A windowed local fdr estimator providing higher resolution and robust thresholds (2007)
Khan, Rishi L., Vadigepalli, Rajanikanth, Gao, Guang, Schwaber, James S.
Motivation: In microarray analysis, special consideration must be given to the issues of multiple statistical tests and typically p-values are adjusted to control family-wise error rate (FWER) or...
Khan, Rishi L, Gonye, Gregory E, Gao, Guang, Schwaber, James S
Abstract Background Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for...
Khan, Rishi L., Gonye, Gregory E., Gao, Guang, Schwaber, James S.
Background Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for...
Robel Y. Kahsay, Guoli Wang, Guang Gao, Li Liao
* To whom correspondence should be addressed.
BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2005)
Robel Y. Kahsay, Guang Gao, Li Liao
doi:10.1093/bioinformatics/bti303 An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2005)
Robel Y. Kahsay, Guang Gao, Li Liao
doi:10.1093/bioinformatics/bti303 An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
Robel Kahsay, Li Liao, Guang Gao
In this work, we proposed a hidden Markov model for transmembrane protein sequences. The architecture of the model, based on an existing model TMHMM by Sonnhammer et al, contains 7 types of states...
Quasi-consensus-based comparison of profile hidden Markov models for protein sequences (2005)
Kahsay, Robel Y., Wang, Guoli, Gao, Guang, Liao, Li, Dunbrack, Roland
A simple approach for the sensitive detection of distant relationships among protein families and for sequence–structure alignment via comparison of hidden Markov models based on their...
Kahsay, Robel Y., Gao, Guang, Liao, Li
Motivation: Knowledge of the transmembrane helical topology can help identify binding sites and infer functions for membrane proteins. However, because membrane proteins are hard to solubilize and...
Kahsay, Robel Y., Gao, Guang, Liao, Li
Motivation: Knowledge of the transmembrane helical topology can help identify binding sites and infer functions for membrane proteins. However, because membrane proteins are hard to solubilize and...
Quasi-consensus based comparison of profile hidden Markov models for protein sequences (2005)
Kahsay, Robel Y., Wang, Guoli, Gao, Guang, Liao, Li, Dunbrack, Roland
A simple approach for sensitive detection of distant relationships among protein families and for sequence-structure alignment via comparison of hidden Markov models based on their quasi-consensus...
CASA: a server for the critical assessment of protein sequence alignment accuracy (2002)
Kahsay, Robel Y., Wang, Guoli, Dongre, Nataraj, Gao, Guang, Dunbrack, Roland L.
Summary: A public server for evaluating the accuracy of protein sequence alignment methods is presented. CASA is an implementation of the alignment accuracy benchmark presented by Sauder et al....
Compiling several classes of communication patterns on a multithreaded architecture (2001)
Rishi Kumar, Gagan Agrawal, Guang Gao
state.edu Communication optimizations play a crucial role in per-formance of parallel applications which are compiled and executed on distributed memory machines. Multithreaded architectures can...
An implementation of a Hopfield network kernel on EARTH (1998)
Jos'e N. Amaral, Guang Gao, Xinan Tang
EARTH is a multithreaded program execution and architecture model that hides communication and synchronization latencies through fine-grain multithreading. EARTH provides a simple synchronization...
Coping with very high latencies in petaflop computer systems (1998)
Sean Ryan, Jos'e N. Amaral, Guang Gao, Zachary Ruiz, Andres Marquez, Kevin Theobald
The very long and highly variable latencies in the deep memory hierarchy of a petaflop-scale architecture design, such as the Hybrid Technology Multi-Threaded Architecture (HTMT) [13], present a new...
A Refinement of the HTMT Program Execution Model (1998)
Guang Gao, José Nelson Amaral, Andres Marquez, Kevin Theobald
We refine the specification of the program execution model for the HTMT architecture that has been presented in previous documents and discussed in HTMT workshops. The parcel percolation model is...
Processing in memory: Chips to petaflops (1997)
Peter M. Kogge, Jay B. Brockman, Thomas Sterling, Guang Gao
This paper discusses the potential use of Processing-InMemory (PIM) Technology in petaflops level computing. It starts with a quick review of a proposed PIM architecture called Shamrock, and follows...
Compiling C for the EARTH Multithreaded Architecture (1996)
Laurie Hendren, Xinan Tang, Yingchun Zhu, Guang Gao, Xun Xue, Haiying Cai, ...
Multithreaded architectures provide an opportunity for efficiently executing programs with irregular parallelism and/or irregular locality. This paper presents a strategy that makes use of the...
Surfactant-aided draining and drying of liquid films on solid surfaces / (1994)
Thesis (Ph. D.)--University of Minnesota, 1994.
The Multi-Threaded Architecture Multiprocessor (1994)
Herbert Hum, Herbert H. J, Humy Olivier, Olivier Maquelin, Kevin Theobald, Xinan Tang, ...
Multithreaded node architectures have been proposed for future multiprocessor systems. However, some open issues remain: can efficient multithreading support be provided in a multiprocessor machine...
Designing Programming Languages for Analyzability: A Fresh Look at Pointer Data Structures (1992)
In this paper we propose a programming language mechanism and associated compiler techniques which significantly enhance the analyzability of pointerbased data structures frequently used in...
Collective Analysis and Transformation of Loop Clusters (1992)
this memo is a new loop analysis and transformation technique which brings compiler technology closer to meeting the needs of newer high-performance computer architectures. In specific terms, the...
A Kahn principle for networks of nonmonotonic real-time processes (1992)
We show that the input-output function computed by a network of asynchronous real-time processes is denoted by the unique fixed point of a Scott continuous functional even though the network or its...
Thesis (Ph. D.)--Michigan Technological University, 1989.
NPAT Expression Is Regulated by E2F and Is Essential for Cell Cycle Progression
Gao, Guang, Bracken, Adrian P., Burkard, Karina, Pasini, Diego, Classon, Marie, Attwooll, Claire, ...
NPAT is an in vivo substrate of cyclin E-Cdk2 kinase and is thought to play a critical role in coordinated transcriptional activation of histone genes during the G1/S-phase transition and in S-phase...
DNA damage induces downregulation of histone gene expression through the G1 checkpoint pathway
Su, Chuan, Gao, Guang, Schneider, Sandra, Helt, Christopher, Weiss, Carsten, O'Reilly, Michael A, ...
Activation of the G1 checkpoint following DNA damage leads to inhibition of cyclin E–Cdk2 and subsequent G1 arrest in higher eucaryotes. Little, however, is known about the molecular events...
Stress-Activated Protein Kinases Are Involved in Coxsackievirus B3 Viral Progeny Release
Si, Xiaoning, Luo, Honglin, Morgan, Andrew, Zhang, Jingchun, Wong, Jerry, Yuan, Ji, ...
Stress-activated protein kinases (SAPKs), consisting of c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (p38 MAPK), are activated upon various environmental stimuli, including...
NPAT Expression Is Regulated by E2F and Is Essential for Cell Cycle Progression
Gao, Guang, Bracken, Adrian P., Burkard, Karina, Pasini, Diego, Classon, Marie, Attwooll, Claire, ...
NPAT is an in vivo substrate of cyclin E-Cdk2 kinase and is thought to play a critical role in coordinated transcriptional activation of histone genes during the G1/S-phase transition and in S-phase...
DNA damage induces downregulation of histone gene expression through the G1 checkpoint pathway
Su, Chuan, Gao, Guang, Schneider, Sandra, Helt, Christopher, Weiss, Carsten, O'Reilly, Michael A, ...
Activation of the G1 checkpoint following DNA damage leads to inhibition of cyclin E–Cdk2 and subsequent G1 arrest in higher eucaryotes. Little, however, is known about the molecular events...
Stress-Activated Protein Kinases Are Involved in Coxsackievirus B3 Viral Progeny Release
Si, Xiaoning, Luo, Honglin, Morgan, Andrew, Zhang, Jingchun, Wong, Jerry, Yuan, Ji, ...
Stress-activated protein kinases (SAPKs), consisting of c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (p38 MAPK), are activated upon various environmental stimuli, including...
Ubiquitination Is Required for Effective Replication of Coxsackievirus B3
Si, Xiaoning, Gao, Guang, Wong, Jerry, Wang, Yahong, Zhang, Jingchun, Luo, Honglin
Autophagosome Supports Coxsackievirus B3 Replication in Host Cells▿
Wong, Jerry, Zhang, Jingchun, Si, Xiaoning, Gao, Guang, Mao, Ivy, McManus, Bruce M., ...
Recent studies suggest a possible takeover of host antimicrobial autophagy machinery by positive-stranded RNA viruses to facilitate their own replication. In the present study, we investigated the...
Proteasome inhibition attenuates coxsackievirus-induced myocardial damage in mice
Gao, Guang, Zhang, Jingchun, Si, Xiaoning, Wong, Jerry, Cheung, Caroline, McManus, Bruce, ...
Coxsackievirus B3 (CVB3) is one of the most prevalent pathogens of viral myocarditis, which may persist chronically and progress to dilated cardiomyopathy. We previously demonstrated a critical role...