Projects/MASSIV: Alternative splicing-inspired protein development - Revision history

Vs at 21:17, 16 February 2024

2024-02-16T21:17:01Z

Wiki: Wiki moved page Projects/ELAPID: Alternative splicing-inspired protein development to Projects/MASSIV: Alternative splicing-inspired protein development: Project title change.

2020-09-24T15:08:51Z

Wiki moved page Projects/ELAPID: Alternative splicing-inspired protein development to Projects/MASSIV: Alternative splicing-inspired protein development: Project title change.

Wiki at 15:04, 24 September 2020

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Wiki at 15:03, 24 September 2020

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Wiki at 14:56, 24 September 2020

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Wiki at 15:37, 28 August 2020

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Wiki at 15:35, 28 August 2020

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 ==Problem 74==
-* Title: MASSIV: Alternative splicing-inspired protein desdign
+* Title: MASSIV: Alternative splicing-inspired protein design
-* Problem: Eukaryotes have evolveda transcription machinery that can augment the protein repertoire without increasing the genome size. It produces several mRNA transcripts from the same gene, by choosing different initiation/termination sites and/or by splicing different exons. This regulatory process is called Alternative Splicing (AS). Although the mechanisms of AS have been well described at the genomic level, the extent to which and how AS modulates protein functions and interactions remains a fundamental open question. Here, we propose to develop a probabilistic model that will learn from the functional AS events observed today in nature to generate new protein functional diversity. The rationale will be that the means AS has produced to generate protein diversity along evolution can be reused and generalized to expand the protein repertoire way beyond what we observe today. The challenge here will be to design an artificial system able to learn the underlying rules of (functional) AS and to generalize to any protein sequence.
+* Problem: Eukaryotes have evolved a transcription machinery that can augment the protein repertoire without increasing the genome size. It produces several mRNA transcripts from the same gene, by choosing different initiation/termination sites and/or by splicing different exons. This regulatory process is called Alternative Splicing (AS). Although the mechanisms of AS have been well described at the genomic level, the extent to which and how AS modulates protein functions and interactions remains a fundamental open question. Here, we propose to develop a probabilistic model that will learn from the functional AS events observed today in nature to generate new protein functional diversity. The rationale will be that the means AS has produced to generate protein diversity along evolution can be reused and generalized to expand the protein repertoire way beyond what we observe today. The challenge here will be to design an artificial system able to learn the underlying rules of (functional) AS and to generalize to any protein sequence.
 <!-- Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms.-->
 * Data: Almost ready to share, could be accessed on request.
@@ Line 10: / Line 16: @@
 *# Protein physics: a course of lectures with color and stereoscopic illustrations and problems by Finkelstein A.V., Ptitsyn O.B. [http://www.mol.bio.msu.ru/res/DOC61/2012_Book_fizika_belka.pdf book in rus]
 *# Image [http://www.lcqb.upmc.fr/laine/images/phylo.png www.lcqb.upmc.fr/laine/images/phylo.png]
-* Basic solution: for now the problem is not strictly formulated. But there is a github project to start with.
+* Basic solution: for now the problem is not strictly formulated. But there is a GitHub project to start with.
 * Novelty:
 * Authors:  Elodie Laine, Sergei Grudinin, and Vadim Strijov

