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上传时间:2016-09-27 13:22:59

Selected publications citing Strand NGS - formerly Avadis NGS

2016

Targeted molecular profiling of rare genetic alterations in colorectal cancer using next-generation sequencing
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Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort
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The LG/J Murine Strain Exhibits Near-Normal Tendon Biomechanical Properties Following a Full-Length Central Patellar Tendon Defect
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Gene Panel Testing in Epileptic Encephalopathies and Familial Epilepsies
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De Novo Assembly of the Transcriptome of Turritopsis, a Jellyfish that Repeatedly Rejuvenates
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HIRA Is Required for Heart Development and Directly Regulates Tnni2 and Tnnt3
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Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway
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Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome
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Genome-wide targets regulated by the OsMADS1 transcription factor reveals its DNA recognition properties
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TNF activation of NF-κB is essential for development of single-positive thymocytes
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Complete in vitro generation of fertile oocytes from mouse primordial germ cells
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Homozygosity mapping guided next generation sequencing to identify the causative genetic variation in inherited retinal degenerative diseases
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Mutations Causing Slow-Channel Myasthenia Reveal that a Valine ring in the Channel Pore of Muscle AChR is Optimized for Stabilizing Channel Gating
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Tungstate treatment of the Dysbiosis associated with Gastrointestinal inflammation
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The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic ComputationalCollaboration within a Consortium
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Design of pathway-preferential estrogens that provide beneficial metabolic and vascular effects without stimulating reproductive tissues
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Next-Generation Sequencing Technology Detects Deletions in the RB1 Gene, Ranging from a Single Base Pair to Whole Gene (~170 kb) with a Higher Sensitivity than FISH
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Utility of Lymphoblastoid Cell Lines for Induced Pluripotent Stem Cell Generation
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Plasma membrane H+-ATPase1 (AHA1) plays a major role in Arabidopsis thaliana for stomatal opening in response to blue light
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Functional Neurons Generated from T Cell-Derived Induced Pluripotent Stem Cells for Neurological Disease Modeling
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Methylation correlates with suppressed expression of immunomodulatory genes in the tumor-adjacent stroma of African American Prostate Cancer compared patients of European American ancestory
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Comprehensive analysis of BRCA (BRCAm) and other germline mutations (GRm) with a clinicopathological association in breast cancer: An Indian study
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SWR1 chromatin-remodelling complex subunits and H2A.Z have non-overlapping functions in immunity and gene regulation in Arabidopsis
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miR-135b, a key regulator of malignancy, is linked to poor prognosis in human myxoid liposarcoma
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Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation
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A homeobox protein, NKX6.1, up-regulates interleukin-6 expression for cell growth in basal-like breast cancer cells
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Laminin regulates PDGFRβ+ cell stemness and muscle development
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Aberrant transcriptional pathways in t(12;21) Acute Lymphoblastic Leukemia
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ZmNAC55, a maize stress-responsive NAC transcription factor, confers drought resistance in transgenic Arabidopsis
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Micro-RNA expression profiling by next-generation sequencing identified novel micro-rnas that are differentially expressed in oa cartilage and chondrocytes
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Efficient in planta detection and dissection of de novo mutation events in the Arabidopsis thaliana disease resistance gene UNI
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A homeobox protein, NKX6.1, up-regulates interleukin-6 expression for cell growth in basal-like breast cancer cells
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Deep sequencing leads to the identification of eukaryotic translation initiation factor 5a as a key element in Rsv1-mediated lethal systemic hypersensitive response to Soybean mosaic virus infection in Soybean
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Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection
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Clinical characteristics of a Japanese family with hearing loss accompanied by compound heterozygous mutations in LOXHD1
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Intratumoral heterogeneity identified at the epigenetic, genetic and transcriptional level in glioblastoma
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Multigene profiling to identify clinically relevant actionable mutations in breast cancer: An Indian study
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The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic Computational Collaboration within a Consortium
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Prenatal genetic diagnosis of retinoblastoma and report of RB1 gene mutation from India
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Delineation of metabolic gene clusters in plant genomes by chromatin signatures
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The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome
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Corona cell RNA sequencing from individual oocytes revealed transcripts and pathways linked to euploid oocyte competence and live birth
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Detection of high frequency of mutations in a breast and/or ovarian cancer cohort: implications of embracing a multi-gene panel in molecular diagnosis in India
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Altered cholesterol biosynthesis causes precocious neurogenesis in the developing mouse forebrain
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Identification and Validation of Housekeeping Genes for Gene Expression Analysis of Cancer Stem Cells
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The renewed battle against RAS-mutant cancers
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Gene expression profiling of white adipose tissue reveals paternal transmission of proneness to obesity
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MicroRNA-27b Enhances the Hepatic Regenerative Properties of Adipose-Derived Mesenchymal Stem Cells
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Systemic Chromosome Instability Resulted in Colonic Transcriptomic Changes in Metabolic, Proliferation, and Stem Cell Regulators in Sgo1−/+ Mice
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Dissecting the molecular mechanisms of the TGF-ß/BMP signal transduction pathways mapping new players and critically assessing established tools
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From Conventional to Next Generation Sequencing of Epstein-Barr Virus Genomes
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A Shh-Foxf-Fgf18-Shh Molecular Circuit Regulating Palate Development
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2015

Simultaneous targeting of 5-LOX-COX and EGFR blocks progression of pancreatic ductal adenocarcinoma
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Transcriptional Regulation of development and tumor-induced Angiogenesis by Etv2 and Fli1b
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Screening of an Indian cohort with breast and/or ovarian cancer by a next-generation sequencing-based panel to detect a high frequency of mutations
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An integrative model of leukocyte genomics and organ dysfunction in heart failure patients requiring mechanical circulatory support
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CRCDA—Comprehensive resources for cancer NGS data analysis
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Genetic and epigenetic characterization of hypodiploid acute lymphoblastic leukemia
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Assessment of individual differences in the rat nucleus accumbens transcriptome following taste-heroin extended access
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The Human Milk Oligosaccharide 2'-Fucosyllactose Augments the Adaptive Response to Extensive Intestinal Resection
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Tie2 Signaling Enhances Mast Cell Progenitor Adhesion to Vascular Cell Adhesion Molecule-1 (VCAM-1) through [alpha] 4[Beta]1 Integrin: e0144436
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Sex Specification and Heterogeneity of Primordial Germ Cells in Mice: e0144836
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Adeno-associated Virus Gene Therapy Vector scAAVIGF-I for Transduction of Equine Articular Chondrocytes and RNA-Seq Analysis
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Translational Regulation of the Mitochondrial Genome Following Redistribution of Mitochondrial MicroRNA in the Diabetic Heart
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Intratumoral heterogeneity of DNA repair pathways in glioblastoma
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Age and Nursing Affect the Neonatal Porcine Uterine Transcriptome
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O-linked β-N-acetylglucosamine (O-GlcNAc) acts as a glucose sensor to epigenetically regulate the insulin gene in pancreatic beta cells
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Changes in Methionine Metabolism and Histone H3 Trimethylation Are Linked to Mitochondrial Defects in Multiple Sclerosis
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The gene expression in rat liver carcinogenesis And exhaustive analysis of DNA methylation
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Identification of Novel Micro-RNAs in IL-1β-Stimulated OA Chondrocytes By Next-Generation Sequencing
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Multi-Omics Analysis for Understanding the Molecular Basis of Lung Adenocarcinoma
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De novo point mutations in the male gamete are directly associated with paternal aging and reduced fecundity
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Clinical utility of profiling somatic alterations in Indian cancer patients using a multi-gene next generation sequencing (NGS) test
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Neuronopathic Gaucher Disease: Dysregulated mRNAs and miRNAs in brain pathogenesis and effects of pharmacologic chaperone treatment in a mouse model
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Nutrigenomics in livestock: systems biology meets nuitrition
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Imbalance between the expression dosages of X-chromosome and autosomal genes in mammalian oocytes
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Sequential Binding of MEIS1 and NKX2-5 on the Popdc2 Gene: A Mechanism for Spatiotemporal Regulation of Enhancers during Cardiogenesis
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Detection, validation and visualization of copy number variations in targeted panels without matched normal samples using next generation sequencing data
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β-Caryophyllene attenuates dextran sulfate sodium-induced colitis in mice via modulation of gene expression associated mainly with colon inflammation
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Detection of translocations in clinical cancer samples using targeted NGS data
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Benchmarking Strand NGS RNA aligner against TopHat2 and other common splice aligners
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An integrated RNA and DNA approach to unravel genetic regulation in cancer
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IDH mutant to activate the Hoxa9 / Meis1 path and the low- oxygen signal in acute myeloid leukemia onset model mice
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β-Naphthoflavone induces oxidative stress in the intertidal copepod, Tigriopus japonicus
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A transposable element in a NAC gene is associated with drought tolerance in maize seedling
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Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain
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Novel roles for LIX1L in promoting cancer cell proliferation through ROS1-mediated LIX1L phosphorylation
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An integrated transcriptomics and proteomics study of Head and Neck Squamous Cell Carcinoma – methodological and analytical considerations
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K-bZIP Mediated SUMO-2/3 Specific Modification on the KSHV Genome Negatively Regulates Lytic Gene Expression and Viral Reactivation
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Testicular dysgenesis/regression without campomelic dysplasia in patients carrying missense mutations and upstream deletion of SOX9
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Multi-Omics Analysis for Understanding the Molecular Basis of Lung Adenocarcinoma
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The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis
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Methods and Techniques for miRNA Data Analysis
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A novel missense mutation of RYR1 in familial idiopathic hyper CK-emia
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A comparative analysis of high-throughput platforms for validation of a circulating microRNA signature in diabetic retinopathy
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Simulating BZIP2 compression using MAPLE and MAPLET interative applications
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A Comprehensive Profile of ChIP-Seq-Based Olig2 Target Genes in Motor Neuron Progenitor Cells Suggests the Possible Involvement of Olig2 in the Pathogenesis of Amyotrophic Lateral Sclerosis
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Lactocrine signaling and neonatal porcine reproductive tract development
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Cellular Response to ATM Deletion: A Multi-Omics Approach
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Information Flow from Strand NGS 2.1 to GeneSpring 13.0
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Correlation Analysis in Agilent GeneSpring and Mass Profiler Professional
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A missense mutation in domain III in HSPG2 in Schwartz–Jampel syndrome compromises secretion of perlecan into the extracellular space
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Epstein–Barr Virus Genetic Variation in Lymphoblastoid Cell Lines Derived from Kenyan Pediatric Population
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Identification of Non-Coding RNAs Associated with Telomeres Using a Combination of enChIP and RNA Sequencing
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IDH2 and NPM1 mutations cooperate to activate Hoxa9/Meis1 and hypoxia pathways in acute myeloid leukemia
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Identification of novel mutations in ABCA4 gene: Clinical and Genetic analysis of Indian patients with Stargardt disease
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Whole transcriptome expression profiling of mouse limb tendon development by using RNA‐seq
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A Cell-Based Systems Biology Assessment of Human Blood to Monitor Immune Responses after Influenza Vaccination
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Bioinformatics data mining approach indicates the expression of chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq)-based hypoxia-inducible factor-1α target genes in periplaque lesions of multiple sclerosis
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FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice
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Long-Term Safety Issues of iPSC-Based Cell Therapy in a Spinal Cord Injury Model: Oncogenic Transformation with Epithelial-Mesenchymal
Transition
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Lysine-specific demethylase LSD2 suppresses lipid influx and metabolism in hepatic cells
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Pathogenesis of Soybean mosaic virus in soybean carrying Rsv1 gene is associated with miRNA and siRNA pathways, and breakdown of AGO1 homeostasis
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A Zap70-dependent feedback circuit is essential for efficient selection of CD4 lineage thymocytes
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2014

A study on the influence of different promoter and 5′ UTR (URM) cassettes from Arabidopsis thaliana on the expression level of the reporter gene β glucuronidase in tobacco and cotton
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Identification of microRNAs involved in acute rejection and spontaneous tolerance in murine hepatic allografts
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Islet Microenvironment, Modulated by Vascular Endothelial Growth Factor-A Signaling, Promotes β Cell Regeneration
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Loss of Ikaros DNA-binding function confers integrin-dependent survival on pre-B cells and progression to acute lymphoblastic leukemia
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Localised Dominant Dystrophic Epidermolysis Bullosa with a Novel de Novo Mutation in COL7A1 Diagnosed by Next-generation Sequencing
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Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development
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A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia
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A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors
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The head and neck cancer cell oncogenome: a platform for the development of precision molecular therapies
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S1P-Yap1 Signaling Regulates Endoderm Formation Required for Cardiac Precursor Cell Migration in Zebrafish
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SDF-1/CXCL12 induces directional cell migration and spontaneous metastasis via a CXCR4/Gαi/mTORC1 axis
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Loss of function mutations in RPL27 and RPS27 identified by whole‐exome sequencing in Diamond‐Blackfan anaemia
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The role of maternal-specific H3K9me3 modification in establishing imprinted X-chromosome inactivation and embryogenesis in mice
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Feasibility of Low-Throughput Next Generation Sequencing for Germline DNA Screening
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RNA-seq analysis of the rat placentation site reveals maternal obesity-associated changes in placental and offspring thyroid hormone signaling
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Transcriptome analysis of Musa and its Applications in Banana improvement
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Method and system for genetic trait search based on the phenotype and the genome of a human subject 
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Sp8 Function During Craniofacial Development - A post-doctoral thesis submitted by AD Kasberg
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H3K36 Histone Methyltransferase Setd2 Is Required for Murine Embryonic Stem Cell Differentiation toward Endoderm
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Integrative Genomics Approach to Identify Genes Important for H2 Production by Rhodopseudomonas 
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A Cross-species Comparison of the Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei Quorum Sensing Regulons
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Whole Genome Sequencing Reveals Novel Non-Synonymous Mutation in Ectodysplasin A (EDA) Associated with Non-Syndromic X-Linked Dominant Congenital Tooth Agenesis
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Comprehensive Next-Generation Sequencing Analyses of Hypoparathyroidism: Identification of Novel GCM2 Mutations
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Google Books: Bioinformatics, Systems Biology, and Systems Medicine
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Targeted deep sequencing of solid tumors to predict response to therapy: A study in an Indian population.
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MicroRNA expression profiling of cat and dog kidneys
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Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature
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Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study
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Milk-borne bioactive factors: effects on neonatal porcine reproductive tissues. KM Rahman - 2014
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Cleavage by signal peptide peptidase is required for the degradation of selected tail-anchored proteins
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Global gene expression analysis following spinal cord injury in non-human primates
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Themis2 Is Not Required for B Cell Development, Activation, and Antibody Responses
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Utility of Neutrophil Fc[gamma] Receptor I (CD64) Index as a Biomarker for Mucosal Inflammation in Pediatric Crohn's Disease
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Searching for Genomic Region of High-Fat Diet-Induced Type 2 Diabetes in Mouse Chromosome 2 by Analysis of Congenic Strains
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Overlapping and Asymmetric Functions of TCR Signaling during Thymic Selection of CD4 and CD8 Lineages
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Avadis NGS DNA Read Aligner - A Benchmarking study
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8-oxoguanine causes spontaneous de novo germline mutations in mice
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A Kir3.4 mutation causes Andersen–Tawil syndrome by an inhibitory effect on Kir2.1
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Vascular endothelial growth factor coordinates islet innervation via vascular scaffolding
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The genetics of chemoreception in the labella and tarsi of Aedes aegypti
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MicroRNA-34c is associated with emphysema severity and modulates SERPINE1 expression
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Cardiac Channelopathy Testing in 274 Ethnically Diverse Sudden Unexplained Deaths
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NF-κB signaling mediates homeostatic maturation of new T cells 
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Genomic reconnaissance of clinical isolates of emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential 
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Glucose Transporter 8 (GLUT8) mediates fructose-induced de novo lipogenesis and macrosteatosis
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Global Analysis of the Burkholderia thailandensis quorum-sensing-controlled regulon
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Maternal Obesity is Associated with a Lipotoxic Placental Environment
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Identification of EMS-induced causal mutations in Arabidopsis thaliana by next-generation sequencing
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2013 

Making a Definitive Diagnosis: A Fast-track from Sequence to Answers 
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Accelerating Disease Diagnosis Through Automated Genomic Analysis 
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Quantitative Transcriptome Analysis Using Next Generation Sequencer Reveals Significant Alternations of Cardiac Gene Expression in Heart Failure 
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Genome-wide Association of Yorkie with Chromatin and Chromatin-Remodeling Complexes 
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Dissecting the molecular mechanisms of the TGF-ß/BMP signal transduction pathways : mapping new players and critically assessing established tools - Post-doctoral thesis submitted by Janis Vogt, 2013, University of Dundee 
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Improved Accuracy and Precision in Clinical Next Generation Sequencing with the SmartChip TE™ Target Enrichment System 
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Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases
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Gustatory receptor expression in the labella and tarsi of Aedes aegypti 
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Aneuploidy and normal cell contamination aware approach to detect copy number variations in cancer using next generation sequencing data. 
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ChIP-Seq Data Mining: Remarkable Differences in NRSF/REST Target Genes between Human ESC and ESC-Derived Neurons
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Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics 
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Functional Development of the Octenol Response in Aedes aegypti 
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Roles of Bmp4 during tooth morphogenesis and sequential tooth formation
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A comprehensive analysis of the human placenta transcriptome
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The chromatin modification by SUMO-2/3 but not SUMO-1 prevents the epigenetic activation of key immune-related genes during Kaposi's sarcoma associated herpesvirus reactivation
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LRP4 third β-propeller domain mutations cause novel congenital myasthenia by compromising agrin-mediated musk signaling in a position-specific manner
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Odd-skipped related-1 controls neural crest chondrogenesis during tongue development
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Diverse spectrum of rare deafness genes underlies early-childhood hearing loss in Japanese patients: a cross-sectional, multi-center next-generation sequencing study
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The mitochondrial RNA landscape of Saccharomyces cerevisiae
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The housekeeping gene Hypoxanthine Guanine Phosphoribosyltransferase (HPRT) regulates multiple developmental and metabolic pathways of murine embryonic stem cell neuronal differentiation
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Gaucher Disease: Transcriptome analyses using microarray or mRNA sequencing in a Gba1 mutant mouse model treated with Velaglucerase alfa or Imiglucerase
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Asymmetric thymocyte death underlies the CD4:CD8 T-cell ratio in the adaptive immune system
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A Role for Hedgehog Signaling in the Differentiation of the Insertion Site of the Patellar Tendon in the Mouse
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Recombineering-based dissection of flanking and paralogous Hox gene functions in mouse reproductive tracts
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Exome sequencing of senescence-accelerated mice (SAM) reveals deleterious mutations in degenerative disease-causing genes
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Study of Global Transcriptional Changes of N-GlcNAc2 Proteins-Producing T24 Bladder Carcinoma Cells under Glucose Deprivation
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Time-series expression analyses using mRNA-Seq: A statistical approach
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Defining Genetic Blueprints–Kidney and Craniofacial Development 
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Poster: 2013 – ZNF9 splicing patterns as potential prognostic markers for severity of Myotonic Dystrophy Type 2
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2012 
MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System
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Identification of a p-Coumarate Degradation Regulon in Rhodopseudomonas palustris by Xpression, an Integrated Tool for Prokaryotic RNA-Seq Data Processing 
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RNA-Seq defines novel genes, RNA processing patterns and enhancer maps for the early stages of nephrogenesis: Hox supergenes 
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Pediatric Biomedical Informatics: Computer Applications in Pediatric Research- By John J. Hutton 
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Bioinformatics for High Throughput Sequencing- By Naiara Rodríguez-Ezpeleta, Michael Hackenberg, Ana M. Aransay
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Human ESC/iPSC-based ‘omics’ and bioinformatics for translational research 
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High-Throughput Sequencing Data Analysis Software: Current State and Future Developments 
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Time Course RNA-seq: A Potential Avenue with Somewhat Different Approach in Tandem of Differential Analysis 
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Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines 
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A Global Transcriptome Analysis of a Dog Model of Congestive Heart Failure With the Human Genome as a Reference 
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Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon
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The ribonuclease Dis3 is an essential regulator of the developmental transcriptome
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Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions
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Exome Sequencing: Capture and Sequencing of All Human Coding Regions for Disease Gene Discovery
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Retinal Transcriptome Profiling by Directional Next-Generation Sequencing Using 100 ng of Total RNA
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Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries
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Mutations in the Glycosylphosphatidylinositol Gene PIGL Cause CHIME Syndrome
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RNA-seq Analysis of the Functional Compartments within the Rat Placentation Site
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Transcriptomic landscape of breast cancers through mRNA sequencing
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A novel mutation in SCN4A causes severe myotonia and school-age-onset paralytic episodes
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2011 
Podbat: a novel genomic tool reveals Swr1-independent H2A. Z incorporation at gene coding sequences through epigenetic meta-analysis 
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An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment 
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Pronounced and Extensive Microtubule Defects in a Saccharomyces cerevisiae DIS3 Mutant 
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LMO7 Mediates Cell-Specific Activation of Rho-MRTF-SRF Pathway and Plays an Important Role in Breast Cancer Cell Migration
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