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		Research article Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia Sherry-Ann Brown, Leslie M Loew BMC Systems Biology 2012, 6:70 (15 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Frequency-based time-series gene expression recomposition using PRIISM Bruce A Rosa, Yuhua Jiao, Sookyung Oh, Beronda L Montgomery, Wensheng Qin, Jin Chen BMC Systems Biology 2012, 6:69 (15 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui BMC Systems Biology 2012, 6:68 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software PathCase-SB: integrating data sources and providing tools for systems biology research Sarp A Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K Dash, Nicola Lai, Gultekin Ozsoyoglu, Zehra Ozsoyoglu BMC Systems Biology 2012, 6:67 (14 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article A simple theoretical framework for understanding heterogeneous differentiation of CD4⁺ T cells Tian Hong, Jianhua Xing, Liwu Li, John J Tyson BMC Systems Biology 2012, 6:66 (14 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases Yu Liu, Mehmet Koyutürk, Jill S Barnholtz-Sloan, Mark R Chance BMC Systems Biology 2012, 6:65 (13 June 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology
		Research article Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level Wenting Li, Rui Wang, Linfu Bai, Zhangming Yan, Zhirong Sun BMC Systems Biology 2012, 6:64 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease Michael C Oldham, Peter Langfelder, Steve Horvath BMC Systems Biology 2012, 6:63 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique Nizamul Morshed, Madhu Chetty, Nguyen Xuan Vinh BMC Systems Biology 2012, 6:62 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Combinatorial network of transcriptional regulation and microRNA regulation in human cancer Hui Yu, Kang Tu, Yi-Jie Wang, Jun-Zhe Mao, Lu Xie, Yuan-Yuan Li, Yi-Xue Li BMC Systems Biology 2012, 6:61 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Mapping the stabilome: a novel computational method for classifying metabolic protein stability Ralph Patrick, Kim-Anh Cao, Melissa Davis, Bostjan Kobe, Mikael Bodén BMC Systems Biology 2012, 6:60 (8 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2) Alexander Wentzel, Per Bruheim, Anders Øverby, Øyvind M Jakobsen, Håvard Sletta, Walid A M Omara, David A Hodgson, Trond E Ellingsen BMC Systems Biology 2012, 6:59 (7 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Stochastic simulations of a synthetic bacteria-yeast ecosystem Konstantinos Biliouris, David Babson, Claudia Schmidt-Dannert, Yiannis N Kaznessis BMC Systems Biology 2012, 6:58 (6 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Analyzing fixed points of intracellular regulation networks with interrelated feedback topology Nicole Radde BMC Systems Biology 2012, 6:57 (6 June 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes Zuguang Gu, Jialin Liu, Kunming Cao, Junfeng Zhang, Jin Wang BMC Systems Biology 2012, 6:56 (6 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network Benjamin D Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P Walker BMC Systems Biology 2012, 6:55 (4 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks Florian Martin, Ty M Thomson, Alain Sewer, David A Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C Peitsch BMC Systems Biology 2012, 6:54 (31 May 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison Michalis K Titsias, Antti Honkela, Neil D Lawrence, Magnus Rattray BMC Systems Biology 2012, 6:53 (30 May 2012) Abstract \| Full text \| PDF \| PubMed
		Database AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yukiko Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka BMC Systems Biology 2012, 6:52 (30 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary AlzPathway is a publicly available database collating known Alzheimer's disease intra, inter and extra cellular signalling pathways into a comprehensive pathway map, providing a useful resource in deciphering Alzheimer's disease pathogenesis.
		Methodology article Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics Paola Lecca, Daniele Morpurgo, Gianluca Fantaccini, Alessandro Casagrande, Corrado Priami BMC Systems Biology 2012, 6:51 (28 May 2012) Abstract \| Full text \| PDF \| PubMed
		Research article A systems biology approach reveals common metastatic pathways in osteosarcoma Ricardo J Flores, Yiting Li, Alexander Yu, Jianhe Shen, Pulivarthi H Rao, Serrine S Lau, Marina Vannucci, Ching C Lau, Tsz-Kwong Man BMC Systems Biology 2012, 6:50 (28 May 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth Seung Sohn, Tae Kim, Jay H Lee, Sang Lee BMC Systems Biology 2012, 6:49 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Trade-offs between drug toxicity and benefit in the multi-antibiotic resistance system underlie optimal growth of E. coli Kevin B Wood, Philippe Cluzel BMC Systems Biology 2012, 6:48 (25 May 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network Rachel S Koh, Mary J Dunlop BMC Systems Biology 2012, 6:47 (20 May 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article A specialized ODE integrator for the efficient computation of parameter sensitivities Pedro Gonnet, Sotiris Dimopoulos, Lukas Widmer, Jörg Stelling BMC Systems Biology 2012, 6:46 (20 May 2012) Abstract \| Full text \| PDF \| PubMed

	All
		Research article Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia Sherry-Ann Brown, Leslie M Loew BMC Systems Biology 2012, 6:70 (15 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Frequency-based time-series gene expression recomposition using PRIISM Bruce A Rosa, Yuhua Jiao, Sookyung Oh, Beronda L Montgomery, Wensheng Qin, Jin Chen BMC Systems Biology 2012, 6:69 (15 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui BMC Systems Biology 2012, 6:68 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software PathCase-SB: integrating data sources and providing tools for systems biology research Sarp A Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K Dash, Nicola Lai, Gultekin Ozsoyoglu, Zehra Ozsoyoglu BMC Systems Biology 2012, 6:67 (14 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article A simple theoretical framework for understanding heterogeneous differentiation of CD4⁺ T cells Tian Hong, Jianhua Xing, Liwu Li, John J Tyson BMC Systems Biology 2012, 6:66 (14 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases Yu Liu, Mehmet Koyutürk, Jill S Barnholtz-Sloan, Mark R Chance BMC Systems Biology 2012, 6:65 (13 June 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology
		Research article Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level Wenting Li, Rui Wang, Linfu Bai, Zhangming Yan, Zhirong Sun BMC Systems Biology 2012, 6:64 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease Michael C Oldham, Peter Langfelder, Steve Horvath BMC Systems Biology 2012, 6:63 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique Nizamul Morshed, Madhu Chetty, Nguyen Xuan Vinh BMC Systems Biology 2012, 6:62 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Combinatorial network of transcriptional regulation and microRNA regulation in human cancer Hui Yu, Kang Tu, Yi-Jie Wang, Jun-Zhe Mao, Lu Xie, Yuan-Yuan Li, Yi-Xue Li BMC Systems Biology 2012, 6:61 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Mapping the stabilome: a novel computational method for classifying metabolic protein stability Ralph Patrick, Kim-Anh Cao, Melissa Davis, Bostjan Kobe, Mikael Bodén BMC Systems Biology 2012, 6:60 (8 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2) Alexander Wentzel, Per Bruheim, Anders Øverby, Øyvind M Jakobsen, Håvard Sletta, Walid A M Omara, David A Hodgson, Trond E Ellingsen BMC Systems Biology 2012, 6:59 (7 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Stochastic simulations of a synthetic bacteria-yeast ecosystem Konstantinos Biliouris, David Babson, Claudia Schmidt-Dannert, Yiannis N Kaznessis BMC Systems Biology 2012, 6:58 (6 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Analyzing fixed points of intracellular regulation networks with interrelated feedback topology Nicole Radde BMC Systems Biology 2012, 6:57 (6 June 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes Zuguang Gu, Jialin Liu, Kunming Cao, Junfeng Zhang, Jin Wang BMC Systems Biology 2012, 6:56 (6 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network Benjamin D Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P Walker BMC Systems Biology 2012, 6:55 (4 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks Florian Martin, Ty M Thomson, Alain Sewer, David A Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C Peitsch BMC Systems Biology 2012, 6:54 (31 May 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison Michalis K Titsias, Antti Honkela, Neil D Lawrence, Magnus Rattray BMC Systems Biology 2012, 6:53 (30 May 2012) Abstract \| Full text \| PDF \| PubMed
		Database AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yukiko Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka BMC Systems Biology 2012, 6:52 (30 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary AlzPathway is a publicly available database collating known Alzheimer's disease intra, inter and extra cellular signalling pathways into a comprehensive pathway map, providing a useful resource in deciphering Alzheimer's disease pathogenesis.
		Methodology article Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics Paola Lecca, Daniele Morpurgo, Gianluca Fantaccini, Alessandro Casagrande, Corrado Priami BMC Systems Biology 2012, 6:51 (28 May 2012) Abstract \| Full text \| PDF \| PubMed
		Research article A systems biology approach reveals common metastatic pathways in osteosarcoma Ricardo J Flores, Yiting Li, Alexander Yu, Jianhe Shen, Pulivarthi H Rao, Serrine S Lau, Marina Vannucci, Ching C Lau, Tsz-Kwong Man BMC Systems Biology 2012, 6:50 (28 May 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth Seung Sohn, Tae Kim, Jay H Lee, Sang Lee BMC Systems Biology 2012, 6:49 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Trade-offs between drug toxicity and benefit in the multi-antibiotic resistance system underlie optimal growth of E. coli Kevin B Wood, Philippe Cluzel BMC Systems Biology 2012, 6:48 (25 May 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network Rachel S Koh, Mary J Dunlop BMC Systems Biology 2012, 6:47 (20 May 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article A specialized ODE integrator for the efficient computation of parameter sensitivities Pedro Gonnet, Sotiris Dimopoulos, Lukas Widmer, Jörg Stelling BMC Systems Biology 2012, 6:46 (20 May 2012) Abstract \| Full text \| PDF \| PubMed