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# Category Archives: Transcription Modeling

## Tuesday 07/30/13

9:30 A – 5:00 P, 9:00 P- 12:00 P STORM set up O/N Ph-wt Pc-cy7 Modeling Using renewal equations which say fano factor of time is eta^2 of transcript count variability (covN) should go like 1/kf for all N for … Continue reading

Posted in Summaries, Transcription Modeling
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## notes from analytical exploration of effects of chain length on mRNA variability

The details of this approach are not valid, since we require reversability to use this form for the variance. excised text from review draft: % Using Sanchez Approach Since only one state in the gestation cycle is transcriptionally competent, all … Continue reading

Posted in Transcription Modeling
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## CoV of a series chain

1 2, 2 3, 4, 3 4, 6, 6, 4 5, 8, 9, 8, 5 6,10, 12, 12, 10, 6 The first term just increases by 1 from the term diagonal above and right of it, the second term increases … Continue reading

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## Finite state Markov model notes

simple switching model. Two systems, 1 and 2, each two states A and B. fi Ai <==> Bi bi Bi –> Bi + mRNA A1 <==> A2 [* f1 s12 0 b1 * 0 0 s2 0 * f2 0 … Continue reading

## Transcription traffic jams

Selth et al Elongation Review: polII collisions yield backtracking, pol II collisions yield reactivation / push through of paused leaders. Longer genes have more traffic jams (Swinburne 2008 G&D, see below). Saeki and Svejstrup 2009 Mol Cell Collisions can push … Continue reading

Posted in Transcription Modeling
Tagged transcription, writing
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## Friday 07/22/11

9:00A -12:30P mRNA counting (see post) numbers synthesis rates, decay modeling sent to ML Discuss merits of mathematical formulation of snail boundary bistability with Jacques. Proofs back for PNAS paper on gap-shadows. Fix yellow shade in fig 2D legend, review … Continue reading

## Protected: mRNA snail numbers and models

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Posted in snail patterning, Transcription Modeling
Tagged modeling, MP06, MP10, mRNA counting, sna
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## Protected: Gal4 gradient LacZ response

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Posted in Transcription Modeling
Tagged activators, Gal4, mRNA counting
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## Protected: bcd 1x and 6x counting

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Posted in Transcription Modeling
Tagged bcd, hb, mRNA counting
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## Protected: Analysis of 5-22 data b

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Posted in AP patterning, Shadow Enhancers, Transcription Modeling
Tagged bcd, hb, mRNA counting, noise, shadow enhancers
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