M. Sikora

Robotic-inspired approach to multi-domain membrane receptor conformation space: theory and SARS-CoV-2 spike protein case study

The paper develops a robotic-inspired method to define the conformational space of the SARS-CoV-2 spike protein using DH parameters, showing improved distinction of conformations compared to spherical coordinates.

The spatiotemporal distribution of human pathogens in ancient Eurasia and the emergence of zoonotic diseases

The paper maps ancient pathogens in Eurasia, showing zoonotic diseases emerged with livestock domestication and spread with pastoralist migrations.

Proteins containing 6-crossing knot types andtheir folding pathways

This paper analyzes 6-crossing protein knots using AlphaFold 2 predictions and a coarse-grained model, identifying two distinct folding mechanisms for the 63 knot.

Two-million-year-old microbial communities from the Kap Kobenhavn Formation in North Greenland

This paper reconstructs microbial communities from 2-million-year-old permafrost in Greenland, finding similarities to modern thawing permafrost microbes and suggesting microbial communities may signal climate change impacts before plants and animals.

Rhizosphere bacterial colonization of beet occurs in discrete phases regardless of bioinoculation with the wild sea beet root community

The paper shows that beet rhizosphere bacterial colonization occurs in two distinct phases regardless of bioinoculation, soil type, or genotype, with stable communities forming after five weeks.

Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius

The paper determines the atomic structure of the two-component S-layer in Sulfolobus acidocaldarius using cryoEM, cryoET, and AlphaFold2.

Elevated genetic risk for multiple sclerosis originated in Steppe Pastoralist populations

This study identifies the origin of genetic risk variants for multiple sclerosis in Steppe pastoralist populations and traces their spread into Europe through migration.

The Selection Landscape and Genetic Legacy of Ancient Eurasians

This study models ancient Eurasian selection landscapes and shows ancestry-specific genetic risk associations with modern phenotypes.

Population Genomics of Postglacial Western Eurasia

This study analyzes ancient genomes from Western Eurasia to trace postglacial human migrations and genetic changes across the Holocene.

Resilience in soil bacterial communities of the boreal forest from one to five years after wildfire across a severity gradient

The paper examines soil bacterial community resilience five years post-wildfire across a severity gradient, finding increased similarity to unburned sites and persistent enrichment of specific taxa.

Human KIR+CD8+ T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19

The paper identifies KIR+CD8+ T cells as regulatory cells in humans that suppress pathogenic CD4+ T cells in autoimmune and infectious diseases.

Obesity affects mitochondrial metabolism and proliferative potential of equine endometrial progenitor cells.

This study examines how obesity impacts mitochondrial metabolism and proliferation of equine endometrial progenitor cells, finding reduced viability, increased oxidative stress, and altered signaling pathways.

Global Structure of the Intrinsically Disordered Protein Tau Emerges from its Local Structure

This study uses a computational method to model the structural ensemble of tau K18, showing how local structure influences global conformational states and disease-related aggregation.

31,600-year-old human virus genomes support a Pleistocene origin for common childhood infections

The paper analyzes ancient virus genomes from 31,600-year-old human remains, showing that common childhood infections originated in the Pleistocene.

Nuclear retention of pre-mRNA involving Cajal bodies during meiotic prophase in plants

The paper identifies nuclear retention of pre-mRNA in Cajal bodies during meiotic prophase in plants, revealing a conserved mechanism for gene regulation in generative cell development.

The evolutionary making of SARS-CoV-2

This study identifies evolutionary innovations in SARS-CoV-2 protein sequences, highlighting functional changes in the spike protein and its furin cleavage site relevant to immune evasion and infection.

Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion

The paper shows that cortical tension stabilizes E-cadherin at cell-cell contacts, limiting contact expansion beyond a critical tension threshold.

Map of SARS-CoV-2 spike epitopes not shielded by glycans.

The paper identifies SARS-CoV-2 spike epitopes not shielded by glycans using molecular dynamics simulations and epitope mapping.

A geostatistical approach to modelling human Holocene migrations in Europe using ancient DNA

This study models Holocene human migrations in Europe using ancient DNA and geostatistical methods, finding links between population movements and changes in vegetation and climate.

Effect of osmoprotectants on the survival of bacterial endophytes in lyophilized beet roots

The paper assesses endophytic bacterial diversity in beet roots and evaluates how osmoprotectants during lyophilization affect bacterial viability, density, and salt tolerance.