Related papers: Apollo: A Sequencing-Technology-Independent, Scala…
Audio-video joint generation has progressed rapidly, yet substantial challenges still remain. Non-commercial approaches still suffer audio-visual asynchrony, poor lip-speech alignment, and unimodal degradation, which can be stemmed from…
The remarkable performance of Large Language Models (LLMs) highly relies on crafted prompts. However, manual prompt engineering is a laborious process, creating a core bottleneck for practical application of LLMs. This phenomenon has led to…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanostructures. A `program' for growing a desired structure…
The study of functional genomics--particularly in non-model organisms has been dramatically improved over the last few years by use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…
The repeat content and heterozygosity rate of a target genome are important factors in determining the feasibility of achieving a complete telomere-to-telomere assembly. The mathematical relationship between the required coverage and read…
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
We present POLO --- a C++ library for large-scale parallel optimization research that emphasizes ease-of-use, flexibility and efficiency in algorithm design. It uses multiple inheritance and template programming to decompose algorithms into…
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…
Leveraging machine learning (ML) to predict an initial solution for mixed-integer linear programming (MILP) has gained considerable popularity in recent years. These methods predict a solution and fix a subset of variables to reduce the…
Lead optimization in drug discovery requires efficiently navigating vast chemical space through iterative cycles to enhance molecular properties while preserving structural similarity to the original lead compound. Despite recent advances,…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…