John D. Aitchison

A tense time for the nuclear envelope.

Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast.

Transcriptome profiling to identify genes involved in peroxisome assembly and function.

Approaching complete peroxisome characterization by gas-phase fractionation.

Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.

YHR150w and YDR479c encode peroxisomal integral membrane proteins involved in the regulation of peroxisome number, size, and distribution in Saccharomyces cerevisiae.

Inventories to insights.

Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae.

Pex11-related proteins in peroxisome dynamics: a role for the novel peroxin Pex27p in controlling peroxisome size and number in Saccharomyces cerevisiae.

Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae.

Virtual gating and nuclear transport: the hole picture.

Cell cycle regulated transport controlled by alterations in the nuclear pore complex.

Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import.

Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane.

Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein.

Proteomic and genomic characterization of chromatin complexes at a boundary.

Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae.

Interactions between Mad1p and the nuclear transport machinery in the yeast Saccharomyces cerevisiae.

A data integration methodology for systems biology: experimental verification.

A data integration methodology for systems biology.

The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control.

The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner.

Pex19p binds Pex30p and Pex32p at regions required for their peroxisomal localization but separate from their peroxisomal targeting signals.

The peroxisomal membrane protein Inp2p is the peroxisome-specific receptor for the myosin V motor Myo2p of Saccharomyces cerevisiae.

Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism.

Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast.

Studying nuclear protein import in yeast.

Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs.

The role of karyopherins in the regulated sumoylation of septins.

Transcriptional responses to fatty acid are coordinated by combinatorial control.

Comprehensive analysis of diverse ribonucleoprotein complexes.

Cell biology: pore puzzle.

Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes.

Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis.

Saccharomyces cerevisiae Yta7 regulates histone gene expression.

Systems biology at the Institute for Systems Biology.

Control of transcriptional variability by overlapping feed-forward regulatory motifs.

Regulation of peroxisome dynamics.

Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes.

A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity.

Myosin-driven peroxisome partitioning in S. cerevisiae.

A role for the karyopherin Kap123p in microtubule stability.

Deterministic and stochastic models of genetic regulatory networks.

Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing.

Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress.

Systems cell biology of the mitotic spindle.

GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome.

Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.

QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments.

Genome-wide analysis of effectors of peroxisome biogenesis.

Expression of the Salmonella spp. virulence factor SifA in yeast alters Rho1 activity on peroxisomes.

Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing.

Role of the nuclear envelope in genome organization and gene expression.

Faster, quantitative, and accurate precursor acquisition independent from ion count.

The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast.

Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.

Statistical analysis of dynamic transcriptional regulatory network structure.

Mathematical modeling of biomolecular network dynamics.

A regression model approach to enable cell morphology correction in high-throughput flow cytometry.

Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests.

The yeast nuclear pore complex and transport through it.

NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions.

Asymmetric positive feedback loops reliably control biological responses.

A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses.

Global analysis of condition-specific subcellular protein distribution and abundance.

Metallochaperones regulate intracellular copper levels.

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.

A role for the nucleoporin Nup170p in chromatin structure and gene silencing.

Multifunctional double-negative T cells in sooty mangabeys mediate T-helper functions irrespective of SIV infection.

PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.

Molecular mechanisms of system responses to novel stimuli are predictable from public data.

Peroxisomes take shape.

Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.

Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity.

An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation.

The multifunctional nuclear pore complex: a platform for controlling gene expression.

Quantitative proteomic analysis of host-virus interactions reveals a role for Golgi brefeldin A resistance factor 1 (GBF1) in dengue infection.

Predicting antidisease immunity using proteome arrays and sera from children naturally exposed to malaria.

Systems cell biology.

Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.

Rapid, optimized interactomic screening.

Signaling dynamics and peroxisomes.

Corrigendum: Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.

The interactome challenge.

Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry.

Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum.

Severe adult malaria is associated with specific PfEMP1 adhesion types and high parasite biomass.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.

Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression.

One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.

An indicator cell assay for blood-based diagnostics.