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The placenta is a complex organ, playing multiple roles during fetal development. Very little is known about the association between placental morphological abnormalities and fetal physiology. In this work, we present an open sourced,…
Complex networks can often be decomposed into less complex sub-networks whose structures can give hints about the functional organization of the network as a whole. However, these structural motifs can only tell one part of the functional…
How do we capture the breadth of behavior in animal movement, from rapid body twitches to aging? Using high-resolution videos of the nematode worm $C. elegans$, we show that a single dynamics connects posture-scale fluctuations with…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyzes the biological reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts…
Plant phenotyping, that is, the quantitative assessment of plant traits including growth, morphology, physiology, and yield, is a critical aspect towards efficient and effective crop management. Currently, plant phenotyping is a manually…
While deep learning has seen many recent applications to drug discovery, most have focused on predicting activity or toxicity directly from chemical structure. Phenotypic changes exhibited in cellular images are also indications of the…
Life science is entering a new era of petabyte-level sequencing data. Converting such big data to biological insights represents a huge challenge for computational analysis. To this end, we developed DeepMetabolism, a biology-guided deep…
The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and…
Deep learning segmentation and fluorescence imaging techniques allow the cellular morphology of living embryos to be constructed spatiotemporally. These development processes involve numerous molecules distributed at the subcellular scale,…
Recent advances in high-throughput sequencing technologies have enabled the extraction of multiple features that depict patient samples at diverse and complementary molecular levels. The generation of such data has led to new challenges in…
Finding a template in a search image is an important task underlying many computer vision applications. Recent approaches perform template matching in a deep feature-space, produced by a convolutional neural network (CNN), which is found to…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
Every year, plant parasitic nematodes, one of the major groups of plant pathogens, cause a significant loss of crops worldwide. To mitigate crop yield losses caused by nematodes, an efficient nematode monitoring method is essential for…
Three-dimensional volumetric imaging of cells allows for in situ visualization, thus preserving contextual insights into cellular processes. Despite recent advances in machine learning methods, morphological analysis of sub-nuclear…
Understanding physical rules underlying collective motions requires perturbation of controllable parameters in self-propelled particles. However, controlling parameters in animals is generally not easy, which makes collective behaviours of…
There is renewed interest in modeling and understanding the nervous system of the nematode $\textit{Caenorhabditis elegans}$ ($\textit{C. elegans}$), as this small model system provides a path to bridge the gap between nervous system…
Determining neuronal identity in imaging data is an essential task in neuroscience, facilitating the comparison of neural activity across organisms. Cross-organism comparison, in turn, enables a wide variety of research including…
The deep learning revolution is touching all scientific disciplines and corners of our lives as a means of harnessing the power of big data. Marine ecology is no exception. These new methods provide analysis of data from sensors, cameras,…
The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching…