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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
The high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
Time-optimal paths for a Dubins airplane
This model extends the Dubins car by L.E. Dubins (1957) to have altitude, which leads to Dubins airplane, and characterize the time-optimal trajectories for the system through the use of the Pontryagin Maximum Principle.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
This work describes an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff, enabling acquisition of genome assemblies for individual uncultivated bacteria using only short reads.
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
- J. McLean, M. Lombardo, R. Lasken
- BiologyProceedings of the National Academy of Sciences
- 10 June 2013
An approach for increasing throughput and effectively improving the likelihood of sampling rare events based on forming small random pools of single-flow–sorted cells, amplifying their DNA by multiple displacement amplification and sequencing all cells in the pool, creating a “mini-metagenome” is developed.
A partition function algorithm for interacting nucleic acid strands
A model for analyzing the thermodynamics of two interacting nucleic acid strands considering the most general type of interactions studied in the literature is presented and a corresponding dynamic programming algorithm that computes the partition function over (almost) all physically possible joint secondary structures formed by two interactingucleic acids in O(n6) time is presented.
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community
- M. Embree, Harish Nagarajan, N. Movahedi, H. Chitsaz, K. Zengler
- BiologyThe ISME Journal
- 1 April 2014
The combination of single-cell genome sequencing and a novel low-input metatranscriptomics protocol is used to reveal the intricate metabolic capabilities and microbial interactions of an alkane-degrading methanogenic community.
De novo assembly of bacterial genomes from single cells
An improved assembly approach tailored for single cell Illumina sequences that incorporates a progressively increasing coverage cutoff is described, enabling acquisition of genome assemblies for individual uncultivated bacteria, providing cell-specific genetic information absent from metagenomic studies.
De novo co-assembly of bacterial genomes from multiple single cells
- N. Movahedi, Elmira Forouzmand, H. Chitsaz
- BiologyIEEE International Conference on Bioinformatics…
- 4 October 2012
This work gives an algorithm for de novo co-assembly of bacterial genomes from multiple single cells that outperforms single cell assembly of each individual one in all standard metrics and outperforms mixed assembly in which the input datasets are simply concatenated.
On Time-optimal Trajectories for a Car-like Robot with One Trailer
- H. Chitsaz
- Computer ScienceSIAM Conf. on Control and its Applications
- 28 January 2013
This work uses the Pontryagin Maximum Principle to characterize extremal trajectories, i.e. candidate geodesics, for a car-like robot with one trailer, and identifies planar elastica as the third piece of motion that occurs along the authors' extr emals.
biRNA: Fast RNA-RNA Binding Sites Prediction
Experimental results show that biRNA outperforms RNAup and also support the accuracy of the approach, and the proposed Bayesian approximation of the Boltzmann joint probability distribution provides a powerful, novel framework that can also be utilized in other applications.