John D. Aitchison

Institute for Systems Biology

Affiliated withInstitute for Systems Biology Center for Infectious Disease Research

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title Cited by 4	2009
Publication title Cited by 4	2017

Other Publications

Article	Year
A tense time for the nuclear envelope. Cell\| PubMed ID: 11853664	2002
Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast. Molecular and cellular biology\| PubMed ID: 11909949	2002
Transcriptome profiling to identify genes involved in peroxisome assembly and function. The Journal of cell biology\| PubMed ID: 12135984	2002
Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis\| PubMed ID: 12298092	2002
Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes. The Journal of cell biology\| PubMed ID: 12403813	2002
YHR150w and YDR479c encode peroxisomal integral membrane proteins involved in the regulation of peroxisome number, size, and distribution in Saccharomyces cerevisiae. The Journal of cell biology\| PubMed ID: 12707309	2003
Inventories to insights. The Journal of cell biology\| PubMed ID: 12743099	2003
Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae. The Journal of biological chemistry\| PubMed ID: 12794079	2003
Pex11-related proteins in peroxisome dynamics: a role for the novel peroxin Pex27p in controlling peroxisome size and number in Saccharomyces cerevisiae. Molecular biology of the cell\| PubMed ID: 14517321	2003
Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae. Molecular biology of the cell\| PubMed ID: 14617799	2004
Virtual gating and nuclear transport: the hole picture. Trends in cell biology\| PubMed ID: 14624840	2003
Cell cycle regulated transport controlled by alterations in the nuclear pore complex. Cell\| PubMed ID: 14697200	2003
Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import. Molecular and cellular biology\| PubMed ID: 15367670	2004
Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. The Journal of cell biology\| PubMed ID: 15596542	2004
Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein. The Biochemical journal\| PubMed ID: 15686447	2005
Proteomic and genomic characterization of chromatin complexes at a boundary. The Journal of cell biology\| PubMed ID: 15824130	2005
Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae. The Journal of cell biology\| PubMed ID: 15928207	2005
Interactions between Mad1p and the nuclear transport machinery in the yeast Saccharomyces cerevisiae. Molecular biology of the cell\| PubMed ID: 16000377	2005
A data integration methodology for systems biology: experimental verification. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16301536	2005
A data integration methodology for systems biology. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16301537	2005
The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control. The Journal of cell biology\| PubMed ID: 16365162	2005
The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner. The Journal of biological chemistry\| PubMed ID: 16520372	2006
Pex19p binds Pex30p and Pex32p at regions required for their peroxisomal localization but separate from their peroxisomal targeting signals. The Journal of biological chemistry\| PubMed ID: 16551610	2006
The peroxisomal membrane protein Inp2p is the peroxisome-specific receptor for the myosin V motor Myo2p of Saccharomyces cerevisiae. Developmental cell\| PubMed ID: 16678774	2006
Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism. Molecular systems biology\| PubMed ID: 16738555	2006
Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nature genetics\| PubMed ID: 16936734	2006
Studying nuclear protein import in yeast. Methods (San Diego, Calif.)\| PubMed ID: 16979507	2006
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. Molecular cell\| PubMed ID: 17157260	2006
The role of karyopherins in the regulated sumoylation of septins. The Journal of cell biology\| PubMed ID: 17403926	2007
Transcriptional responses to fatty acid are coordinated by combinatorial control. Molecular systems biology\| PubMed ID: 17551510	2007
Comprehensive analysis of diverse ribonucleoprotein complexes. Nature methods\| PubMed ID: 17922018	2007
Cell biology: pore puzzle. Nature\| PubMed ID: 18046388	2007
Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 18370030	2008
Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis. The Journal of cell biology\| PubMed ID: 18426976	2008
Saccharomyces cerevisiae Yta7 regulates histone gene expression. Genetics\| PubMed ID: 18493054	2008
Systems biology at the Institute for Systems Biology. Briefings in functional genomics & proteomics\| PubMed ID: 18579616	2008
Control of transcriptional variability by overlapping feed-forward regulatory motifs. Biophysical journal\| PubMed ID: 18621837	2008
Regulation of peroxisome dynamics. Current opinion in cell biology\| PubMed ID: 19188056	2009
Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes. Molecular and cellular biology\| PubMed ID: 19273605	2009
A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity. Molecular and cellular biology\| PubMed ID: 19581291	2009
Myosin-driven peroxisome partitioning in S. cerevisiae. The Journal of cell biology\| PubMed ID: 19687257	2009
A role for the karyopherin Kap123p in microtubule stability. Traffic (Copenhagen, Denmark)\| PubMed ID: 19761543	2009
Deterministic and stochastic models of genetic regulatory networks. Methods in enzymology\| PubMed ID: 19897099	2009
Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing. Nucleic acids research\| PubMed ID: 20008511	2010
Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. The Journal of biological chemistry\| PubMed ID: 20026609	2010
Systems cell biology of the mitotic spindle. The Journal of cell biology\| PubMed ID: 20065087	2010
GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Molecular systems biology\| PubMed ID: 20212525	2010
Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Molecular & cellular proteomics : MCP\| PubMed ID: 20395639	2010
QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. Journal of the American Society for Mass Spectrometry\| PubMed ID: 20451407	2010
Genome-wide analysis of effectors of peroxisome biogenesis. PloS one\| PubMed ID: 20694151	2010
Expression of the Salmonella spp. virulence factor SifA in yeast alters Rho1 activity on peroxisomes. Molecular biology of the cell\| PubMed ID: 20739463	2010
Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Molecular systems biology\| PubMed ID: 21206489	2011
Role of the nuclear envelope in genome organization and gene expression. Wiley interdisciplinary reviews. Systems biology and medicine\| PubMed ID: 21305702	2011
Faster, quantitative, and accurate precursor acquisition independent from ion count. Analytical chemistry\| PubMed ID: 21341720	2011
The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast. Molecular biology of the cell\| PubMed ID: 21441307	2011
Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues. PLoS computational biology\| PubMed ID: 21738459	2011
Statistical analysis of dynamic transcriptional regulatory network structure. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 21877289	2011
Mathematical modeling of biomolecular network dynamics. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 21877294	2011
A regression model approach to enable cell morphology correction in high-throughput flow cytometry. Molecular systems biology\| PubMed ID: 21952134	2011
Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Molecular & cellular proteomics : MCP\| PubMed ID: 22186714	2011
The yeast nuclear pore complex and transport through it. Genetics\| PubMed ID: 22419078	2012
NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions. PLoS biology\| PubMed ID: 22479148	2012
Asymmetric positive feedback loops reliably control biological responses. Molecular systems biology\| PubMed ID: 22531117	2012
A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses. Nature\| PubMed ID: 22982991	2012
Global analysis of condition-specific subcellular protein distribution and abundance. Molecular & cellular proteomics : MCP\| PubMed ID: 23349476	2013
Metallochaperones regulate intracellular copper levels. PLoS computational biology\| PubMed ID: 23349626	2013
Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23388641	2013
A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell\| PubMed ID: 23452847	2013
Multifunctional double-negative T cells in sooty mangabeys mediate T-helper functions irrespective of SIV infection. PLoS pathogens\| PubMed ID: 23825945	2013
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. Bioinformatics (Oxford, England)\| PubMed ID: 23832245	2013
Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic acids research\| PubMed ID: 24185701	2014
Peroxisomes take shape. Nature reviews. Molecular cell biology\| PubMed ID: 24263361	2013
Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature\| PubMed ID: 24284630	2014
Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity. Molecular biology of the cell\| PubMed ID: 24600046	2014
An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Molecular microbiology\| PubMed ID: 24612392	2014
The multifunctional nuclear pore complex: a platform for controlling gene expression. Current opinion in cell biology\| PubMed ID: 24657998	2014
Quantitative proteomic analysis of host-virus interactions reveals a role for Golgi brefeldin A resistance factor 1 (GBF1) in dengue infection. Molecular & cellular proteomics : MCP\| PubMed ID: 24855065	2014
Predicting antidisease immunity using proteome arrays and sera from children naturally exposed to malaria. Molecular & cellular proteomics : MCP\| PubMed ID: 25023128	2014
Systems cell biology. The Journal of cell biology\| PubMed ID: 25225336	2014
Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. BMC systems biology\| PubMed ID: 25881257	2015
Rapid, optimized interactomic screening. Nature methods\| PubMed ID: 25938370	2015
Signaling dynamics and peroxisomes. Current opinion in cell biology\| PubMed ID: 26042681	2015
Corrigendum: Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature\| PubMed ID: 26153856	2015
The interactome challenge. The Journal of cell biology\| PubMed ID: 26572620	2015
Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry. Journal of proteomics & bioinformatics\| PubMed ID: 26962293	2015
Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum. The Journal of biological chemistry\| PubMed ID: 27129769	2016
Severe adult malaria is associated with specific PfEMP1 adhesion types and high parasite biomass. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 27185931	2016
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell\| PubMed ID: 27453469	2016
Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression. Nucleic acids research\| PubMed ID: 27625397	2016
One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY! G3 (Bethesda, Md.)\| PubMed ID: 27856698	2017
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. PLoS computational biology\| PubMed ID: 28520713	2017
An indicator cell assay for blood-based diagnostics. PloS one\| PubMed ID: 28594877	2017