Liu, Jinfeng, Zhang, Yan, Lei, Xingye, Zhang, Zemin
Abstract Background The rates of molecular evolution for protein-coding genes depend on the stringency of functional or structural constraints. The Ka/Ks ratio has been commonly used as an indicator...
Natively Unstructured Loops Differ from Other Loops (2007)
Avner Schlessinger, Jinfeng Liu, Burkhard Rost
Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many...
Natively Unstructured Loops Differ from Other Loops (2007)
Avner Schlessinger, Jinfeng Liu, Burkhard Rost
Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many...
Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines (2006)
Jinfeng Liu, Julian Gough, Burkhard Rost
RIKEN's FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever...
System-lever optimization and validation for power-constrained embedded systems / (2006)
Thesis (Ph. D., Electrical and Computer Engineering)--University of California, Irvine, 2006.
Powers, Robert, Mirkovic, Nebojsa, Goldsmith-Fischman, Sharon, Acton, Thomas B., Chiang, Yi-wen, Huang, Yuanpeng J., ...
The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123- residue (13.6-kDa) protein, has been determined by NMR methods. The structure of AF2095 is...
1H, 13C, and 15N assignments for the Archaeglobus fulgidis protein AF2095 (2004)
Powers, Robert, Acton, Thomas B., Chiang, Yi-wen, Rajan, P. K., Cort, John R., Kennedy, Michael A., ...
Structural genomics is providing a means to determine the molecular and cellular function for the vast amount of proteins in the Human proteome that lack any explicit experimental information by...
Distributed Embedded Systems for Low Power: (2004)
A multiple-processor system can potentially achieve higher energy savings than a single processor, because the reduced workload on each processor creates new opportunities for dynamic voltage scaling...
Combined Functional Partitioning (2004)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
This paper presents a new technique for global energy optimization through coordinated functional partitioning and speed selection for embedded processors interconnected by a high-speed serial bus....
Energy Optimization of Distributed Embedded Processors (2004)
Transmitting compressed data can reduce inter-processor communication traffic and create new opportunities for DVS (dynamic voltage scaling) in distributed embedded systems. However, data compression...
The explosion of sequence information in post-genomic era is increasingly widening the gap between the number of protein sequences deposited in public databases and the experimental characterization...
Communication Speed Selection and Functional Partitioning (2003)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
High-speed serial network interfaces are becoming the primary way for modern embedded systems and systems-onchip to connect with each other and with peripheral devices. Modern communication...
Energy Optimization of Distributed Embedded Processors (2003)
Transmitting compressed data can reduce inter-processor communication traffic and create new opportunities for DVS (dynamic voltage scaling) in distributed embedded systems. However, data compression...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
Transmitting compressed data can reduce inter-processor communication traffic and create new opportunities for DVS (dynamic voltage scaling) in distributed embedded systems. However, data compression...
Communication Speed Selection for Embedded Systems with Networked Voltage-Scalable Processors (2003)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
High-speed serial network interfaces are gaining wide use in connecting multiple processors and peripherals in modern embedded systems, thanks to their size advantage and power efficiency. Many such...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
This paper presents a new technique for global energy optimization through coordinated functional partitioning and speed selection for embedded processors interconnected by a high-speed serial bus....
Phil Carter, Jinfeng Liu, East Structural Genomics
PEP is a databaseo Predictioz fo Entire Proxfl mes. The database coS ains summarieso analyses o proSzfi sequencesfro a range o oSfi isms representing all three majo kingdon o life: eukary oary pro...
Communication Speed Selection for Embedded Systems (2002)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
High-speed serial network interfaces are gaining wide use in connecting multiple processors and peripherals in modern embedded systems, thanks to their size advantage and power efficiency. Many such...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
High-speed serial network interfaces are becoming the primary way for modern embedded systems and systems-onchip to connect with each other and with peripheral devices. Modern communication...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
New embedded systems are being built with new types of energy sources, including solar panels and energy scavenging devices, in order to maximize their utility when battery or A/C power is...
Power-Aware Task Motion: Dynamic Range Enhancement for Power-Aware Embedded Systems (2002)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
New embedded systems are being built with new types of energy sources, including solar panels and energy scavenging devices, in order to maximize their utility when battery and A/C power are...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
Dynamic voltage scaling (DVS) is a popular approach to power and energy reduction in microprocessors: it not only reduces the average power level, but also increases the processor's energy efficiency...
A Constraint-based Application Model and Scheduling Techniques for Power-aware Systems (2002)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh, Fadi Kurdahi
For new embeddedsystems to operate under an increasingly diverse range of power and performance constraints, they must be poweraware, not just low-power. That is, they must track their power sources...
Power-aware Scheduling for Embedded Systems under Min/Max Power and Timing Constraints (2002)
Nikzad "benny Toomarian, Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh, Nazeeh Aranki
Power-aware systems are those that must make the best use of available power. They subsume traditional low-power systems in that they must not only minimize power when the budget is low, but also...
Power-Aware Scheduling under Timing Constraints for Mission-Critical Embedded Systems (2002)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh, Fadi Kurdahi
Power-aware systems are those that must make the best use of available power. They subsume traditional low-power systems in that they must be able to not only minimize power when the budget is low,...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
New embedded systems are being built with new types of energy sources, including solar panels and energy scavenging devices, in order to maximize their utility when battery and A/C power are...
