Science Communication

Talks by our Members and Guests

Understanding genomes' evolutionary history is key to comprehending genes' role in species diversification and adaptation. Moreover, identifying ortholog and paralog genes is fundamental for comparative biology studies. Still, detecting orthology through sequence similarity remains challenging and computationally intensive for gene families containing numerous duplications and losses.

In this talk, I will first introduce REvolutionH-tl, a tool designed for orthology prediction and reconstruction of evolutionary histories free of horizontal gene transfers. Furthermore, I show how REvolutionH-tl can be used to estimate the evolution of antibiotic-resistance genes in a selected group of bacteria.

REvolutionH-tl employs a novel graph-based method to identify biologically plausible gene best-matches, as well as determine orthology and paralogy relationships. This information naturally entails knowledge about gene and species tree topology, which is further reconstructed and unified in an evolutionary scenario that explicitly delineates gene evolution across species.

The accuracy of REvolutionH-tl is comparable to competing tools at substantially reduced computational cost. It is freely available at https://pypi.org/project/revolutionhtl/. REvolutionH-tl stands as a potent addition to the toolkit of comparative genomics researchers. Its significance stands out in the age of massive genome sequencing, where efficient methods to organize and make sense of thousands of genes across numerous species are indispensable.

https://uni-leipzig.zoom.us/j/7147246625

Chemical reaction networks (CRNs) play a central role in the mathematical modeling of complex systems due to their capacity to capture a wide range of nonlinear phenomena. Autocatalysis is a topological feature with essential consequences for dynamical organization in CRNs for conceptual, theoretical, and practical reasons. In this talk, I will review different definitions of autocatalysis and discuss the polyhedral geometry induced by the minimal autocatalytic subnetworks (MASs) on the stoichiometric subspace. I will discuss linear-programming algorithms for exhaustively enumerating and a scheme for visualizing the list of MASs in a generic CRN. Next, I will introduce a formal paradigm for coarse-graining realistic biochemical reactions using their conservation laws and display the ‘combinatorial explosion’ of MASs in fully connected hypergraphs of CRNs with one conservation law. Finally, I will discuss applications of autocatalysis in understanding the origins of life and economics. (For details, see https://arxiv.org/abs/2303.14238 .)

https://uni-leipzig.zoom.us/j/7147246625?omn=61833399298

The modular decomposition (MD) of an undirected graph G is a natural
construction to capture key features of G in terms of a rooted labeled tree
(T,t) whose vertices are labeled as "series" (1), "parallel" (0) or "prime".
If a graph G does not contain prime modules, then all structural information of G
can be directly derived from its MD tree (T,t). As a consequence, many hard
problems become polynomial-time solvable on graphs without prime modules, since
the MD tree serves as a guide for algorithms to find efficient exact solutions
(e.g.\ for optimal colorings, maximum clique, isomorphism test, ... ).

However, the class of graphs without prime modules (aka cographs) is rather
restricted. We introduce here the novel concept of explicit modular decomposition
that aims at replacing "prime" vertices in the MD tree by suitable substructures
to obtain 0/1-labeled networks (N,t). Understanding which graphs can be
explained by which type of network does not only provide novel graph classes but
is crucial to understand which hard problem can be solved on which graph class
efficiently. We will mainly focus on graphs that can be explained by networks
(N,t) whose bi-connected components are simple cycles. These graphs are called
GaTEx, can be recognized in linear-time and are characterized by a set of 25
forbidden induced subgraphs. In particular, GaTEx graphs are closely related to
many other well-known graph classes such as P4-sparse and P4-reducible graphs,
weakly-chordal graphs, perfect graphs with perfect order, comparability and
permutation graphs. As a consequence, one can prove that many hard problems
become linear-time solvable on GaTEx graphs as well.

https://marc-hellmuth.github.io/

In this talk, I will give an overview on the relationship between the
structure of a reaction network and the possible dynamics of the
species concentrations. To this aim, I will focus on systems with
sufficiently nonlinear interaction functions (parameter-rich kinetic
models) and address the structure of the Jacobian matrix at a steady
state. Results are of two kinds: “existence” results that assert the
possibility of a dynamical feature for a specific choice of parameter
and “exclusion” results that assert a dynamical feature independently
from any choice of parameters. I will provide examples of both types.

https://uni-leipzig.zoom.us/j/7147246625

*What?*

TikZ (acronym for "TikZ ist kein Zeichenprogramm")is a tool to create
graphic elements in LaTeX. Not only graphs, but all kind of figures you
might think of.

*When/Where?*

Session 1: Tuesday November 21st, 11am to 1pm, in room 109.

There might be a zoom link to attend remotely, if interest in such an
arrangement is shown. Recording of the sessions will also be considered.

*For who?*

Any LaTeX user (not only graph enthusiasts) interested in creating nice
figures for their papers, posters, presentations...

The first session will introduce the basics. No previous knowledge of TikZ
is required.

*What?*

TikZ (acronym for "TikZ ist kein Zeichenprogramm")is a tool to create
graphic elements in LaTeX. Not only graphs, but all kind of figures you
might think of.

*When/Where?*

Session 2: Tuesday November 28th, 11am to 1pm, in room 109.

There might be a zoom link to attend remotely, if interest in such an
arrangement is shown. Recording of the sessions will also be considered.

*For who?*

Any LaTeX user (not only graph enthusiasts) interested in creating nice
figures for their papers, posters, presentations...

The second session will present some advanced techniques to draw more
complex figures. Experience with TikZ, or attendance of the first session,
is expected.

Autocatalysis refers to the situation that a chemical
species catalyzes its own formation. A chemical reaction is
autocatalytic whenever one of its educts or reactants catalyzes its
own formation. Autocatalysis combines two features of the essence of
living systems, the ability to survive on an ambient food source and
the fact that each biochemical reaction in the system requires only
reactants and (most often) a catalyst that are provided by other
reactions in the system or are present in the food set. A chemical
reaction network, abbreviated to CRN, comprises a set of chemical
species and a set of chemical reactions. A CRN is represented as a
stoichiometric matrix S in which columns correspond to reactions and
rows correspond to chemical species. CRN can also be naturally
represented as a directed hypergraph H = (V, E) where V is the set of
chemical species and E is the set of chemical reactions.

Unfortunately, it is not easy to characterize the substructures that
define an autocatalytic process in a CRN. We will explore, and analyze
the mutual relations of five concepts regarding autocatalysis, which
are: autocatalytic cycles, Milo flows, autocatalytic cores, Nghe
flows, and strongly connected König digraphs. We will end with some
open questions about the topic and ideas for future research

https://uni-leipzig.zoom.us/j/7147246625

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