Journal: BMC Systems Biology

Volume 11, Issue S-7

0 -- 0Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng, Lei Shi. A linear programming computational framework integrates phosphor-proteomics and prior knowledge to predict drug efficacy
15 -- 27Lichun Ma, Jie Zheng. A polynomial based model for cell fate prediction in human diseases
29 -- 44Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai, Tzong-Yi Lee. Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas
45 -- 56Ying Xu, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan. CPredictor3.0: detecting protein complexes from PPI networks with expression data and functional annotations
57 -- 68Cong-Doan Truong, Yung-Keun Kwon. Investigation on changes of modularity and robustness by edge-removal mutations in signaling networks
69 -- 80Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi, Tzong-Yi Lee. Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions
81 -- 90Daniel Trejo-Baños, Pauline Trébulle, Mohamed Elati. Integrating transcriptional activity in genome-scale models of metabolism
91 -- 99Huipeng Li, Lakshmi Venkatraman, Balakrishnan Chakrapani Narmada, Jacob K. White, Hanry Yu, Lisa Tucker-Kellogg. Computational analysis reveals the coupling between bistability and the sign of a feedback loop in a TGF-β1 activation model
101 -- 111Maulida Mazaya, Hung-Cuong Trinh, Yung-Keun Kwon. Construction and analysis of gene-gene dynamics influence networks based on a Boolean model
113 -- 125Qingping Liu, Jiahao Wang, Yan Zhu, Yongqun He. Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism
127 -- 140Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang, Tzong-Yi Lee. MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs
141 -- 150Ben-gong Zhang, Weibo Li, Yazhou Shi, Xiaoping Liu, Luonan Chen. Detecting causality from short time-series data based on prediction of topologically equivalent attractors
151 -- 162Shun Asami, Daisuke Kiga, Akihiko Konagaya. Constraint-based perturbation analysis with cluster Newton method: a case study of personalized parameter estimations with irinotecan whole-body physiologically based pharmacokinetic model
163 -- 174Hao Jiang, Wai-Ki Ching, Wai Shun Cheung, Wenpin Hou, Hong Yin. Hadamard Kernel SVM with applications for breast cancer outcome predictions

Volume 11, Issue S-5

0 -- 0Jingchun Sun, Qiang Wei, Yubo Zhou, Jingqi Wang, Qi Liu, Hua Xu. A systematic analysis of FDA-approved anticancer drugs
0 -- 0W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao, Zhangdong Liu. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work
0 -- 0Jin Li, Yang Wang, Xi Rao, Yue Wang, Weixing Feng, Hong Liang, Yunlong Liu. Roles of alternative splicing in modulating transcriptional regulation
0 -- 0Turki Turki, Zhi Wei. A link prediction approach to cancer drug sensitivity prediction
0 -- 0Biao Li, Amanda Sierra, Juan Jose Deudero, Fatih Semerci, Andrew Laitman, Marek Kimmel, Mirjana Maletic-Savatic. Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis
0 -- 0Xinan Holly Yang, Fangming Tang, Jisu Shin, John M. Cunningham. Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma
0 -- 0Ru-Dong Li, Yin Wang, Hui Cheng, Gang Liu, Tao Cheng, Yunlong Liu, Lei Liu. System modeling reveals the molecular mechanisms of HSC cell cycle alteration mediated by Maff and Egr3 under leukemia
0 -- 0Haoyang Wu, Elise Miller, Denethi Wijegunawardana, Kelly Regan, Philip R. O. Payne, Fuhai Li. MD-Miner: a network-based approach for personalized drug repositioning

Volume 11, Issue S-4

0 -- 0Yong Wang 0001, Xiang-Sun Zhang, Luonan Chen. Understanding biological systems through the lens of data
3 -- 16Mingxin Gan, Wenran Li, Wanwen Zeng, Xiaojian Wang, Rui Jiang. Mimvec: a deep learning approach for analyzing the human phenome
17 -- 25Bo Tian, Can Zhao, Feiyang Gu, Zengyou He. A two-step framework for inferring direct protein-protein interaction network from AP-MS data
27 -- 33Zehua Zhang, Kecheng Guo, Gaofeng Pan, Jijun Tang, Fei Guo. Improvement of phylogenetic method to analyze compositional heterogeneity
35 -- 42Changhe Fu, Su Deng, Guangxu Jin, Xinxin Wang, Zu-Guo Yu. Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data
43 -- 60Fei Liu, Deshun Sun, Ryutaro Murakami, Hiroshi Matsuno. Modeling and analysis of the Delta-Notch dependent boundary formation in the Drosophila large intestine
61 -- 74Duanchen Sun, Yinliang Liu, Xiang-Sun Zhang, Ling-Yun Wu. NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis
75 -- 84Xiaofei Shi, Ruiqi Wang. Glioma cell fate decisions mediated by Dll1-Jag1-Fringe in Notch1 signaling pathway
85 -- 97Jing He, Zhou Zhou, Michael Reed, Andrea Califano. Accelerated parallel algorithm for gene network reverse engineering
99 -- 111Yuzhen Guo, Fengying Tao, Zikai Wu, Yong Wang 0001. Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations
113 -- 119Jie Gao, Kang Wang, Tao Ding, Shanshan Zhu. Forecasting influenza A pandemic outbreak using protein dynamical network biomarkers

