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Parameterization of a Stochastic Model of Gene Expression from Adaptive Imaging Cytometry Data

Parameterization of a Stochastic Model of Gene Expression from Adaptive Imaging Cytometry Data

Supplementary material to a manuscript under review. The manuscript can be downloaded from the link below. 

Abstract

Recent decades have yielded an understanding of cellular behavior as arising from a complicated soup of noisy molecular interactions. Systems biologists [...]

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Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology

Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology

Supplementary material to a manuscript under review. The manuscript can be downloaded from the link below. 

Abstract

Recent decades have yielded an understanding of cellular behavior as arising from a complicated soup of noisy molecular interactions. Systems biologists [...]

430
Views
545
DLs

Measurement of transcriptional noise in the cell cycle regulatory network

Measurement of transcriptional noise in the cell cycle regulatory network

These are the raw images collected to analyze the noise affecting transcription in the control of the cell cycle in yeast. 

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This data set is almost complete. We are still working on uploading the NET1 and SIC1 data.

GenoCAD Grammar to design synthetic transcription factors in eukaryotes

GenoCAD Grammar to design synthetic transcription factors in eukaryotes

This file can be imported into GenoCAD for the design of synthetic transcription factors (sTFs) in eukaryotic cells. Knowledge derived from experimental evidence was captured in this grammar to guide the user to create designer transcription factors that should operate as intended. The grammar [...]

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We like to use Figshare as a central repository of grammars for GenoCAD. This grammar is described in a paper published in ACS Synthetic Biology doi:10.1021/sb400134k

GenoCAD Grammar to design Chlamydomonas reinhardtii expression vectors

GenoCAD Grammar to design Chlamydomonas reinhardtii expression vectors

This is a grammar that can be imported into the web-based application GenoCAD to design expression vectors for expressing genes in the chloroplast of Chlamydomonas reinhardtii. Please refer to the publication linked to this entry for more information about this dataset. 

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This dataset was included in the online supplement of a publication in Bioinformatics:   http://dx.doi.org/10.1093/bioinformatics/btt646 Even though this article is published open access, we like to use Figshare as our central repository of GenoCAD grammars.

Genetic Design Automation Workflow

Comparison between the design automation loop in EDA and GDA. Projects follow parallel paths in both fields. Understanding what lessons from EDA can be applied for GDA is crucial to accelerating discovery in synthetic biology.

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We prepared this figure a few years ago but it did not make it in the final version of the paper. I still like it. I put it on Figshare to share the love! Hopefully it will be useful to...

SBOL: A community standard for communicating designs in synthetic biology

SBOL: A community standard for communicating designs in synthetic biology

Abstract

The Synthetic Biology Open Language (SBOL) is a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-adopted, formalized format for exchange between software tools, research groups, and commercial service providers. The [...]

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Several current and former members the Peccoud Lab are co-authors of this manuscript.

Improving DNA Manufacturing Through Standardization

Improving DNA Manufacturing Through Standardization

 

By framing gene synthesis as a manufacturing problem, it is possible to utilize common Industrial Engineering (IE) principles that have been applied to numerous macroscale systems in the burgeoning realm of DNA fabrication. These techniques have been successfully employed in an academic [...]

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This manuscript was submitted for presentation at IWBDA 2013. It was not accepted. The reviews we received are copied below. The manuscript will eventually be revised and published elsewhere. ----------------------- REVIEW 1 --------------------- PAPER: 11 TITLE: Improving DNA Manufacturing Through...

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