Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

(2012) Aaron K. Wong et al.   NUCLEIC ACIDS RESEARCH

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

A global genomic view of MIF knockdown-mediated cell cycle arrest

(2011) Lingfeng Liu et al.   CELL CYCLE

Two additional midline barriers function with midline lefty1 expression to maintain asymmetric Nodal signaling during left-right axis specification in zebrafish

(2011) K. F. Lenhart et al.   DEVELOPMENT

Zebrafish cardiac development requires a conserved secondary heart field

(2011) D. Hami et al.   DEVELOPMENT

Centriolar satellites are assembly points for proteins implicated in human ciliopathies, including oral-facial-digital syndrome 1

(2011) C. A. M. Lopes et al.   JOURNAL OF CELL SCIENCE

Birth Prevalence of Congenital Heart Disease Worldwide

(2011) Denise van der Linde et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Regression shrinkage and selection via the lasso: a retrospective

(2011) Robert Tibshirani   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

(2011) Sohyun Hwang et al.   Nature Protocols

PILGRM: an interactive data-driven discovery platform for expert biologists

(2011) C. S. Greene et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Def6 Is Required for Convergent Extension Movements during Zebrafish Gastrulation Downstream of Wnt5b Signaling

(2011) Katerina Goudevenou et al.   PLoS One

BioMart: driving a paradigm change in biological data management

(2011) A. Kasprzyk   Database-The Journal of Biological Databases and Curation

Accurate Quantification of Functional Analogy among Close Homologs

(2011) Maria D. Chikina et al.   PLoS Computational Biology

Bmp and Nodal Independently Regulate lefty1 Expression to Maintain Unilateral Nodal Activity during Left-Right Axis Specification in Zebrafish

(2011) Kelly A. Smith et al.   PLoS Genetics

Fast integration of heterogeneous data sources for predicting gene function with limited annotation

(2010) Sara Mostafavi et al.   BIOINFORMATICS

Sox17 and chordin are required for formation of Kupffer's vesicle and left-right asymmetry determination in zebrafish

(2010) Emil Aamar et al.   DEVELOPMENTAL DYNAMICS

Mutations in N-cadherin and a Stardust homolog, Nagie oko, affect cell-cycle exit in zebrafish retina

(2010) Masahiro Yamaguchi et al.   MECHANISMS OF DEVELOPMENT

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

(2010) D. Abdulrehman et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations

(2010) Yuanfang Guan et al.   PLoS Computational Biology

The Zn Finger protein Iguana impacts Hedgehog signaling by promoting ciliogenesis

(2009) Andrew M. Glazer et al.   DEVELOPMENTAL BIOLOGY

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

(2009) David C. Hess et al.   PLoS Genetics

The Sleipnir library for computational functional genomics

(2008) C. Huttenhower et al.   BIOINFORMATICS

Asymmetric Involution of the Myocardial Field Drives Heart Tube Formation in Zebrafish

(2008) Stefan Rohr et al.   CIRCULATION RESEARCH

Rotation and Asymmetric Development of the Zebrafish Heart Requires Directed Migration of Cardiac Progenitor Cells

(2008) Kelly A. Smith et al.   DEVELOPMENTAL CELL

Initiation and propagation of posterior to anterior (PA) waves in zebrafish left-right development

(2008) Xinghao Wang et al.   DEVELOPMENTAL DYNAMICS

Nodal signaling promotes the speed and directional movement of cardiomyocytes in zebrafish

(2008) Maria Ines Medeiros de Campos-Baptista et al.   DEVELOPMENTAL DYNAMICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Direct and indirect roles for Nodal signaling in two axis conversions during asymmetric morphogenesis of the zebrafish heart

(2008) K. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy

(2008) Wan Kim et al.   GENOME BIOLOGY

Predicting gene function in a hierarchical context with an ensemble of classifiers

(2008) Yuanfang Guan et al.   GENOME BIOLOGY

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

(2008) Lourdes Peña-Castillo et al.   GENOME BIOLOGY

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY