John D. Aitchison Institute for Systems Biology Biography Publications Institution JoVE Articles John D. Aitchison has not added a biography. If you are John D. Aitchison and would like to personalize this page please email our Author Liaison for assistance. Publications An Indicator Cell Assay for Blood-based Diagnostics PloS One. 2017 | Pubmed ID: 28594877 Combining Inferred Regulatory and Reconstructed Metabolic Networks Enhances Phenotype Prediction in Yeast PLoS Computational Biology. May, 2017 | Pubmed ID: 28520713 One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY! G3 (Bethesda, Md.). Jan, 2017 | Pubmed ID: 27856698 Co-dependence Between Trypanosome Nuclear Lamina Components in Nuclear Stability and Control of Gene Expression Nucleic Acids Research. Sep, 2016 | Pubmed ID: 27625397 Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome Cell. Jul, 2016 | Pubmed ID: 27453469 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. Jun, 2016 | Pubmed ID: 27185931 Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum The Journal of Biological Chemistry. Jul, 2016 | Pubmed ID: 27129769 Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry Journal of Proteomics & Bioinformatics. 2015 | Pubmed ID: 26962293 The Interactome Challenge The Journal of Cell Biology. Nov, 2015 | Pubmed ID: 26572620 Corrigendum: Pan-viral Specificity of IFN-induced Genes Reveals New Roles for CGAS in Innate Immunity Nature. Sep, 2015 | Pubmed ID: 26153856 Signaling Dynamics and Peroxisomes Current Opinion in Cell Biology. Aug, 2015 | Pubmed ID: 26042681 Rapid, Optimized Interactomic Screening Nature Methods. Jun, 2015 | Pubmed ID: 25938370 Bicluster Sampled Coherence Metric (BSCM) Provides an Accurate Environmental Context for Phenotype Predictions BMC Systems Biology. 2015 | Pubmed ID: 25881257 Systems Cell Biology The Journal of Cell Biology. Sep, 2014 | Pubmed ID: 25225336 Predicting Antidisease Immunity Using Proteome Arrays and Sera from Children Naturally Exposed to Malaria Molecular & Cellular Proteomics : MCP. Oct, 2014 | Pubmed ID: 25023128 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. Nov, 2014 | Pubmed ID: 24855065 The Multifunctional Nuclear Pore Complex: a Platform for Controlling Gene Expression Current Opinion in Cell Biology. Jun, 2014 | Pubmed ID: 24657998 An Evolutionarily Conserved RNase-based Mechanism for Repression of Transcriptional Positive Autoregulation Molecular Microbiology. Apr, 2014 | Pubmed ID: 24612392 Nuclear Pore Complex Evolution: a Trypanosome Mlp Analogue Functions in Chromosomal Segregation but Lacks Transcriptional Barrier Activity Molecular Biology of the Cell. May, 2014 | Pubmed ID: 24600046 Pan-viral Specificity of IFN-induced Genes Reveals New Roles for CGAS in Innate Immunity Nature. Jan, 2014 | Pubmed ID: 24284630 Molecular Mechanisms of System Responses to Novel Stimuli Are Predictable from Public Data Nucleic Acids Research. Feb, 2014 | Pubmed ID: 24185701 Peroxisomes Take Shape Nature Reviews. Molecular Cell Biology. Dec, 2013 | Pubmed ID: 24263361 PhosphoChain: a Novel Algorithm to Predict Kinase and Phosphatase Networks from High-throughput Expression Data Bioinformatics (Oxford, England). Oct, 2013 | Pubmed ID: 23832245 Multifunctional Double-negative T Cells in Sooty Mangabeys Mediate T-helper Functions Irrespective of SIV Infection PLoS Pathogens. 2013 | Pubmed ID: 23825945 A Role for the Nucleoporin Nup170p in Chromatin Structure and Gene Silencing Cell. Feb, 2013 | Pubmed ID: 23452847 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. Feb, 2013 | Pubmed ID: 23388641 Metallochaperones Regulate Intracellular Copper Levels PLoS Computational Biology. 2013 | Pubmed ID: 23349626 Global Analysis of Condition-specific Subcellular Protein Distribution and Abundance Molecular & Cellular Proteomics : MCP. May, 2013 | Pubmed ID: 23349476 A FOXO3-IRF7 Gene Regulatory Circuit Limits Inflammatory Sequelae of Antiviral Responses Nature. Oct, 2012 | Pubmed ID: 22982991 Asymmetric Positive Feedback Loops Reliably Control Biological Responses Molecular Systems Biology. Apr, 2012 | Pubmed ID: 22531117 NUP-1 Is a Large Coiled-coil Nucleoskeletal Protein in Trypanosomes with Lamin-like Functions PLoS Biology. 2012 | Pubmed ID: 22479148 The Yeast Nuclear Pore Complex and Transport Through It Genetics. Mar, 2012 | Pubmed ID: 22419078 Nanospray FAIMS Fractionation Provides Significant Increases in Proteome Coverage of Unfractionated Complex Protein Digests Molecular & Cellular Proteomics : MCP. Dec, 2011 | Pubmed ID: 22186714 A Regression Model Approach to Enable Cell Morphology Correction in High-throughput Flow Cytometry Molecular Systems Biology. 2011 | Pubmed ID: 21952134 Mathematical Modeling of Biomolecular Network Dynamics Methods in Molecular Biology (Clifton, N.J.). 2011 | Pubmed ID: 21877294 Statistical Analysis of Dynamic Transcriptional Regulatory Network Structure Methods in Molecular Biology (Clifton, N.J.). 2011 | Pubmed ID: 21877289 Trade-off Between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues PLoS Computational Biology. Jun, 2011 | Pubmed ID: 21738459 The Peroxin Pex34p Functions with the Pex11 Family of Peroxisomal Divisional Proteins to Regulate the Peroxisome Population in Yeast Molecular Biology of the Cell. May, 2011 | Pubmed ID: 21441307 Faster, Quantitative, and Accurate Precursor Acquisition Independent from Ion Count Analytical Chemistry. Mar, 2011 | Pubmed ID: 21341720 Role of the Nuclear Envelope in Genome Organization and Gene Expression Wiley Interdisciplinary Reviews. Systems Biology and Medicine. Mar-Apr, 2011 | Pubmed ID: 21305702 Environment-responsive Transcription Factors Bind Subtelomeric Elements and Regulate Gene Silencing Molecular Systems Biology. Jan, 2011 | Pubmed ID: 21206489 Expression of the Salmonella Spp. Virulence Factor SifA in Yeast Alters Rho1 Activity on Peroxisomes Molecular Biology of the Cell. Oct, 2010 | Pubmed ID: 20739463 Genome-wide Analysis of Effectors of Peroxisome Biogenesis PloS One. 2010 | Pubmed ID: 20694151 QTIPS: a Novel Method of Unsupervised Determination of Isotopic Amino Acid Distribution in SILAC Experiments Journal of the American Society for Mass Spectrometry. Aug, 2010 | Pubmed ID: 20451407 Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction Molecular & Cellular Proteomics : MCP. Sep, 2010 | Pubmed ID: 20395639 GINS Motion Reveals Replication Fork Progression is Remarkably Uniform Throughout the Yeast Genome Molecular Systems Biology. 2010 | Pubmed ID: 20212525 Systems Cell Biology of the Mitotic Spindle The Journal of Cell Biology. Jan, 2010 | Pubmed ID: 20065087 Dynamic Changes in the Subcellular Distribution of Gpd1p in Response to Cell Stress The Journal of Biological Chemistry. Feb, 2010 | Pubmed ID: 20026609 Histone Chaperone Chz1p Regulates H2B Ubiquitination and Subtelomeric Anti-silencing Nucleic Acids Research. Mar, 2010 | Pubmed ID: 20008511 Deterministic and Stochastic Models of Genetic Regulatory Networks Methods in Enzymology. 2009 | Pubmed ID: 19897099 A Role for the Karyopherin Kap123p in Microtubule Stability Traffic (Copenhagen, Denmark). Nov, 2009 | Pubmed ID: 19761543 Myosin-driven Peroxisome Partitioning in S. Cerevisiae The Journal of Cell Biology. Aug, 2009 | Pubmed ID: 19687257 A Noncanonical Bromodomain in the AAA ATPase Protein Yta7 Directs Chromosomal Positioning and Barrier Chromatin Activity Molecular and Cellular Biology. Sep, 2009 | Pubmed ID: 19581291 Role of the Histone Variant H2A.Z/Htz1p in TBP Recruitment, Chromatin Dynamics, and Regulated Expression of Oleate-responsive Genes Molecular and Cellular Biology. May, 2009 | Pubmed ID: 19273605 Regulation of Peroxisome Dynamics Current Opinion in Cell Biology. Feb, 2009 | Pubmed ID: 19188056 Control of Transcriptional Variability by Overlapping Feed-forward Regulatory Motifs Biophysical Journal. Oct, 2008 | Pubmed ID: 18621837 Systems Biology at the Institute for Systems Biology Briefings in Functional Genomics & Proteomics. Jul, 2008 | Pubmed ID: 18579616 Saccharomyces Cerevisiae Yta7 Regulates Histone Gene Expression Genetics. May, 2008 | Pubmed ID: 18493054 Genome-wide Analysis of Signaling Networks Regulating Fatty Acid-induced Gene Expression and Organelle Biogenesis The Journal of Cell Biology. Apr, 2008 | Pubmed ID: 18426976 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.). 2008 | Pubmed ID: 18370030 Cell Biology: Pore Puzzle Nature. Nov, 2007 | Pubmed ID: 18046388 Comprehensive Analysis of Diverse Ribonucleoprotein Complexes Nature Methods. Nov, 2007 | Pubmed ID: 17922018 Transcriptional Responses to Fatty Acid Are Coordinated by Combinatorial Control Molecular Systems Biology. 2007 | Pubmed ID: 17551510 The Role of Karyopherins in the Regulated Sumoylation of Septins The Journal of Cell Biology. Apr, 2007 | Pubmed ID: 17403926 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. Dec, 2006 | Pubmed ID: 17157260 Studying Nuclear Protein Import in Yeast Methods (San Diego, Calif.). Aug, 2006 | Pubmed ID: 16979507 Dual Feedback Loops in the GAL Regulon Suppress Cellular Heterogeneity in Yeast Nature Genetics. Sep, 2006 | Pubmed ID: 16936734 Expression and Functional Profiling Reveal Distinct Gene Classes Involved in Fatty Acid Metabolism Molecular Systems Biology. 2006 | Pubmed ID: 16738555 The Peroxisomal Membrane Protein Inp2p is the Peroxisome-specific Receptor for the Myosin V Motor Myo2p of Saccharomyces Cerevisiae Developmental Cell. May, 2006 | Pubmed ID: 16678774 Pex19p Binds Pex30p and Pex32p at Regions Required for Their Peroxisomal Localization but Separate from Their Peroxisomal Targeting Signals The Journal of Biological Chemistry. May, 2006 | Pubmed ID: 16551610 The Dynamin-like Protein Vps1p of the Yeast Saccharomyces Cerevisiae Associates with Peroxisomes in a Pex19p-dependent Manner The Journal of Biological Chemistry. May, 2006 | Pubmed ID: 16520372 The Mobile Nucleoporin Nup2p and Chromatin-bound Prp20p Function in Endogenous NPC-mediated Transcriptional Control The Journal of Cell Biology. Dec, 2005 | Pubmed ID: 16365162 A Data Integration Methodology for Systems Biology Proceedings of the National Academy of Sciences of the United States of America. Nov, 