IMPACCT: Methodology and Tools for Power-Aware Embedded Systems (2001)
Pai H. Chou, Jinfeng Liu, Dexin Li, Nader Bagherzadeh
Power-aware systems are those that must exploit a wide range of power/performance tradeoffs in order to adapt to the power availability and application requirements. They require the integration of...
Comparing function and structure between entire proteomes Jinfeng Liu '2 Burkhard Rost (2001)
More than 30 organisms have been entirely sequenced. Here, we applied a variety of simple bioinformatics tools to analyse 29 proteomes for representatives from all three kingdoms: eukaryotes,...
Power-Aware Scheduling under Timing Constraints for Mission-Critical Embedded Systems (2001)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh, Fadi Kurdahi
Power-aware systems are those that must make the best use of available power. They subsume traditional low-power systems in that they must not only minimize power when the budget is low, but also...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh, Fadi Kurdahi
Power-aware systems are those that must make the best use of available power. They subsume traditional low-power systems in that they must not only minimize power when the budget is low, but also...
A Constraint-based Application Model and Scheduling Techniques for Power-aware Systems (2001)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh, Fadi Kurdahi
New embedded systems must be power-aware, not just low-power. That is, they must track their power sources and the changingpower and performance constraints imposed by the environment. Moreover, they...
PEP: Predictions for Entire Proteomes
Carter, Phil, Liu, Jinfeng, Rost, Burkhard
PEP is a database of Predictions for Entire Proteomes. The database contains summaries of analyses of protein sequences from a range of organisms representing all three major kingdoms of life:...
PredictProtein (PP, http://cubic.bioc.columbia.edu/pp/) is an internet service for sequence analysis and the prediction of aspects of protein structure and function. Users submit protein sequence or...
NORSp: predictions of long regions without regular secondary structure
Many structurally flexible regions play important roles in biological processes. It has been shown that extended loopy regions are very abundant in the protein universe and that they have been...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Predicting transmembrane beta-barrels in proteomes
Bigelow, Henry R., Petrey, Donald S., Liu, Jinfeng, Przybylski, Dariusz, Rost, Burkhard
Very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. One reason is that only very few high-resolution structures for transmembrane beta-barrel...
Rost, Burkhard, Yachdav, Guy, Liu, Jinfeng
PredictProtein (http://www.predictprotein.org) is an Internet service for sequence analysis and the prediction of protein structure and function. Users submit protein sequences or alignments;...
CHOP: parsing proteins into structural domains
Sequence-based domain assignment is one of the most important and challenging problems in structural biology. We have developed a method, CHOP, that chops proteins into domain-like fragments. The...
Sequence-based prediction of protein domains
Guessing the boundaries of structural domains has been an important and challenging problem in experimental and computational structural biology. Predictions were based on intuition, biochemical...
Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines
Liu, Jinfeng, Gough, Julian, Rost, Burkhard
RIKEN's FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever...
PEP: Predictions for Entire Proteomes
Carter, Phil, Liu, Jinfeng, Rost, Burkhard
PEP is a database of Predictions for Entire Proteomes. The database contains summaries of analyses of protein sequences from a range of organisms representing all three major kingdoms of life:...
PredictProtein (PP, http://cubic.bioc.columbia.edu/pp/) is an internet service for sequence analysis and the prediction of aspects of protein structure and function. Users submit protein sequence or...
NORSp: predictions of long regions without regular secondary structure
Many structurally flexible regions play important roles in biological processes. It has been shown that extended loopy regions are very abundant in the protein universe and that they have been...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Predicting transmembrane beta-barrels in proteomes
Bigelow, Henry R., Petrey, Donald S., Liu, Jinfeng, Przybylski, Dariusz, Rost, Burkhard
Very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. One reason is that only very few high-resolution structures for transmembrane beta-barrel...
Rost, Burkhard, Yachdav, Guy, Liu, Jinfeng
PredictProtein (http://www.predictprotein.org) is an Internet service for sequence analysis and the prediction of protein structure and function. Users submit protein sequences or alignments;...
CHOP: parsing proteins into structural domains
Sequence-based domain assignment is one of the most important and challenging problems in structural biology. We have developed a method, CHOP, that chops proteins into domain-like fragments. The...
Sequence-based prediction of protein domains
Guessing the boundaries of structural domains has been an important and challenging problem in experimental and computational structural biology. Predictions were based on intuition, biochemical...
Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines
Liu, Jinfeng, Gough, Julian, Rost, Burkhard
RIKEN's FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever...
Natively Unstructured Loops Differ from Other Loops
Schlessinger, Avner, Liu, Jinfeng, Rost, Burkhard
Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many...
Powers, Robert, Mirkovic, Nebojsa, Goldsmith-Fischman, Sharon, Acton, Thomas B., Chiang, Yiwen, Huang, Yuanpeng J., ...
The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123-residue (13.6-kDa) protein, has been determined by NMR methods. The structure of AF2095 is...
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii
Aramini, James M., Huang, Yuanpeng J., Cort, John R., Goldsmith-Fischman, Sharon, Xiao, Rong, Shih, Liang-Yu, ...
We report NMR assignments and solution structure of the 71-residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii, target JR19 of the Northeast Structural Genomics Consortium. The...
Comparing function and structure between entire proteomes
More than 30 organisms have been sequenced entirely. Here, we applied a variety of simple bioinformatics tools to analyze 29 proteomes for representatives from all three kingdoms: eukaryotes,...