Related papers: Exploring nervous system transcriptomes during emb…
During embryonic development, a complex organism is formed from a single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, which are following the expression and activity of…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
The Transiting Exoplanet Survey Satellite (TESS) is surveying a large fraction of the sky, generating a vast database of photometric time series data that requires thorough analysis to identify exoplanetary transit signals. Automated…
We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of…
This study introduces the first 3D spectral-element method (SEM) simulation of ultrasonic wave propagation in a bottlenose dolphin (Tursiops truncatus) head. Unlike traditional finite-element methods (FEM), which struggle with…
Nearly neutral theory predicts that evolutionary processes will differ in small populations compared to large populations, a key point of concern for endangered species. The nearly-neutral threshold, the span of neutral variation, and the…
Background: Transposable elements (TEs) have played an important role in the diversification and enrichment of mammalian transcriptomes through various mechanisms such as exonization and intronization (the birth of new exons/introns from…
We present ECToNAS, a cost-efficient evolutionary cross-topology neural architecture search algorithm that does not require any pre-trained meta controllers. Our framework is able to select suitable network architectures for different tasks…
The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence…
Tuna are large pelagic fish whose populations are close to panmixia. In addition, they are threatened species, so it is important for the maintenance and monitoring of genetic diversity that genetic information at a genome level be…
Spatial transcriptomics (ST) is essential for understanding diseases and developing novel treatments. It measures gene expression of each fine-grained area (i.e., different windows) in the tissue slide with low throughput. This paper…
In this work, six convolutional neural networks (CNNs) have been trained based on %different feature images and arrays from the database including 15,638 superflare candidates on solar-type stars, which are collected from the three-years…
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic…
Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
We present the case for developing the tardigrade (Hypsibius exemplaris) into a model organism for systems neuroscience. These microscopic, transparent animals (~300-500 microns) are among the smallest known to possess both limbs (eight)…
The performance of a deep neural network is heavily dependent on its architecture and various neural architecture search strategies have been developed for automated network architecture design. Recently, evolutionary neural architecture…
The voxelized Allen Atlas of the adult mouse brain (at a resolution of 200 microns) has been used in [arXiv:1303.0013] to estimate the region-specificity of 64 cell types whose transcriptional profile in the mouse brain has been measured in…
The tracing of neural pathways through large volumes of image data is an incredibly tedious and time-consuming process that significantly encumbers progress in neuroscience. We are exploring deep learning's potential to automate…
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes…