Integrated approaches to uncovering transcription regulatory networks in mammalian cells (Q37055842)

18 August 2017

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title

Integrated approaches to uncovering transcription regulatory networks in mammalian cells (English)

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18 August 2017

Timothy Ravasi

3

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Jesper Tegnér

series ordinal

2

object named as

Jesper Tegner

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18 August 2017

Kai Tan

1

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18 August 2017

8 January 2008

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18 August 2017

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18 August 2017

91

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18 August 2017

219-231

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18 August 2017

3

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The Sequence of the Human Genome

18 August 2017

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Initial sequencing and analysis of the human genome

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Gene regulatory networks and the evolution of animal body plans

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Regulatory gene networks and the properties of the developmental process

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Gene regulatory networks for development

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Logic of gene regulatory networks

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Analysis of extended genomic rearrangements in oncological research.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Single-nucleotide polymorphisms and lung disease: clinical implications

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Functional single nucleotide polymorphism-based association studies

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Beyond the sequence: cellular organization of genome function

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Chromosome territories--a functional nuclear landscape.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Chromatin organization in the mammalian nucleus

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

The transcriptional landscape of the mammalian genome

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Antisense transcription in the mammalian transcriptome

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Perturbations to uncover gene networks

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

How to infer gene networks from expression profiles.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Inferring genetic networks and identifying compound mode of action via expression profiling

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

The uses of spatial analysis in medical geography: a review

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Review of uses of network and graph theory concepts within proteomics

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Networks and epidemic models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

The hippocampus as a cognitive graph

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Random graphs with arbitrary degree distributions and their applications

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Use of a cDNA microarray to analyse gene expression patterns in human cancer

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Evaluation of DNA microarray results with quantitative gene expression platforms

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Microarray analysis and tumor classification

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Microarray analysis and tumor classification

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Serial analysis of gene expression

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Using the transcriptome to annotate the genome

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Tagging mammalian transcription complexity

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Genome-wide analysis of mammalian promoter architecture and evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

CAGE: cap analysis of gene expression

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Transcriptional network dynamics in macrophage activation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Systems biology of innate immunity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Transcript abundance in yeast varies over six orders of magnitude

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Stimulus-specific assembly of enhancer complexes on the tumor necrosis factor alpha gene promoter

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

The mechanism of transcriptional synergy of an in vitro assembled interferon-beta enhanceosome.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Considerations of transcriptional control mechanisms: do TFIID-core promoter complexes recapitulate nucleosome-like functions?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Transcription of class III genes: formation of preinitiation complexes

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Topology and reorganization of a human TFIID–promoter complex

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Site-specific heterodimerization by paired class homeodomain proteins mediates selective transcriptional responses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Transcription of chromatin: these are complex times

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Molecular chaperones in signal transduction.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Chromatin remodeling and transcriptional regulation

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Chromatin remodeling and transcription

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Mechanism of transcription initiation and promoter escape by RNA polymerase II.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Initiation of translation in prokaryotes and eukaryotes

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

The transcriptional apparatus required for mRNA encoding genes in the yeast Saccharomyces cerevisiae emerges from a jigsaw puzzle of transcription factors

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Isolation of the yeast regulatory gene GAL4 and analysis of its dosage effects on the galactose/melibiose regulon

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Protein-protein interaction panel using mouse full-length cDNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Large-scale mapping of human protein-protein interactions by mass spectrometry

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Mass spectrometry-based proteomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Advances in protein complex analysis using mass spectrometry

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Analysis of proteins and proteomes by mass spectrometry

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Large-scale protein identification using mass spectrometry

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

An evaluation of human protein-protein interaction data in the public domain

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Towards a proteome-scale map of the human protein–protein interaction network

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

How complete are current yeast and human protein-interaction networks?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Genome-wide location and function of DNA binding proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A global map of p53 transcription-factor binding sites in the human genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Global analysis of protein expression in yeast

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Transcriptional regulatory code of a eukaryotic genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Transcriptional regulatory networks in Saccharomyces cerevisiae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Mammalian cell expression

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A unique role for enhancers is revealed during early mouse development

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Mediator of Transcriptional Regulation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Genomic strategies to identify mammalian regulatory sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Exploiting human--fish genome comparisons for deciphering gene regulation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Highly conserved non-coding sequences are associated with vertebrate development

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Distribution and intensity of constraint in mammalian genomic sequence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A model of the statistical power of comparative genome sequence analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Integrating regulatory motif discovery and genome-wide expression analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A boosting approach for motif modeling using ChIP-chip data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Extensive low-affinity transcriptional interactions in the yeast genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Genomic analysis of regulatory network dynamics reveals large topological changes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Identification of regulatory regions which confer muscle-specific gene expression.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A Discriminative Model for Identifying Spatial cis-Regulatory Modules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Decoding human regulatory circuits

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

De novo cis-regulatory module elicitation for eukaryotic genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A probabilistic method to detect regulatory modules.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

MSCAN: identification of functional clusters of transcription factor binding sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Computational discovery of gene modules and regulatory networks

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Network component analysis: reconstruction of regulatory signals in biological systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Transcriptional regulation of protein complexes in yeast

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Transcriptional regulation of protein complexes within and across species

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Dynamic Complex Formation During the Yeast Cell Cycle

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Discovering regulatory and signalling circuits in molecular interaction networks

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

7 January 2021

Physical network models.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A gene atlas of the mouse and human protein-encoding transcriptomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Integrative molecular concept modeling of prostate cancer progression.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

From signatures to models: understanding cancer using microarrays

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A network-based analysis of systemic inflammation in humans

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Global reconstruction of the human metabolic network based on genomic and bibliomic data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Toward predictive models of mammalian cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A network-based analysis of allergen-challenged CD4+ T cells from patients with allergic rhinitis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

A high-density SNP genome-wide linkage search of 206 families identifies susceptibility loci for chronic lymphocytic leukemia

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2007.11.005

10.1016/J.YGENO.2007.11.005

7 January 2021

Identifiers

DOI

1 reference

18 August 2017

1 reference

PubMed ID

18191937