-
Chapter and Conference Paper
Alternating Optimization Method Based on Nonnegative Matrix Factorizations for Deep Neural Networks
The backpropagation algorithm for calculating gradients has been widely used in computation of weights for deep neural networks (DNNs). This method requires derivatives of objective functions and has some diff...
-
Article
Open AccessTranscriptome analysis of hormone-induced gene expression in Brachypodium distachyon
Brachypodium distachyon is a new model plant closely related to wheat and other cereals. In this study, we performed a comprehensive analysis of hormone-regulated genes in Brachypodium distachyon using RNA sequen...
-
Article
Open AccessContent of intrinsic disorder influences the outcome of cell-free protein synthesis
Cell-free protein synthesis is used to produce proteins with various structural traits. Recent bioinformatics analyses indicate that more than half of eukaryotic proteins possess long intrinsically disordered ...
-
Article
Genome-wide analysis reveals phytohormone action during cassava storage root initiation
Development of storage roots is a process associated with a phase change from cell division and elongation to radial growth and accumulation of massive amounts of reserve substances such as starch. Knowledge o...
-
Article
Open AccessTranscriptome analysis of thermogenic Arum concinnatum reveals the molecular components of floral scent production
Several plant species can generate enough heat to increase their internal floral temperature above ambient temperature. Among thermogenic plants, Arum concinnatum shows the highest respiration activity during the...
-
Article
In vivo anteroposterior translation after meniscal-bearing total knee arthroplasty: effects of soft tissue conditions and flexion angle
Anteroposterior (AP) joint translation is an important indicator of good clinical outcome following total knee arthroplasty (TKA). This study evaluated the in vivo relationship between changes in the degree of...
-
Chapter and Conference Paper
Efficient Algorithm for Linear Systems Arising in Solutions of Eigenproblems and Its Application to Electronic-Structure Calculations
We consider an eigenproblem derived from first-principles electronic-structure calculations. Eigensolvers based on a rational filter require solutions of linear systems with multiple shifts and multiple right ...
-
Article
Open AccessA second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica
Microsatellites or simple sequence repeats (SSRs) in expressed sequence tags (ESTs) are useful resources for genome analysis because of their abundance, functionality and polymorphism. The advent of commercial...
-
Article
RIKEN Cassava Initiative: Establishment of a Cassava Functional Genomics Platform
Cassava (Manihot esculenta Crantz) is an important tropical root crop that provides food security and income generation for many farmers. Cassava ranks as the third most important source of calories in the tropic...
-
Article
A numerical method for polynomial eigenvalue problems using contour integral
We propose a numerical method using contour integral to solve polynomial eigenvalue problems (PEPs). The method finds eigenvalues contained in a certain domain which is defined by a surrounding integral path. ...
-
Article
Erratum: Genome sequence of the palaeopolyploid soybean
Nature 463, 178–183 (2010) During resubmission of this work, a paper was published1 that used a comparative genomics approach between soybean and maize to show that a single-base mutation in chromosome 19 acco...
-
Article
Toward genome-wide metaboloty** and elucidation of metabolic system: metabolic profiling of large-scale bioresources
An improvement in plant production is increasingly important for a sustainable human society. For this purpose, understanding the mechanism of plant production, that is, the plant metabolic system, is an immed...
-
Article
Open AccessGenome sequence of the palaeopolyploid soybean
Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the...
-
Article
Open AccessLarge-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila
Thellungiella halophila (also known as Thellungiella salsuginea) is a model halophyte with a small plant size, short life cycle, and small genome. It easily undergoes genetic transformation by the floral dip** ...
-
Article
Open AccessTriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae
The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL) analysis as well as the holistic population ...
-
Chapter and Conference Paper
On Single Precision Preconditioners for Krylov Subspace Iterative Methods
Large sparse linear systems Ax= b arise in many scientific applications. Krylov subspace iterative methods are often used for solving such linear systems. Preconditioning techniques are efficient to reduce the nu...
-
Article
Open AccessSequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response
Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA li...
-
Article
Open AccessFunctional annotation of 19,841 Populus nigra full-length enriched cDNA clones
Populus is one of favorable model plants because of its small genome. Structural genomics of Populus has reached a breakpoint as nucleotides of the entire genome have been determined. Reaching the post genome era...
-
Article
Open AccessIdentification of plant promoter constituents by analysis of local distribution of short sequences
Plant promoter architecture is important for understanding regulation and evolution of the promoters, but our current knowledge about plant promoter structure, especially with respect to the core promoter, is ...
-
Chapter and Conference Paper
A Master-Worker Type Eigensolver for Molecular Orbital Computations
We consider a parallel method for solving generalized eigenvalue problems that arise from molecular orbital computations. We use a moment-based method that finds several eigenvalues and their corresponding eig...
