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Publications
An improved bimolecular fluorescence complementation assay with a high signal-to-noise ratioYutaka Kodama
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
Biotechniques 49:793-805. 2010..This mutation allows a 4-fold increase in the S/N ratio of the BiFC assay in living cells. This improved Venus-based BiFC system will facilitate PPI studies in various biological research fields...
Assessment of chromosomal integrity using a novel live-cell imaging technique in mouse embryos produced by intracytoplasmic sperm injectionKazuo Yamagata
Laboratory for Genomic Reprogramming, Center for Developmental Biology, RIKEN Kobe, Minatojima minamimachi 2 2 3, Chuo Ku, Kobe City, Hyogo 651 0047, Japan
Hum Reprod 24:2490-9. 2009..One major cause is thought to be embryonic chromosomal abnormalities. However, there is no direct evidence of how these occur or how they affect pregnancy outcomes...
Next-generation gene targeting in the mouse for functional genomicsYoichi Gondo
Mutagenesis and Genomics Team, RIKEN BioResource Center, 3 1 1 Koyadai, Tsukuba, Ibaraki 305 0074, Japan
BMB Rep 42:315-23. 2009....
Age-related spatial and nonspatial short-term memory in Cav2.1alpha1 mutant mice, Rolling NagoyaEiki Takahashi
RIKEN Brain Science Institute, Research Resources Center, Hirosawa 2 1, Wako, Saitama 351 0198, Japan
Behav Brain Res 204:241-5. 2009..In perirhinal cortex, there were no significantly different expressions. Alteration of age-dependent expressions of Cav2.1 channels differs in different regions with related effects on behavioral performances...
Short communication: Establishment of a new polymerase chain reaction-sequence-based typing method for genotyping cattle major histocompatibility complex class II DRB3S N Takeshima
Viral Infectious Diseases Unit, RIKEN, Wako, Saitama 351 0198, Japan
J Dairy Sci 92:2965-70. 2009..This new method will contribute to high-throughput genotyping of BoLA-DRB3 by sequence-based typing...
Genetic analysis of glucosidase II beta-subunit in trimming of high-mannose-type glycansTaisuke Watanabe
RIKEN Advanced Science Institute, Wako, Saitama, Japan
Glycobiology 19:834-40. 2009..These results suggested that the beta-subunit confers the substrate specificity toward di- and monoglucosylated glycans on the glucose-trimming activity of the alpha-subunit...
Prevotella falsenii sp. nov., a Prevotella intermedia-like organism isolated from monkey dental plaqueMitsuo Sakamoto
Microbe Division Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351 0198, Japan
Int J Syst Evol Microbiol 59:319-22. 2009..nov. is proposed. The type strain is 04052(T) (=JCM 15124(T) =CCUG 56137(T))...
Taste reactivity and its modulation by morphine and methamphetamine in C57BL/6 and DBA/2 miceBarbara Cagniard
Molecular Neuropathology Group, RIKEN Brain Science Institute, 2 1 Hirosawa, Wako Shi, Saitama, 351 0198, Japan
Physiol Behav 96:412-20. 2009....
Ca2+ induces macropinocytosis via F-actin depolymerization during growth cone collapseHiroyuki Kabayama
Laboratory for Developmental Neurobiology, Brain Science Institute, The Institute of Physical and Chemical Research RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
Mol Cell Neurosci 40:27-38. 2009..We propose that the coordinated regulation of actin cytoskeletal reorganization and macropinocytosis-mediated retrograde membrane trafficking may contribute to Ca(2+)-induced axon growth inhibition...
Generation of mice derived from embryonic stem cells using blastocysts of different developmental agesHiroshi Ohta
Laboratory for Genomic Reprogramming, Center for Developmental Biology, RIKEN, Chuo Ku, Kobe 650 0047, Japan
Reproduction 136:581-7. 2008..We also discuss a comparison of the present findings with those of our previous study, where ES mice were generated using an aggregation method employing the same ES cell lines...
Microbacterium hatanonis sp. nov., isolated as a contaminant of hairsprayMohammad Abdul Bakir
Microbe Division Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351 0198, Japan
Int J Syst Evol Microbiol 58:654-8. 2008..nov. is proposed. The type strain is FCC-01(T) (=JCM 14558(T) =DSM 19179(T))...
