Shultzaberger, Ryan K., Chiang, Derek Y., Moses, Alan M., Eisen, Michael B.
Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we...
Characterizing the cancer genome in lung adenocarcinoma (2007)
Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, ...
Somatic alterations in cellular DNA underlie almost all human cancers(1). The prospect of targeted therapies(2) and the development of high-resolution, genome-wide approaches(3-8) are now spurring...
Derek Y. Chiang, Patrick O. Brown, Michael B. Eisen
Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
Characterizing the cancer genome in lung adenocarcinoma (2007)
Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, ...
Flexible promoter architecture requirements for coactivator recruitment (2006)
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Abstract Background The spatial organization of transcription factor binding sites in regulatory DNA, and the composition of intersite sequences, influences the assembly of the multiprotein complexes...
Derek Y Chiang, David A Nix, Ryan K Shultzaberger, Audrey P Gasch, Michael B Eisen, Derek Y Chiang, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available shortly after the date of publication, from the URL listed below....
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
A systematic examination of the gene regulatory elements in ascomycete fungi reveals striking conservation along with some examples of the ways in which regulatory systems can evolve.
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
Abstract We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding-site...
Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
Conservation and evolution of cis-regulatory systems in ascomycete fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Position specific variation in the rate of evolution in transcription factor binding sites (2003)
Moses, Alan M., Chiang, Derek Y., Kellis, Manolis, Lander, Eric S., Eisen, Michael B.
Background: The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental...
Position specific variation in the rate of evolution in transcription factor binding sites (2003)
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Abstract Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of...
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Abstract Background Transcriptional regulation in eukaryotes often involves multiple transcription factors binding to the same transcription control region, and to understand the regulatory content...
BMC Evolutionary Biology BioMed Central (2003)
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S L, Michael B Eisen, Eric S Lander, ...
Research article Position specific variation in the rate of evolution in transcription factor binding sites
2003 Chiang et Volume al. 4, Issue 7, Article R43 Open Access (2003)
Derek Y Chiang, Alan M Moses, Manolis Kellis, Eric S L, Michael B Eisen
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
Derek Y. Chiang, Dept Of Molecular, Cell Biology, Eric S. Lander
Background. Transcriptional regulation in eukaryotes is often multifactorial, involving multiple transcription factors binding to the same transcription control region (e.g., upstream activating...
BMC Evolutionary Biology BioMed Central (2003)
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S L, Michael B Eisen, Eric S Lander, ...
Research article Position specific variation in the rate of evolution in transcription factor binding sites
Chiang, Derek Y., Brown, Patrick O., Eisen, Michael B.
The combination of genome-wide expression patterns and full genome sequences offers a great opportunity to further our understanding of the mechanisms and logic of transcriptional regulation. Many...
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts...
Position specific variation in the rate of evolution in transcription factor binding sites
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Gasch, Audrey P, Moses, Alan M, Chiang, Derek Y, Fraser, Hunter B, Berardini, Mark, Eisen, Michael B
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.
Flexible promoter architecture requirements for coactivator recruitment
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts...
Position specific variation in the rate of evolution in transcription factor binding sites
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Gasch, Audrey P, Moses, Alan M, Chiang, Derek Y, Fraser, Hunter B, Berardini, Mark, Eisen, Michael B
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.
Flexible promoter architecture requirements for coactivator recruitment
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Determining Physical Constraints in Transcriptional Initiation Complexes Using DNA Sequence Analysis
Shultzaberger, Ryan K., Chiang, Derek Y., Moses, Alan M., Eisen, Michael B.
Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we...
Astrocyte elevated gene-1 regulates hepatocellular carcinoma development and progression
Yoo, Byoung Kwon, Emdad, Luni, Su, Zao-zhong, Villanueva, Augusto, Chiang, Derek Y., Mukhopadhyay, Nitai D., ...
Hepatocellular carcinoma (HCC) is a highly aggressive vascular cancer characterized by diverse etiology, activation of multiple signal transduction pathways, and various gene mutations. Here, we have...