CHPP

• Rare tissue studies

  • Abbey, S. R. et al. (2018) The Human Odontoblast Cell Layer and Dental Pulp Proteomes and N-Terminomes. J. Dent. Res., 97, 338-346. 
  • Eckhard, U. et al. (2015) TAILS N-terminomic and proteomic datasets of healthy human dental pulp. Data Brief, 5, 542-548. 
  • Eckhard, U. et al. (2015) The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues. J. Proteome Res., 14, 3568-3582. 
  • Lange, P. F. et al. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J. Proteome Res., 13, 2028-2044. 
  • Prudova, A. et al. (2014) TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage. Blood, 124, e49-60. 

• Database search tools

  • Lange, P. F. et al. (2012) TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. Nucleic Acids Res., 40, D351-D361. 
  • Lange, P. F. and Overall, C. M. (2011) TopFIND, a knowledgebase linking protein termini with function. Nat. Methods, 8, 703-704. 

• 2018 JPR Special Issue

  • Paik, Y. K. et al. (2018) Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods. J. Proteome Res., 17, 4023-4030. 
  • Omenn, G. S. et al. (2018) Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. J. Proteome Res., 17, 4031-4041. 
  • Paik, Y. K. et al. (2018) Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. J. Proteome Res., 17, 4042-4050. 
  • Deutsch, E. W. et al. (2018) Expanding the Use of Spectral Libraries in Proteomics. J. Proteome Res., 17, 4051-4060. 
  • Siddiqui, O. et al. (2018) Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge. J. Proteome Res., 17, 4061-4071. 
  • Boersema, P. J. et al. (2018) Biology/Disease-Driven Initiative on Protein-Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date. J. Proteome Res., 17, 4072-4084. 
  • Naryzhny, S. N. et al. (2018) Next Steps on in Silico 2DE Analyses of Chromosome 18 Proteoforms. J. Proteome Res., 17, 4085-4096. 
  • Narimatsu, H. et al. (2018) Current Technologies for Complex Glycoproteomics and Their Applications to Biology/Disease-Driven Glycoproteomics. J. Proteome Res., 17, 4097-4112. 
  • Macron, C. et al. (2018) Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification. J. Proteome Res., 17, 4113-4126. 
  • Sjöstedt, E. et al. (2018) Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues. J. Proteome Res., 17, 4127-4137. 
  • Weldemariam, M. M. et al. (2018) Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins. J. Proteome Res., 17, 4138-4151. 
  • Zhang, Y. et al. (2018) Improvement of Peptide Separation for Exploring the Missing Proteins Localized on Membranes. J. Proteome Res., 17, 4152-4159. 
  • Robin, T. et al. (2018) Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project. J. Proteome Res., 17, 4160-4170. 
  • Sun, J. et al. (2018) Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue. J. Proteome Res., 17, 4171-4177. 
  • He, C. et al. (2018) Digging for Missing Proteins Using Low-Molecular-Weight Protein Enrichment and a "Mirror Protease" Strategy. J. Proteome Res., 17, 4178-4185. 
  • Zhang, C. et al. (2018) Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17. J. Proteome Res., 17, 4186-4196. 
  • Melaine, N. et al. (2018) Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins. J. Proteome Res., 17, 4197-4210. 
  • Duek, P. et al. (2018) Exploring the Uncharacterized Human Proteome Using neXtProt. J. Proteome Res., 17, 4211-4226. 
  • Pullman, B. S. et al. (2018) ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets. J. Proteome Res., 17, 4227-4234. 
  • Jeong, S. K. et al. (2018) ASV-ID, a Proteogenomic Workflow To Predict Candidate Protein Isoforms on the Basis of Transcript Evidence. J. Proteome Res., 17, 4235-4242. 
  • Wang, J. et al. (2018) Integrated Dissection of Cysteine Oxidative Post-translational Modification Proteome During Cardiac Hypertrophy. J. Proteome Res., 17, 4243-4257. 
  • Ilgisonis, E. V. et al. (2018) Increased Sensitivity of Mass Spectrometry by Alkaline Two-Dimensional Liquid Chromatography: Deep Cover of the Human Proteome in Gene-Centric Mode. J. Proteome Res., 17, 4258-4266. 
  • Lau, E. et al. (2018) Identifying High-Priority Proteins Across the Human Diseasome Using Semantic Similarity. J. Proteome Res., 17, 4267-4278. 
  • Marshall, N. C. et al. (2018) Global Profiling of Proteolysis from the Mitochondrial Amino Terminome during Early Intrinsic Apoptosis Prior to Caspase-3 Activation. J. Proteome Res., 17, 4279-4296. 
  • Monti, C. et al. (2018) Update of the Functional Mitochondrial Human Proteome Network. J. Proteome Res., 17, 4297-4306. 
  • Ronci, M. et al. (2018) Sequential Fractionation Strategy Identifies Three Missing Proteins in the Mitochondrial Proteome of Commonly Used Cell Lines. J. Proteome Res., 17, 4307-4314. 
  • Macron, C. et al. (2018) Identification of Missing Proteins in Normal Human Cerebrospinal Fluid. J. Proteome Res., 17, 4315-4319. 
  • Hwang, H. et al. (2018) Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry. J. Proteome Res., 17, 4320-4324. 
  • Clemente, L. F. et al. (2018) Identification of the Missing Protein Hyaluronan Synthase 1 in Human Mesenchymal Stem Cells Derived from Adipose Tissue or Umbilical Cord. J. Proteome Res., 17, 4325-4328. 
  • Sajulga, R. et al. (2018) Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics. J. Proteome Res., 17, 4329-4336. 
  • Mendoza, L. et al. (2018) Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper. J. Proteome Res., 17, 4337-4344. 
  • Yu, K. H. et al. (2018) A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project. J. Proteome Res., 17, 4345-4357. 