2005 | Pubmed ID: 16301537 A Data Integration Methodology for Systems Biology: Experimental Verification Proceedings of the National Academy of Sciences of the United States of America. Nov, 2005 | Pubmed ID: 16301536 Interactions Between Mad1p and the Nuclear Transport Machinery in the Yeast Saccharomyces Cerevisiae Molecular Biology of the Cell. Sep, 2005 | Pubmed ID: 16000377 Inp1p is a Peroxisomal Membrane Protein Required for Peroxisome Inheritance in Saccharomyces Cerevisiae The Journal of Cell Biology. Jun, 2005 | Pubmed ID: 15928207 Proteomic and Genomic Characterization of Chromatin Complexes at a Boundary The Journal of Cell Biology. Apr, 2005 | Pubmed ID: 15824130 Nop53p is a Novel Nucleolar 60S Ribosomal Subunit Biogenesis Protein The Biochemical Journal. Jun, 2005 | Pubmed ID: 15686447 Quantitative Mass Spectrometry Reveals a Role for the GTPase Rho1p in Actin Organization on the Peroxisome Membrane The Journal of Cell Biology. Dec, 2004 | Pubmed ID: 15596542 Characterization of Karyopherin Cargoes Reveals Unique Mechanisms of Kap121p-mediated Nuclear Import Molecular and Cellular Biology. Oct, 2004 | Pubmed ID: 15367670 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. Feb, 2004 | Pubmed ID: 14617799 Cell Cycle Regulated Transport Controlled by Alterations in the Nuclear Pore Complex Cell. Dec, 2003 | Pubmed ID: 14697200 Virtual Gating and Nuclear Transport: the Hole Picture Trends in Cell Biology. Dec, 2003 | Pubmed ID: 14624840 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. Oct, 2003 | Pubmed ID: 14517321 Utp8p is an Essential Intranuclear Component of the Nuclear TRNA Export Machinery of Saccharomyces Cerevisiae The Journal of Biological Chemistry. Aug, 2003 | Pubmed ID: 12794079 Inventories to Insights The Journal of Cell Biology. May, 2003 | Pubmed ID: 12743099 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. Apr, 2003 | Pubmed ID: 12707309 Karyopherins in Nuclear Pore Biogenesis: a Role for Kap121p in the Assembly of Nup53p into Nuclear Pore Complexes The Journal of Cell Biology. Oct, 2002 | Pubmed ID: 12403813 Approaching Complete Peroxisome Characterization by Gas-phase Fractionation Electrophoresis. Sep, 2002 | Pubmed ID: 12298092 Transcriptome Profiling to Identify Genes Involved in Peroxisome Assembly and Function The Journal of Cell Biology. Jul, 2002 | Pubmed ID: 12135984 Kap121p-mediated Nuclear Import is Required for Mating and Cellular Differentiation in Yeast Molecular and Cellular Biology. Apr, 2002 | Pubmed ID: 11909949 A Tense Time for the Nuclear Envelope Cell. Feb, 2002 | Pubmed ID: 11853664 ODELAY: En storskalig metod för multiparameterkvantificering av jästtillväxt Thurston Herricks1, Fred D. Mast1,2, Song Li1, John D. Aitchison1,2 1Institute for Systems Biology, 2Center for Infectious Disease Research JoVE 55879 Biology Kvantitativa Phosphoproteomics i Fatty Acid Stimulerade Saccharomyces cerevisiae Ramsey A. Saleem1, John D. Aitchison1 1Institute for Systems Biology JoVE 1474 Biology
ODELAY: En storskalig metod för multiparameterkvantificering av jästtillväxt Thurston Herricks1, Fred D. Mast1,2, Song Li1, John D. Aitchison1,2 1Institute for Systems Biology, 2Center for Infectious Disease Research JoVE 55879 Biology
Kvantitativa Phosphoproteomics i Fatty Acid Stimulerade Saccharomyces cerevisiae Ramsey A. Saleem1, John D. Aitchison1 1Institute for Systems Biology JoVE 1474 Biology