Multilayer nonnegative matrix factorization using projected gradient approachesAndrzej Cichocki
Laboratory for Advanced Brain Signal Processing, RIKEN Brain Science Institute, Wako Shi, Saitama 351 0198, Japan
Int J Neural Syst 17:431-46. 2007..Our new implementations of NMF are demonstrated with the simulations performed for Blind Source Separation (BSS) data...
An artificial aptazyme-based riboswitch and its cascading system in E. coliAtsushi Ogawa
Bioengineering Laboratory, RIKEN (The Institute of Physical and Chemical Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Chembiochem 9:206-9. 2008
Molecular characterization of microbial mutations induced by ion beam irradiationHiroyuki Ichida
Graduate School of Science and Technology, Chiba University, Matsudo, Chiba 271 8510, Japan
Mutat Res 639:101-7. 2008..We found also that ion beams, particularly "heavier" ion beams, can produce single gene disruptions and may present an effective alternative to transgenic approaches...
Biomimetic approach to tacit learning based on compound controlShingo Shimoda
RIKEN Brain Science Institute BSI Toyota Collaboration Center, Nagoya 463 0003, Japan
IEEE Trans Syst Man Cybern B Cybern 40:77-90. 2010..We show that the individual activities can generate optimized behaviors from a particular global viewpoint, i.e., autonomous rhythm generation and learning of balanced postures, without using global performance indices...
Kernel bandwidth optimization in spike rate estimationHideaki Shimazaki
RIKEN Brain Science Institute, Saitama, Japan
J Comput Neurosci 29:171-82. 2010....
Physiological function and molecular basis of STIM1-mediated calcium entry in immune cellsYoshihiro Baba
Laboratory for Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
Immunol Rev 231:174-88. 2009....
[Recognition of dynamic facial expressions in peripheral and central vision]Tomomi Fujimura
JST ERATO Okanoya Emotional Information Project, RIKEN, Hirosawa, Wako 351 0198, Japan
Shinrigaku Kenkyu 81:348-55. 2010..These findings suggest that an effect of dynamic information is more salient in peripheral vision than in central vision for recognizing certain facial expressions...
A global single-cell cDNA amplification method for quantitative microarray analysisKazuki Kurimoto
Laboratory for Mammalian Germ Cell Biology, RIKEN Center for Developmental Biology, Kobe, Japan
Methods Mol Biol 687:91-111. 2011..The promoter-tagged cDNA is purified with gel electrophoresis and amplified with one final cycle of PCR...
Vapochromic and mechanochromic tetrahedral gold(I) complexes based on the 1,2-bis(diphenylphosphino)benzene ligandMasahisa Osawa
Luminescent Materials Laboratory, RIKEN The Institute of Physical and Chemical Research, Hirosawa 2 1, Wako Shi, 351 0198 Japan
Chemistry 16:12114-26. 2010..We have demonstrated that the symmetry reductions are responsible for the phosphorescence color alteration caused by external stimuli (volatile organic compounds and mechanical grinding)...
Sex determination: insights from the silkwormMasataka G Suzuki
The Institute of Physical and Chemical Research, Hirosawa, Wako, Saitama 351 0198, Japan
J Genet 89:357-63. 2010..Since BmPSI does not exhibit any sequence relationship to known SR proteins, such as Tra and Tra2, the regulatory mechanism of sex-specific alternative splicing of Bmdsx is distinct from that of dsx...
GeneWaltz--A new method for reducing the false positives of gene findingKazuharu Misawa
Research Program for Computational Science, Research and Development Group for Next Generation Integrated Living Matter Simulation, Fusion of Data and Analysis Research and Development Team, RIKEN, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
BioData Min 3:6. 2010..These false positives are problematic because they waste time and resources of experimental studies...
Development of selective inhibitors of necrosisMikiko Sodeoka
RIKEN Advanced Science Institute, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
Chem Rec 10:308-14. 2010..IM-54 inhibits necrosis induced by oxidative stress, but not apoptosis induced by anticancer drugs...
DNA methylation profiling using live-cell imagingKazuo Yamagata
Laboratory for Genomic Reprogramming, Center for Developmental Biology, RIKEN Kobe, Minatojima minamimachi 2 2 3, Chuo Ku, Kobe City, Hyogo 651 0047, Japan
Methods 52:259-66. 2010..In this review, I describe the theoretical basis of this imaging and discuss its usefulness and potential for studies on epigenetic regulation, especially in early mammalian development...
Autonomous right-screw rotation of growth cone filopodia drives neurite turningAtsushi Tamada
Laboratory for Neuronal Growth Mechanisms, RIKEN Brain Science Institute, Wako, Saitama 351 0198, Japan
J Cell Biol 188:429-41. 2010..Although the growth cone itself has been regarded as functionally symmetric, our study reveals the asymmetric nature of growth cone motility...
sORF finder: a program package to identify small open reading frames with high coding potentialKousuke Hanada
Plant Science Center, RIKEN, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
Bioinformatics 26:399-400. 2010....
Optimization of SSVEP brain responses with application to eight-command Brain-Computer InterfaceHovagim Bakardjian
Laboratory for Advanced Brain Signal Processing, Brain Science Institute, RIKEN, Wako Shi, Saitama, Japan
Neurosci Lett 469:34-8. 2010..These results emphasize the need for SSVEP applications to optimize not only the analysis algorithms but also the stimuli in order to maximize the brain responses they rely on...
NGSView: an extensible open source editor for next-generation sequencing dataErik Arner
RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
Bioinformatics 26:125-6. 2010..NGSView is available under an open source license and can be extended through a well documented API. AVAILABILITY: http://ngsview.sourceforge.net..
Pd(0)-Mediated rapid coupling between methyl iodide and heteroarylstannanes: an efficient and general method for the incorporation of a positron-emitting (11)C radionuclide into heteroaromatic frameworksMasaaki Suzuki
RIKEN Center for Molecular Imaging Science, 6 7 3 Minatojima minamimachi, Chuo Ku, Kobe 650 0047, Japan
Chemistry 15:12489-95. 2009....
Relative importance of the tyrosine phosphorylation sites of Disabled-1 to the transmission of Reelin signalingToshifumi Morimura
Ogawa Research Unit, Brain Science Institute, RIKEN, 2 1 Hirosawa, Wako Shi, Saitama 351 0198, Japan
Brain Res 1304:26-37. 2009..The results also suggest that phosphorylation of either one of the residues in each pair is sufficient for the transmission of Reelin signaling...
Cytoplasmic peptide:N-glycanase and catabolic pathway for free N-glycans in the cytosolTadashi Suzuki
Department of Biochemistry, 21st Center of Excellence Program, Osaka University Graduate School of Medicine, Japan
Semin Cell Dev Biol 18:762-9. 2007..Taken together, these observations indicate that C-terminus of mammalian PNGase is important for recognition of the substrates while N-terminus of this enzyme is involved in assembly of a degradation complex...
Multiplex PCR-based real-time invader assay (mPCR-RETINA): a novel SNP-based method for detecting allelic asymmetries within copy number variation regionsNaoya Hosono
Laboratory for Genotyping, SNP Research Center, The Institute of Physical and Chemical Research RIKEN, Kanagawa, Japan
Hum Mutat 29:182-9. 2008..We believe mPCR-RETINA will provide a significant contribution to identifying functional alleles in CNV regions...
Tlx acts as a proangiogenic switch by regulating extracellular assembly of fibronectin matrices in retinal astrocytesAkiyoshi Uemura
Laboratory for Stem Cell Biology, Center for Developmental Biology, Institute of Physical and Chemical Research RIKEN, Kobe, Japan
J Clin Invest 116:369-77. 2006..This work identifies Tlx as an essential component of the molecular network involved in the hypoxia-inducible proangiogenic switch in retinal astrocytes...
Improved Golgi-like visualization in retrogradely projecting neurons after EGFP-adenovirus infection in adult rat and monkeyRyohei Tomioka
Laboratory for Cortical Organization and Systematics, RIKEN Brain Science Institute, 2 1 Hirosawa, Wako Shi, Saitama 351 0198, Japan
J Histochem Cytochem 54:539-48. 2006..The native EGFP signal (without antibody enhancement) may be sufficient for studies involving cultured cells or slices...
