iEnhancer-RF: Identifying enhancers and their strength by enhanced feature representation using random forest

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

(2020) Zohar Shipony et al.   NATURE METHODS

A Pretraining-Retraining Strategy of Deep Learning Improves Cell-Specific Enhancer Predictions

(2020) Xiaohui Niu et al.   Frontiers in Genetics

AE-LGBM: Sequence-based novel approach to detect interacting protein pairs via ensemble of autoencoder and LightGBM

(2020) Abhibhav Sharma et al.   COMPUTERS IN BIOLOGY AND MEDICINE

PyFeat: A Python-based Effective Feature Generation Tool for DNA, RNA, and Protein Sequences

(2019) Rafsanjani Muhammod et al.   BIOINFORMATICS

Iterative feature representations improve N4-methylcytosine site prediction

(2019) Leyi Wei et al.   BIOINFORMATICS

A dense initialization for limited-memory quasi-Newton methods

(2019) Johannes Brust et al.   COMPUTATIONAL OPTIMIZATION AND APPLICATIONS

Predicting subcellular localization of multisite proteins using differently weighted multi-label k-nearest neighbors sets

(2019) Zhongting Jiang et al.   TECHNOLOGY AND HEALTH CARE

dForml(KNN)-PseAAC: Detecting formylation sites from protein sequences using K-nearest neighbor algorithm via Chou's 5-step rule and pseudo components

(2019) Qiao Ning et al.   JOURNAL OF THEORETICAL BIOLOGY

Introducing of an integrated artificial neural network and Chou's pseudo amino acid composition approach for computational epitope-mapping of Crimean-Congo haemorrhagic fever virus antigens

(2019) Mokhtar Nosrati et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

Paclitaxel Response Can Be Predicted With Interpretable Multi-Variate Classifiers Exploiting DNA-Methylation and miRNA Data

(2019) Alexandra Bomane et al.   Frontiers in Genetics

iProtease-PseAAC(2L): A two-layer predictor for identifying proteases and their types using Chou's 5-step-rule and general PseAAC

(2019) Yaser Daanial Khan et al.   ANALYTICAL BIOCHEMISTRY

DeepDRBP-2L: A New Genome Annotation Predictor for Identifying DNA-Binding Proteins and RNA-Binding Proteins Using Convolutional Neural Network and Long Short-Term Memory

(2019) Jun Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

iEnhancer-EL: Identifying enhancers and their strength with ensemble learning approach

(2018) Bin Liu et al.   BIOINFORMATICS

Integrating ChIP-seq with other functional genomics data

(2018) Shan Jiang et al.   Briefings in Functional Genomics

TOBMI: Trans-omics block missing data imputation using a k-Nearest Neighbor weighted approach

(2018) Xuesi Dong et al.   BIOINFORMATICS

LVQ-KNN: Composition-based DNA/RNA binning of short nucleotide sequences utilizing a prototype-based k-nearest neighbor approach

(2018) Ariane Belka et al.   VIRUS RESEARCH

EnhancerPred2.0: predicting enhancers and their strength based on position-specific trinucleotide propensity and electron–ion interaction potential feature selection

(2017) Wenying He et al.   Molecular BioSystems

NNAlign: a platform to construct and evaluate artificial neural network models of receptor–ligand interactions

(2017) Morten Nielsen et al.   NUCLEIC ACIDS RESEARCH

EnhancerPred: a predictor for discovering enhancers based on the combination and selection of multiple features

(2016) Cangzhi Jia et al.   Scientific Reports

iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudok-tuple nucleotide composition

(2015) Bin Liu et al.   BIOINFORMATICS

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

DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications

(2015) Yiming Lu et al.   PLoS One

Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome

(2015) Wei Chen et al.   Scientific Reports

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

Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis

(2014) Hui Ding et al.   Molecular BioSystems

Enhancer Function: Mechanistic and Genome-Wide Insights Come Together

(2014) Jennifer L. Plank et al.   MOLECULAR CELL

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

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

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

(2014) Genevieve D. Erwin et al.   PLoS Computational Biology

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis

(2013) Chuanxin Zou et al.   BMC BIOINFORMATICS

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

(2013) Karin J. Ferrari et al.   MOLECULAR CELL

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines

(2012) Michael Fernández et al.   NUCLEIC ACIDS RESEARCH

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Discover regulatory DNA elements using chromatin signatures and artificial neural network

(2010) Hiram A. Firpi et al.   BIOINFORMATICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS