Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments

(2015) Ning Leng et al.   BIOINFORMATICS

Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop

(2015) Vladimir Yu. Kiselev et al.   NUCLEIC ACIDS RESEARCH

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis

(2015) Daniel Spies et al.   Computational and Structural Biotechnology Journal

TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information

(2014) Yongsoo Kim et al.   BIOINFORMATICS

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

(2014) Tarmo Äijö et al.   BIOINFORMATICS

timeClip: pathway analysis for time course data without replicates

(2014) Paolo Martini et al.   BMC BIOINFORMATICS

Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress

(2014) Kyuri Jo et al.   METHODS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Inference of dynamic networks using time-course data

(2013) Y. Kim et al.   BRIEFINGS IN BIOINFORMATICS

Differential Expression Analysis for Pathways

(2013) Winston A. Haynes et al.   PLoS Computational Biology

Role of PI3K-AKT-mTOR and Wnt Signaling Pathways in Transition of G1-S Phase of Cell Cycle in Cancer Cells

(2013) Lakshmipathi Vadlakonda et al.   Frontiers in Oncology

More power via graph-structured tests for differential expression of gene networks

(2012) Laurent Jacob et al.   Annals of Applied Statistics

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

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Along signal paths: an empirical gene set approach exploiting pathway topology

(2012) Paolo Martini et al.   NUCLEIC ACIDS RESEARCH

Disruption of epithelial architecture caused by loss of PTEN or by oncogenic mutant p110α/PIK3CA but not by HER2 or mutant AKT1

(2012) F M Berglund et al.   ONCOGENE

Pathway analysis of genomic data: concepts, methods, and prospects for future development

(2012) Vijay K. Ramanan et al.   TRENDS IN GENETICS

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Akt, FoxO and regulation of apoptosis

(2011) Xinbo Zhang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Cooperation between both Wnt/ -catenin and PTEN/PI3K/Akt signaling promotes primitive hematopoietic stem cell self-renewal and expansion

(2011) J. M. Perry et al.   GENES & DEVELOPMENT

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

GSA-SNP: a general approach for gene set analysis of polymorphisms

(2010) Dougu Nam et al.   NUCLEIC ACIDS RESEARCH

Coordination of Fc receptor signaling regulates cellular commitment to phagocytosis

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

Model-based method for transcription factor target identification with limited data

(2010) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

(2009) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Calmodulin modulates Akt activity in human breast cancer cell lines

(2008) Christine M. Coticchia et al.   BREAST CANCER RESEARCH AND TREATMENT