@@ Line 2: / Line 2: @@
 * Title: MASSIV: Alternative splicing-inspired protein desdign
-* Problem: Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms.
+* Problem: Eukaryotes have evolveda transcription machinery that can augment the protein repertoire without increasing the genome size. It produces several mRNA transcripts from the same gene, by choosing different initiation/termination sites and/or by splicing different exons. This regulatory process is called Alternative Splicing (AS). Although the mechanisms of AS have been well described at the genomic level, the extent to which and how AS modulates protein functions and interactions remains a fundamental open question. Here, we propose to develop a probabilistic model that will learn from the functional AS events observed today in nature to generate new protein functional diversity. The rationale will be that the means AS has produced to generate protein diversity along evolution can be reused and generalized to expand the protein repertoire way beyond what we observe today. The challenge here will be to design an artificial system able to learn the underlying rules of (functional) AS and to generalize to any protein sequence.
 * Data: Almost ready to share, could be accessed on request.
 * References:
@@ Line 10: / Line 11: @@
 *# Image [http://www.lcqb.upmc.fr/laine/images/phylo.png www.lcqb.upmc.fr/laine/images/phylo.png]
 * Basic solution: for now the problem is not strictly formulated. But there is a github project to start with.
-* Novelty: Eukaryotes have evolveda transcription machinery that can augment the protein repertoire without increasing the genome size. It produces several mRNA transcripts from the same gene, by choosing different initiation/termination sites and/or by splicing different exons. This regulatory process is called Alternative Splicing (AS). Although the mechanisms of AS have been well described at the genomic level, the extent to which and how AS modulates protein functions and interactions remains a fundamental open question. Here, we propose to develop a probabilistic model that will learn from the functional AS events observed today in nature to generate new protein functional diversity. The rationale will be that the means AS has produced to generate protein diversity along evolution can be reused and generalized to expand the protein repertoire way beyond what we observe today. The challenge here will be to design an artificial system able to learn the underlying rules of (functional) AS and to generalize to any protein sequence.
+* Novelty:
 * Authors:  Elodie Laine, Sergei Grudinin, and Vadim Strijov

@@ Line 1: / Line 1: @@
 ==Problem 74==
-* Title: ELAPID: Alternative splicing-inspired protein desdign
+* Title: MASSIV: Alternative splicing-inspired protein desdign
 * Problem: Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms.
 * Data: Almost ready to share, could be accessed on request.
@@ Line 10: / Line 10: @@
 *# Image [http://www.lcqb.upmc.fr/laine/images/phylo.png www.lcqb.upmc.fr/laine/images/phylo.png]
 * Basic solution: for now the problem is not strictly formulated. But there is a github project to start with.
-* Method: structural biology
+* Novelty: Eukaryotes have evolveda transcription machinery that can augment the protein repertoire without increasing the genome size. It produces several mRNA transcripts from the same gene, by choosing different initiation/termination sites and/or by splicing different exons. This regulatory process is called Alternative Splicing (AS). Although the mechanisms of AS have been well described at the genomic level, the extent to which and how AS modulates protein functions and interactions remains a fundamental open question. Here, we propose to develop a probabilistic model that will learn from the functional AS events observed today in nature to generate new protein functional diversity. The rationale will be that the means AS has produced to generate protein diversity along evolution can be reused and generalized to expand the protein repertoire way beyond what we observe today. The challenge here will be to design an artificial system able to learn the underlying rules of (functional) AS and to generalize to any protein sequence.
 * Authors:  Elodie Laine, Sergei Grudinin, and Vadim Strijov

@@ Line 1: / Line 1: @@
 ==Problem 74==
-* Title: ELAPID: Alternative splicing-inspired protein development
+* Title: ELAPID: Alternative splicing-inspired protein desdign
 * Problem: Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms.
 * Data: Almost ready to share, could be accessed on request.

@@ Line 2: / Line 2: @@
 * Title: ELAPID: Alternative splicing-inspired protein development
-Problem: Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms.
+* Problem: Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms.
 * Data: Almost ready to share, could be accessed on request.
 * References:
@@ Line 8: / Line 8: @@
 *# Disentangle homology relationships between exons by [http://www.lcqb.upmc.fr/ LCQB UPMC], 2020, [https://github.com/PhyloSofS-Team/thoraxe github]
 *# Protein physics: a course of lectures with color and stereoscopic illustrations and problems by Finkelstein A.V., Ptitsyn O.B. [http://www.mol.bio.msu.ru/res/DOC61/2012_Book_fizika_belka.pdf book in rus]
-# [http://www.lcqb.upmc.fr/laine/images/phylo.png www.lcqb.upmc.fr/laine/images/phylo.png]
+*# Image [http://www.lcqb.upmc.fr/laine/images/phylo.png www.lcqb.upmc.fr/laine/images/phylo.png]
 * Basic solution: for now the problem is not strictly formulated. But there is a github project to start with.
 * Method: structural biology
 * Authors:  Elodie Laine, Sergei Grudinin, and Vadim Strijov

← Older revision	Revision as of 15:08, 24 September 2020
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← Older revision		Revision as of 15:31, 28 August 2020
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	* Title: ELAPID: Alternative splicing-inspired protein development		* Title: ELAPID: Alternative splicing-inspired protein development