The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization.

Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement

Improving large vocabulary continuous speech recognition by combining GMM-based and reservoir-based acoustic modeling

In earlier work we have shown that good phoneme recognition is possible with a so-called reservoir, a special type of recurrent neural network. In this paper, different architectures based on Reservoir Computing (RC) for large vocabulary continuous speech recognition are investigated. Besides experiments with HMM hybrids, it is shown that a RC-HMM tandem can achieve the same recognition accuracy as a classical HMM, which is a promising result for such a fairly new paradigm. It is also demonstrated that a state-level combination of the scores of the tandem and the baseline HMM leads to a significant improvement over the baseline. A word error rate reduction of the order of 20\% relative is possible

Current trends in multilingual speech processing

In this paper, we describe recent work at Idiap Research Institute in the domain of multilingual speech processing and provide some insights into emerging challenges for the research community. Multilingual speech processing has been a topic of ongoing interest to the research community for many years and the field is now receiving renewed interest owing to two strong driving forces. Firstly, technical advances in speech recognition and synthesis are posing new challenges and opportunities to researchers. For example, discriminative features are seeing wide application by the speech recognition community, but additional issues arise when using such features in a multilingual setting. Another example is the apparent convergence of speech recognition and speech synthesis technologies in the form of statistical parametric methodologies. This convergence enables the investigation of new approaches to unified modelling for automatic speech recognition and text-to-speech synthesis (TTS) as well as cross-lingual speaker adaptation for TTS. The second driving force is the impetus being provided by both government and industry for technologies to help break down domestic and international language barriers, these also being barriers to the expansion of policy and commerce. Speech-to-speech and speech-to-text translation are thus emerging as key technologies at the heart of which lies multilingual speech processin