• 2017 JPR Special Issue

  • Paik, Y. K. et al. (2017) Progress and Future Direction of Chromosome-Centric Human Proteome Project. J. Proteome Res., 16, 4253-4258. 
  • Meyfour, A. et al. (2017) Chromosome-Centric Human Proteome Project Allies with Developmental Biology: A Case Study of the Role of Y Chromosome Genes in Organ Development. J. Proteome Res., 16, 4259-4272. 
  • Tholey, A. et al. (2017) We Are Not Alone: The iMOP Initiative and Its Roles in a Biology- and Disease-Driven Human Proteome Project. J. Proteome Res., 16, 4273-4280. 
  • Omenn, G. S. et al. (2017) Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project. J. Proteome Res., 16, 4281-4287. 
  • Deutsch, E. W. et al. (2017) Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. J. Proteome Res., 16, 4288-4298. 
  • Schwenk, J. M. et al. (2017) The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. J. Proteome Res., 16, 4299-4310. 
  • Poverennaya, E. V. et al. (2017) Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18? J. Proteome Res., 16, 4311-4318. 
  • Alberio, T. et al. (2017) Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative. J. Proteome Res., 16, 4319-4329. 
  • Li, S. et al. (2017) Digging More Missing Proteins Using an Enrichment Approach with ProteoMiner. J. Proteome Res., 16, 4330-4339. 
  • Carapito, C. et al. (2017) Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods. J. Proteome Res., 16, 4340-4351. 
  • Wang, Y. et al. (2017) Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue. J. Proteome Res., 16, 4352-4363. 
  • Peng, X. et al. (2017) Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer. J. Proteome Res., 16, 4364-4373. 
  • Guruceaga, E. et al. (2017) Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach. J. Proteome Res., 16, 4374-4390. 
  • Meyfour, A. et al. (2017) Y Chromosome Missing Protein, TBL1Y, May Play an Important Role in Cardiac Differentiation. J. Proteome Res., 16, 4391-4402. 
  • Elguoshy, A. et al. (2017) Identification and Validation of Human Missing Proteins and Peptides in Public Proteome Databases: Data Mining Strategy. J. Proteome Res., 16, 4403-4414. 
  • Choong, W. K. et al. (2017) Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome. J. Proteome Res., 16, 4415-4424. 
  • Hwang, H. et al. (2017) Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases. J. Proteome Res., 16, 4425-4434. 
  • Cho, J. Y. et al. (2017) Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification. J. Proteome Res., 16, 4435-4445. 
  • Zhao, P. et al. (2017) Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage. J. Proteome Res., 16, 4446-4454. 
  • Na, K. et al. (2017) Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins. J. Proteome Res., 16, 4455-4467. 
  • Zhang, W. et al. (2017) Detergent-Insoluble Proteome Analysis Revealed Aberrantly Aggregated Proteins in Human Preeclampsia Placentas. J. Proteome Res., 16, 4468-4480. 
  • Velásquez, E. et al. (2017) Synaptosomal Proteome of the Orbitofrontal Cortex from Schizophrenia Patients Using Quantitative Label-Free and iTRAQ-Based Shotgun Proteomics. J. Proteome Res., 16, 4481-4494. 
  • Togayachi, A. et al. (2017) Glycobiomarker, Fucosylated Short-Form Secretogranin III Levels Are Increased in Serum of Patients with Small Cell Lung Carcinoma. J. Proteome Res., 16, 4495-4505. 
  • Mora, M. I. et al. (2017) Prioritizing Popular Proteins in Liver Cancer: Remodelling One-Carbon Metabolism. J. Proteome Res., 16, 4506-4514. 
  • Zhang, S. et al. (2017) Profiling B-Type Natriuretic Peptide Cleavage Peptidoforms in Human Plasma by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometry. J. Proteome Res., 16, 4515-4522. 
  • Zhou, J. Y. et al. (2017) Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues. J. Proteome Res., 16, 4523-4530. 
  • Mohamedali, A. et al. (2017) Human Prestin: A Candidate PE1 Protein Lacking Stringent Mass Spectrometric Evidence? J. Proteome Res., 16, 4531-4535. 