Raman probe using a single hollow waveguideYuichi Komachi
Probing Technology Laboratory, RIKEN, The Institute of Physical and Chemical Research, Hirosawa, Wako Shi 351 0198, Japan
Opt Lett 30:2942-4. 2005..In addition, the measured Raman spectra showed better signal-to-noise ratios than a conventional Raman fiber probe. The HW's suitability as a Raman fiber probe was also demonstrated...
Robustness, evolvability, and optimality of evolutionary neural networksP P Palmes
RIKEN Brain Science Institute, Hirosawa Wako City, Saitama 351 198, Japan
Biosystems 82:168-88. 2005..Our results strongly suggest that proper ANN design requires simultaneous adaptation of ANN structure and weights to avoid one-sided or bias convergence to either the weight or architecture space...
Generation of progeny from embryonic stem cells by microinsemination of male germ cells from chimeric miceEiji Mizutani
Laboratory for Genomic Reprogramming, Center for Developmental Biology, RIKEN Kobe, Japan
Genesis 43:34-42. 2005..Thus, this technique allowed us to generate the ES cell-derived progeny even from the low contributed chimeric mice, which cannot produce ES-origin offspring by natural mating...
Gene expression and association analyses of LIM (PDLIM5) in bipolar disorder and schizophreniaT Kato
Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako Shi, Saitama, Japan
Mol Psychiatry 10:1045-55. 2005..No association was observed in case-control analysis and family-based association analysis in schizophrenia. These results suggest that SNPs in the upstream region of LIM may confer the genetic risk for bipolar disorder...
Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the HypermastigeaMoriya Ohkuma
Environmental Molecular Biology Laboratory, RIKEN, Wako, Saitama 351 0198, Japan
Mol Phylogenet Evol 35:646-55. 2005..The monophyletic lineage composed by Spirotrichonymphida exhibited a narrower branching pattern than Trichonymphida. The root of parabasalids was examined but could not be discerned accurately...
[Future views on genome network projects]Yoshihide Hayashizaki
Tanpakushitsu Kakusan Koso 49:3017. 2004
[Orthologue, paralogue and comparative genomics for gene network analysis]Nobuyuki Kawagashira
Tanpakushitsu Kakusan Koso 49:2909-15. 2004
[Protein-protein interaction assay by dual-color fluorescence cross correlation spectroscopy]Rieko Oyama
Tanpakushitsu Kakusan Koso 49:2775-9. 2004
Isofrequency band-like zones of activation revealed by optical imaging of intrinsic signals in the cat primary auditory cortexH Ojima
Cortical Organization Systematics, BSI, RIKEN, 2 1 Hirosawa, Wako, Saitama, 351 0198 Japan
Cereb Cortex 15:1497-509. 2005....
[Functional coupling between neuron and glia in neuronal sphingolipid biosynthesis]Yoshio Hirabayashi
Tanpakushitsu Kakusan Koso 49:2391-6. 2004
pDUAL, a multipurpose, multicopy vector capable of chromosomal integration in fission yeastAkihisa Matsuyama
Chemical Genetics Laboratory, RIKEN, Saitama 351 0198, Japan
Yeast 21:1289-305. 2004..Using these all-in-one vectors, a suitable mode of expression of a cloned gene can be selected for individual analysis without any complicated subcloning processes...
New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)Hideyuki Miyatake
RIKEN Harima Institute SPring 8, Sayo cho, Sayo gun, Hyogo, Japan
Acta Crystallogr D Biol Crystallogr 62:280-9. 2006..The effectiveness of these techniques was assessed using five different crystals. Four of the crystals were successfully iodinated, providing sufficient phasing power for structure determination...
Neural correlates of priming on occluded figure interpretation in human fusiform cortexL C Liu
Laboratory for Human Brain Dynamics, RIKEN Brain Science Institute BSI, 2 1 Hirosawa, Wakoshi, Saitama 351 0198, Japan
Neuroscience 141:1585-97. 2006....
Lipid rafts: new tools and a new componentToshihide Kobayashi
Lipid Biology Laboratory, RIKEN Institute of Physical and Chemical Research, Japan
Biol Pharm Bull 29:1526-31. 2006..Recent findings have uncovered a previously unrecognized activity of a glycosphingolipid synthesis inhibitor, D-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol (D-PDMP)...