Volume 11, Issue S-2

0 -- 0Qiao Liu, Mingxin Gan, Rui Jiang. A sequence-based method to predict the impact of regulatory variants using random forest
0 -- 0Zhanzhan Cheng, Kai Huang, Yang Wang, Hui Liu, Jihong Guan, Shuigeng Zhou. Selecting high-quality negative samples for effectively predicting protein-RNA interactions
0 -- 0Weiqi Chen, Jing Liu, Shan He. Prior knowledge guided active modules identification: an integrated multi-objective approach
0 -- 0Pavithra K. Balasubramanian, Anand Balupuri, Hee Young Kang, Seung Joo Cho. Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors
0 -- 0Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo, Sun Kim. PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI
0 -- 0Daesik Choi, Byungkyu Park, Hanju Chae, Wook Lee, Kyungsook Han. Predicting protein-binding regions in RNA using nucleotide profiles and compositions

Volume 11, Issue S-1

1 -- 15Andjela Rodic, Bojana Blagojevic, Evgeny M. Zdobnov, Magdalena Djordjevic, Marko Djordjevic. Understanding key features of bacterial restriction-modification systems through quantitative modeling
17 -- 26Leonid V. Omelyanchuk, Alina F. Munzarova. Theoretical model of mitotic spindle microtubule growth for FRAP curve interpretation
27 -- 42Olga A. Podkolodnaya, Natalya N. Tverdokhleb, Nikolay Podkolodnyy. Computational modeling of the cell-autonomous mammalian circadian oscillator

Volume 11, Issue 6

0 -- 0Morteza ZiHayat, Heidar Davoudi, Aijun An. Mining significant high utility gene regulation sequential patterns
15 -- 21Quan Zou, Shixiang Wan, Xiangxiang Zeng, Zhanshan (Sam) Ma. Reconstructing evolutionary trees in parallel for massive sequences
23 -- 34Wen Zhang, Xiang Yue, Feng Liu, Yanlin Chen, Shikui Tu, Xining Zhang. A unified frame of predicting side effects of drugs by using linear neighborhood similarity
35 -- 44Qi Li, Yongyi Gong. A geometric method for contour extraction of Drosophila embryos
45 -- 61Hao Jiang, Wai-Ki Ching, Yushan Qiu, Xiaoqing Cheng. Optimal projection method determination by Logdet Divergence and perturbed von-Neumann Divergence
63 -- 73Jin-Xing Liu, Dong-Qin Wang, Chun-Hou Zheng, Ying-Lian Gao, Sha-Sha Wu, Junliang Shang. Identifying drug-pathway association pairs based on L2, 1-integrative penalized matrix decomposition
75 -- 88Ou Wei, Zonghao Guo, Yun Niu, Wenyuan Liao. Model checking optimal finite-horizon control for probabilistic gene regulatory networks

Volume 11, Issue 3

0 -- 0Amin Zollanvari, Gil Alterovitz. SNP by SNP by environment interaction network of alcoholism
0 -- 0Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons, Zhiyong Lu. DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks
0 -- 0Minghan Chen, Fei Li, Shuo Wang, Young Cao. Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics
0 -- 0Hyundoo Jeong, Byung-Jun Yoon. SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance
0 -- 0Yijie Wang, Xiaoning Qian. Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction

Volume 11, Issue 1

0 -- 0Wenbin 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
0 -- 0Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García, Elena R. Alvarez-Buylla. Gene regulatory network underlying the immortalization of epithelial cells
0 -- 0Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner, Mustafa Khammash. Parameter inference for stochastic single-cell dynamics from lineage tree data
0 -- 0Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer, Fabian J. Theis. Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
0 -- 0Anne 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
0 -- 0Athanasios D. Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P. Tampakaki, Konstantinos P. Koutsoumanis, Elias S. Manolakos. Image analysis driven single-cell analytics for systems microbiology
0 -- 0Thomas J. Snowden, Piet H. Van Der Graaf, Marcus J. Tindall. A combined model reduction algorithm for controlled biochemical systems
0 -- 0Tatsuaki Tsuruyama. Kinetic stability analysis of protein assembly on the center manifold around the critical point
0 -- 0Raghvendra Mall, Luigi Cerulo, Halima Bensmail, Antonio Iavarone, Michele Ceccarelli. Detection of statistically significant network changes in complex biological networks
0 -- 0Sara 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
0 -- 0Walter 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
0 -- 0Joyatee 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
0 -- 0Hugo 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
0 -- 0Anat Zimmer, Shlomit Amar-Farkash, Tamar Danon, Uri Alon. Dynamic proteomics reveals bimodal protein dynamics of cancer cells in response to HSP90 inhibitor
0 -- 0Philipp 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
0 -- 0Cihan Oguz, Layne T. Watson, William T. Baumann, John J. Tyson. Predicting network modules of cell cycle regulators using relative protein abundance statistics
0 -- 0Eleftherios Avramidis, Ozgur E. Akman. Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination
0 -- 0Niklas Hartung, Uwe Benary, Jana Wolf, Bente Kofahl. Paracrine and autocrine regulation of gene expression by Wnt-inhibitor Dickkopf in wild-type and mutant hepatocytes
0 -- 0Michael A. Rowland, Edward J. Perkins, Michael L. Mayo. Physiological fidelity or model parsimony? The relative performance of reverse-toxicokinetic modeling approaches
0 -- 0David 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
0 -- 0Mostafa Herajy, Fei Liu 0006, Christian Rohr, Monika Heiner. Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models
0 -- 0Francisco Saitua, Paulina Torres, J. Ricardo PéRez-Correa, Eduardo Agosin. Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris
0 -- 0Patricia 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
0 -- 0S. 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
0 -- 0Deepanwita 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
0 -- 0Anna 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
0 -- 0Brian K. Chu, Margaret J. Tse, Royce R. Sato, Elizabeth L. Read. Markov State Models of gene regulatory networks
0 -- 0Kerri-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
0 -- 0Jian Yang, Tinghong Yang, Duzhi Wu, Limei Lin, Fan Yang, Jing Zhao. The integration of weighted human gene association networks based on link prediction
0 -- 0Theofilos 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 0002. Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction
0 -- 0Jun Hyuk Kang, Kwang-Hyun Cho. A novel interaction perturbation analysis reveals a comprehensive regulatory principle underlying various biochemical oscillators
0 -- 0Thierry 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
0 -- 0Abraham A. Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang, Feng-Biao Guo. SSER: Species specific essential reactions database
0 -- 0Yulin Wang, Hongyu Miao. Parameter identifiability-based optimal observation remedy for biological networks
0 -- 0Nicolás Loira, Sebastian 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
0 -- 0Chihyun 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
0 -- 0Leonie Amstein, Jörg Ackermann, Jennifer Scheidel, Simone Fulda, Ivan Dikic, Ina Koch. Manatee invariants reveal functional pathways in signaling networks
0 -- 0Matthew 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
0 -- 0Attila Gábor, Alejandro Fernández Villaverde, Julio R. Banga. Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems
0 -- 0Tao 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
0 -- 0Juan 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
0 -- 0Duc-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
0 -- 0Mariana Esther Martinez-Sanchez, Marcia Hiriart, Elena R. Alvarez-Buylla. The CD4+ T cell regulatory network mediates inflammatory responses during acute hyperinsulinemia: a simulation study
0 -- 0Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma, Ziv Bar-Joseph. Reconstructing cancer drug response networks using multitask learning
0 -- 0Dimos 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
0 -- 0Thorsten Will, Volkhard Helms. Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare
0 -- 0Wenfei Zhang, Ying Liu, Mindy Zhang, Cheng Zhu, Yuefeng Lu. Quantitative reproducibility analysis for identifying reproducible targets from high-throughput experiments
0 -- 0Diala Abd-Rabbo, Stephen W. Michnick. Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast
0 -- 0Anna Doloman, Honey Varghese, Charles D. Miller, Nicholas S. Flann. Modeling de novo granulation of anaerobic sludge
0 -- 0Antje 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
0 -- 0Annie 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
0 -- 0Luis 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
0 -- 0Shabnam 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
0 -- 0Niek 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
0 -- 0Saskia Trescher, Jannes Münchmeyer, Ulf Leser. Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization
0 -- 0Marilena M. Bourdakou, George M. Spyrou. Informed walks: whispering hints to gene hunters inside networks' jungle
0 -- 0Jignesh H. Parmar, Grey Davis, Hope Shevchuk, Pedro Mendes. Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient
0 -- 0Milan 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
0 -- 0Luis 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
0 -- 0Piero Dalle Pezze, Nicolas Le Novère. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks
0 -- 0Ranjita Dutta Roy, Christian Rosenmund, Melanie I. Stefan. Cooperative binding mitigates the high-dose hook effect
0 -- 0Xiulan Lai, Avner Friedman. Combination therapy for melanoma with BRAF/MEK inhibitor and immune checkpoint inhibitor: a mathematical model
0 -- 0Yunseong 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