Related papers: SlopMap: a software application tool for quick and…
We introduce LLMmap, a first-generation fingerprinting technique targeted at LLM-integrated applications. LLMmap employs an active fingerprinting approach, sending carefully crafted queries to the application and analyzing the responses to…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
The Connectivity Map (CMap) is a large publicly available database of cellular transcriptomic responses to chemical and genetic perturbations built using a standardized acquisition protocol known as the L1000 technique. Databases such as…
Sequential pattern mining (SPM) has excellent prospects and application spaces and has been widely used in different fields. The non-overlapping SPM, as one of the data mining techniques, has been used to discover patterns that have…
AMRScan is a hybrid bioinformatics toolkit implemented in both R and [Nextflow](https://www.nextflow.io/) for the rapid and reproducible detection of antimicrobial resistance (AMR) genes from next-generation sequencing (NGS) data. The…
Summary: Mapping ancient DNA to a reference genome is challenging as it involves numerous steps, is time-consuming and has to be repeated within a study to assess the quality of extracts and libraries; as a result, the mapping needs to be…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and…
We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and…
Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…
As an increasing number of genome-wide association studies reveal the limitations of attempting to explain phenotypic heritability by single genetic loci, there is growing interest for associating complex phenotypes with sets of genetic…
Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…