Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy

Early Steps in Autophagy Depend on Direct Phosphorylation of Atg9 by the Atg1 Kinase

(2014) Daniel Papinski et al.   MOLECULAR CELL

Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration

(2014) Tapesh Santra et al.   PLoS Computational Biology

SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

(2013) Dávid Fazekas et al.   BMC Systems Biology

Androgen receptor (AR) positive vs negative roles in prostate cancer cell deaths including apoptosis, anoikis, entosis, necrosis and autophagic cell death

(2013) Simeng Wen et al.   CANCER TREATMENT REVIEWS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Apoptosis and autophagy contribute to gender difference in cardiac ischemia–reperfusion induced injury in rats

(2013) Chen Chen et al.   LIFE SCIENCES

ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase

(2013) Ryan C. Russell et al.   NATURE CELL BIOLOGY

Emerging regulation and functions of autophagy

(2013) Patricia Boya et al.   NATURE CELL BIOLOGY

Autophagy in the brain of neonates following hypoxia–ischemia shows sex- and region-specific effects

(2013) S.N. Weis et al.   NEUROSCIENCE

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

(2013) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

Complex regulation of autophagy in cancer – Integrated approaches to discover the networks that hold a double-edged sword

(2013) János Kubisch et al.   SEMINARS IN CANCER BIOLOGY

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

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

MicroRNA regulation of autophagy

(2012) L. B. Frankel et al.   CARCINOGENESIS

miRDeathDB: a database bridging microRNAs and the programmed cell death

(2012) J Xu et al.   CELL DEATH AND DIFFERENTIATION

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

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

Autophagy, signaling and obesity

(2012) Vanessa J. Lavallard et al.   PHARMACOLOGICAL RESEARCH

Cell Surface Estrogen Receptor Alpha Is Upregulated during Subchronic Metabolic Stress and Inhibits Neuronal Cell Degeneration

(2012) Cristiana Barbati et al.   PLoS One

Autophagy Regulation and Integration with Cell Signaling

(2011) Anne Hamacher-Brady   ANTIOXIDANTS & REDOX SIGNALING

The acquisition of resistance to TNFα in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray

(2011) Etienne Moussay et al.   Autophagy

Rule-based multi-level modeling of cell biological systems

(2011) Carsten Maus et al.   BMC Systems Biology

Autophagy as a therapeutic target in cancer

(2011) Ning Chen et al.   CANCER BIOLOGY & THERAPY

Genome-wide Localization of SREBP-2 in Hepatic Chromatin Predicts a Role in Autophagy

(2011) Young-Kyo Seo et al.   Cell Metabolism

On the role of autophagy in human diseases: a gender perspective

(2011) Pasquale Lista et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

(2011) T. Vergoulis et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

TFEB Links Autophagy to Lysosomal Biogenesis

(2011) C. Settembre et al.   SCIENCE

A GRAPH-BASED SEMANTIC SIMILARITY MEASURE FOR THE GENE ONTOLOGY

(2011) MARCO A. ALVAREZ et al.   Journal of Bioinformatics and Computational Biology

Sex-related resistance to myocardial ischemia-reperfusion injury is associated with high constitutive ARC expression

(2010) Wobbe Bouma et al.   AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

PuTmiR: A database for extracting neighboring transcription factors of human microRNAs

(2010) Sanghamitra Bandyopadhyay et al.   BMC BIOINFORMATICS

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research

(2010) K. Homma et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

A structure filter for the Eukaryotic Linear Motif Resource

(2009) Allegra Via et al.   BMC BIOINFORMATICS

TransmiR: a transcription factor–microRNA regulation database

(2009) Juan Wang et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

The Negatome database: a reference set of non-interacting protein pairs

(2009) Pawel Smialowski et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

FoxO transcription factors in the maintenance of cellular homeostasis during aging

(2008) Dervis AM Salih et al.   CURRENT OPINION IN CELL BIOLOGY

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

(2008) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH

miR2Disease: a manually curated database for microRNA deregulation in human disease

(2008) Q. Jiang et al.   NUCLEIC ACIDS RESEARCH