Ideker Lab - UC San Diego
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1 News 161 Publications 32 Members

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate.

Lin, Yin C Jhunjhunwala, Suchit Benner, Christopher Heinz, Sven Welinder, Eva Mansson, Robert Sigvardsson, Mikael Hagman, James Espinoza, Celso A Dutkowski, Janusz ...

Published in Nature immunology

It is now established that the transcription factors E2A, EBF1 and Foxo1 have critical roles in B cell development. Here we show that E2A and EBF1 bound regulatory elements present in the Foxo1 locus. E2A and EBF1, as well as E2A and Foxo1, in turn, were wired together by a vast spectrum of cis-regulatory sequences. These associations were dynamic ...

Genome-wide profiling of salt fractions maps physical properties of chromatin.

Henikoff, Steven Henikoff, Jorja G Sakai, Akiko Loeb, Gabriel B Ahmad, Kami

Published in Genome research

We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosome...

Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.

K, Lee D, Thorneycroft P, Achuthan H, Hermjakob T, Ideker

Published in The Plant Cell

Most cellular processes are enabled by cohorts of interacting proteins that form dynamic networks within the plant proteome. The study of these networks can provide insight into protein function and provide new avenues for research. This article informs the plant science community of the currently available sources of protein interaction data and d...

A decade of systems biology.

Chuang, Han-Yu Hofree, Matan Ideker, Trey

Published in Annual review of cell and developmental biology

Systems biology provides a framework for assembling models of biological systems from systematic measurements. Since the field was first introduced a decade ago, considerable progress has been made in technologies for global cell measurement and in computational analyses of these data to map and model cell function. It has also greatly expanded int...

Integrative systems biology

Bandyopadhyay, S Trey Ideker

Published in Nature Genetics

An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neur...

M, Gersten M, Alirezaei Mc, Marcondes C, Flynn T, Ravasi T, Ideker Hs, Fox

Published in Journal of Neuroscience

Human immunodeficiency virus (HIV)-associated dementia (HAD) is a syndrome occurring in HIV-infected patients with advanced disease that likely develops as a result of macrophage and microglial activation as well as other immune events triggered by virus in the central nervous system. The most relevant experimental model of HAD, rhesus macaques exh...

Cost-effective strategies for completing the interactome.

As, Schwartz J, Yu Kr, Gardenour Jr, Finley Rl T, Ideker

Published in Nature Methods

Comprehensive protein-interaction mapping projects are underway for many model species and humans. A key step in these projects is estimating the time, cost and personnel required for obtaining an accurate and complete map. Here we modeled the cost of interaction-map completion for various experimental designs. We showed that current efforts may re...

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export... PDF available through Get Fulltext Research

Gm, Wilmes M, Bergkessel S, Bandyopadhyay M, Shales H, Braberg G, Cagney Sr, Collins Gb, Whitworth Tl, Kress Js, Weissman ...

Published in Molecular Cell

We used a quantitative, high-density genetic interaction map, or E-MAP (Epistatic MiniArray Profile), to interrogate the relationships within and between RNA-processing pathways. Due to their complexity and the essential roles of many of the components, these pathways have been difficult to functionally dissect. Here, we report the results for 107,...

Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. PDF available through Get Fulltext Research

Lee, Kiyoung Chuang, Han-Yu Beyer, Andreas Sung, Min-Kyung Huh, Won-Ki Lee, Bonghee Ideker, Trey

Published in Nucleic acids research

The function of a protein is intimately tied to its subcellular localization. Although localizations have been measured for many yeast proteins through systematic GFP fusions, similar studies in other branches of life are still forthcoming. In the interim, various machine-learning methods have been proposed to predict localization using physical ch...

Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. PDF available through Get Fulltext Research

R, König Y, Zhou D, Elleder Tl, Diamond Gm, Bonamy Jt, Irelan Cy, Chiang Bp, Tu Pd, De Jesus Ce, Lilley ...

Published in Cell

Human Immunodeficiency Viruses (HIV-1 and HIV-2) rely upon host-encoded proteins to facilitate their replication. Here, we combined genome-wide siRNA analyses with interrogation of human interactome databases to assemble a host-pathogen biochemical network containing 213 confirmed host cellular factors and 11 HIV-1-encoded proteins. Protein complex...

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