Genomics
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…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Non-coding RNA (ncRNA) are RNA sequences which don't code for a gene but instead carry important biological functions. The task of ncRNA classification consists in classifying a given ncRNA sequence into its family. While it has been shown…
Motivation: P values derived from the null hypothesis significance testing framework are strongly affected by sample size, and are known to be irreproducible in underpowered studies, yet no suitable replacement has been proposed. Results:…
The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called $\alpha$ and $\beta$, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human…
Tumor microenvironment has complex effects on tumorigenesis and metastasis. However, there is still a lack of comprehensive understanding of the relationship among molecular and cellular characteristics in tumor microenvironment, clinical…
RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the…
Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is…
In recent years the publication of genome sequences for the Chinese hamster and Chinese hamster ovary (CHO) cell lines have facilitated study of these biopharmaceutical cell factories with unprecedented resolution. Our understanding of the…
We introduce a method to generate synthetic protein sequences which are predicted to be resistant to certain antibiotics. We did this using 6,023 genes that were predicted to be resistant to antibiotics in the intestinal region of the human…
Background: Many genome-wide association studies have detected genomic regions associated with traits, yet understanding the functional causes of association often remains elusive. Utilizing systems approaches and focusing on intermediate…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
Neuroinflammation in utero may result in lifelong neurological disabilities. Astrocytes play a pivotal role, but the mechanisms are poorly understood. No early postnatal treatment strategies exist to enhance neuroprotective potential of…
The Oxford Nanopore Technologies's MinION is the first portable DNA sequencing device. It is capable of producing long reads, over 100 kBp were reported. However, it has significantly higher error rate than other methods. In this study, we…
Summary: The advent of Web-based tools that assist in the analysis and visualization of macromolecules require application programming interfaces (APIs) designed for modern web frameworks. To this end, we have developed a Node.js module…
Transgenerational inheritance of a trait is presumably affected by both genetic and environmental factors but remains poorly understood. We studied the effect of genetic polymorphisms on transgenerational inheritance of yeast segregants…
Most common SNPs are popularly assumed to be neutral. We here developed novel methods to examine in animal models and humans whether extreme amount of minor alleles (MAs) carried by an individual may represent extreme trait values and…
Background. A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region…
Summary: Human alpha satellite and satellite 2/3 contribute to several percent of the human genome. However, identifying these sequences with traditional algorithms is computationally intensive. Here we develop dna-brnn, a recurrent neural…
Single Molecule Real-Time (SMRT) sequencing is a recent advancement of Next Gen technology developed by Pacific Bio (PacBio). It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it. To deal…