Constructing an integrated genetic and epigenetic cellular network for whole cellular mechanism using high-throughput next-generation sequencing data

On the Calculation of System Entropy in Nonlinear Stochastic Biological Networks

(2015) Bor-Sen Chen et al.   Entropy

Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis under a Natural Selection Scheme

(2015) Bor-Sen Chen et al.   Evolutionary Bioinformatics

Deregulation of Immune Response Genes in Patients With Epstein-Barr Virus-Associated Gastric Cancer and Outcomes

(2015) Sun Young Kim et al.   GASTROENTEROLOGY

Competition between RNA-binding proteins CELF1 and HuR modulates MYC translation and intestinal epithelium renewal

(2015) Lan Liu et al.   MOLECULAR BIOLOGY OF THE CELL

Robust sensorimotor control of human arm model under state-dependent noises, control-dependent noises and additive noises

(2015) Cheng-Wei Li et al.   NEUROCOMPUTING

Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data

(2015) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

Liver disease in menopause

(2015) Carla W Brady   WORLD JOURNAL OF GASTROENTEROLOGY

miR-145 mediates the antiproliferative and gene regulatory effects of vitamin D3 by directly targeting E2F3 in gastric cancer cells

(2015) Su’e Chang et al.   Oncotarget

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

The Interaction of RNA Helicase DDX3 with HIV-1 Rev-CRM1-RanGTP Complex during the HIV Replication Cycle

(2015) Seyed Hanif Mahboobi et al.   PLoS One

Canolol Inhibits Gastric Tumors Initiation and Progression through COX-2/PGE2 Pathway in K19-C2mE Transgenic Mice

(2015) Donghui Cao et al.   PLoS One

Identification and Replication of a Combined Epigenetic and Genetic Biomarker Predicting Suicide and Suicidal Behaviors

(2014) Jerry Guintivano et al.   AMERICAN JOURNAL OF PSYCHIATRY

Reciprocal activation between ATPase inhibitory factor 1 and NF-κB drives hepatocellular carcinoma angiogenesis and metastasis

(2014) Ruipeng Song et al.   HEPATOLOGY

Reduction of HIV-1 Infectivity through Endoplasmic Reticulum-Associated Degradation-Mediated Env Depletion

(2014) Antonio Casini et al.   JOURNAL OF VIROLOGY

microRNA-124 inhibits proliferation and induces apoptosis by directly repressing EZH2 in gastric cancer

(2014) Liming Xie et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

USP15 stabilizes MDM2 to mediate cancer-cell survival and inhibit antitumor T cell responses

(2014) Qiang Zou et al.   NATURE IMMUNOLOGY

The role of genetics and epigenetics in the pathogenesis of systemic sclerosis

(2014) Jasper C. A. Broen et al.   Nature Reviews Rheumatology

HIV-1 Vpr Induces Interferon-Stimulated Genes in Human Monocyte-Derived Macrophages

(2014) Muhammad Atif Zahoor et al.   PLoS One

Role of MicroRNA Modulation in the Interferon-α/Ribavirin Suppression of HIV-1 In Vivo

(2014) Mohamed Abdel-Mohsen et al.   PLoS One

HIV-1 Tat induces DNMT over-expression through microRNA dysregulation in HIV-related non Hodgkin lymphomas

(2014) Anna Luzzi et al.   Infectious Agents and Cancer

Expression of steroid receptor coactivator 3 in ovarian epithelial cancer is a poor prognostic factor and a marker for platinum resistance

(2013) C Palmieri et al.   BRITISH JOURNAL OF CANCER

miR-141, a new player, joins the senescence orchestra

(2013) Yoko Itahana et al.   CELL CYCLE

Microvesicle microRNA profiles and functional roles between chronic hepatitis B and hepatocellular carcinoma

(2013) H. Li et al.   Clinical & Translational Oncology

Integrated analysis of genome-wide genetic and epigenetic association data for identification of disease mechanisms

(2013) Xiayi Ke et al.   Epigenetics

microRNAs in gastric cancer invasion and metastasis

(2013) Xiaoning Zhao   Frontiers in Bioscience-Landmark

Design of synthetic biological logic circuits based on evolutionary algorithm

(2013) Chia-Hua Chuang et al.   IET Systems Biology

JMJD1C demethylates MDC1 to regulate the RNF8 and BRCA1–mediated chromatin response to DNA breaks

(2013) Sugiko Watanabe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MiR-10a* up-regulates coxsackievirus B3 biosynthesis by targeting the 3D-coding sequence

(2013) Lei Tong et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

TRAF2 is an NF-κB-activating oncogene in epithelial cancers

(2013) R R Shen et al.   ONCOGENE

Downregulation of the Mitochondrial Phosphatase PTPMT1 Is Sufficient to Promote Cancer Cell Death

(2013) Natalie M. Niemi et al.   PLoS One

The MAPK Pathway Signals Telomerase Modulation in Response to Isothiocyanate-Induced DNA Damage of Human Liver Cancer Cells

(2013) Evelyn Lamy et al.   PLoS One

Smg1 haploinsufficiency predisposes to tumor formation and inflammation

(2013) Tara L. Roberts et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PML mediates glioblastoma resistance to mammalian target of rapamycin (mTOR)-targeted therapies

(2013) Akio Iwanami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

17β-Estradiol inhibits HIV-1 by inducing a complex formation between β-catenin and estrogen receptor α on the HIV promoter to suppress HIV transcription

(2013) Erika L. Szotek et al.   VIROLOGY

Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression

(2013) Kathryn Miller-Jensen et al.   PLoS Computational Biology

24 Hours in the Life of HIV-1 in a T Cell Line

(2013) Pejman Mohammadi et al.   PLoS Pathogens

miR-182 and miR-10a Are Key Regulators of Treg Specialisation and Stability during Schistosome and Leishmania-associated Inflammation

(2013) Samir Kelada et al.   PLoS Pathogens

Illuminating Potential Technical Artifacts of DNA-Methylation Array Probes

(2012) John D. Blair et al.   AMERICAN JOURNAL OF HUMAN GENETICS

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

Integrated cellular network of transcription regulations and protein-protein interactions

(2012) Yu-Chao Wang et al.   BMC Systems Biology

Crosstalk between transcription factors and microRNAs in human protein interaction network

(2012) Chen-Ching Lin et al.   BMC Systems Biology

miR-101 is down-regulated by the hepatitis B virus x protein and induces aberrant DNA methylation by targeting DNA methyltransferase 3A

(2012) Xufu Wei et al.   CELLULAR SIGNALLING

Small Ubiquitin-like Modifier (SUMO) Modification of Zinc Finger Protein 131 Potentiates Its Negative Effect on Estrogen Signaling

(2012) Yohan Oh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

miRNA-145 Targets v-ets Erythroblastosis Virus E26 Oncogene Homolog 1 to Suppress the Invasion, Metastasis, and Angiogenesis of Gastric Cancer Cells

(2012) L. Zheng et al.   MOLECULAR CANCER RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

CTGC motifs within the HIV core promoter specify Tat-responsive pre-initiation complexes

(2012) Emmanuelle Wilhelm et al.   Retrovirology

Global cancer statistics

(2011) Ahmedin Jemal et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Sterol Regulatory Element-Binding Protein 2 Couples HIV-1 Transcription to Cholesterol Homeostasis and T Cell Activation

(2011) H. E. Taylor et al.   JOURNAL OF VIROLOGY

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tat RNA silencing suppressor activity contributes to perturbation of lymphocyte miRNA by HIV-1

(2011) Amy M Hayes et al.   Retrovirology

Rev-ing up post-transcriptional HIV-1 RNA expression

(2011) Venkat S.R.K. Yedavalli et al.   RNA Biology

Network integration meets network dynamics

(2010) Teresa M Przytycka et al.   BMC BIOLOGY

On the Interplay between Entropy and Robustness of Gene Regulatory Networks

(2010) Bor-Sen Chen et al.   Entropy

Down-regulated microRNA-152 induces aberrant DNA methylation in hepatitis B virus-related hepatocellular carcinoma by targeting DNA methyltransferase 1

(2010) Jinfeng Huang et al.   HEPATOLOGY

Nutlin-3 cooperates with doxorubicin to induce apoptosis of human hepatocellular carcinoma cells through p53 or p73 signaling pathways

(2010) Tongsen Zheng et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

RAF translocations expand cancer targets

(2010) Martin McMahon   NATURE MEDICINE

On the Noise-Enhancing Ability of Stochastic Hodgkin-Huxley Neuron Systems

(2010) Bor-Sen Chen et al.   NEURAL COMPUTATION

Robust Observer-Based Tracking Control of Hodgkin-Huxley Neuron Systems Under Environmental Disturbances

(2010) Bor-Sen Chen et al.   NEURAL COMPUTATION

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Constraints Acting on DDX3X Protein Potentially Interferes with Rev-Mediated Nuclear Export of HIV-1 RNA

(2010) Deepak Sharma et al.   PLoS One

Triplex-forming MicroRNAs Form Stable Complexes With HIV-1 Provirus and Inhibit its Replication

(2010) Mazhar Kanak et al.   APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

miRNA-regulated dynamics in circadian oscillator models

(2009) Amitabha Nandi et al.   BMC Systems Biology

System identification: DNA computing approach

(2009) Ching-Huei Huang et al.   ISA TRANSACTIONS

A Dynamic Stochastic Model of Frequency-Dependent Stress Fiber Alignment Induced by Cyclic Stretch

(2009) Hui-Ju Hsu et al.   PLoS One

ITFP: an integrated platform of mammalian transcription factors

(2008) G. Zheng et al.   BIOINFORMATICS

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The HIV-1 Rev Binding Family of Proteins: The Dog Proteins as a Study Model

(2008) Maria Panaro et al.   Endocrine Metabolic & Immune Disorders-Drug Targets