A new method to improve network topological similarity search: applied to fold recognition

Global view of the protein universe

(2014) S. Nepomnyachiy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

(2014) Jianzhu Ma et al.   PLoS Computational Biology

Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses

(2013) U. Martin Singh-Blom et al.   PLoS One

A single source k-shortest paths algorithm to infer regulatory pathways in a gene network

(2012) Yu-Keng Shih et al.   BIOINFORMATICS

A conditional neural fields model for protein threading

(2012) Jianzhu Ma et al.   BIOINFORMATICS

gbase: an efficient analysis platform for large graphs

(2012) U Kang et al.   VLDB JOURNAL

Uncover disease genes by maximizing information flow in the phenome-interactome network

(2011) Y. Chen et al.   BIOINFORMATICS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

In Silico Gene Prioritization by Integrating Multiple Data Sources

(2011) Yixuan Chen et al.   PLoS One

Genome-wide inferring gene–phenotype relationship by walking on the heterogeneous network

(2010) Yongjin Li et al.   BIOINFORMATICS

On the evolutionary origins of “Fold Space Continuity”: A study of topological convergence and divergence in mixed alpha-beta domains

(2010) M.I. Sadowski et al.   JOURNAL OF STRUCTURAL BIOLOGY

Protein interface conservation across structure space

(2010) Q. C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systems Pharmacology of Arrhythmias

(2010) S. I. Berger et al.   Science Signaling

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

Predicting genetic interactions with random walks on biological networks

(2009) Kyle C Chipman et al.   BMC BIOINFORMATICS

Discrete–continuous duality of protein structure space

(2009) Ruslan I Sadreyev et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

Structural relationships among proteins with different global topologies and their implications for function annotation strategies

(2009) D. Petrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nature of the protein universe

(2009) M. Levitt   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The continuity of protein structure space is an intrinsic property of proteins

(2009) J. Skolnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation

(2009) Alberto Pascual-García et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

(2009) Alberto Pascual-García et al.   PLoS Computational Biology

Simultaneous inference: When should hypothesis testing problems be combined?

(2008) Bradley Efron   Annals of Applied Statistics

RANKPROP: a web server for protein remote homology detection

(2008) I. Melvin et al.   BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA