Regulatory network inferred using expression data of small sample size: application and validation in erythroid system

Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation

(2014) Fan Zhu et al.   BIOINFORMATICS

Predicting dynamic signaling network response under unseen perturbations

(2014) Fan Zhu et al.   BIOINFORMATICS

Developmental transcriptome analysis of human erythropoiesis

(2014) L. Shi et al.   HUMAN MOLECULAR GENETICS

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies

(2014) Lonnie Welch et al.   PLoS Computational Biology

Biased, Non-equivalent Gene-Proximal and -Distal Binding Motifs of Orphan Nuclear Receptor TR4 in Primary Human Erythroid Cells

(2014) Lihong Shi et al.   PLoS Genetics

Lysine-specific demethylase 1 is a therapeutic target for fetal hemoglobin induction

(2013) Lihong Shi et al.   NATURE MEDICINE

Lesion Area Detection Using Source Image Correlation Coefficient for CT Perfusion Imaging

(2013) Fan Zhu et al.   IEEE Journal of Biomedical and Health Informatics

An effective framework for reconstructing gene regulatory networks from genetical genomics data

(2012) R. J. Flassig et al.   BIOINFORMATICS

Parallel perfusion imaging processing using GPGPU

(2012) Fan Zhu et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

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

Computed tomography perfusion imaging denoising using Gaussian process regression

(2012) Fan Zhu et al.   PHYSICS IN MEDICINE AND BIOLOGY

Experimental Design for Parameter Estimation of Gene Regulatory Networks

(2012) Bernhard Steiert et al.   PLoS One

Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes

(2012) Yuanfang Guan et al.   PLoS Computational Biology

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana

(2011) Ana Pop et al.   BMC Systems Biology

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Nuclear Receptors TR2 and TR4 Recruit Multiple Epigenetic Transcriptional Corepressors That Associate Specifically with the Embryonic  -Type Globin Promoters in Differentiated Adult Erythroid Cells

(2011) S. Cui et al.   MOLECULAR AND CELLULAR BIOLOGY

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang et al.   NUCLEIC ACIDS RESEARCH

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

(2011) R. J. Prill et al.   Science Signaling

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data

(2010) Kevin Y. Yip et al.   PLoS One

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge

(2010) Patricia Menéndez et al.   PLoS One

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

(2010) Christopher Y. Park et al.   PLoS Computational Biology

Detailing regulatory networks through large scale data integration

(2009) C. Huttenhower et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

(2009) Tom Michoel et al.   BMC Systems Biology

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans

(2009) Maria D. Chikina et al.   PLoS Computational Biology

The Sleipnir library for computational functional genomics

(2008) C. Huttenhower et al.   BIOINFORMATICS

SIRENE: supervised inference of regulatory networks

(2008) F. Mordelet et al.   BIOINFORMATICS

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

Drug discovery approaches targeting the PI3K/Akt pathway in cancer

(2008) C Garcia-Echeverria et al.   ONCOGENE

A Genomewide Functional Network for the Laboratory Mouse

(2008) Yuanfang Guan et al.   PLoS Computational Biology

A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli

(2008) Jason Ernst et al.   PLoS Computational Biology