TileMap: create chromosomal map of tiling array hybridizations (2008)
Gene Expression, Hongkai Ji, Wing Hung Wong
doi:10.1093/bioinformatics/bti593
Vokes, Steven A., Ji, Hongkai, Wong, Wing H., McMahon, Andrew P.
Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We characterized the Gli-dependent cis-regulatory network through a combination...
Kim, Ryung S, Ji, Hongkai, Wong, Wing H
Abstract Background Many statistical algorithms combine microarray expression data and genome sequence data to identify transcription factor binding motifs in the low eukaryotic genomes. Finding...
Ji, Hongkai, Vokes, Steven A., Wong, Wing H.
Genome-wide location analysis (ChIP-chip, ChIP-PET) is a powerful technique to study mammalian transcriptional regulation. In order to obtain a basic understanding of the location data generated for...
Ji, Hongkai, Vokes, Steven A., Wong, Wing H.
Genome-wide location analysis (ChIP-chip, ChIP-PET) is a powerful technique to study mammalian transcriptional regulation. In order to obtain a basic understanding of the location data generated for...
Ji, Hongkai, Vokes, Steven A., Wong, Wing H.
Genome-wide location analysis (ChIP-chip, ChIP-PET) is a powerful technique to study mammalian transcriptional regulation. In order to obtain a basic understanding of the location data generated for...
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
TileMap: create chromosomal map of tiling array hybridizations (2005)
Motivation: Tiling array is a new type of microarray that can be used to survey genomic transcriptional activities and transcription factor binding sites at high resolution. The goal of this paper is...
TileMap: create chromosomal map of tiling array hybridizations (2005)
Motivation: Tiling array is a new type of microarray that can be used to survey genomic transcriptional activities and transcription factor binding sites at high resolution. The goal of this paper is...
AsMamDB: an alternative splice database of mammals (2001)
Ji, Hongkai, Zhou, Qing, Wen, Fang, Xia, Huiyu, Lu, Xin, Li, Yanda
The objective of database AsMamDB is to facilitate the systematic study of alternatively spliced genes of mammals. Version 1.0 of AsMamDB contains 1563 alternatively spliced genes of human, mouse and...
AsMamDB: an alternative splice database of mammals
Ji, Hongkai, Zhou, Qing, Wen, Fang, Xia, Huiyu, Lu, Xin, Li, Yanda
The objective of database AsMamDB is to facilitate the systematic study of alternatively spliced genes of mammals. Version 1.0 of AsMamDB contains 1563 alternatively spliced genes of human, mouse and...
Why do human diversity levels vary at a megabase scale?
Hellmann, Ines, Prüfer, Kay, Ji, Hongkai, Zody, Michael C., Pääbo, Svante, Ptak, Susan E.
Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of...
AsMamDB: an alternative splice database of mammals
Ji, Hongkai, Zhou, Qing, Wen, Fang, Xia, Huiyu, Lu, Xin, Li, Yanda
The objective of database AsMamDB is to facilitate the systematic study of alternatively spliced genes of mammals. Version 1.0 of AsMamDB contains 1563 alternatively spliced genes of human, mouse and...
Why do human diversity levels vary at a megabase scale?
Hellmann, Ines, Prüfer, Kay, Ji, Hongkai, Zody, Michael C., Pääbo, Svante, Ptak, Susan E.
Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of...
Ji, Hongkai, Vokes, Steven A., Wong, Wing H.
Genome-wide location analysis (ChIP-chip, ChIP-PET) is a powerful technique to study mammalian transcriptional regulation. In order to obtain a basic understanding of the location data generated for...
Vokes, Steven A., Ji, Hongkai, Wong, Wing H., McMahon, Andrew P.
Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We characterized the Gli-dependent cis-regulatory network through a combination...
TileProbe: modeling tiling array probe effects using publicly available data
Judy, Jennifer Toolan, Ji, Hongkai
Motivation: Individual probes on an Affymetrix tiling array usually behave differently. Modeling and removing these probe effects are critical for detecting signals from the array data. Current data...