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Documents authored by Flamm, Christoph

Document
DOI: 10.4230/DagRep.12.9.121
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381)

Authors: Sven Findeiß, Christoph Flamm, and Yann Ponty

Published in: Dagstuhl Reports, Volume 12, Issue 9 (2023)

Abstract
This report documents the program and outcomes of Dagstuhl Seminar 22381 "Rational Design of RiboNucleic Acids" (RNAs). The seminar covered a wide array of models, algorithmic strategies, molecular scales and modalities, all targeting in silico design of RNAs performing predefined biological functions. It consisted in a series of talks, each being allocated a generous time budget enabling frequent (welcomed!) interruptions and fruitful discussions. Applications of rational RNA design include mRNA vaccines; RNAs acting as sensors; self-replicating RNAs, relevant to RNA world/origin of life studies; populations of RNAs performing computations, e.g. through strand-displacement systems; RNA origamis forming nano-architectures through self-assembly; weakly interacting RNAs inducing the formation of droplets within cells through liquid-liquid phase separation. Those diverse applications are typically tackled by Bioinformatics-inclined scientists, contributing to distinct areas of life science and, as a result, somewhat isolated and sometimes unaware of similar pursuits in neighboring fields. The overarching goals of this meeting were to gather computational scientists from multiple fields, increase awareness of relevant efforts in distant communities, and ultimately contribute to a transversal perspective where RNA design becomes an object of study in itself.
Cite as

Sven Findeiß, Christoph Flamm, and Yann Ponty. Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). In Dagstuhl Reports, Volume 12, Issue 9, pp. 121-149, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{findei_et_al:DagRep.12.9.121,
  author =	{Findei{\ss}, Sven and Flamm, Christoph and Ponty, Yann},
  title =	{{Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381)}},
  pages =	{121--149},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2023},
  volume =	{12},
  number =	{9},
  editor =	{Findei{\ss}, Sven and Flamm, Christoph and Ponty, Yann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.12.9.121},
  URN =		{urn:nbn:de:0030-drops-178110},
  doi =		{10.4230/DagRep.12.9.121},
  annote =	{Keywords: RNA, RNA design, Inverse folding, RNA structure, mRNA design, RNA sensors, Co-transcriptional folding, Molecular evolution, Distant homology, Drug design}
}
Document
DOI: 10.4230/DagRep.7.11.28
Algorithmic Cheminformatics (Dagstuhl Seminar 17452)

Authors: Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler

Published in: Dagstuhl Reports, Volume 7, Issue 11 (2018)

Abstract
Dagstuhl Seminar 17452 "Algorithmic Cheminformatics" brought together leading researchers from both chemistry and computer science. The seminar was the second in a series of the Dagstuhl seminars and had a focus on concurrency theory as chemical systems are highly concurrent by nature. Within computer science we focused on formal approaches for chemistry and concurrency theory, including process calculi and Petri nets. The participants surveyed areas of overlapping interests and identified possible fields of joint future research.
Cite as

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler. Algorithmic Cheminformatics (Dagstuhl Seminar 17452). In Dagstuhl Reports, Volume 7, Issue 11, pp. 28-45, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@Article{andersen_et_al:DagRep.7.11.28,
  author =	{Andersen, Jakob L. and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.},
  title =	{{Algorithmic Cheminformatics (Dagstuhl Seminar 17452)}},
  pages =	{28--45},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2018},
  volume =	{7},
  number =	{11},
  editor =	{Andersen, Jakob L. and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.7.11.28},
  URN =		{urn:nbn:de:0030-drops-86692},
  doi =		{10.4230/DagRep.7.11.28},
  annote =	{Keywords: Modelling, Simulation, Networks, Semantics / Formal Methods}
}
Document
DOI: 10.4230/DagRep.4.11.22
Algorithmic Cheminformatics (Dagstuhl Seminar 14452)

Authors: Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, and Peter F. Stadler

Published in: Dagstuhl Reports, Volume 4, Issue 11 (2015)

Abstract
Dagstuhl Seminar 14452 "Algorithmic Cheminformatics" brought together leading researchers from both chemistry and computer science. The meeting successfully aimed at bridging in the apparent gap between the two disciplines. The participants surveyed areas of overlapping interests and identified possible fields of joint future research.
Cite as

Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, and Peter F. Stadler. Algorithmic Cheminformatics (Dagstuhl Seminar 14452). In Dagstuhl Reports, Volume 4, Issue 11, pp. 22-39, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@Article{banzhaf_et_al:DagRep.4.11.22,
  author =	{Banzhaf, Wolfgang and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.},
  title =	{{Algorithmic Cheminformatics (Dagstuhl Seminar 14452)}},
  pages =	{22--39},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2015},
  volume =	{4},
  number =	{11},
  editor =	{Banzhaf, Wolfgang and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.4.11.22},
  URN =		{urn:nbn:de:0030-drops-49686},
  doi =		{10.4230/DagRep.4.11.22},
  annote =	{Keywords: Graph Transformation Systems, Graph and Hypergraph Invariants, Graph Comparison, Network Flows, Hypergraphs, Formal Languages, Algebraic Chemistry}
}
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