Category Archives: Transcription Modeling

Fundamentals of Transcription How Number of TF binding sites affects transcription increase binding rate increase probability > n TFs are bound increase probability an enhancer promoter interaction activates the gene. Affinity: relation from multiple weak sites to strong sites predicting … Continue reading →

Final edits: conversation of ‘IR/ER model’ to ‘IR/ER scheme’, (the models are ‘toy’ and ‘complex’, for which we compare two regulatory ‘schemes’). Upload Paper, Response to Reviewers, 6 Figures, Supplemental Text, 6 Supplemental Figures, Code with readme linking to webpage … Continue reading →

Received Steve’s revisions of response to reviewers.  Read and submitted final edits back to Steve and Peter. Labeled and exported all figures as F1/S1_name.tif and .eps (Illustrator, vector graphics format).  Sent zipped tif files to Peter and Steve for conformation.

Fixed figure 1 and S3 to label state 4 as 4B, keeping with dual state model.

Meeting with Peter and Steve 3:00P – 5:15P Revise model state description.  Revise discussion of two types of pausing: regulated pausing and other pausing. Need to fix reference citation in Appendix G. Fix labeling of supplemental figures: S1 sample chip, … Continue reading →

Revisions back from Steve.  Review and respond to comments.   Send back to Peter and Steve. Revisions to Supplement also received.  Still need to review and reply.