• 2016 JPR Special Issue

  • Paik, Y. K. et al. (2016) Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV. J. Proteome Res., 15, 3945-3950. 
  • Omenn, G. S. et al. (2016) Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications. J. Proteome Res., 15, 3951-3960. 
  • Deutsch, E. W. et al. (2016) Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. J. Proteome Res., 15, 3961-3970. 
  • Duek, P. et al. (2016) Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status. J. Proteome Res., 15, 3971-3978. 
  • Van Eyk, J. E. et al. (2016) Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016. J. Proteome Res., 15, 3979-3987. 
  • Wei, W. et al. (2016) Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer. J. Proteome Res., 15, 3988-3997. 
  • Vandenbrouck, Y. et al. (2016) Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update. J. Proteome Res., 15, 3998-4019. 
  • Zhao, M. et al. (2016) Searching Missing Proteins Based on the Optimization of Membrane Protein Enrichment and Digestion Process. J. Proteome Res., 15, 4020-4029. 
  • Poverennaya, E. V. et al. (2016) State of the Art of Chromosome 18-Centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells. J. Proteome Res., 15, 4030-4038. 
  • Kopylov, A. T. et al. (2016) Targeted Quantitative Screening of Chromosome 18 Encoded Proteome in Plasma Samples of Astronaut Candidates. J. Proteome Res., 15, 4039-4046. 
  • Guo, J. et al. (2016) Drug Resistance in Colorectal Cancer Cell Lines is Partially Associated with Aneuploidy Status in Light of Profiling Gene Expression. J. Proteome Res., 15, 4047-4059. 
  • Guo, J. et al. (2016) Phosphoproteome Characterization of Human Colorectal Cancer SW620 Cell-Derived Exosomes and New Phosphosite Discovery for C-HPP. J. Proteome Res., 15, 4060-4072. 
  • Weiland, F. et al. (2016) Novel IEF Peptide Fractionation Method Reveals a Detailed Profile of N-Terminal Acetylation in Chemotherapy-Responsive and -Resistant Ovarian Cancer Cells. J. Proteome Res., 15, 4073-4081. 
  • Park, G. W. et al. (2016) Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate. J. Proteome Res., 15, 4082-4090. 
  • Deutsch, E. W. et al. (2016) Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics. J. Proteome Res., 15, 4091-4100. 
  • Garin-Muga, A. et al. (2016) Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence. J. Proteome Res., 15, 4101-4115. 
  • Kim, J. W. et al. (2016) gFinder: A Web-Based Bioinformatics Tool for the Analysis of N-Glycopeptides. J. Proteome Res., 15, 4116-4125. 
  • Lam, M. P. et al. (2016) Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. J. Proteome Res., 15, 4126-4134.

