Integration of omic networks in a developmental atlas of maize

Genome-Wide Characterization ofcis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework ofOpaque2in Maize

(2015) Chaobin Li et al.   PLANT CELL

A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes

(2015) Caroline Marcon et al.   PLANT PHYSIOLOGY

Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast

(2015) Gábor Csárdi et al.   PLoS Genetics

Correlation of mRNA and protein abundance in the developing maize leaf

(2014) Lalit Ponnala et al.   PLANT JOURNAL

Parallel Proteomic and Phosphoproteomic Analyses of Successive Stages of Maize Leaf Development

(2013) M. R. Facette et al.   PLANT CELL

Reconstruction of protein networks from an atlas of maize seed proteotypes

(2013) J. W. Walley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

(2013) Katherine Noelani Chang et al.   eLife

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Unraveling the KNOTTED1 regulatory network in maize meristems

(2012) N. Bolduc et al.   GENES & DEVELOPMENT

Modification Site Localization Scoring: Strategies and Performance

(2012) Robert J. Chalkley et al.   MOLECULAR & CELLULAR PROTEOMICS

Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit

(2012) Katja Baerenfaller et al.   Molecular Systems Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas

(2012) H. Qiao et al.   SCIENCE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize

(2011) James C. Schnable et al.   PLoS One

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

Refinements to Label Free Proteome Quantitation: How to Deal with Peptides Shared by Multiple Proteins

(2010) Ying Zhang et al.   ANALYTICAL CHEMISTRY

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

The control of axillary meristem fate in the maize ramosa pathway

(2010) A. Gallavotti et al.   DEVELOPMENT

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

(2008) A. Yilmaz et al.   PLANT PHYSIOLOGY

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE

Geometric Interpretation of Gene Coexpression Network Analysis

(2008) Steve Horvath et al.   PLoS Computational Biology