Positive selection for the male functionality of a co-retroposed gene in the hominoids (2009)
Zhang, Yong, Lu, Shujuan, Zhao, Shuqi, Zheng, Xiaofeng, Long, Manyuan, Wei, Liping
Abstract Background New genes generated by retroposition are widespread in humans and other mammalian species. Usually, this process copies a single parental gene and inserts it into a distant...
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules (2009)
Li, Chuan-Yun, Liu, Qing-Rong, Zhang, Ping-Wu, Li, Xiao-Mo, Wei, Liping, Uhl, George R.
‘Cell adhesion molecules’ (CAMs) are essential elements of cell/cell communication that are important for proper development and plasticity of a variety of organs and tissues. In the brain,...
Li, Zheng, Liu, Min, Zhang, Li, Zhang, Wenxia, Gao, Ge, Zhu, Zuoyan, ...
How many intergenically encoded non-coding RNAs (ncRNAs) are expressed during various developmental stages in Drosophila? Previous analyses in one or a few developmental stages indicated abundant...
Application Note DRTF: a database of rice transcription factors (2008)
Ge Gao, Yingfu Zhong, Anyuan Guo, Qihui Zhu, Wen Tang, Weimou Zheng, ...
Summary: DRTF contains 2,025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2,384 in ssp. japonica, distributed in 63 families, identified by computational prediction and...
Allison Waugh, Glenn A. Williams, Liping Wei, Russ B. Altman
Given the high rate at which biological data are being collected and made public, it is essential that computational tools be developed that are capable of efficiently accessing and analyzing these...
Jeffrey Chang, Michelle Whirl Carrillo, Allison Waugh, Liping Wei, Russ B Altman
this paper, we studied diverse globin-like structures with sequence identities ranging from 9 to 25 percent. The set contains proteins that are closely related in terms of function, as well as two...
Genes and (Common) Pathways Underlying Drug Addiction (2008)
Chuan-Yun Li, Xizeng Mao, Liping Wei
Drug addiction is a serious worldwide problem with strong genetic and environmental influences. Different technologies have revealed a variety of genes and pathways underlying addiction; however,...
Li, Jiong-Tang, Zhang, Yong, Kong, Lei, Liu, Qing-Rong, Wei, Liping
Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse...
Steven C. Bagley, Liping Wei, Carol Cheng, Russ B. Altman
Bagley et al
An Automated System for Generating Comparative Disease Profiles and Making Diagnoses (2007)
We define comparative disease profile (CDP) as a collection of facts and/or symptoms that are significantly different between a disease group and a user-defined control group. We have developed a...
Chuan-Yun Li, Xizeng Mao, Liping Wei
Drug addiction is a serious worldwide problem with strong genetic and environmental influences. Different technologies have revealed a variety of genes and pathways underlying addiction, however,...
Kong, Lei, Zhang, Yong, Ye, Zhi-Qiang, Liu, Xiao-Qiao, Zhao, Shu-Qi, Wei, Liping, ...
Recent transcriptome studies have revealed that a large number of transcripts in mammals and other organisms do not encode proteins but function as noncoding RNAs (ncRNAs) instead. As millions of...
Ye, Zhi-Qiang, Zhao, Shu-Qi, Gao, Ge, Liu, Xiao-Qiao, Langlois, Robert E., Lu, Hui, ...
Motivation: The rapid accumulation of single amino acid polymorphisms (SAPs), also known as non-synonymous single nucleotide polymorphisms (nsSNPs), brings the opportunities and needs to understand...
Liang, Chao, Fujinuma, Ryosuke, Wei, Liping, Balser, Teri C.
Microbial contribution to carbon and nitrogen cycling in forest soils is important, and may depend on tree species. The amount of amino sugars and their ratios can serve as reliable indicators for...
Yong Zhang, Jiongtang Li, Lei Kong, Ge Gao, Qing-rong Liu, Liping Wei
Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense...
NATsDB: Natural Antisense Transcripts DataBase (2007)
Zhang, Yong, Li, Jiongtang, Kong, Lei, Gao, Ge, Liu, Qing-Rong, Wei, Liping
Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense...
SynDB: a Synapse protein DataBase based on synapse ontology (2007)
Zhang, Wuxue, Zhang, Yong, Zheng, Hui, Zhang, Chen, Xiong, Wei, Olyarchuk, John G., ...
A synapse is the junction across which a nerve impulse passes from an axon terminal to a neuron, muscle cell or gland cell. The functions and building molecules of the synapse are essential to almost...