• 2015 JPR Special Issue

  • Paik, Y. K. et al. (2015) Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J. Proteome Res., 14, 3409-3414. 
  • Horvatovich, P. et al. (2015) Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3415-3431. 
  • Jayaram, S. et al. (2015) Insights from Chromosome-Centric Mapping of Disease-Associated Genes: Chromosome 12 Perspective. J. Proteome Res., 14, 3432-3440. 
  • Horvatovich, P. et al. (2015) In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins. J. Proteome Res., 14, 3441-3451. 
  • Omenn, G. S. et al. (2015) Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J. Proteome Res., 14, 3452-3460. 
  • Deutsch, E. W. et al. (2015) State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. J. Proteome Res., 14, 3461-3473. 
  • Vakilian, H. et al. (2015) DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation. J. Proteome Res., 14, 3474-3483. 
  • Li, H. D. et al. (2015) Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. J. Proteome Res., 14, 3484-3491. 
  • Jangravi, Z. et al. (2015) Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145). J. Proteome Res., 14, 3492-3502. 
  • Rengaraj, D. et al. (2015) Bioinformatics Annotation of Human Y Chromosome-Encoded Protein Pathways and Interactions. J. Proteome Res., 14, 3503-3518. 
  • Menon, R. et al. (2015) Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study. J. Proteome Res., 14, 3519-3529. 
  • Díez, P. et al. (2015) Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3530-3540. 
  • Tay, A. P. et al. (2015) Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data. J. Proteome Res., 14, 3541-3554. 
  • Woo, S. et al. (2015) Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. J. Proteome Res., 14, 3555-3567. 
  • Eckhard, U. et al. (2015) The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues. J. Proteome Res., 14, 3568-3582. 
  • Zhang, Y. et al. (2015) Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins. J. Proteome Res., 14, 3583-3594. 
  • Ahmadi Rastegar, D. et al. (2015) Isoform-Level Gene Expression Profiles of Human Y Chromosome Azoospermia Factor Genes and Their X Chromosome Paralogs in the Testicular Tissue of Non-Obstructive Azoospermia Patients. J. Proteome Res., 14, 3595-3605. 
  • Jumeau, F. et al. (2015) Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3606-3620. 
  • Carapito, C. et al. (2015) Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14. J. Proteome Res., 14, 3621-3634. 
  • Fan, Y. et al. (2015) Insights from ENCODE on Missing Proteins: Why β-Defensin Expression Is Scarcely Detected. J. Proteome Res., 14, 3635-3644. 
  • Yang, L. et al. (2015) Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria. J. Proteome Res., 14, 3645-3657. 
  • Kitata, R. B. et al. (2015) Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. J. Proteome Res., 14, 3658-3669. 
  • Hoover, H. et al. (2015) Quantitative Proteomic Verification of Membrane Proteins as Potential Therapeutic Targets Located in the 11q13 Amplicon in Cancers. J. Proteome Res., 14, 3670-3679. 
  • Su, N. et al. (2015) Special Enrichment Strategies Greatly Increase the Efficiency of Missing Proteins Identification from Regular Proteome Samples. J. Proteome Res., 14, 3680-3692. 
  • Chen, Y. et al. (2015) Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins. J. Proteome Res., 14, 3693-3709. 
  • Jeong, S. K. et al. (2015) GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3710-3719. 
  • Yang, S. et al. (2015) CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets. J. Proteome Res., 14, 3720-3728. 
  • Krasnov, G. S. et al. (2015) PPLine: An Automated Pipeline for SNP, SAP, and Splice Variant Detection in the Context of Proteogenomics. J. Proteome Res., 14, 3729-3737. 
  • Tabas-Madrid, D. et al. (2015) Proteogenomics Dashboard for the Human Proteome Project. J. Proteome Res., 14, 3738-3749. 
  • Dong, Q. et al. (2015) Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. J. Proteome Res., 14, 3750-3761. 
  • Panwar, B. et al. (2015) MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. J. Proteome Res., 14, 3762-3767. 

• 2014 JPR Special Issue

  • Paik, Y. K. et al. (2014) Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II. J. Proteome Res., 13, 1-4. 
  • Horvatovich, P. et al. (2014) Proteomic studies related to genetic determinants of variability in protein concentrations. J. Proteome Res., 13, 5-14. 
  • Lane, L. et al. (2014) Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J. Proteome Res., 13, 15-20. 
  • Woo, S. et al. (2014) Proteogenomic database construction driven from large scale RNA-seq data. J. Proteome Res., 13, 21-28. 
  • Teo, G. et al. (2014) PECA: a novel statistical tool for deconvoluting time-dependent gene expression regulation. J. Proteome Res., 13, 29-37. 
  • Chang, C. et al. (2014) Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP. J. Proteome Res., 13, 38-49. 
  • Zhong, J. et al. (2014) Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. J. Proteome Res., 13, 50-59. 
  • Farrah, T. et al. (2014) State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J. Proteome Res., 13, 60-75. 
  • Islam, M. T. et al. (2014) Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome. J. Proteome Res., 13, 76-83. 
  • Pang, C. N. et al. (2014) Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing. J. Proteome Res., 13, 84-98. 
  • Wang, D. et al. (2014) CAPER 2.0: an interactive, configurable, and extensible workflow-based platform to analyze data sets from the Chromosome-centric Human Proteome Project. J. Proteome Res., 13, 99-106. 
  • Higdon, R. et al. (2014) MOPED enables discoveries through consistently processed proteomics data. J. Proteome Res., 13, 107-113. 
  • Zhang, C. et al. (2014) Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1. J. Proteome Res., 13, 114-125. 
  • Liu, Y. et al. (2014) Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications. J. Proteome Res., 13, 126-136. 
  • Ahn, J. M. et al. (2014) Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. J. Proteome Res., 13, 137-146. 
  • Martins-de-Souza, D. et al. (2014) Deciphering the human brain proteome: characterization of the anterior temporal lobe and corpus callosum as part of the Chromosome 15-centric Human Proteome Project. J. Proteome Res., 13, 147-157. 
  • Segura, V. et al. (2014) Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome. J. Proteome Res., 13, 158-172. 
  • Shargunov, A. V. et al. (2014) Tissue-specific alternative splicing analysis reveals the diversity of chromosome 18 transcriptome. J. Proteome Res., 13, 173-182. 
  • Ponomarenko, E. A. et al. (2014) Chromosome 18 transcriptoproteome of liver tissue and HepG2 cells and targeted proteome mapping in depleted plasma: update 2013. J. Proteome Res., 13, 183-190. 
  • Lichti, C. F. et al. (2014) Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. J. Proteome Res., 13, 191-199. 
  • Wang, Q. et al. (2014) Omics evidence: single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines. J. Proteome Res., 13, 200-211. 
  • Menon, R. et al. (2014) Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. J. Proteome Res., 13, 212-227. 
  • Sheynkman, G. M. et al. (2014) Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. J. Proteome Res., 13, 228-240. 
  • Song, C. et al. (2014) Large-scale quantification of single amino-acid variations by a variation-associated database search strategy. J. Proteome Res., 13, 241-248. 
  • Peng, M. et al. (2014) Identification of enriched PTM crosstalk motifs from large-scale experimental data sets. J. Proteome Res., 13, 249-259. 
  • Edwards, A. V. et al. (2014) Spatial and temporal effects in protein post-translational modification distributions in the developing mouse brain. J. Proteome Res., 13, 260-267. 
  • Leng, L. et al. (2014) A proteomics strategy for the identification of FAT10-modified sites by mass spectrometry. J. Proteome Res., 13, 268-276. 
  • Sethi, M. K. et al. (2014) Comparative N-glycan profiling of colorectal cancer cell lines reveals unique bisecting GlcNAc and α-2,3-linked sialic acid determinants are associated with membrane proteins of the more metastatic/aggressive cell lines. J. Proteome Res., 13, 277-288. 
  • Gbormittah, F. O. et al. (2014) Characterization of glycoproteins in pancreatic cyst fluid using a high-performance multiple lectin affinity chromatography platform. J. Proteome Res., 13, 289-299. 
  • Kiel, C. et al. (2014) Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins. J. Proteome Res., 13, 300-313. 
  • Aquino, P. F. et al. (2014) Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer. J. Proteome Res., 13, 314-320. 
  • Fujimoto, G. M. et al. (2014) Accounting for population variation in targeted proteomics. J. Proteome Res., 13, 321-323. 

