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Current Flash X-ray single-particle diffraction Imaging (FXI) experiments, which operate on modern X-ray Free Electron Lasers (XFELs), can record millions of interpretable diffraction patterns from individual biomolecules per day. Due to…
13C-based metabolic flux analysis (13C-MFA) is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a…
Single-pixel imaging (SPI) is significant for applications constrained by transmission bandwidth or lighting band, where 3D SPI can be further realized through capturing signals carrying depth. Sampling strategy and reconstruction algorithm…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
Multiview light sheet fluorescence microscopy (LSFM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing…
Cell type identification from single-cell transcriptomic data is a common goal of single-cell RNA sequencing (scRNAseq) data analysis. Neural networks have been employed to identify cell types from scRNAseq data with high performance.…
Designing architectures for deep neural networks requires expert knowledge and substantial computation time. We propose a technique to accelerate architecture selection by learning an auxiliary HyperNet that generates the weights of a main…
As deep learning methods continue to improve medical image segmentation performance, data annotation is still a big bottleneck due to the labor-intensive and time-consuming burden on medical experts, especially for 3D images. To…
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the…
It has been demonstrated in the recent years that nanomechanical mass spectrometry was well suited for the analysis of specific high mass species such as viruses. Still, the exclusive use of one-dimensional devices such as vibrating beams…
Manual annotation of pathology slides for cancer diagnosis is laborious and repetitive. Therefore, much effort has been devoted to develop computer vision solutions. Our approach, (FLASH), is based on a Deep Convolutional Neural Network…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and…
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…
Deep image hashing aims to enable effective large-scale image retrieval by mapping the input images into simple binary hash codes through deep neural networks. More recently, Vision Mamba with linear time complexity has attracted extensive…
Multiple Sclerosis (MS) is a chronic autoimmune disease of the central nervous system whose molecular mechanisms remain incompletely understood. In this study, we developed an end-to-end machine learning pipeline to analyze transcriptomic…
Modern data science relies on data analytic pipelines to organize interdependent computational steps. Such analytic pipelines often involve different algorithms across multiple steps, each with its own hyperparameters. To achieve the best…
MINFLUX (Minimal Photon Flux) is a single-molecule imaging technique capable of resolving fluorophores at a precision of <5 nm. Interpretation of the point patterns generated by this technique presents challenges due to variable emitter…
We present a light and fast, public available, ray-tracer {\tt Splotch} software tool which supports the effective visualization of cosmological simulations data. We describe the algorithm it relies on, which is designed in order to deal…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…