RNA-seq data integration into genome-scale metabolic model

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Bhushan Dhamale

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May 16, 2018, 12:56:45 PM5/16/18
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I am looking for a good guide/tutorial source for the integration of RNA-seq data into genome-scale metabolic models.
I have the raw read FASTQ files for Mycobacterium tuberculosis. Despite several searches, I was unable to find a way to integrate data from the FASTQ files into the model.
I am quite new to this, and I would really appreciate some links to any sources that would demonstrate ways to do what I am aiming for.

Ronan M.T. Fleming

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May 16, 2018, 2:26:41 PM5/16/18
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Hi Bhushan,
you could start with this:
See also the referenced papers, esp the review by Opdam et al.
Regards,
Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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Assistant Professor,
Division of Systems Biomedicine and Pharmacology,
Leiden Academic Centre for Drug Research,
Faculty of Science,
Leiden University.
&
H2020 Project Coordinator
Systems Medicine of Mitochondrial Parkinson’s Disease
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Andres Mauricio Pinzon Velasco

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May 16, 2018, 3:20:55 PM5/16/18
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Hi Bhushan,
This can be helpful too:

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models

Methods for integration of transcriptomic data in genome-scale metabolic models


Hope it helps,

Regards,
Andrés M. Pinzón Ph.D.
Assistant Professor
Group Leader - Bioinformatics and Systems Biology
Instituto de Genética, Off. 218
Universidad Nacional de Colombia
+57 (1) 3165000 Ext. 11618

Bhushan Dhamale

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May 29, 2018, 2:37:23 AM5/29/18
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Thank you for the suggestion Dr. Fleming.


On Wednesday, May 16, 2018 at 11:56:41 PM UTC+5:30, Ronan M.T. Fleming wrote:
Hi Bhushan,
you could start with this:
See also the referenced papers, esp the review by Opdam et al.
Regards,
Ronan
On 16 May 2018 at 18:56, Bhushan Dhamale <bhushan....@gmail.com> wrote:
I am looking for a good guide/tutorial source for the integration of RNA-seq data into genome-scale metabolic models.
I have the raw read FASTQ files for Mycobacterium tuberculosis. Despite several searches, I was unable to find a way to integrate data from the FASTQ files into the model.
I am quite new to this, and I would really appreciate some links to any sources that would demonstrate ways to do what I am aiming for.

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Bhushan Dhamale

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May 29, 2018, 2:38:29 AM5/29/18
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Thank you for the helpful reviews Dr. Pinzón.

On Thursday, May 17, 2018 at 12:50:55 AM UTC+5:30, Andres Mauricio Pinzon Velasco wrote:
Hi Bhushan,
This can be helpful too:

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models

Methods for integration of transcriptomic data in genome-scale metabolic models


Hope it helps,

Regards,
2018-05-16 13:26 GMT-05:00 Ronan M.T. Fleming <ronan.mt...@gmail.com>:
Hi Bhushan,
you could start with this:
See also the referenced papers, esp the review by Opdam et al.
Regards,
Ronan
On 16 May 2018 at 18:56, Bhushan Dhamale <bhushan....@gmail.com> wrote:
I am looking for a good guide/tutorial source for the integration of RNA-seq data into genome-scale metabolic models.
I have the raw read FASTQ files for Mycobacterium tuberculosis. Despite several searches, I was unable to find a way to integrate data from the FASTQ files into the model.
I am quite new to this, and I would really appreciate some links to any sources that would demonstrate ways to do what I am aiming for.

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--
--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
----------------------------------------------------------------------------
Assistant Professor,
Division of Systems Biomedicine and Pharmacology,
Leiden Academic Centre for Drug Research,
Faculty of Science,
Leiden University.
&
H2020 Project Coordinator
Systems Medicine of Mitochondrial Parkinson’s Disease
----------------------------------------------------------------------------
Mobile:  +352 621 175 112
Skype: ronan.fleming
----------------------------------------------------------------------------
(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

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