| review article | Q7318358 |
| scholarly article | Q13442814 |
| P50 | author | Michael R Brent | Q87900417 |
| P2093 | author name string | Michael R Brent | |
| P2860 | cites work | Transposon Calling Cards | Q87203081 |
| Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles | Q21145898 | ||
| ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context | Q21284234 | ||
| An integrated encyclopedia of DNA elements in the human genome | Q22122150 | ||
| The accessible chromatin landscape of the human genome | Q24595581 | ||
| Wisdom of crowds for robust gene network inference | Q24604615 | ||
| DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells | Q24633746 | ||
| Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data | Q24798371 | ||
| Inferring yeast cell cycle regulators and interactions using transcription factor activities | Q24814940 | ||
| Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach | Q24816788 | ||
| Dam it's good! DamID profiling of protein-DNA interactions | Q26783494 | ||
| Expanding the Biologist's Toolkit with CRISPR-Cas9 | Q26863745 | ||
| Affinity regression predicts the recognition code of nucleic acid–binding proteins | Q27313925 | ||
| Transcriptional regulatory code of a eukaryotic genome | Q27933887 | ||
| Identifying transcription factor functions and targets by phenotypic activation | Q27936626 | ||
| Quantitative and logic modelling of molecular and gene networks | Q28083248 | ||
| ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia | Q28274448 | ||
| Transcriptional networks controlling the cell cycle. | Q39211167 | ||
| The discrepancy between chromatin factor location and effect. | Q39619277 | ||
| Adaptively inferring human transcriptional subnetworks | Q40511836 | ||
| De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins | Q42027009 | ||
| Predicting the effects of copy-number variation in double and triple mutant combinations | Q42132833 | ||
| Prediction of phenotype and gene expression for combinations of mutations | Q42860872 | ||
| Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors. | Q44256796 | ||
| gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation | Q44687571 | ||
| Generating realistic in silico gene networks for performance assessment of reverse engineering methods | Q45719256 | ||
| Inferring gene regulatory networks by ANOVA. | Q47954037 | ||
| The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models. | Q51769911 | ||
| Predicting expression patterns from regulatory sequence in Drosophila segmentation. | Q51897395 | ||
| Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project | Q28301622 | ||
| Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters | Q28302903 | ||
| Inferring binding energies from selected binding sites | Q28472054 | ||
| DNA-binding specificities of human transcription factors | Q28854562 | ||
| Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities | Q29301030 | ||
| The long-range interaction landscape of gene promoters | Q29615403 | ||
| Identification of functional elements and regulatory circuits by Drosophila modENCODE | Q29617551 | ||
| limma powers differential expression analyses for RNA-sequencing and microarray studies | Q29617988 | ||
| Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments. | Q30404787 | ||
| The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo | Q30478837 | ||
| Mapping functional transcription factor networks from gene expression data | Q30620797 | ||
| ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells | Q30651227 | ||
| Identification of active transcriptional regulatory elements from GRO-seq data | Q30914286 | ||
| Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data | Q31111868 | ||
| Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression | Q33366448 | ||
| Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data | Q33529097 | ||
| ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs | Q33564556 | ||
| Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. | Q33659512 | ||
| Inferring regulatory networks from expression data using tree-based methods | Q33711877 | ||
| DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models | Q33737739 | ||
| A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity | Q33878190 | ||
| Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). | Q33886781 | ||
| Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets | Q34044099 | ||
| A predictive computational framework for direct reprogramming between human cell types | Q34045862 | ||
| Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position | Q34375601 | ||
| A high-resolution map of the three-dimensional chromatin interactome in human cells | Q34378943 | ||
| Use of pleiotropy to model genetic interactions in a population | Q34446684 | ||
| Transcription factor binding dynamics during human ES cell differentiation | Q34463538 | ||
| Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans | Q34475541 | ||
| TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. | Q34485897 | ||
| CellNet: network biology applied to stem cell engineering | Q34520877 | ||
| Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers | Q34626036 | ||
| An atlas of active enhancers across human cell types and tissues | Q34660689 | ||
| Yeast Gal4: a transcriptional paradigm revisited | Q34683120 | ||
| Network component analysis: reconstruction of regulatory signals in biological systems | Q34788818 | ||
| Integrating regulatory motif discovery and genome-wide expression analysis | Q34869275 | ||
| The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. | Q34976601 | ||
| Widespread misinterpretable ChIP-seq bias in yeast | Q35071005 | ||
| Principles of regulatory information conservation between mouse and human | Q35128631 | ||
| Determination and inference of eukaryotic transcription factor sequence specificity | Q35249717 | ||
| A mammalian transcription factor-specific peptide repository for targeted proteomics. | Q35434417 | ||
| Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation | Q35561962 | ||
| Generation of mouse ES cell lines engineered for the forced induction of transcription factors. | Q35619663 | ||
| Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences. | Q35662980 | ||
| "Calling cards" for DNA-binding proteins in mammalian cells | Q35810814 | ||
| Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. | Q35860667 | ||
| Recognition models to predict DNA-binding specificities of homeodomain proteins | Q36022098 | ||
| Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay | Q36549689 | ||
| Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins | Q36653801 | ||
| Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells | Q36660738 | ||
| Predictive modeling of genome-wide mRNA expression: from modules to molecules | Q36740482 | ||
| Dynamic regulatory network controlling TH17 cell differentiation | Q36799525 | ||
| Insights into the regulation of protein abundance from proteomic and transcriptomic analyses | Q36846022 | ||
| RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II | Q37031377 | ||
| Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases | Q37140821 | ||
| Mapping yeast transcriptional networks | Q37142704 | ||
| Predicting the binding preference of transcription factors to individual DNA k-mers. | Q37153250 | ||
| Global mapping of protein-DNA interactions in vivo by digital genomic footprinting | Q37157318 | ||
| Benchmarking regulatory network reconstruction with GRENDEL. | Q37319654 | ||
| Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins | Q37319659 | ||
| ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells | Q37463190 | ||
| Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments | Q37631782 | ||
| An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins | Q37734422 | ||
| Transcriptional enhancers: from properties to genome-wide predictions | Q38194866 | ||
| Genetic reconstruction of a functional transcriptional regulatory network | Q38302919 | ||
| Chromatin profiling using targeted DNA adenine methyltransferase | Q38303417 | ||
| The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae | Q38494570 | ||
| DNA Motif Databases and Their Uses | Q38579661 | ||
| Precise maps of RNA polymerase reveal how promoters direct initiation and pausing | Q38606913 | ||
| P433 | issue | 11 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 736-750 | |
| P577 | publication date | 2016-10-06 | |
| P1433 | published in | Trends in Genetics | Q2451468 |
| P1476 | title | Past Roadblocks and New Opportunities in Transcription Factor Network Mapping | |
| P478 | volume | 32 |
| Q41063962 | A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a. |
| Q38807143 | Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes |
| Q49436822 | Genomic and molecular control of cell type and cell type conversions. |
| Q47875614 | Mammalian Transcription Factor Networks: Recent Advances in Interrogating Biological Complexity |
| Q37451136 | Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast |
| Q42696593 | NetProphet 2.0: Mapping Transcription Factor Networks by Exploiting Scalable Data Resources. |
| Q52359757 | The Genome-Scale Integrated Networks in Microorganisms. |
Search more.