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We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
State Space Models (SSMs), particularly the Mamba architecture, have recently emerged as powerful alternatives to Transformers for sequence modeling, offering linear computational complexity while achieving competitive performance. Yet,…
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR…
MSstatsQC [3] is an open-source software that provides longitudinal system suitability monitoring tools in the form of control charts for proteomic experiments. It includes simultaneous tools for the mean and dispersion of suitability…
In the rapidly evolving domain of next generation sequencing and bioinformatics analysis, data generation is one aspect that is increasing at a concomitant rate. The burden associated with processing large amounts of sequencing data has…
We developed a software pipeline for quality control (QC) of histopathology whole slide images (WSIs) that segments various regions, such as blurs of different levels, tissue regions, tissue folds, and pen marks. Given the necessity and…
Multiplex Imaging (MI) enables the simultaneous visualization of multiple biological markers in separate imaging channels at subcellular resolution, providing valuable insights into cell-type heterogeneity and spatial organization. However,…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Recent advancements in generative AI have made text-guided image inpainting - adding, removing, or altering image regions using textual prompts - widely accessible. However, generating semantically correct photorealistic imagery, typically…
Multiple sequence alignment (MSA) is a core operation for comparing genome sequences and is widely used in bio-informatics. MAFFT, a practical MSA tool, repeatedly shifts a pair of sequences and computes a distance. Because the number of…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
Whole slide image (WSI) classification requires repetitive zoom-in and out for pathologists, as only small portions of the slide may be relevant to detecting cancer. Due to the lack of patch-level labels, multiple instance learning (MIL) is…
By activating blocked users and altering successive interference cancellation (SIC) sequences, reconfigurable intelligent surfaces (RISs) become promising for enhancing non-orthogonal multiple access (NOMA) systems. The downlink RIS-aided…
Recent developments in self-supervised learning (SSL) have made it possible to learn data representations without the need for annotations. Inspired by the non-contrastive SSL approach (SimSiam), we introduce a novel framework SIMSAM to…
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…