7 papers · ranked by Valyu relevance
Lotte Pollaris, Bavo Vanneste, Benjamin Rombaut, Arne Defauw + 15 more
Current spatial transcriptomics technologies are increasingly able to measure large gene panels at subcellular resolution, but a major bottleneck in this rapidly advancing field is the computational analysis and interpretation of the data. To bridge this gap, here we present SPArrOW, a flexible, modular and scalable…
Peiyao A Zhao, Jessica Garber, Claire Gustafson, June Kim + 4 more
Spatially resolved transcriptomics technologies have significantly enhanced our ability to understand cellular characteristics within tissue contexts. However, they present a trade-off between spatial resolution and transcriptome coverage. This limitation, compounded with analytical tools treating cell type inference…
Tian Jiang, P. Douglas Renfrew, Kevin Drew, Noah Youngs + 3 more
A wide variety of protein and peptidomimetic design tasks require matching functional three-dimensional motifs to potential oligomeric scaffolds. Enzyme design, for example, aims to graft active-site patterns typically consisting of 3 to 15 residues onto new protein surfaces. Identifying suitable proteins capable of…
Phred M. Benham, Carla Cicero, Merly Escalona, Eric Beraut + 9 more
Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps. This makes it difficult to decipher the impact of these elements on the dynamics of genome evolution. The increased capacity of long-read sequencing…
Prasad U. Bandodkar, Razeen R. Shaikh, Gregory T. Reeves
Model development is essential to gain a mathematical understanding of the underlying phenomena in systems biology. In most models, it is typically hard to estimate the values of the biophysical/phenomenological parameters that characterize the model. The parameters are estimated by minimizing a function that reduces a…
Daniel Campos, Vicenç Méndez, John Palmer, Javier Cristín + 1 more
There is a widespread belief in ecology that the capacity of animals to orchestrate systematic and planned paths should represent a significant benefit for efficient search and exploration. Within this view, stochasticity observed in real animal trajectories is mostly understood as undesirable noise caused by internal…
Wayo Matsushima, Kristiana Brink, Julia Schroeder, Eric A. Miska + 1 more
Mammalian sperm RNA has recently received a lot of interest due to its involvement in epigenetic germline inheritance. Studies of epigenetic germline inheritance have shown that environmental exposures can induce effects in the offspring without altering the DNA sequence of germ cells. Most mechanistic studies were…