• 2013 JPR Special Issue

  • Marko-Varga, G. et al. (2013) A first step toward completion of a genome-wide characterization of the human proteome. J. Proteome Res., 12, 1-5.
  • Jangravi, Z. et al. (2013) A fresh look at the male-specific region of the human Y chromosome. J. Proteome Res., 12, 6-22.
  • Aebersold, R. et al. (2013) The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J. Proteome Res., 12, 23-27.
  • Huhmer, A. F. et al. (2013) The chromosome-centric human proteome project: a call to action. J. Proteome Res., 12, 28-32.
  • Chen, L. C. et al. (2013) Decoding the disease-associated proteins encoded in the human chromosome 4. J. Proteome Res., 12, 33-44.
  • Liu, S. et al. (2013) A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J. Proteome Res., 12, 45-57.
  • Yamamoto, T. et al. (2013) Integrated view of the human chromosome X-centric proteome project. J. Proteome Res., 12, 58-61.
  • Imanishi, T. et al. (2013) Full-length transcriptome-based H-InvDB throws a new light on chromosome-centric proteomics. J. Proteome Res., 12, 62-66.
  • Wu, S. et al. (2013) First proteomic exploration of protein-encoding genes on chromosome 1 in human liver, stomach, and colon. J. Proteome Res., 12, 67-80.
  • Zhang, Y. et al. (2013) Proteome atlas of human chromosome 8 and its multiple 8p deficiencies in tumorigenesis of the stomach, colon, and liver. J. Proteome Res., 12, 81-88.
  • Fanayan, S. et al. (2013) Chromosome 7-centric analysis of proteomics data from a panel of human colon carcinoma cell lines. J. Proteome Res., 12, 89-96.
  • Kwon, K. H. et al. (2013) Chromosome 11-centric human proteome analysis of human brain hippocampus tissue. J. Proteome Res., 12, 97-105.
  • Jeong, S. K. et al. (2013) GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes. J. Proteome Res., 12, 106-111.
  • Segura, V. et al. (2013) Spanish human proteome project: dissection of chromosome 16. J. Proteome Res., 12, 112-122.
  • Zgoda, V. G. et al. (2013) Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells. J. Proteome Res., 12, 123-134.
  • Nilsson, C. L. et al. (2013) Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium. J. Proteome Res., 12, 135-150.
  • Wang, Q. et al. (2013) Qualitative and quantitative expression status of the human chromosome 20 genes in cancer tissues and the representative cell lines. J. Proteome Res., 12, 151-161.
  • Farrah, T. et al. (2013) The state of the human proteome in 2012 as viewed through PeptideAtlas. J. Proteome Res., 12, 162-171.
  • Goode, R. J. et al. (2013) The proteome browser web portal. J. Proteome Res., 12, 172-178.
  • Guo, F. et al. (2013) CAPER: a chromosome-assembled human proteome browsER. J. Proteome Res., 12, 179-186.
  • Peng, Y. et al. (2013) Top-down targeted proteomics for deep sequencing of tropomyosin isoforms. J. Proteome Res., 12, 187-198.
  • Maurer, A. et al. (2013) A periodate-cleavable linker for functional proteomics under slightly acidic conditions: application for the analysis of intracellular aspartic proteases. J. Proteome Res., 12, 199-207.
  • Muraoka, S. et al. (2013) In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list. J. Proteome Res., 12, 208-213.
  • Yamana, R. et al. (2013) Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot NanoLC-MS/MS analysis with meter-scale monolithic silica columns. J. Proteome Res., 12, 214-221.
  • Percy, A. J. et al. (2013) Standardized protocols for quality control of MRM-based plasma proteomic workflows. J. Proteome Res., 12, 222-233.
  • Mortstedt, H. et al. (2013) Screening method using selected reaction monitoring for targeted proteomics studies of nasal lavage fluid. J. Proteome Res., 12, 234-247.