Genome comparison using Gene Ontology (GO) with statistical testing (2006)
Cai, Zhaotao, Mao, Xizeng, Li, Songgang, Wei, Liping
Abstract Background Automated comparison of complete sets of genes encoded in two genomes can provide insight on the genetic basis of differences in biological traits between species. Gene ontology...
CEAS: cis-regulatory element annotation system (2006)
Xuwo Ji, Wei Li, Jun Song, Liping Wei, X. Shirley Liu
The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP– chip experiments to locate the in vivo-binding sites of transcription factors in the human...
Databases and ontologies (2006)
Ge Gao, Yingfu Zhong, Anyuan Guo, Qihui Zhu, Wen Tang, Weimou Zheng, ...
DRTF: a database of rice transcription factors
Bmc Bioinformatics, Zhaotao Cai, Xizeng Mao, Songgang Li, Liping Wei, Liping Wei
Genome comparison using Gene Ontology (GO) with statistical
CEAS: cis-regulatory element annotation system (2006)
Ji, Xuwo, Li, Wei, Song, Jun, Wei, Liping, Liu, X. Shirley
The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP–chip experiments to locate the in vivo-binding sites of transcription factors in the human...
KOBAS server: a web-based platform for automated annotation and pathway identification (2006)
Wu, Jianmin, Mao, Xizeng, Cai, Tao, Luo, Jingchu, Wei, Liping
There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experiments) using controlled vocabularies and...
DRTF: a database of rice transcription factors (2006)
Gao, Ge, Zhong, Yingfu, Guo, Anyuan, Zhu, Qihui, Tang, Wen, Zheng, Weimou, ...
Summary: DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and...
Li, Jigang, Li, Xiaojuan, Guo, Lei, Lu, Feng, Feng, Xiaojie, He, Kun, ...
MYB transcription factor genes play important roles in many developmental processes and in various defence responses of plants. Two Arabidopsis R2R3-type MYB genes, AtMYB59 and AtMYB48, were found to...
NATsDB: Natural Antisense Transcripts DataBase (2006)
Zhang, Yong, Li, Jiongtang, Kong, Lei, Gao, Ge, Liu, Qing-Rong, Wei, Liping
Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense...
Liang, Chao, Fujinuma, Ryosuke, Wei, Liping, Balser, Teri C.
Microbial contribution to carbon and nitrogen cycling in forest soils is important, and may depend on tree species. The amount of amino sugars and their ratios can serve as reliable indicators for...
Zhang, Yong, Liu, X. Shirley, Liu, Qing-Rong, Wei, Liping
We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to...
Li, Jigang, Li, Xiaojuan, Guo, Lei, Lu, Feng, Feng, Xiaojie, He, Kun, ...
MYB transcription factor genes play important roles in many developmental processes and in various defence responses of plants. Two Arabidopsis R2R3-type MYB genes, AtMYB59 and AtMYB48, were found to...
NATsDB: Natural Antisense Transcripts DataBase (2006)
Zhang, Yong, Li, Jiongtang, Kong, Lei, Gao, Ge, Liu, Qing-Rong, Wei, Liping
Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense...
GBA server: EST-based digital gene expression profiling (2005)
Xin Wu, Michael G. Walker, Jingchu Luo, Liping Wei
Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding...
Running Head: Genome Annotation and Pathway Identification Using KO (2005)
Xizeng Mao, Tao Cai, John G. Olyarchuk, Liping Wei
Motivation: High-throughput technologies, such as DNA sequencing and microarrays, have created the need for automated annotation of large sets of genes, including whole genomes, and automated...
Databases and ontologies (2005)
Anyuan Guo, Kun He, Shunong Bai, Xiaocheng Gu, Liping Wei, Jingchu Luo
doi:10.1093/bioinformatics/bti334
GBA server: EST-based digital gene expression profiling (2005)
Wu, Xin, Walker, Michael G., Luo, Jingchu, Wei, Liping
Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding...
DATF: a database of Arabidopsis transcription factors (2005)
Guo, Anyuan, He, Kun, Liu, Di, Bai, Shunong, Gu, Xiaocheng, Wei, Liping, ...
Summary: We have probably developed the most comprehensive database of Arabidopsis transcription factors (DATF). The DATF contains known and predicted Arabidopsis transcription factors (1827 genes in...
DATF: a database of Arabidopsis transcription factors (2005)
Guo, Anyuan, He, Kun, Liu, Di, Bai, Shunong, Gu, Xiaocheng, Wei, Liping, ...
