Related papers: Reducing assembly complexity of microbial genomes …
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
Single-stranded libraries generated from ancient DNA extracts have specific sequencing requirements. The short library molecules typically associated with ancient DNA templates are expected to behave differently during the annealing to the…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
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…
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing…
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples, and to prepare these cells for bulk whole genome sequencing without cultivation. We characterize this approach by…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
Single particle cryo-electron microscopy has become a critical tool in structural biology over the last decade, able to achieve atomic scale resolution in three dimensional models from hundreds of thousands of (noisy) two-dimensional…