DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery

6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes

(2020) Haodong Xu et al.   BIOINFORMATICS

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network

(2020) Guangsheng Pei et al.   ONCOGENE

Integration of A Deep Learning Classifier with A Random Forest Approach for Predicting Malonylation Sites

(2019) Zhen Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

MicroRNA-374a, -4680, and -133b suppress cell proliferation through the regulation of genes associated with human cleft palate in cultured human palate cells

(2019) Akiko Suzuki et al.   BMC Medical Genomics

Epigenetic inactivation of LHX6 mediated microcystin-LR induced hepatocarcinogenesis via the Wnt/β-catenin and P53 signaling pathways

(2019) Hong-qiang Chen et al.   ENVIRONMENTAL POLLUTION

VISDB: a manually curated database of viral integration sites in the human genome

(2019) Deyou Tang et al.   NUCLEIC ACIDS RESEARCH

pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks

(2018) Stefan Budach et al.   BIOINFORMATICS

Deep Learning and Its Applications in Biomedicine

(2018) Chensi Cao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning

(2018) Yubin Xie et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

DeepHINT: understanding HIV-1 integration via deep learning with attention

(2018) Hailin Hu et al.   BIOINFORMATICS

HOXB7 accelerates the malignant progression of hepatocellular carcinoma by promoting stemness and epithelial-mesenchymal transition

(2017) Hong-bo Huan et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Analysis of Plasma Epstein–Barr Virus DNA to Screen for Nasopharyngeal Cancer

(2017) K.C. Allen Chan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Dysfunction of IKZF1/MYC/MDIG axis contributes to liver cancer progression through regulating H3K9me3/p21 activity

(2017) Qi Huo et al.   Cell Death & Disease

HOXB7 promotes tumor progression via bFGF-induced activation of MAPK/ERK pathway and indicated poor prognosis in hepatocellular carcinoma

(2017) Wei-Min Wang et al.   Oncotarget

Generalising Ward’s Method for Use with Manhattan Distances

(2017) Trudie Strauss et al.   PLoS One

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma

(2016) Ling-Hao Zhao et al.   Nature Communications

Human Papillomavirus Carcinogenesis: an Identity Crisis in the Retinoblastoma Tumor Suppressor Pathway

(2015) Karl Munger et al.   JOURNAL OF VIROLOGY

Identification of MEF2B , EBF1 , and IL6R as Direct Gene Targets of Epstein-Barr Virus (EBV) Nuclear Antigen 1 Critical for EBV-Infected B-Lymphocyte Survival

(2015) Italo Tempera et al.   JOURNAL OF VIROLOGY

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism

(2015) Zheng Hu et al.   NATURE GENETICS

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization

(2015) Qingguo Wang et al.   Genome Medicine

Viral Carcinogenesis: Factors Inducing DNA Damage and Virus Integration

(2014) Yan Chen et al.   Cancers

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Reactivation of hepatitis B virus and hepatitis C virus in patients with cancer

(2012) Harrys A. Torres et al.   Nature Reviews Clinical Oncology

Recurrent Targeted Genes of Hepatitis B Virus in the Liver Cancer Genomes Identified by a Next-Generation Sequencing–Based Approach

(2012) Dong Ding et al.   PLoS Genetics

Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

(2011) Luisa Barzon et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Hybrid Capture and Next-Generation Sequencing Identify Viral Integration Sites from Formalin-Fixed, Paraffin-Embedded Tissue

(2011) Eric J. Duncavage et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

(2011) David Sims et al.   GENOME BIOLOGY

Mechanisms of HBV-related hepatocarcinogenesis

(2010) Christine Neuveut et al.   JOURNAL OF HEPATOLOGY

HPV-associated head and neck cancer: a virus-related cancer epidemic

(2010) Shanthi Marur et al.   LANCET ONCOLOGY

Interferon regulatory factor (IRF)-2 activates the HPV-16 E6–E7 promoter in keratinocytes

(2010) Michael J. Lace et al.   VIROLOGY

Human tumor-associated viruses and new insights into the molecular mechanisms of cancer

(2009) D Martin et al.   ONCOGENE

Molecular mechanisms of cervical carcinogenesis by high-risk human papillomaviruses: novel functions of E6 and E7 oncoproteins

(2009) Takashi Yugawa et al.   REVIEWS IN MEDICAL VIROLOGY

Persistent activation of an innate immune response translates respiratory viral infection into chronic lung disease

(2008) Edy Y Kim et al.   NATURE MEDICINE