Summary: We have developed likely the most comprehensive database of Arabidopsis transcription factors. The Database of Arabidopsis Transcription Factors (DATF) contains known and predicted...
Mao, Xizeng, Cai, Tao, Olyarchuk, John G., Wei, Liping
Motivation: High-throughput technologies, such as DNA sequencing and microarrays, have created the need for automated annotation of large sets of genes, including whole genomes, and automated...
Mao, Xizeng, Cai, Tao, Olyarchuk, John G., Wei, Liping
Motivation: High-throughput technologies such as DNA sequencing and microarrays have created the need for automated annotation of large sets of genes, including whole genomes, and automated...
Thesis (Ph. D.)--Cornell University, Jan., 2004.
Yueyi Liu, X. Shirley Liu, Liping Wei, Russ B. Altman, Serafim Batzoglou
Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from...
Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, X. Shirley Liu
A suite of web-based programs to search for
Liu, Yueyi, Liu, X. Shirley, Wei, Liping, Altman, Russ B., Batzoglou, Serafim
Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from...
A suite of web-based programs to search for transcriptional regulatory motifs (2004)
Liu, Yueyi, Wei, Liping, Batzoglou, Serafim, Brutlag, Douglas L., Liu, Jun S., Liu, X. Shirley
The identification of regulatory motifs is important for the study of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i)...
Liping Wei, L. Wei, R. B. Altman
this paper, we report a new, improved FEATURE system and investigate the FEATURE's ability to recognize sites that are geometrically complex and asymmetric, such as ATP-binding sites, redoxin...
Zhou, Yan, Huang, Guyang Matthew, Wei, Liping
Motivation: More and more often, a gene is epitomized by a large number of sequences in GenBank. This high redundancy makes it very difficult to identify a unique best match for a query sequence from...
Using meta computing tools to facilitate large-scale analyses of biological databases (2001)
Allison Waugh, Glenn A. Williams, Liping Wei, Russ B. Altman
Given the high rate at which biological data are being collected and made public, it is essential that computational tools be developed that are capable of efficiently accessing and analyzing these...
Using Metacomputing Tools To Facilitate Largescale (2001)
Analyses Of Biological, Allison Waugh, Glenn A. Williams, Liping Wei, Russ B. Altman
Given the high rate at which biological data are being collected and made public, it is essential that computational tools be developed that are capable of efficiently accessing and analyzing these...
Are Predicted Structures Good Enough to Preserve Functional Sites? (1999)
Liping Wei Enoch, Liping Wei, Enoch S Huang, Russ B Altman
this paper, we analyze the preservation of calciumbinding sites in model structures of a vitamin D dependent calcium-binding protein from bovine intestine. The native structure of the vitamin D...
Liping Wei, Russ B. Altman, Jeffrey T. Chang
We have performed a comprehensive analysis of the microenvironments surrounding the twenty amino acids. Our analysis includes comparison of amino acid environments with random control environments as...
Saifee, Owais, Wei, Liping, Nonet, Michael L.
We describe the molecular cloning and characterization of the unc-64 locus of Caenorhabditis elegans. unc-64 expresses three transcripts, each encoding a molecule with 63–64% identity to human...
Nonet, Michael L., Holgado, Andrea M., Brewer, Faraha, Serpe, Craig J., Norbeck, Betty A., Holleran, Julianne, ...
The unc-11 gene of Caenorhabditis elegans encodes multiple isoforms of a protein homologous to the mammalian brain-specific clathrin-adaptor protein AP180. The UNC-11 protein is expressed at high...
Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics
Liu, Yueyi, Liu, X. Shirley, Wei, Liping, Altman, Russ B., Batzoglou, Serafim
Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from...
A suite of web-based programs to search for transcriptional regulatory motifs
Liu, Yueyi, Wei, Liping, Batzoglou, Serafim, Brutlag, Douglas L., Liu, Jun S., Liu, X. Shirley
The identification of regulatory motifs is important for the study of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i)...
GBA server: EST-based digital gene expression profiling
Wu, Xin, Walker, Michael G., Luo, Jingchu, Wei, Liping
Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding...
Zhang, Yong, Liu, X. Shirley, Liu, Qing-Rong, Wei, Liping
We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to...
CEAS: cis-regulatory element annotation system
Ji, Xuwo, Li, Wei, Song, Jun, Wei, Liping, Liu, X. Shirley
The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP–chip experiments to locate the in vivo-binding sites of transcription factors in the human...
KOBAS server: a web-based platform for automated annotation and pathway identification
Wu, Jianmin, Mao, Xizeng, Cai, Tao, Luo, Jingchu, Wei, Liping
There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experiments) using controlled vocabularies and...
