References of "Scientific Reports"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailAlignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction
Laczny, Cedric Christian UL; Pinel, Nicolás; Vlassis, Nikos UL et al

in Scientific Reports (2014)

The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An ideal visualization ... [more ▼]

The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An ideal visualization method should, among others, enable clear distinction of congruent groups of sequences of closely related taxa, be applicable to fragments of lengths typically achievable following assembly, and allow the efficient analysis of the growing amounts of community genomic sequence data. Here, we report a scalable approach for the visualization of metagenomic data that is based on nonlinear dimension reduction via Barnes-Hut Stochastic Neighbor Embedding of centered log-ratio transformed oligonucleotide signatures extracted from assembled genomic sequence fragments. The approach allows for alignment-free assessment of the data-inherent taxonomic structure, and it can potentially facilitate the downstream binning of genomic fragments into uniform clusters reflecting organismal origin. We demonstrate the performance of our approach by visualizing community genomic sequence data from simulated as well as groundwater, human-derived and marine microbial communities. [less ▲]

Detailed reference viewed: 266 (22 UL)
Full Text
Peer Reviewed
See detailEfficient Gate-tunable light-emitting device made of defective boron nitride nanotubes: from ultraviolet to the visible
Attaccalite, Claudio; Wirtz, Ludger UL; Marini, Andrea et al

in Scientific Reports (2013), 3

Boron nitride is a promising material for nanotechnology applications due to its two-dimensional graphene-like, insulating, and highly-resistant structure. Recently it has received a lot of attention as a ... [more ▼]

Boron nitride is a promising material for nanotechnology applications due to its two-dimensional graphene-like, insulating, and highly-resistant structure. Recently it has received a lot of attention as a substrate to grow and isolate graphene as well as for its intrinsic UV lasing response. Similar to carbon, one-dimensional boron nitride nanotubes (BNNTs) have been theoretically predicted and later synthesised. Here we use first principles simulations to unambiguously demonstrate that i) BN nanotubes inherit the highly efficient UV luminescence of hexagonal BN; ii) the application of an external perpendicular field closes the electronic gap keeping the UV lasing with lower yield; iii) defects in BNNTS are responsible for tunable light emission from the UV to the visible controlled by a transverse electric field (TEF). Our present findings pave the road towards optoelectronic applications of BN-nanotube-based devices that are simple to implement because they do not require any special doping or complex growth. [less ▲]

Detailed reference viewed: 168 (4 UL)
Full Text
Peer Reviewed
See detailEnhancement of Vibronic and Ground-State Vibrational Coherences in 2D Spectra of Photosynthetic Complexes
Chenu, Aurélia UL; Christensson, Niklas; Kauffmann, Harald F. et al

in Scientific Reports (2013)

Detailed reference viewed: 21 (0 UL)