Revisiting the Saccharomyces cerevisiae predicted ORFeome (2008)
Li, Qian-Ru, Carvunis, Anne-Ruxandra, Yu, Haiyuan, Han, Jing-Dong J., Zhong, Quan, Simonis, Nicolas, ...
Accurately defining the coding potential of an organism, i.e., all protein-encoding open reading frames (ORFs) or “ORFeome,” is a prerequisite to fully understand its biology. ORFeome annotation...
Inferring causal relationships among different histone modifications and gene expression (2008)
Yu, Hong, Zhu, Shanshan, Zhou, Bing, Xue, Huiling, Han, Jing-Dong J.
Histone modifications are major epigenetic factors regulating gene expression. They play important roles in maintaining stem cell pluripotency and in cancer pathogenesis. Different modifications may...
Impacts of protein-protein interaction domains on organism and network complexity (2008)
Xia, Kai, Fu, Zheng, Hou, Lei, Han, Jing-Dong J.
It has been a puzzle that genome or proteome sizes are not correlated with the complexity of the organisms. Although alternative splicing and noncoding and regulatory elements explain some of the...
Xia, Kai, Dong, Dong, Han, Jing-Dong J
Abstract Background Although protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further...
Han, Jing-Dong J., Bertin, Nicolas, Hao, Tong, Goldberg, Debra S., Berriz, Gabriel F., Zhang, Lan V., ...
In apparently scale-free protein-protein interaction networks, or 'interactome' networks, most proteins interact with few partners, whereas a small but significant proportion of proteins, the 'hubs',...
Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs (2004)
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Xia, Kai, Xue, Huiling, Dong, Dong, Zhu, Shanshan, Wang, Jiamu, Zhang, Qingpeng, ...
The protein–protein interaction networks, or interactome networks, have been shown to have dynamic modular structures, yet the functional connections between and among the modules are less well...
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Xia, Kai, Xue, Huiling, Dong, Dong, Zhu, Shanshan, Wang, Jiamu, Zhang, Qingpeng, ...
The protein–protein interaction networks, or interactome networks, have been shown to have dynamic modular structures, yet the functional connections between and among the modules are less well...
Confirmation of Organized Modularity in the Yeast Interactome
Bertin, Nicolas, Simonis, Nicolas, Dupuy, Denis, Cusick, Michael E, Han, Jing-Dong J, Fraser, Hunter B, ...
A modular network model of aging
Xue, Huiling, Xian, Bo, Dong, Dong, Xia, Kai, Zhu, Shanshan, Zhang, Zhongnan, ...
Many fundamental questions on aging are still unanswered or are under intense debate. These questions are frequently not addressable by examining a single gene or a single pathway, but can best be...
Inferring causal relationships among different histone modifications and gene expression
Yu, Hong, Zhu, Shanshan, Zhou, Bing, Xue, Huiling, Han, Jing-Dong J.
Histone modifications are major epigenetic factors regulating gene expression. They play important roles in maintaining stem cell pluripotency and in cancer pathogenesis. Different modifications may...
Revisiting the Saccharomyces cerevisiae predicted ORFeome
Li, Qian-Ru, Carvunis, Anne-Ruxandra, Yu, Haiyuan, Han, Jing-Dong J., Zhong, Quan, Simonis, Nicolas, ...
Accurately defining the coding potential of an organism, i.e., all protein-encoding open reading frames (ORFs) or “ORFeome,” is a prerequisite to fully understand its biology. ORFeome annotation...
Impacts of protein–protein interaction domains on organism and network complexity
Xia, Kai, Fu, Zheng, Hou, Lei, Han, Jing-Dong J.
It has been a puzzle that genome or proteome sizes are not correlated with the complexity of the organisms. Although alternative splicing and noncoding and regulatory elements explain some of the...