相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Dynamic regulatory module networks for inference of cell type-specific transcriptional networks
Alireza Fotuhi Siahpirani et al.
GENOME RESEARCH (2022)
Twelve years of SAMtools and BCFtools
Petr Danecek et al.
GIGASCIENCE (2021)
Salt Stress Enhances Early Symbiotic Gene Expression in Medicago truncatula and Induces a Stress-Specific Set of Rhizobium-Responsive Genes
Sanhita Chakraborty et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2021)
Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation([OPEN])
Sonali Roy et al.
PLANT CELL (2020)
Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development
Deborah Chasman et al.
CELL SYSTEMS (2019)
A shared gene drives lateral root development and root nodule symbiosis pathways in Lotus
Takashi Soyano et al.
SCIENCE (2019)
Ca2+-regulated Ca2+ channels with an RCK gating ring control plant symbiotic associations
Sunghoon Kim et al.
NATURE COMMUNICATIONS (2019)
A Novel Positive Regulator of the Early Stages of Root Nodule Symbiosis Identified by Phosphoproteomics
Oswaldo Valdes-Lopez et al.
PLANT AND CELL PHYSIOLOGY (2019)
A Remote cis-Regulatory Region Is Required for NIN Expression in the Pericycle to Initiate Nodule Primordium Formation in Medicago truncatula
Jieyu Liu et al.
PLANT CELL (2019)
Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules
Kelsey A. Maher et al.
PLANT CELL (2018)
Dynamics of Ethylene Production in Response to Compatible Nod Factor
Dugald Reid et al.
PLANT PHYSIOLOGY (2018)
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
Jianhong Ou et al.
BMC GENOMICS (2018)
Whole-genome landscape of Medicago truncatula symbiotic genes
Yann Pecrix et al.
NATURE PLANTS (2018)
Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes
Zefu Lu et al.
NUCLEIC ACIDS RESEARCH (2017)
Differential analysis of RNA-seq incorporating quantification uncertainty
Harold Pimentel et al.
NATURE METHODS (2017)
ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development1[CC-BY]
Li-Qun Chen et al.
PLANT PHYSIOLOGY (2017)
Ploidy-dependent changes in the epigenome of symbiotic cells correlate with specific patterns of gene expression
Marianna Nagymihaly et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
New insights into Nod factor biosynthesis: Analyses of chitooligomers and lipo-chitooligomers of Rhizobium sp IRBG74 mutants
Verena Poinsot et al.
CARBOHYDRATE RESEARCH (2016)
Near-optimal probabilistic RNA-seq quantification
Nicolas L. Bray et al.
NATURE BIOTECHNOLOGY (2016)
LOB Domain Proteins: Beyond Lateral Organ Boundaries
Changzheng Xu et al.
TRENDS IN PLANT SCIENCE (2016)
Does a Common Pathway Transduce Symbiotic Signals in Plant-Microbe Interactions?
Andrea Genre et al.
FRONTIERS IN PLANT SCIENCE (2016)
Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula
Carine Satge et al.
NATURE PLANTS (2016)
Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals
Estibaliz Larrainzar et al.
PLANT PHYSIOLOGY (2015)
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
Matthew T. Weirauch et al.
CELL (2014)
Hormonal control of cell division and elongation along differentiation trajectories in roots
Hirotomo Takatsuka et al.
JOURNAL OF EXPERIMENTAL BOTANY (2014)
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
Richard I. Sherwood et al.
NATURE BIOTECHNOLOGY (2014)
An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing
Brice Roux et al.
PLANT JOURNAL (2014)
A Positive Regulator of Nodule Organogenesis, NODULE INCEPTION, Acts as a Negative Regulator of Rhizobial Infection in Lotus japonicus
Emiko Yoro et al.
PLANT PHYSIOLOGY (2014)
Timing Mechanism Dependent on Cell Division Is Invoked by Polycomb Eviction in Plant Stem Cells
Bo Sun et al.
SCIENCE (2014)
Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany
C. Wasternack et al.
ANNALS OF BOTANY (2013)
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Helga Thorvaldsdottir et al.
BRIEFINGS IN BIOINFORMATICS (2013)
Symbiosis and the social network of higher plants
Muthusubramanian Venkateshwaran et al.
CURRENT OPINION IN PLANT BIOLOGY (2013)
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
Jason D. Buenrostro et al.
NATURE METHODS (2013)
Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants
Giles E. D. Oldroyd
NATURE REVIEWS MICROBIOLOGY (2013)
Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks
Sushmita Roy et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models
Thais G. do Rego et al.
BIOINFORMATICS (2012)
Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis
Christopher M. Rose et al.
MOLECULAR & CELLULAR PROTEOMICS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Two Direct Targets of Cytokinin Signaling Regulate Symbiotic Nodulation in Medicago truncatula
Federico Ariel et al.
PLANT CELL (2012)
Transcriptional Responses toward Diffusible Signals from Symbiotic Microbes Reveal MtNFP- and MtDMI3-Dependent Reprogramming of Host Gene Expression by Arbuscular Mycorrhizal Fungal Lipochitooligosaccharides
Lisa F. Czaja et al.
PLANT PHYSIOLOGY (2012)
SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors
Miin-Feng Wu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
The Rules of Engagement in the Legume-Rhizobial Symbiosis
Giles E. D. Oldroyd et al.
ANNUAL REVIEW OF GENETICS, VOL 45 (2011)
Nuclear membranes control symbiotic calcium signaling of legumes
Ward Capoen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Lihua J. Zhu et al.
BMC BIOINFORMATICS (2010)
Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome
Soichi Inagaki et al.
EMBO JOURNAL (2010)
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz et al.
MOLECULAR CELL (2010)
Plant flotillins are required for infection by nitrogen-fixing bacteria
Cara H. Haney et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Differential expression analysis for sequence count data
Simon Anders et al.
GENOME BIOLOGY (2010)
Spontaneous access to DNA target sites in folded chromatin fibers
Michael G. Poirier et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
Abscisic Acid Coordinates Nod Factor and Cytokinin Signaling during the Regulation of Nodulation in Medicago truncatula
Yiliang Ding et al.
PLANT CELL (2008)
A positive regulatory role for LjERF1 in the nodulation process is revealed by systematic analysis of nodule-associated transcription factors of Lotus japonicus
Erika Asamizu et al.
PLANT PHYSIOLOGY (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
The Medicago truncatula CRE1 cytokinin receptor regulates lateral root development and early symbiotic interaction with Sinorhizobium meliloti
Silvina Gonzalez-Rizzo et al.
PLANT CELL (2006)
The Medicago truncatula lysine motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes
Jean-Francois Arrighi et al.
PLANT PHYSIOLOGY (2006)
A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses
J Lévy et al.
SCIENCE (2004)
LysM domain receptor kinases regulating rhizobial Nod factor-induced infection
E Limpens et al.
SCIENCE (2003)
Agrobacterium rhizogenes-transformed roots of Medicago truncatula for the study of nitrogen-fixing and endomycorrhizal symbiotic associations
A Boisson-Dernier et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2001)
Four genes of Medicago truncatula controlling components of a nod factor transduction pathway
R Catoira et al.
PLANT CELL (2000)