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Phylogenetic tree
Related publications (123)
From trees to barcodes and back again II: Combinatorial and probabilistic aspects of a topological inverse problem
Kathryn Hess Bellwald, Lida Kanari, Adélie Eliane Garin
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general position, based ...
2024The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem
Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...
EPFL2024Impact of phylogeny on structural contact inference from protein sequence data
Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Umberto Lupo
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...
ROYAL SOC2023From Trees to Barcodes and Back Again:A Combinatorial, Probabilistic and Geometric Study of a Topological Inverse Problem
In this thesis, we investigate the inverse problem of trees and barcodes from a combinatorial, geometric, probabilistic and statistical point of view.Computing the persistent homology of a merge tree yields a barcode B. Reconstructing a tree from B involve ...
EPFL2022Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis
Didier Trono, Laurence Gouzi Abrami, Evaristo Jose Planet Letschert, Julien Léonard Duc, Laia Simo Riudalbas, Sandra Eloise Kjeldsen, Alexandre Coudray, Sagane Dind
The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we ...
2022Extracting phylogenetic dimensions of coevolution reveals hidden functional signals
Anne-Florence Raphaëlle Bitbol
Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...
NATURE PORTFOLIO2022Protein language models trained on multiple sequence alignments learn phylogenetic relationships
Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo
Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...
NATURE PORTFOLIO2022Key factors determining the presence of Tree-related Microhabitats: A synthesis of potential factors at site, stand and tree scales, with perspectives for further research
Tree-related microhabitats (TreMs) have been identified as key features for forest-dwelling taxa and are often employed as measures for biodiversity conservation in integrative forest management. However, managing forests to ensure an uninterrupted resourc ...
2022Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium
Rizlan Bernier-Latmani, Karin Lederballe Meibom, Karen Elda Viacava Romo, Nicolas Louis Maurice Jacquemin, Matthew Charles Reid, Jiangtao Qiao
Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype ...
2022