Dynamic cell and microparticle control via optoelectronic tweezers (2007)
Ohta, Aaron Takami, Chiou, Pei-Yu, Han, Tae H., Liao, James C., Bhardwaj, Urvashi, McCabe, Edward R. B., ...
This paper reports on cell and microparticle manipulation using optically induced dielectrophoresis. Our novel optoelectronic tweezers (OET) device enables optically controlled trapping,...
Dynamic cell and microparticle control via optoelectronic tweezers (2007)
Ohta, Aaron T., Chiou, Pei-Yu, Han, Tae H., Liao, James C., Bhardwaj, Urvashi, McCabe, Edward R.B., ...
This paper reports on cell and microparticle manipulation using optically induced dielectrophoresis. Our novel optoelectronic tweezers (OET) device enables optically controlled trapping,...
A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering (2007)
Hatzimanikatis, Vassily, Liao, James C.
A review, with refs. When mentioning prokaryotic metabolic engineering, most people will immediately think of Jay Bailey. Jay's contribution to this fast-growing field is evident and familiar to...
Liao, James C., Roychawdhury, Vwani
During the course of the project four software tools for BioSPICE were developed. These include Network Component Analysis (NCA), GeneScreen, 1cDNA, and MIcroArray Experimental Spice (MIAMESpice)....
Inferring yeast cell cycle regulators and interactions using transcription factor activities (2005)
Yang, Young-Lyeol, Suen, Jason, Brynildsen, Mark P, Galbraith, Simon J, Liao, James C
Abstract Background Since transcription factors are often regulated at the post-transcriptional level, their activities, rather than expression levels may provide valuable information for...
George C. Tseng, Lars Rohlin, James C. Liao
We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the...
Using Fuzzy Logic and a Hybrid Genetic Algorithm for Metabolic Modeling (1996)
John Yen, Bogju Lee, James C. Liao
The identification of metabolic systems such as metabolic pathways, enzyme actions, and gene regulations is a complex task due to the complexity of the system and limited knowledge about the model....
Using A Hybrid Genetic Algorithm and Fuzzy Logic for Metabolic Modeling (1996)
John Yen, Bogju Lee, James C. Liao
The identification of metabolic systems is a complex task due to the complexity of the system and limited knowledge about the model. Mathematical equations and ODE's have been used to capture the...
Intravascular flow decreases erythrocyte consumption of nitric oxide
Liao, James C., W. Hein, Travis, Vaughn, Mark W., Huang, Kuang-Tse, Kuo, Lih
Nitric oxide (NO) produced by the endothelium diffuses both into the lumen and to the smooth muscle cells according to the concentration gradient in each direction. The extremely high reaction rate...
Tseng, George C., Oh, Min-Kyu, Rohlin, Lars, Liao, James C., Wong, Wing Hung
We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the...
Modulation of nitric oxide bioavailability by erythrocytes
Huang, Kuang-Tse, Han, Tae H., Hyduke, Daniel R., Vaughn, Mark W., Van Herle, Helga, Hein, Travis W., ...
Nitric oxide (NO) activates soluble guanylyl cyclase in smooth muscle cells to induce vasodilation in the vasculature. However, as hemoglobin (Hb) is an effective scavenger of NO and is present in...
Co-expression pattern from DNA microarray experiments as a tool for operon prediction
Sabatti, Chiara, Rohlin, Lars, Oh, Min-Kyu, Liao, James C.
The prediction of operons, the smallest unit of transcription in prokaryotes, is the first step towards reconstruction of a regulatory network at the whole genome level. Sequence information, in...
Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions
Han, Tae H., Hyduke, Daniel R., Vaughn, Mark W., Fukuto, Jon M., Liao, James C.
Understanding the interaction of nitric oxide (NO) with red blood cells (RBCs) is vital to elucidating the metabolic fate of NO in the vasculature. Because hemoglobin (Hb) is the most abundant...
Joshi, Mahesh S., Ferguson, T. Bruce, Han, Tae H., Hyduke, Daniel R., Liao, James C., Rassaf, Tienush, ...
Although irreversible reaction of NO with the oxyheme of hemoglobin (producing nitrate and methemoglobin) is extremely rapid, it has been proposed that, under normoxic conditions, NO binds...
Regulation of nitric oxide consumption by hypoxic red blood cells
Han, Tae H., Qamirani, Erion, Nelson, Allyson G., Hyduke, Daniel R., Chaudhuri, Gautam, Kuo, Lih, ...
The homeostasis of nitric oxide (NO) is attained through a balance between its production and consumption. Shifts in NO bioavailability have been linked to a variety of diseases. Although the...
Network component analysis: Reconstruction of regulatory signals in biological systems
Liao, James C., Boscolo, Riccardo, Yang, Young-Lyeol, Tran, Linh My, Sabatti, Chiara, Roychowdhury, Vwani P.
High-dimensional data sets generated by high-throughput technologies, such as DNA microarray, are often the outputs of complex networked systems driven by hidden regulatory signals. Traditional...
Kao, Katy C., Yang, Young-Lyeol, Boscolo, Riccardo, Sabatti, Chiara, Roychowdhury, Vwani, Liao, James C.
Cells adjust gene expression profiles in response to environmental and physiological changes through a series of signal transduction pathways. Upon activation or deactivation, the terminal regulators...
Design of artificial cell–cell communication using gene and metabolic networks
Bulter, Thomas, Lee, Sun-Gu, Wong, Wilson WaiChun, Fung, Eileen, Connor, Michael R., Liao, James C.
Artificial transcriptional networks have been used to achieve novel, nonnative behavior in bacteria. Typically, these artificial circuits are isolated from cellular metabolism and are designed to...
Inferring yeast cell cycle regulators and interactions using transcription factor activities
Yang, Young-Lyeol, Suen, Jason, Brynildsen, Mark P, Galbraith, Simon J, Liao, James C
Heat Shock Response of Archaeoglobus fulgidus†
Rohlin, Lars, Trent, Jonathan D., Salmon, Kirsty, Kim, Unmi, Gunsalus, Robert P., Liao, James C.
The heat shock response of the hyperthermophilic archaeon Archaeoglobus fulgidus strain VC-16 was studied using whole-genome microarrays. On the basis of the resulting expression profiles,...
Markov Chain Modeling of Pyelonephritis-Associated Pili Expression in Uropathogenic Escherichia coli
Zhou, Baiyu, Beckwith, David, Jarboe, Laura R., Liao, James C.
Pyelonephritis-associated pili (Pap) expression in uropathogenic Escherichia coli is regulated by a complex phase variation mechanism involving the competition between leucine-responsive regulatory...
Intravascular flow decreases erythrocyte consumption of nitric oxide
Liao, James C., W. Hein, Travis, Vaughn, Mark W., Huang, Kuang-Tse, Kuo, Lih
Nitric oxide (NO) produced by the endothelium diffuses both into the lumen and to the smooth muscle cells according to the concentration gradient in each direction. The extremely high reaction rate...
Tseng, George C., Oh, Min-Kyu, Rohlin, Lars, Liao, James C., Wong, Wing Hung
We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the...
Modulation of nitric oxide bioavailability by erythrocytes
Huang, Kuang-Tse, Han, Tae H., Hyduke, Daniel R., Vaughn, Mark W., Van Herle, Helga, Hein, Travis W., ...
Nitric oxide (NO) activates soluble guanylyl cyclase in smooth muscle cells to induce vasodilation in the vasculature. However, as hemoglobin (Hb) is an effective scavenger of NO and is present in...
Co-expression pattern from DNA microarray experiments as a tool for operon prediction
Sabatti, Chiara, Rohlin, Lars, Oh, Min-Kyu, Liao, James C.
The prediction of operons, the smallest unit of transcription in prokaryotes, is the first step towards reconstruction of a regulatory network at the whole genome level. Sequence information, in...
Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions
Han, Tae H., Hyduke, Daniel R., Vaughn, Mark W., Fukuto, Jon M., Liao, James C.
Understanding the interaction of nitric oxide (NO) with red blood cells (RBCs) is vital to elucidating the metabolic fate of NO in the vasculature. Because hemoglobin (Hb) is the most abundant...
Joshi, Mahesh S., Ferguson, T. Bruce, Han, Tae H., Hyduke, Daniel R., Liao, James C., Rassaf, Tienush, ...
Although irreversible reaction of NO with the oxyheme of hemoglobin (producing nitrate and methemoglobin) is extremely rapid, it has been proposed that, under normoxic conditions, NO binds...
Regulation of nitric oxide consumption by hypoxic red blood cells
Han, Tae H., Qamirani, Erion, Nelson, Allyson G., Hyduke, Daniel R., Chaudhuri, Gautam, Kuo, Lih, ...
The homeostasis of nitric oxide (NO) is attained through a balance between its production and consumption. Shifts in NO bioavailability have been linked to a variety of diseases. Although the...
Network component analysis: Reconstruction of regulatory signals in biological systems
Liao, James C., Boscolo, Riccardo, Yang, Young-Lyeol, Tran, Linh My, Sabatti, Chiara, Roychowdhury, Vwani P.
High-dimensional data sets generated by high-throughput technologies, such as DNA microarray, are often the outputs of complex networked systems driven by hidden regulatory signals. Traditional...
Kao, Katy C., Yang, Young-Lyeol, Boscolo, Riccardo, Sabatti, Chiara, Roychowdhury, Vwani, Liao, James C.
Cells adjust gene expression profiles in response to environmental and physiological changes through a series of signal transduction pathways. Upon activation or deactivation, the terminal regulators...
Design of artificial cell–cell communication using gene and metabolic networks
Bulter, Thomas, Lee, Sun-Gu, Wong, Wilson WaiChun, Fung, Eileen, Connor, Michael R., Liao, James C.
Artificial transcriptional networks have been used to achieve novel, nonnative behavior in bacteria. Typically, these artificial circuits are isolated from cellular metabolism and are designed to...
Inferring yeast cell cycle regulators and interactions using transcription factor activities
Yang, Young-Lyeol, Suen, Jason, Brynildsen, Mark P, Galbraith, Simon J, Liao, James C
Heat Shock Response of Archaeoglobus fulgidus†
Rohlin, Lars, Trent, Jonathan D., Salmon, Kirsty, Kim, Unmi, Gunsalus, Robert P., Liao, James C.
The heat shock response of the hyperthermophilic archaeon Archaeoglobus fulgidus strain VC-16 was studied using whole-genome microarrays. On the basis of the resulting expression profiles,...
Single-Gene Disorders: What Role Could Moonlighting Enzymes Play?
Sriram, Ganesh, Martinez, Julian A., McCabe, Edward R. B., Liao, James C., Dipple, Katrina M.
Single-gene disorders with “simple” Mendelian inheritance do not always imply that there will be an easy prediction of the phenotype from the genotype, which has been shown for a number of...
Markov Chain Modeling of Pyelonephritis-Associated Pili Expression in Uropathogenic Escherichia coli
Zhou, Baiyu, Beckwith, David, Jarboe, Laura R., Liao, James C.
Pyelonephritis-associated pili (Pap) expression in uropathogenic Escherichia coli is regulated by a complex phase variation mechanism involving the competition between leucine-responsive regulatory...
Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator
Wong, Wilson W, Tsai, Tony Y, Liao, James C
In Escherichia coli, protein degradation in synthetic circuits is commonly achieved by the ssrA-tagged degradation system. In this work, we show that the degradation kinetics for the green...
Versatility and Connectivity Efficiency of Bipartite Transcription Networks
Brynildsen, Mark P., Tran, Linh M., Liao, James C.
The modulation of promoter activity by DNA-binding transcription regulators forms a bipartite network between the regulators and genes, in which a smaller number of regulators control a much lager...
Hyduke, Daniel R., Jarboe, Laura R., Tran, Linh M., Chou, Katherine J. Y., Liao, James C.
Nitric oxide (NO) is used by mammalian immune systems to counter microbial invasions and is produced by bacteria during denitrification. As a defense, microorganisms possess a complex network to cope...