Affiliation: University of California
- Discovering tightly regulated and differentially expressed gene sets in whole genome expression dataChun Ye
Bioinformatics Program, University of California San Diego, La Jolla, CA 92093 0404, USA
Bioinformatics 23:e84-90. 2007..We present a new method based on notions of tight regulation and differential expression to look for sets of genes which appear to be significantly affected by genetic variation...
- Using network component analysis to dissect regulatory networks mediated by transcription factors in yeastChun Ye
Bioinformatics Program, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 5:e1000311. 2009..The software package implementing the algorithms discussed in this work is available as a MATLAB package upon request...
- Orthologous repeats and mammalian phylogenetic inferenceAli Bashir
Bioinformatics Program, University of California San Diego, La Jolla, California 92093 0114, USA
Genome Res 15:998-1006. 2005..With rapid expansion of available partial sequence data, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference...
- Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approachesJae Hoon Sul
Computer Science Department, University of California, Los Angeles, California, USA
PLoS Genet 9:e1003491. 2013..Additionally, our method provides an interpretation framework that accurately predicts whether an eQTL has an effect in a particular tissue...
- Assessing computational tools for the discovery of transcription factor binding sitesMartin Tompa
Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
Nat Biotechnol 23:137-44. 2005..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
- Molecular evolution of growth hormone gene family in old world monkeys and hominoidsChun Ye
Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
Gene 350:183-92. 2005..Our results disclosed the complex history of the primate growth hormone gene family and raised intriguing questions on the consequences of these evolutionary events...
- Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoidsYing Li
Laboratory of Molecular Evolution and Genome Diversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
J Mol Endocrinol 35:399-409. 2005..Detailed analysis of the evolution of pseudogenes showed that the evolutionary pattern of this gene family in platyrrhines is in agreement with the so-called birth-and-death process...
- PKD1 inhibits cancer cells migration and invasion via Wnt signaling pathway in vitroKe Zhang
State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, and School of Life Science, Sichuan University, Chengdu 610041, China
Cell Biochem Funct 25:767-74. 2007..And we also showed that PC-1 regulated these processes in a process that may be at least partially through the Wnt pathway. Collectively, our data suggest that PKD1 may act as a novel member of the tumor suppressor family of genes...