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Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cells without sample pooling or RNA extraction. Currently, there is no algorithm optimized…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…
In the past two decades a range of fluorescence cell microscopy techniques have been developed which can achieve ~10 nm spatial resolution, i.e. substantially beating the usual limits set by optical diffraction. However, these methods rely…
Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better…
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by…
We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of $k$-mer…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
In this work, we introduce a new type of linear classifier that is implemented in a chemical form. We propose a novel encoding technique which simultaneously represents multiple datasets in an array of microliter-scale chemical mixtures.…
This paper presents a method for time-lapse 3D cell analysis. Specifically, we consider the problem of accurately localizing and quantitatively analyzing sub-cellular features, and for tracking individual cells from time-lapse 3D confocal…
Tip-Enhanced Raman Spectroscopy (TERS) provides nanoscale chemical fingerprints alongside high-resolution topographic mapping of molecules, offering a powerful tool for materials discovery. However, TERS image datasets are challenging to…
Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short…
We study multilabel classification of chest X-rays and present a simple, strong pipeline built on SE-ResNeXt101 $(32 \times 4d)$. The backbone is finetuned for 14 thoracic findings with a sigmoid head, trained using Multilabel Iterative…
Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties.…
Inter-symbol interference (ISI) with heteroscedastic, or state-dependent, noise is a defining feature of molecular communication via diffusion (MCvD). However, such noise variance dependency across ISI states has not been systematically…
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…
Estimating and testing for differences in molecular phenotypes (e.g. gene expression, chromatin accessibility, transcription factor binding) across conditions is an important part of understanding the molecular basis of gene regulation.…
Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…
Media-based modulation (MBM) is a novel modulation technique that can improve the spectral efficiency of the existing wireless systems. In MBM, multiple radio frequency (RF) mirrors are placed near the transmit antenna(s) and are switched…
Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…