Notch: filling a hole in T helper 2 cell differentiationMasato Kubo
Laboratory for Signal Network, Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Suehiro cho 1 7 22, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
Immunity 27:3-5. 2007..In this issue of Immunity, Amsen et al. (2007) and Fang et al. (2007) propose a direct role for Notch signaling in the expression of GATA-3 transcription factor and T helper 2 cell differentiation...
A novel dominant-negative mutation in Gdf5 generated by ENU mutagenesis impairs joint formation and causes osteoarthritis in miceHiroshi Masuya
Mouse Functional Genomics Research Group, RIKEN GSC, Tsukuba, Ibaraki, Japan
Hum Mol Genet 16:2366-75. 2007..This study further highlights a critical role of GDF5 in joint formation and the development of OA, and this mouse should serve as a good model for OA...
Structural and functional analysis of the apoptosis-associated tyrosine kinase (AATYK) familyM Tomomura
Laboratory for Molecular Neurogenesis, Laboratory for Neuronal Growth Mechanisms, RIKEN Brain Science Institute, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
Neuroscience 148:510-21. 2007....
Lymphocytic choriomeningitis infection undetected by dirty-bedding sentinel monitoring and revealed after embryo transfer of an inbred strain derived from wild miceFumio Ike
RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
Comp Med 57:272-81. 2007..111..
Simultaneous pattern classification and multidomain association using self-structuring kernel memory networksTetsuya Hoya
Department of Mathematics, College of Science and Technology, Nihon University, Tokyo 101 8308, Japan
IEEE Trans Neural Netw 18:732-44. 2007....
Two new non-competitive mGlu1 receptor antagonists are potent tools to unravel functions of this mGlu receptor subtypeT Knopfel
Laboratory for Neuronal Circuit Dynamics, RIKEN BSI, Wako Shi, Saitama, Japan
Br J Pharmacol 151:723-4. 2007....
Dynamic functional connectivityAndreas A Ioannides
Laboratory for Human Brain Dynamics, RIKEN Brain Science Institute, 2 1 Hirosawa, Wakoshi, Saitama, Japan 351 0198
Curr Opin Neurobiol 17:161-70. 2007..As shown at the end of this review, a correspondence principle can be formulated to guide the interpretation across network levels and to relate nodes to well defined anatomical entities...
Mechanisms of COPII vesicle formation and protein sortingKen Sato
Molecular Membrane Biology Laboratory, RIKEN Discovery Research Institute, Hirosawa, Wako, Saitama 351 0198, Japan
FEBS Lett 581:2076-82. 2007..In the present review, we summarize current knowledge of COPII-mediated vesicle formation from the ER, as well as highlighting non-canonical roles of COPII components...
Precise mapping of early visual responses in space and timeVahe Poghosyan
Laboratory for Human Brain Dynamics, BSI, RIKEN, 2 1 Hirosawa, Wako Shi, Saitama, 351 0198, Japan
Neuroimage 35:759-70. 2007..These results show for the first time in humans, significantly shorter onset latencies in V1 for peripheral than parafoveal VF stimulations...
Molecular genetics of bipolar disorder and depressionTadafumi Kato
Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan
Psychiatry Clin Neurosci 61:3-19. 2007..Finally, this report addresses some possible causes for the lack of replication in this field...
[ADLib system for rapid and flexible design of monoclonal antibodies]Kunihiro Ohta
Genetic System Regulation Laboratory, RIKEN Discovery Research Institute, Wako City, Saitama, Japan
Yakugaku Zasshi 127:81-9. 2007..The ADLib system is applicable to self- or highly conserved antigens, polysaccharide chains, peptides, and haptens...
Acid-base catalysis of chiral Pd complexes: development of novel catalytic asymmetric reactions and their application to synthesis of drug candidatesYoshitaka Hamashima
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
Chem Pharm Bull (Tokyo) 54:1351-64. 2006..This aza-Michael reaction was successfully applied to asymmetric synthesis of the CETP inhibitor torcetrapib...
Clathrin-associated adaptor protein complexesHiroshi Ohno
Laboratory for Epithelial Immunobiology, Research Center for Allergy and Immunology (RCAI, RIKEN, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Japan
J Cell Sci 119:3719-21. 2006
Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCRHarukazu Suzuki
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
FEBS Lett 573:214-8. 2004..These results provide unique molecular markers that may account for the molecular basis of the unique functions of specific brain regions...
