Systems Biology in the Context of Big Data and Networks

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

(2013) Yao Xu et al.   NATURE

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Systematization of the Protein Sequence Diversity in Enzymes Related to Secondary Metabolic Pathways in Plants, in the Context of Big Data Biology Inspired by the KNApSAcK Motorcycle Database

(2013) Shun Ikeda et al.   PLANT AND CELL PHYSIOLOGY

KNApSAcK Metabolite Activity Database for Retrieving the Relationships Between Metabolites and Biological Activities

(2013) Y. Nakamura et al.   PLANT AND CELL PHYSIOLOGY

Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases

(2013) Erika Asamizu et al.   PLANT AND CELL PHYSIOLOGY

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants

(2013) Takeshi Obayashi et al.   PLANT AND CELL PHYSIOLOGY

Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network

(2013) Jialiang Huang et al.   PLoS Computational Biology

DATA MINING METHODS FOR OMICS AND KNOWLEDGE OF CRUDE MEDICINAL PLANTS TOWARD BIG DATA BIOLOGY

(2013) Farit M. Afendi et al.   Computational and Structural Biotechnology Journal

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure

(2012) V. Reinharz et al.   BIOINFORMATICS

Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug

(2012) Hee Lee et al.   BMC Systems Biology

Studying protein complexes by the yeast two-hybrid system

(2012) Seesandra V. Rajagopala et al.   METHODS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling

(2011) Zhiyong Wang et al.   BIOINFORMATICS

GraphCrunch 2: Software tool for network modeling, alignment and clustering

(2011) Oleksii Kuchaiev et al.   BMC BIOINFORMATICS

PREDICT: a method for inferring novel drug indications with application to personalized medicine

(2011) A. Gottlieb et al.   Molecular Systems Biology

KNApSAcK Family Databases: Integrated Metabolite–Plant Species Databases for Multifaceted Plant Research

(2011) Farit Mochamad Afendi et al.   PLANT AND CELL PHYSIOLOGY

Predicting conformation of protein complexes by determining statistically significant domain-domain interactions

(2011) Kensaku Nishikata et al.   Plant Biotechnology

Computational approaches to 3D modeling of RNA

(2010) Christian Laing et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

DDBJ progress report

(2010) E. Kaminuma et al.   NUCLEIC ACIDS RESEARCH

Dynamics of Time-Lagged Gene-to-Metabolite Networks of Escherichia coli Elucidated by Integrative Omics Approach

(2010) Hiroki Takahashi et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Network-Based Relating Pharmacological and Genomic Spaces for Drug Target Identification

(2010) Shiwen Zhao et al.   PLoS One

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

Massively Parallel Sequencing: The Next Big Thing in Genetic Medicine

(2009) Tracy Tucker et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exploring biological network structure with clustered random networks

(2009) Shweta Bansal et al.   BMC BIOINFORMATICS

Disease candidate gene identification and prioritization using protein interaction networks

(2009) Jing Chen et al.   BMC BIOINFORMATICS

A core-attachment based method to detect protein complexes in PPI networks

(2009) Min Wu et al.   BMC BIOINFORMATICS

Predicting Protein Complexes from PPI Data: A Core-Attachment Approach

(2009) Henry C.M. Leung et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Human Disease-Drug Network Based on Genomic Expression Profiles

(2009) Guanghui Hu et al.   PLoS One

COMPUTER SCIENCE: Beyond the Data Deluge

(2009) G. Bell et al.   SCIENCE

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Keeping Up With the Next Generation

(2008) John R. ten Bosch et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Discovery and Scoring of Protein Interaction Subnetworks Discriminative of Late Stage Human Colon Cancer

(2008) Rod K. Nibbe et al.   MOLECULAR & CELLULAR PROTEOMICS