Margaret J. Tse, Royce R. Sato, Elizabeth L. Read:
Markov State Models of gene regulatory networks. 14:1-14:17 - Thomas J. Snowden, Piet H. Van Der Graaf, Marcus J. Tindall:
A combined model reduction algorithm for controlled biochemical systems. 17:1-17:18 - Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García, Elena R. Álvarez-Buylla:
Gene regulatory network underlying the immortalization of epithelial cells. 24:1-24:15 - Sara Saheb Kashaf, Claudio Angione, Pietro Liò:
Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization. 25:1-25:13 - Luis U. Aguilera, Christoph Zimmer, Ursula Kummer:
A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study. 26:1-26:14 - Francisco Saitua, Paulina Torres, José Ricardo Pérez-Correa, Eduardo Agosin:
Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris. 27:1-27:21 - Dimos Kapetis, Jenny Sassone, Yang Yang, Barbara Galbardi, Markos N. Xenakis, Ronald L. Westra, Radek Szklarczyk, Patrick Lindsey, Catharina G. Faber, Monique Gerrits, Ingemar S. J. Merkies, Sulayman D. Dib-Hajj, Massimo Mantegazza, Stephen G. Waxman, Giuseppe Lauria, Michela Taiana, Margherita Marchi, Raffaella Lombardi, Daniele Cazzato, Filippo Martinelli-Boneschi, Andrea Zauli, Ferdinando Clarelli, Silvia Santoro, Ignazio Lopez, Angelo Quattrini, Janneke Hoeijmakers, Maurice Sopacua, Bianca de Greef, Hubert J. M. Smeets, Rowida Al Momani, Jo Michel Vanoevelen, Ivo Eijkenboom, Sandrine Cestèle, Oana Chever, Rayaz A. Malik, Mitra Tavakoli, Dan Ziegler:
Network topology of NaV1.7 mutations in sodium channel-related painful disorders. 28:1-28:16 - Walter Bottje, Byung-Whi Kong, Antonio Reverter, Ashley J. Waardenberg, Kentu Lassiter, Nicholas J. Hudson:
Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency. 29:1-29:16 - Cihan Oguz, Layne T. Watson, William T. Baumann, John J. Tyson:
Predicting network modules of cell cycle regulators using relative protein abundance statistics. 30:1-30:24 - Theofilos Papadopoulos, Audrey Casemayou, Eric Neau, Benjamin Breuil, Cécile Caubet, Denis Calise, Barbara A. Thornhill, Magdalena Bachvarova, Julie Belliere, Robert L. Chevalier, Panagiotis Moulos, Dimcho Bachvarov, Benedicte Buffin-Meyer, Stéphane Decramer, Françoise Conte Auriol, Jean-Loup Bascands, Joost P. Schanstra, Julie Klein:
Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction. 31:1-31:11 - Raghvendra Mall, Luigi Cerulo, Halima Bensmail, Antonio Iavarone, Michele Ceccarelli:
Detection of statistically significant network changes in complex biological networks. 32:1-32:17 - Anat Zimmer, Shlomit Amar-Farkash, Tamar Danon, Uri Alon:
Dynamic proteomics reveals bimodal protein dynamics of cancer cells in response to HSP90 inhibitor. 33:1-33:11 - S. D. Pavithra Jayasundara, S. S. N. Perera, Gathsaurie Neelika Malavige, Saroj Jayasinghe:
Mathematical modelling and a systems science approach to describe the role of cytokines in the evolution of severe dengue. 34:1-34:14 - Michael A. Rowland, Edward J. Perkins, Michael L. Mayo:
Physiological fidelity or model parsimony? The relative performance of reverse-toxicokinetic modeling approaches. 35:1-35:11 - Chihyun Park, So Jeong Yun, Sung Jin Ryu, Soyoung Lee, Young Sam Lee, Youngmi Yoon, Sang-Chul Park:
Systematic identification of an integrative network module during senescence from time-series gene expression. 36:1-36:13 - Anne Mathilde Lund, Christian Schrøder Kaas, Julian Brandl, Lasse Ebdrup Pedersen, Helene Faustrup Kildegaard, Claus Kristensen, Mikael Rørdam Andersen:
Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data. 37:1-37:17 - Diala Abd-Rabbo, Stephen W. Michnick:
Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast. 38:1-38:14 - Matthew J. Simpson, Kai-Yin Lo, Yung-Shin Sun:
Quantifying the roles of random motility and directed motility using advection-diffusion theory for a 3T3 fibroblast cell migration assay stimulated with an electric field. 39:1-39:9 - Eleftherios Avramidis, Ozgur E. Akman:
Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination. 40:1-40:23 - Saskia Trescher, Jannes Münchmeyer, Ulf Leser:
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. 41:1-41:18 - Philipp Kügler, M. A. K. Bulelzai, André H. Erhardt:
Period doubling cascades of limit cycles in cardiac action potential models as precursors to chaotic early Afterdepolarizations. 42:1-42:13 - Athanasios D. Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P. Tampakaki, Konstantinos P. Koutsoumanis, Elias S. Manolakos:
Image analysis driven single-cell analytics for systems microbiology. 43:1-43:21 - Thorsten Will, Volkhard Helms:
Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare. 44:1-44:19 - Yunseong Kim, Sea Choi, Dongkwan Shin, Kwang-Hyun Cho:
Quantitative evaluation and reversion analysis of the attractor landscapes of an intracellular regulatory network for colorectal cancer. 45:1-45:11 - Piero Dalle Pezze, Nicolas Le Novère:
SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. 46:1-46:5 - Juan A. Botía, Jana Vandrovcova, Paola Forabosco, Sebastian Guelfi, Karishma D'Sa, John Hardy, Cathryn M. Lewis, Mina Ryten, Michael E. Weale:
An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks. 47:1-47:16 - Shabnam Khatibi, Hong-Jian Zhu, John Wagner, Chin Wee Tan, Jonathan H. Manton, Antony W. Burgess:
Mathematical model of TGF-βsignalling: feedback coupling is consistent with signal switching. 48:1-48:15 - Hugo F. Cueto-Rojas, Nicholas Milne, Ward van Helmond, Mervin M. Pieterse, Antonius J. A. van Maris, Jean-Marc Daran, Sebastian Aljoscha Wahl:
Membrane potential independent transport of NH3 in the absence of ammonium permeases in Saccharomyces cerevisiae. 49:1-49:13 - Abraham A. Labena, Yuan-Nong Ye, Chuan Dong, Fa-Zhan Zhang, Feng-Biao Guo:
SSER: Species specific essential reactions database. 50:1-50:8 - Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula, Anu Raghunathan:
A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance. 51:1-51:20 - Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner, Mustafa Khammash:
Parameter inference for stochastic single-cell dynamics from lineage tree data. 52:1-52:13 - Yulin Wang, Hongyu Miao:
Parameter identifiability-based optimal observation remedy for biological networks. 53:1-53:13 - Attila Gábor, Alejandro Fernández Villaverde, Julio R. Banga:
Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems. 54:1-54:16 - Tao Peng, Linan Liu, Adam L. Maclean, Chi Wut Wong, Weian Zhao, Qing Nie:
A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions. 55:1-55:15 - Milan J. A. van Hoek, Roeland M. H. Merks:
Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism. 56:1-56:18 - Jignesh H. Parmar, Grey Davis, Hope Shevchuk, Pedro Mendes:
Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. 57:1-57:13 - Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas, Dolly Montoya Castaño:
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol. 58:1-58:13 - Niek Welkenhuysen, Johannes Borgqvist, Mattias Backman, Loubna Bendrioua, Mattias Goksör, Caroline Beck Adiels, Marija Cvijovic, Stefan Hohmann:
Single-cell study links metabolism with nutrient signaling and reveals sources of variability. 59:1-59:10 - Thierry Chénard, Frédéric Guénard, Marie-Claude Vohl, André Carpentier, André Tchernof, Rafael J. Najmanovich:
Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes. 60:1-60:15 - Duc-Hau Le, Van-Huy Pham:
HGPEC: a Cytoscape app for prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network. 61:1-61:10 - Wenbin Guo, Cristiane P. G. Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W. S. Brown, Runxuan Zhang:
Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size. 62:1-62:12 - Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer, Fabian J. Theis:
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems. 63:1-63:18 - Mariana Esther Martinez-Sanchez, Marcia Hiriart, Elena R. Álvarez-Buylla:
The CD4+ T cell regulatory network mediates inflammatory responses during acute hyperinsulinemia: a simulation study. 64:1-64:12 - Anna Huhtinen, Vesa Hongisto, Asta Laiho, Eliisa Löyttyniemi, Dirk Pijnenburg, Mika Scheinin:
Gene expression profiles and signaling mechanisms in α2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells. 65:1-65:30 - Nicolás Loira, Sebastián N. Mendoza, María Paz Cortés, Natalia Rojas, Dante Travisany, Alex Di Génova, Natalia Gajardo, Nicole Ehrenfeld, Alejandro Maass:
Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production. 66:1-66:17 - Annie Glatigny, Philippe Gambette, Alexa Bourand-Plantefol, Geneviève Dujardin, Marie-Hélène Mucchielli-Giorgi:
Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae. 67:1-67:12 - Kerri-Ann Norton, Travis Wallace, Niranjan B. Pandey, Aleksander S. Popel:
An agent-based model of triple-negative breast cancer: the interplay between chemokine receptor CCR5 expression, cancer stem cells, and hypoxia. 68:1-68:15 - Anna Doloman, Honey Varghese, Charles D. Miller, Nicholas S. Flann:
Modeling de novo granulation of anaerobic sludge. 69:1-69:12 - Xiulan Lai, Avner Friedman:
Combination therapy for melanoma with BRAF/MEK inhibitor and immune checkpoint inhibitor: a mathematical model. 70:1-70:18 - Mostafa Herajy, Fei Liu, Christian Rohr, Monika Heiner:
Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models. 71:1-71:16 - Leonie Amstein, Jörg Ackermann, Jennifer Scheidel, Simone Fulda, Ivan Dikic, Ina Koch:
Manatee invariants reveal functional pathways in signaling networks. 72:1-72:11 - Wenfei Zhang, Ying Liu, Mindy Zhang, Cheng Zhu, Yuefeng Lu:
Quantitative reproducibility analysis for identifying reproducible targets from high-throughput experiments. 73:1-73:7 - Ranjita Dutta Roy, Christian Rosenmund, Melanie I. Stefan:
Cooperative binding mitigates the high-dose hook effect. 74:1-74:10 - Joyatee M. Sarker, Serena M. Pearce, Robert P. Nelson Jr., Tamara Kinzer-Ursem, David M. Umulis, Ann E. Rundell:
An Integrative multi-lineage model of variation in leukopoiesis and acute myelogenous leukemia. 78:1-78:18 - Jun Hyuk Kang, Kwang-Hyun Cho:
A novel interaction perturbation analysis reveals a comprehensive regulatory principle underlying various biochemical oscillators. 95:1-95:12 - Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma, Ziv Bar-Joseph:
Reconstructing cancer drug response networks using multitask learning. 96:1-96:15 - Marilena M. Bourdakou, George M. Spyrou:
Informed walks: whispering hints to gene hunters inside networks' jungle. 97:1-97:11 - Niklas Hartung, Uwe Benary, Jana Wolf, Bente Kofahl:
Paracrine and autocrine regulation of gene expression by Wnt-inhibitor Dickkopf in wild-type and mutant hepatocytes. 98:1-98:16
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