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DNA encoded libraries (DELs) are used for rapid large-scale screening of small molecules against a protein target. These combinatorial libraries are built through several cycles of chemistry and DNA ligation, producing large sets of…
Within the preprocessing pipeline of a Next Generation Sequencing sample, its set of Single-Base Mismatches is one of the first outcomes, together with the number of correctly aligned reads. The union of these two sets provides a 4x4 matrix…
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…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
For large libraries of small molecules, exhaustive combinatorial chemical screens become infeasible to perform when considering a range of disease models, assay conditions, and dose ranges. Deep learning models have achieved state of the…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
This paper proposes a general network fingerprinting framework, Seqnature, that uses packet sequences as its basic data unit and that makes it simple to implement any fingerprinting technique that can be formulated as a problem of…
A new open-source cluster finding library ''Common Clusterization Library'' (CCL) is proposed to describe the clusters production when applied to the transport codes. The new library was applied to the Parton-Hadron-Quantum-Molecular…
DNA-encoded small molecule libraries (DELs) have enabled discovery of novel inhibitors for many distinct protein targets of therapeutic value through screening of libraries with up to billions of unique small molecules. We demonstrate a new…
Single-cell RNA sequencing (scRNA-seq) has the potential to provide powerful, high-resolution signatures to inform disease prognosis and precision medicine. This paper takes an important first step towards this goal by developing an…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
Viroids are small circular single-stranded infectious RNAs that are characterized by a relatively high mutation level. Knowledge of their sequence heterogeneity remains largely elusive, and, as yet, no strategy attempting to address this…
Next Generation Sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
Motivation: Single-cell RNA sequencing (scRNA-seq) is a groundbreaking technology extensively utilized in biological research, facilitating the examination of gene expression at the individual cell level within a given tissue sample. While…
The use of deep learning models in computational biology has increased massively in recent years, and it is expected to continue with the current advances in the fields such as Natural Language Processing. These models, although able to…
Contrastive learning has gained significant attention in short text clustering, yet it has an inherent drawback of mistakenly identifying samples from the same category as negatives and then separating them in the feature space (false…
This paper tackles the challenging problem of automating code updates to fix deprecated API usages of open source libraries by analyzing their release notes. Our system employs a three-tier architecture: first, a web crawler service…