John D. Aitchison

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