Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks

iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition

(2015) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

iPPI-Esml: An ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC

(2015) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

Impacts of Bioinformatics to Medicinal Chemistry

(2015) Kuo-Chen Chou   Medicinal Chemistry

Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

(2015) Wei Chen et al.   Molecular BioSystems

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

(2015) Weiwei Zhang et al.   GENOME BIOLOGY

iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition

(2014) Shou-Hui Guo et al.   BIOINFORMATICS

iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking

(2014) Yue-Nong Fan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components

(2014) Wang-Ren Qiu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

(2014) Ruifeng Xu et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

(2014) Hao Lin et al.   NUCLEIC ACIDS RESEARCH

iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach

(2014) Wang-Ren Qiu et al.   Biomed Research International

iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types

(2013) Xuan Xiao et al.   ANALYTICAL BIOCHEMISTRY

Long noncoding RNAs and the genetics of cancer

(2013) S W Cheetham et al.   BRITISH JOURNAL OF CANCER

Origins of aberrant DNA methylation in acute myeloid leukemia

(2013) T Schoofs et al.   LEUKEMIA

Some remarks on predicting multi-label attributes in molecular biosystems

(2013) Kuo-Chen Chou   Molecular BioSystems

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types

(2013) Zheng Wang et al.   PLoS One

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Methylation of human papillomavirus 16, 18, 31, and 45 L2 and L1 genes and the cellular DAPK gene: Considerations for use as biomarkers of the progression of cervical neoplasia

(2013) Mina Kalantari et al.   VIROLOGY

iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteineS-nitrosylation sites in proteins

(2013) Yan Xu et al.   PeerJ

Epigenetic reprogramming of cancer cells via targeted DNA methylation

(2012) Ashley G. Rivenbark et al.   Epigenetics

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

(2012) Altuna Akalin et al.   PLoS Genetics

iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites

(2011) Kuo-Chen Chou et al.   Molecular BioSystems

The functional role of long non-coding RNA in human carcinomas

(2011) Ewan A Gibb et al.   Molecular Cancer

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

(2010) Maria E. Figueroa et al.   CANCER CELL

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH