Levin, Joshua Z, Berger, Michael F, Adiconis, Xian, Rogov, Peter, Melnikov, Alexandre, Fennell, Timothy, ...
Abstract Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by...
High-resolution DNA-binding specificity analysis of yeast transcription factors (2009)
Zhu, Cong, McCord, Rachel Patton, Shi, Zhenwei, Berger, Michael F., Newburger, Daniel E., ...
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by...
Predicting the binding preference of transcription factors to individual DNA k-mers (2009)
Alleyne, Trevis M., Peña-Castillo, Lourdes, Badis, Gwenael, Talukder, Shaheynoor, Berger, Michael F., Gehrke, Andrew R., ...
Motivation: Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly...
Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments (2008)
Aaron M. Qureshi, Michael F. Berger, Martha L
equally to this work.
Rachel Patton Mccord, Michael F Berger, Martha L Bulyk
www.molecularsystemsbiology.com
Hu, Yanhui, Rolfs, Andreas, Bhullar, Bhupinder, Murthy, Tellamraju V. S., Zhu, Cong, Berger, Michael F., ...
The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein–protein interactions. These...
Hu, Yanhui, Rolfs, Andreas, Bhullar, Bhupinder, Murthy, Tellamraju V. S., Zhu, Cong, Berger, Michael F., ...
The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein–protein interactions. These...
Inferring condition-specific transcription factor function from DNA binding and gene expression data
McCord, Rachel Patton, Berger, Michael F, Philippakis, Anthony A, Bulyk, Martha L
Numerous genomic and proteomic datasets are permitting the elucidation of transcriptional regulatory networks in the yeast Saccharomyces cerevisiae. However, predicting the condition dependence of...
Hu, Yanhui, Rolfs, Andreas, Bhullar, Bhupinder, Murthy, Tellamraju V. S., Zhu, Cong, Berger, Michael F., ...
The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein–protein interactions. These...
Pompeani, Audra J, Irgon, Joseph J, Berger, Michael F, Bulyk, Martha L, Wingreen, Ned S, Bassler, Bonnie L
Quorum sensing is the process of cell-to-cell communication by which bacteria communicate via secreted signal molecules called autoinducers. As cell population density increases, the accumulation of...
High-resolution DNA-binding specificity analysis of yeast transcription factors
Zhu, Cong, McCord, Rachel Patton, Shi, Zhenwei, Berger, Michael F., Newburger, Daniel E., ...
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by...
Predicting the binding preference of transcription factors to individual DNA k-mers
Alleyne, Trevis M., Peña-Castillo, Lourdes, Badis, Gwenael, Talukder, Shaheynoor, Berger, Michael F., Gehrke, Andrew R., ...
Motivation: Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly...