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。FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update
Yanhui Hu et al.
NUCLEIC ACIDS RESEARCH (2021)
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets
Damian Szklarczyk et al.
NUCLEIC ACIDS RESEARCH (2021)
Mediator subunit MED1 is required for E2A-PBX1-mediated oncogenic transcription and leukemic cell growth
Yu-Ling Lee et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)
Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data
Aditya Pratapa et al.
NATURE METHODS (2020)
Polycomb regulation is coupled to cell cycle transition in pluripotent stem cells
Helena G. Asenjo et al.
SCIENCE ADVANCES (2020)
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
Emily R. Miraldi et al.
GENOME RESEARCH (2019)
Polycomb/Trithorax Antagonism: Cellular Memory in Stem Cell Fate and Function
Marjorie Brand et al.
CELL STEM CELL (2019)
Benchmark and integration of resources for the estimation of human transcription factor activities
Luz Garcia-Alonso et al.
GENOME RESEARCH (2019)
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim et al.
NATURE BIOTECHNOLOGY (2019)
An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms
Oguz Kanca et al.
eLife (2019)
GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks
Thomas Moerman et al.
BIOINFORMATICS (2019)
FlyBase 2.0: the next generation
Jim Thurmond et al.
NUCLEIC ACIDS RESEARCH (2019)
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
Heonjong Han et al.
NUCLEIC ACIDS RESEARCH (2018)
YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae
Miguel C. Teixeira et al.
NUCLEIC ACIDS RESEARCH (2018)
Realizing drug repositioning by adapting a recommendation system to handle the process
Makbule Guclin Ozsoy et al.
BMC BIOINFORMATICS (2018)
Parallel roles of transcription factors dFOXO and FER2 in the development and maintenance of dopaminergic neurons
Damla Tas et al.
PLOS GENETICS (2018)
Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila
Yijie Wang et al.
NATURE COMMUNICATIONS (2018)
ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data
Shinya Oki et al.
EMBO REPORTS (2018)
A collaborative filtering-based approach to biomedical knowledge discovery
Jake Lever et al.
BIOINFORMATICS (2018)
A prior-based integrative framework for functional transcriptional regulatory network inference
Alireza F. Siahpirani et al.
NUCLEIC ACIDS RESEARCH (2017)
Polycomb and Trithorax Group Genes in Drosophila
Judith A. Kassis et al.
GENETICS (2017)
Multilineage communication regulates human liver bud development from pluripotency
J. Gray Camp et al.
NATURE (2017)
Polycomb and Trithorax Group Genes in Drosophila
Judith A. Kassis et al.
GENETICS (2017)
Atropos: specific, sensitive, and speedy trimming of sequencing reads
John P. Didion et al.
PEERJ (2017)
Fused Regression for Multi-source Gene Regulatory Network Inference
Kari Y. Lam et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Hangnoh Lee et al.
PLOS GENETICS (2016)
Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm
Li-Fang Chu et al.
GENOME BIOLOGY (2016)
c-Fos importance for brain development
Fabiola N. Velazquez et al.
AGING-US (2015)
An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network
Mario L. Arrieta-Ortiz et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse
Zhi-Ping Liu et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2015)
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Yang Liao et al.
BIOINFORMATICS (2014)
The Metazoan-Specific Mediator Subunit 26 (Med26) Is Essential for Viability and Is Found at both Active Genes and Pericentric Heterochromatin in Drosophila melanogaster
Sharon K. Marr et al.
MOLECULAR AND CELLULAR BIOLOGY (2014)
Proximal alternating linearized minimization for nonconvex and nonsmooth problems
Jerome Bolte et al.
MATHEMATICAL PROGRAMMING (2014)
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites
Shula Shazman et al.
NUCLEIC ACIDS RESEARCH (2014)
Polycomb proteins control proliferation and transformation independently of cell cycle checkpoints by regulating DNA replication
Andrea Piunti et al.
NATURE COMMUNICATIONS (2014)
DNA copy number evolution in Drosophila cell lines
Hangnoh Lee et al.
GENOME BIOLOGY (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network
Ashish Misra et al.
BMC SYSTEMS BIOLOGY (2013)
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
Federico Zambelli et al.
BRIEFINGS IN BIOINFORMATICS (2013)
PRC2 Controls Drosophila Oocyte Cell Fate by Repressing Cell Cycle Genes
Nicola Iovino et al.
DEVELOPMENTAL CELL (2013)
The Med1 Subunit of the Mediator Complex Induces Liver Cell Proliferation and Is Phosphorylated by AMP Kinase
Navin Viswakarma et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2013)
The Drosophila Ortholog of MLL3 and MLL4, trithorax related, Functions as a Negative Regulator of Tissue Growth
Hiroshi Kanda et al.
MOLECULAR AND CELLULAR BIOLOGY (2013)
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
Daniel Marbach et al.
GENOME RESEARCH (2012)
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
NATURE (2012)
Wisdom of crowds for robust gene network inference
Daniel Marbach et al.
NATURE METHODS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing
Justin M. Zook et al.
PLOS ONE (2012)
Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism
Joerg Martin Buescher et al.
SCIENCE (2012)
Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation
Jun Zhu et al.
PLOS BIOLOGY (2012)
FIMO: scanning for occurrences of a given motif
Charles E. Grant et al.
BIOINFORMATICS (2011)
A transcriptional dynamic network during Arabidopsis thaliana pollen development
Jigang Wang et al.
BMC SYSTEMS BIOLOGY (2011)
A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces
Bryan J. Venters et al.
MOLECULAR CELL (2011)
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
Lihua Julie Zhu et al.
NUCLEIC ACIDS RESEARCH (2011)
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
Raluca Gordan et al.
GENOME BIOLOGY (2011)
Trimming of mammalian transcriptional networks using network component analysis
Linh M. Tran et al.
BMC BIOINFORMATICS (2010)
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets
Jueri Reimand et al.
NUCLEIC ACIDS RESEARCH (2010)
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
Van Anh Huynh-Thu et al.
PLOS ONE (2010)
Revealing strengths and weaknesses of methods for gene network inference
Daniel Marbach et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Sushmita Roy et al.
SCIENCE (2010)
Motif discovery and motif finding from genome-mapped DNase footprint data
Ivan V. Kulakovskiy et al.
BIOINFORMATICS (2009)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
MATRIX FACTORIZATION TECHNIQUES FOR RECOMMENDER SYSTEMS
Yehuda Koren et al.
COMPUTER (2009)
A genetic pathway composed of Sox14 and Mical governs severing of dendrites during pruning
Daniel Kirilly et al.
NATURE NEUROSCIENCE (2009)
Normal dendrite growth in Drosophila motor neurons requires the AP-1 transcription factor
Cortnie L. Hartwig et al.
DEVELOPMENTAL NEUROBIOLOGY (2008)
Network inference using informative priors
Sach Mukherjee et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Gene-environment interaction in yeast gene expression
Erin N. Smith et al.
PLOS BIOLOGY (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
GENE REGULATORY NETWORK RECONSTRUCTION BY BAYESIAN INTEGRATION OF PRIOR KNOWLEDGE AND/OR DIFFERENT EXPERIMENTAL CONDITIONS
ADRIANO V. WERHLI et al.
Journal of Bioinformatics and Computational Biology (2008)
Genetic reconstruction of a functional transcriptional regulatory network
Zhanzhi Hu et al.
NATURE GENETICS (2007)
Design and implementation of high-throughput RNAi screens in cultured Drosophila cells
Nadire Ramadan et al.
NATURE PROTOCOLS (2007)
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
A Subramanian et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila
GH Baeg et al.
GENES & DEVELOPMENT (2005)
Functional genomic analysis of the Wnt-Wingless signaling pathway
R DasGupta et al.
SCIENCE (2005)
Drosophila DNase I footprint database:: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
CM Bergman et al.
BIOINFORMATICS (2005)
The landscape of genetic complexity across 5,700 gene expression traits in yeast
RB Brem et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Genome-wide RNAi analysis of growth and viability in Drosophila cells
M Boutros et al.
SCIENCE (2004)
Transcriptional regulatory code of a eukaryotic genome
CT Harbison et al.
NATURE (2004)
Network component analysis: Reconstruction of regulatory signals in biological systems
JC Liao et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Cell cycle-dependent and cell cycle-independent control of transcription by Drosophila E2F/RB pathway
DK Dimova et al.
GENES & DEVELOPMENT (2003)
Role for a Drosophila Myb-containing protein complex in site-specific DNA replication
EL Beall et al.
NATURE (2002)
The SIN3/RPD3 deacetylase complex is essential for G2 phase cell cycle progression and regulation of SMRTER corepressor levels
LA Pile et al.
MOLECULAR AND CELLULAR BIOLOGY (2002)
Myb controls G2/M progression by inducing cyclin B expression in the Drosophila eye imaginal disc
M Okada et al.
EMBO JOURNAL (2002)
c-Jun and the transcriptional control of neuronal apoptosis
J Ham et al.
BIOCHEMICAL PHARMACOLOGY (2000)