4.8 Article

DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool

Related references

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

Predicting DNA binding proteins using support vector machine with hybrid fractal features

Xiao-Hui Niu et al.

JOURNAL OF THEORETICAL BIOLOGY (2014)

Review Cell Biology

The structure, function and evolution of proteins that bind DNA and RNA

William H. Hudson et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Pfam: the protein families database

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Protein-DNA binding: complexities and multi-protein codes

Trevor Siggers et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemical Research Methods

A large-scale evaluation of computational protein function prediction

Predrag Radivojac et al.

NATURE METHODS (2013)

Review Biochemistry & Molecular Biology

Single-Stranded DNA-Binding Proteins: Multiple Domains for Multiple Functions

Thayne H. Dickey et al.

STRUCTURE (2013)

Review Plant Sciences

DNA-binding domains of plant-specific transcription factors: structure, function, and evolution

Kazuhiko Yamasaki et al.

TRENDS IN PLANT SCIENCE (2013)

Article Multidisciplinary Sciences

The tomato genome sequence provides insights into fleshy fruit evolution

Shusei Sato et al.

NATURE (2012)

Review Biochemistry & Molecular Biology

Transcription factors regulating the progression of monocot and dicot seed development

Pinky Agarwal et al.

BIOESSAYS (2011)

Article Biochemistry & Molecular Biology

Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex

Trevor Siggers et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Review Biochemistry & Molecular Biology

Transcription Dynamics in Plant Immunity

John W. Moore et al.

PLANT CELL (2011)

Article Multidisciplinary Sciences

iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model

Wei-Zhong Lin et al.

PLOS ONE (2011)

Article Computer Science, Artificial Intelligence

LIBSVM: A Library for Support Vector Machines

Chih-Chung Chang et al.

ACM TRANSACTIONS ON INTELLIGENT SYSTEMS AND TECHNOLOGY (2011)

Article Biochemistry & Molecular Biology

PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences

Yoichi Murakami et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

Boosting the prediction and understanding of DNA-binding domains from sequence

Robert E. Langlois et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

agriGO: a GO analysis toolkit for the agricultural community

Zhou Du et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Genetics & Heredity

Lineage-specific expansion of DNA-binding transcription factor families

Varodom Charoensawan et al.

TRENDS IN GENETICS (2010)

Article Biochemical Research Methods

AmiGO: online access to ontology and annotation data

Seth Carbon et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

QuickGO: a web-based tool for Gene Ontology searching

David Binns et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

DNA-Prot: Identification of DNA Binding Proteins from Protein Sequence Information using Random Forest

K. Krishna Kumar et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2009)

Article Biochemical Research Methods

A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome

Mu Gao et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Review Biochemistry & Molecular Biology

The zinc finger network of plants

S. Ciftci-Yilmaz et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2008)

Article Biochemical Research Methods

Classifying RNA-Binding Proteins Based on Electrostatic Properties

Shula Shazman et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Review Cell Biology

Predicting protein function from sequence and structure

David Lee et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2007)

Article Biochemical Research Methods

Identification of DNA-binding proteins using support vector machines and evolutionary profiles

Manish Kumar et al.

BMC BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

WoLF PSORT: protein localization predictor

Paul Horton et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biotechnology & Applied Microbiology

Predicting protein function by machine learning on amino acid sequences - a critical evaluation

Ali Al-Shahib et al.

BMC GENOMICS (2007)

Review Genetics & Heredity

The evolution of gene regulation by transcription factors and microRNAs

Kevin Chen et al.

NATURE REVIEWS GENETICS (2007)

Review Biochemistry & Molecular Biology

Protein families and RNA recognition

Y Chen et al.

FEBS JOURNAL (2005)

Article Biochemistry & Molecular Biology

Zinc finger proteins: new insights into structural and functional diversity

JH Laity et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2001)

Article Multidisciplinary Sciences

Arabidopsis transcription factors:: Genome-wide comparative analysis among eukaryotes

JL Riechmann et al.

SCIENCE (2000)

Article Multidisciplinary Sciences

The language of covalent histone modifications

BD Strahl et al.

NATURE (2000)