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7 papers · 1 filter
From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction
Simona Cocco, Remi Monasson, Martin Weigt
Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural information. Among those ar…
Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
Magnus Ekeberg, Cecilia Lövkvist, Yueheng Lan +2
Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse…
Speed of evolution in large asexual populations with diminishing returns
Maria Rita Fumagalli, Matteo Osella, Philippe Thomen +2
The adaptive evolution of large asexual populations is generally characterized by competition between clones carrying different beneficial mutations. This interference phenomenon s…
Growth-rate-dependent dynamics of a bacterial genetic oscillator
Matteo Osella, Marco Cosentino Lagomarsino
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied…
Gene silencing and large-scale domain structure of the E. coli genome
Mina Zarei, Bianca Sclavi, Marco Cosentino Lagomarsino
The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link…
Gene autoregulation via intronic microRNAs and its functions
Carla Bosia, Matteo Osella, Mariama El Baroudi +2
Background: MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their d…