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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...
2 Battery Emulation B#: A Battery Emulator and Power-Profiling Instrument (2008)
Chulsung Park, Jinfeng Liu, Pai H. Chou
B # (B sharp) is a programmable power supply that emulates battery behavior. It measures current load, calls a battery simulation program to compute voltage in real time, and controls a linear...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
communication speed selection, communication/computation trade-offs, embedded multi-processor, lowpower design This paper presents a new technique for global energy optimization through coordinated...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
Abstract. 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...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
Abstract. 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...
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...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
communication speed selection, communication/computation trade-offs, embedded multi-processor, lowpower design This paper presents a new technique for global energy optimization through coordinated...
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 changing power and performance constraints imposed by the environment. Moreover,...
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
Abstract. 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 Scheduling for Embedded Systems under Min/Max Power and Timing Constraints £ (2007)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh, Nazeeh Aranki, Nikzad “benny Toomarian
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...
Supplementary material: "supplement.pdf" (2007)
NOTE to the printer: Please maintain the italic typesetting for the first sentence of each paragraph instead of sub-headings. 1 More than 30 organisms have been entirely sequenced. Here, we applied a...
Communication Speed Selection and Functional Partitioning (2007)
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...
Distributed Embedded Systems for Low Power: A Case Study (2007)
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...
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
communication speed selection, communication/computation trade-offs, embedded multi-processor, lowpower design This paper presents a new technique for global energy optimization through coordinated...
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.
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....
Tapper: a lightweight scripting engine for highly constrained wireless sensor nodes (2006)
Qiang Xie, Jinfeng Liu, Pai H. Chou
Tapper is a lightweight scripting engine for highly constrained wireless sensor nodes. Many such nodes run on 8-bit microcontrollers (MCUs) with only a few kilobytes of on-chip memory, often with...
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...
B#: a battery emulator and power profiling instrument (2005)
Chulsung Park, Jinfeng Liu, Pai H. Chou
This paper describes B # (B-sharp), a programmable power supply that emulates the behavior of a battery. It measures the current load, calls a battery simulation program to compute the voltage in...
Eco: an Ultra-Compact Low-Power Wireless Sensor Node for Real-Time Motion Monitoring (2005)
Chulsung Park, Jinfeng Liu, Pai H. Chou
Eco is an ultra-compact wireless sensor node. Only 648 mm 3 in volume and weighing under 1.6 grams, Eco was initially designed to monitor the spontaneous motion of preterm infants over 2.4GHz radio...
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...
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...
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...
Chop: parsing proteins into structural domains (2004)
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...
Department: Pharmacology.
The PredictProtein server (2004)
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 (2004)
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...
Predicting transmembrane beta-barrels in proteomes (2004)
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...
Sequence-based prediction of protein domains (2004)
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...
PEP: Predictions fo Entire Proteomes (2003)
Phil Carter, Jinfeng Liu, Burkhard Rost
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...
The PredictProtein Server (2003)
PredictProfiWD (PP, http://cubic.bio c.coV mbia.edu/pp/) is an internet servicefo sequence analysis and the predictio o aspectso fproKxK structure and functioc Users submitpro tein sequenceo r...
NORSp: predictions of long regions without regular secondary structure (2003)
Many structurallyflexil eregiEplay iay2 tant rolesi bies2 ies processes. It has been shown that extended loopy regi/G are very abundanti the protei n uniKP2fi and that they have been conserved...
The PredictProtein server (2003)
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 (2003)
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...
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii (2003)
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...
PEP: Predictions for Entire Proteomes (2003)
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:...
Communication speed selection for embedded systems with networked voltage-scalable processors (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...
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...
Communication speed selection for embedded systems with networked voltage-scalable processors (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...
Communication speed selection for embedded systems with networked voltage-scalable processors (2002)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
High-speed serial network interfaces are gaining wide use in con-necting multiple processors and peripherals in modem embedded systems, thanks to their size advantage and power efficiency. Many such...
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...
Target space for structural genomics revisited (2002)
Motivation: Structural genomics eventually aims at determining structures for all proteins. However, in the beginning experimentalists are likely to focus on globular proteins to achieve a rapid...
Power-Aware Scheduling under Timing Constraints for Mission-Critical Embedded Systems (2001)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh, Fadi Kurdahi
1 This research was sponsored by DARPA under contract F33615-00-1-1719 Power-aware systems are those that must make the best use of available power. They subsume traditional low-power systems in that...
Power-aware task motion: Dynamic range enhancement for power-aware embedded systems (2001)
Jinfeng Liu, Pai H. Chou, Nader Bagherzadeh
1 This research was sponsored by DARPA under contract F33615-00-1-1719 New embedded systems are being built with new types of energy sources, including solar panels and energy scavenging devices, in...
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...
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...
Comparing function and structure between entire proteomes (2001)
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,...
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,...
Liu, Jinfeng, Zhang, Yan, Lei, Xingye, Zhang, Zemin
A large-scale survey using single nucleotide polymorphism data from dbSNP provides insights into the evolutionary selection constraints on human proteins of different structural and functional...
Structural genomics is the largest contributor of novel structural leverage
Nair, Rajesh, Liu, Jinfeng, Soong, Ta-Tsen, Acton, Thomas B., Everett, John K., Kouranov, Andrei, ...
The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers for structural genomics (SG). These centers systematically target many large...
Misaghi, Shahram, Ottosen, Søren, Izrael-Tomasevic, Anita, Arnott, David, Lamkanfi, Mohamed, Lee, James, ...
Protein ubiquitination provides an efficient and reversible mechanism to regulate cell cycle progression and checkpoint control. Numerous regulatory proteins direct the addition of ubiquitin to...