Saifee, Owais, Wei, Liping, Nonet, Michael L.
We describe the molecular cloning and characterization of the unc-64 locus of Caenorhabditis elegans. unc-64 expresses three transcripts, each encoding a molecule with 63–64% identity to human...
Nonet, Michael L., Holgado, Andrea M., Brewer, Faraha, Serpe, Craig J., Norbeck, Betty A., Holleran, Julianne, ...
The unc-11 gene of Caenorhabditis elegans encodes multiple isoforms of a protein homologous to the mammalian brain-specific clathrin-adaptor protein AP180. The UNC-11 protein is expressed at high...
Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics
Liu, Yueyi, Liu, X. Shirley, Wei, Liping, Altman, Russ B., Batzoglou, Serafim
Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from...
A suite of web-based programs to search for transcriptional regulatory motifs
Liu, Yueyi, Wei, Liping, Batzoglou, Serafim, Brutlag, Douglas L., Liu, Jun S., Liu, X. Shirley
The identification of regulatory motifs is important for the study of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i)...
GBA server: EST-based digital gene expression profiling
Wu, Xin, Walker, Michael G., Luo, Jingchu, Wei, Liping
Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding...
Zhang, Yong, Liu, X. Shirley, Liu, Qing-Rong, Wei, Liping
We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to...
CEAS: cis-regulatory element annotation system
Ji, Xuwo, Li, Wei, Song, Jun, Wei, Liping, Liu, X. Shirley
The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP–chip experiments to locate the in vivo-binding sites of transcription factors in the human...
KOBAS server: a web-based platform for automated annotation and pathway identification
Wu, Jianmin, Mao, Xizeng, Cai, Tao, Luo, Jingchu, Wei, Liping
There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experiments) using controlled vocabularies and...
Zhou, Min, Xu, Honglin, Wei, Xiaoli, Ye, Zhiqiang, Wei, Liping, Gong, Weimin, ...
5-Enolpyruvylshikimate 3-phosphate synthase (EPSPS) is a key enzyme in the shikimate pathway and is targeted by the wide-spectrum herbicide glyphosate. Here, we describe the use of a selection system...
NATsDB: Natural Antisense Transcripts DataBase
Zhang, Yong, Li, Jiongtang, Kong, Lei, Gao, Ge, Liu, Qing-Rong, Wei, Liping
Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense...
SynDB: a Synapse protein DataBase based on synapse ontology
Zhang, Wuxue, Zhang, Yong, Zheng, Hui, Zhang, Chen, Xiong, Wei, Olyarchuk, John G., ...
A synapse is the junction across which a nerve impulse passes from an axon terminal to a neuron, muscle cell or gland cell. The functions and building molecules of the synapse are essential to almost...
Kong, Lei, Zhang, Yong, Ye, Zhi-Qiang, Liu, Xiao-Qiao, Zhao, Shu-Qi, Wei, Liping, ...
Recent transcriptome studies have revealed that a large number of transcripts in mammals and other organisms do not encode proteins but function as noncoding RNAs (ncRNAs) instead. As millions of...
Genes and (Common) Pathways Underlying Drug Addiction
Li, Chuan-Yun, Mao, Xizeng, Wei, Liping
Drug addiction is a serious worldwide problem with strong genetic and environmental influences. Different technologies have revealed a variety of genes and pathways underlying addiction; however,...
Automated annotation of sites in protein structures / by Liping Wei.
Submitted to the Program in Medical Information Sciences and the Committee on Graduate Studies of Stanford University.
Automated annotation of sites in protein structures /
Submitted to the Program in Medical Information Sciences and the Committee on Graduate Studies of Stanford University.
Li, Jiong-Tang, Zhang, Yong, Kong, Lei, Liu, Qing-Rong, Wei, Liping
Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse...
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules
Li, Chuan-Yun, Liu, Qing-Rong, Zhang, Ping-Wu, Li, Xiao-Mo, Wei, Liping, Uhl, George R.
‘Cell adhesion molecules’ (CAMs) are essential elements of cell/cell communication that are important for proper development and plasticity of a variety of organs and tissues. In the brain,...
Li, Zheng, Liu, Min, Zhang, Li, Zhang, Wenxia, Gao, Ge, Zhu, Zuoyan, ...
How many intergenically encoded non-coding RNAs (ncRNAs) are expressed during various developmental stages in Drosophila? Previous analyses in one or a few developmental stages indicated abundant...