AIMC Topic: Caenorhabditis elegans
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Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning.
Nature methods
May 27, 2019
In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impair...
Multiple tracking and machine learning reveal dopamine modulation for area-restricted foraging behaviors via velocity change in Caenorhabditis elegans.
Neuroscience letters
May 10, 2019
Food exploration is an essential survival behavior in organisms. To find food efficiently, many organisms use a foraging strategy called area-restricted search (ARS) wherein individuals first turn more frequently, restricting their search to one area...
Mass Surveilance of -Smartphone-Based DIY Microscope and Machine-Learning-Based Approach for Worm Detection.
Sensors (Basel, Switzerland)
Mar 26, 2019
The nematode is often used as an alternative animal model due to several advantages such as morphological changes that can be seen directly under a microscope. Limitations of the model include the usage of expensive and cumbersome microscopes, and r...
MAPLE (modular automated platform for large-scale experiments), a robot for integrated organism-handling and phenotyping.
eLife
Aug 17, 2018
Lab organisms are valuable in part because of large-scale experiments like screens, but performing such experiments over long time periods by hand is arduous and error-prone. Organism-handling robots could revolutionize large-scale experiments in the...
Multi-Domain Networks Association for Biological Data Using Block Signed Graph Clustering.
IEEE/ACM transactions on computational biology and bioinformatics
Jun 25, 2018
Multi-domain biological network association and clustering have attracted a lot of attention in biological data integration and understanding, which can provide a more global and accurate understanding of biological phenomenon. In many problems, diff...
A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters.
Nature chemical biology
Feb 26, 2018
We developed a new way to engineer complex proteins toward multidimensional specifications using a simple, yet scalable, directed evolution strategy. By robotically picking mammalian cells that were identified, under a microscope, as expressing prote...
WorMachine: machine learning-based phenotypic analysis tool for worms.
BMC biology
Jan 16, 2018
BACKGROUND: Caenorhabditis elegans nematodes are powerful model organisms, yet quantification of visible phenotypes is still often labor-intensive, biased, and error-prone. We developed WorMachine, a three-step MATLAB-based image analysis software th...
The Si elegans project at the interface of experimental and computational Caenorhabditis elegans neurobiology and behavior.
Journal of neural engineering
Oct 14, 2016
OBJECTIVE: In light of recent progress in mapping neural function to behavior, we briefly and selectively review past and present endeavors to reveal and reconstruct nervous system function in Caenorhabditis elegans through simulation.
MiRNATIP: a SOM-based miRNA-target interactions predictor.
BMC bioinformatics
Sep 22, 2016
BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNA sequences with regulatory functions to post-transcriptional level for several biological processes, such as cell disease progression and metastasis. MiRNAs interact with target messenger RNA (mR...
Tissue enrichment analysis for C. elegans genomics.
BMC bioinformatics
Sep 13, 2016
BACKGROUND: Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses base...
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