Computational and Systems Biology

Latest articles

1. 1. Computational and Systems Biology

   Essential metabolism for a minimal cell

   Marian Breuer et al.

   A near-complete flux balance analysis model of a minimal cell demonstrates the high essentiality of its metabolic genes, agrees well with experimental essentiality data and suggests some further gene removals.
2. 1. Cell Biology
   2. Computational and Systems Biology

   Saccharomyces cerevisiae goes through distinct metabolic phases during its replicative lifespan

   Simeon Leupold et al.

   With replicative age, S. cerevisiae shifts from a fermentative towards an unusual respiratory metabolism, accompanied by a decrease in growth and glucose uptake rate.
3. 1. Cell Biology
   2. Computational and Systems Biology

   Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury

   Nona Farbehi et al.

   Comprehensive scRNA-seq analysis of cardiac stromal cells in healthy and injured hearts reveals novel cell types and non-linear cell dynamics, providing new insights into cardiac inflammation, fibrosis and repair.
4. 1. Computational and Systems Biology
   2. Human Biology and Medicine

   In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta

   Maria Pernemalm et al.
5. 1. Computational and Systems Biology

   Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies

   Ye Zheng et al.

   A statistical model rescues multi-mapping reads with high accuracy and demonstrates their impact in all facets of the analysis of genome-wide high throughput conformation capture datasets.
6. 1. Computational and Systems Biology
   2. Neuroscience

   Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions

   Yanxian Lin et al.

   Liquid-liquid phase separation of tau is demonstrated to be an equilibrium state, stable only within a narrow range near physiological conditions, and thus has the capacity to regulate biological processes.
7. 1. Computational and Systems Biology
   2. Physics of Living Systems

   Learning protein constitutive motifs from sequence data

   Jérôme Tubiana et al.

   A new machine-learning toolbox unveils coevolutionary protein motifs related to structure, function, and phylogeny from sequence information only.
8. 1. Computational and Systems Biology
   2. Stem Cells and Regenerative Medicine

   Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming

   Mirko Francesconi et al.

   Variation in efficiency, speed and path during transdifferentiation and reprogramming originates from two pre-B cell subpopulations with reciprocal propensity towards each fate conversion.
9. 1. Computational and Systems Biology
   2. Developmental Biology

   Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish

   Erika Tsingos et al.
10. 1. Computational and Systems Biology
    2. Neuroscience

    Biophysical mechanisms in the mammalian respiratory oscillator re-examined with a new data-driven computational model

    Ryan S Phillips et al.

    Computational modeling motivated by recent experiments clarifies biophysical mechanisms generating the rhythm and amplitude of breathing at the level of neurons and brain circuits in mammals.