4.8 Article

Extracting sequence features to predict proteinDNA interactions: a comparative study

Related references

Note: Only part of the references are listed.
Article Cell Biology

A core Klf circuitry regulates self-renewal of embryonic stem cells

Jianming Jiang et al.

NATURE CELL BIOLOGY (2008)

Article Biochemical Research Methods

Genomic sequence is highly predictive of local nucleosome depletion

Guo-Cheng Yuan et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Induction of pluripotent stem cells from adult human fibroblasts by defined factors

Kazutoshi Takahashi et al.

Article Multidisciplinary Sciences

A gene regulatory network in mouse embryonic stem cells

Qing Zhou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Statistics & Probability

COUPLING HIDDEN MARKOV MODELS FOR THE DISCOVERY OF Cis-REGULATORY MODULES IN MULTIPLE SPECIES

Qing Zhou et al.

ANNALS OF APPLIED STATISTICS (2007)

Review Biochemistry & Molecular Biology

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques

Laura Elnitski et al.

GENOME RESEARCH (2006)

Article Multidisciplinary Sciences

A protein interaction network for pluripotency of embryonic stem cells

Jianlong Wang et al.

NATURE (2006)

Article Biotechnology & Applied Microbiology

High-resolution computational models of genome binding events

Yuan Qi et al.

NATURE BIOTECHNOLOGY (2006)

Article Biotechnology & Applied Microbiology

Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae

Guo-Cheng Yuan et al.

GENOME BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Core transcriptional regulatory circuitry in human embryonic stem cells

LA Boyer et al.

Article Biochemistry & Molecular Biology

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

A Siepel et al.

GENOME RESEARCH (2005)

Article Biochemical Research Methods

Finding short DNA motifs using permuted Markov models

XY Zhao et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2005)

Article Biochemical Research Methods

A boosting approach for motif modeling using ChIP-chip data

PY Hong et al.

BIOINFORMATICS (2005)

Article Multidisciplinary Sciences

De novo cis-regulatory module elicitation for eukaryotic genomes

M Gupta et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Identifying tissue-selective transcription factor bindings sites in vertebrate promoters

AD Smith et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Predicting gene expression from sequence

MA Beer et al.

Article Biochemical Research Methods

Modeling within-motif dependence for transcription factor binding site predictions

Q Zhou et al.

BIOINFORMATICS (2004)

Article Statistics & Probability

Computational discovery of gene regulatory binding motifs: A Bayesian perspective

ST Jensen et al.

STATISTICAL SCIENCE (2004)

Article Multidisciplinary Sciences

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

Q Zhou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Multidisciplinary Sciences

Interacting models of cooperative gene regulation

D Das et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

Decoding human regulatory circuits

W Thompson et al.

GENOME RESEARCH (2004)

Article Multidisciplinary Sciences

Integrating regulatory motif discovery and genome-wide expression analysis

EM Conlon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Biochemistry & Molecular Biology

TRANSFAC (R): transcriptional regulation, from patterns to profiles

V Matys et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Probabilistic code for DNA recognition by proteins of the EGR family

PV Benos et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Biochemical Research Methods

Identification of regulatory elements using a feature selection method

S Keles et al.

BIOINFORMATICS (2002)

Article Statistics & Probability

Greedy function approximation: A gradient boosting machine

JH Friedman

ANNALS OF STATISTICS (2001)

Article Biochemical Research Methods

Detection of cis-element clusters in higher eukaryotic DNA

MC Frith et al.

BIOINFORMATICS (2001)

Article Genetics & Heredity

Regulatory element detection using correlation with expression

HJ Bussemaker et al.

NATURE GENETICS (2001)