  • Malerod, H. et al. (2013) Comprehensive profiling of N-linked glycosylation sites in HeLa cells using hydrazide enrichment. J. Proteome Res., 12, 248-259.
  • Zhou, H. et al. (2013) Toward a comprehensive characterization of a human cancer cell phosphoproteome. J. Proteome Res., 12, 260-271.
  • Lavallee-Adam, M. et al. (2013) Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J. Proteome Res., 12, 272-281.
  • Buanne, P. et al. (2013) Characterization of carbonic anhydrase IX interactome reveals proteins assisting its nuclear localization in hypoxic cells. J. Proteome Res., 12, 282-292.
  • Gaudet, P. et al. (2013) neXtProt: organizing protein knowledge in the context of human proteome projects. J. Proteome Res., 12, 293-298.
  • Danielsson, F. et al. (2013) RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins. J. Proteome Res., 12, 299-307.
  • Meding, S. et al. (2013) Tryptic peptide reference data sets for MALDI imaging mass spectrometry on formalin-fixed ovarian cancer tissues. J. Proteome Res., 12, 308-315.
  • Wu, Y. et al. (2013) Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation. J. Proteome Res., 12, 316-327.
  • Xiao, C. L. et al. (2013) Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information. J. Proteome Res., 12, 328-335.
  • Sharma, A. et al. (2013) Identification of potential universal vaccine candidates against group A Streptococcus by using high throughput in silico and proteomics approach. J. Proteome Res., 12, 336-346.
  • Maris, M. et al. (2013) Role of the saturated nonesterified fatty acid palmitate in beta cell dysfunction. J. Proteome Res., 12, 347-362.
  • Ye, Y. et al. (2013) Quantitative proteomics by amino acid labeling in foot-and-mouth disease virus (FMDV)-infected cells. J. Proteome Res., 12, 363-377.
  • Kliemt, S. et al. (2013) Sulfated hyaluronan containing collagen matrices enhance cell-matrix-interaction, endocytosis, and osteogenic differentiation of human mesenchymal stromal cells. J. Proteome Res., 12, 378-389.
  • Sun, D. et al. (2013) Quantitative proteome of medulla oblongata in spontaneously hypertensive rats. J. Proteome Res., 12, 390-395.
  • Klatt, S. et al. (2013) Production of glycosylated soluble amyloid precursor protein alpha (sAPPalpha) in Leishmania tarentolae. J. Proteome Res., 12, 396-403.
  • Fujita, T. et al. (2013) Proteomic analysis of the royal jelly and characterization of the functions of its derivation glands in the honeybee. J. Proteome Res., 12, 404-411.
  • Torsetnes, S. B. et al. (2013) Digging deeper into the field of the small cell lung cancer tumor marker ProGRP: a method for differentiation of its isoforms. J. Proteome Res., 12, 412-420.
  • Cirillo, F. et al. (2013) Molecular mechanisms of selective estrogen receptor modulator activity in human breast cancer cells: identification of novel nuclear cofactors of antiestrogen-ERα complexes by interaction proteomics. J. Proteome Res., 12, 421-431.
  • Lee, J. Y. et al. (2013) Proteomic and transcriptional analysis of Lactobacillus johnsonii PF01 during bile salt exposure by iTRAQ shotgun proteomics and quantitative RT-PCR. J. Proteome Res., 12, 432-443.
  • Adamczyk, B. et al. (2013) Characterization of fibrinogen glycosylation and its importance for serum/plasma N-glycome analysis. J. Proteome Res., 12, 444-454.
  • Hrabakova, R. et al. (2013) Cancer cell resistance to aurora kinase inhibitors: identification of novel targets for cancer therapy. J. Proteome Res., 12, 455-469.
  • Pechlivanis, A. et al. (2013) 1H NMR study on the short- and long-term impact of two training programs of sprint running on the metabolic fingerprint of human serum. J. Proteome Res., 12, 470-480.
  • O'Sullivan, A. et al. (2013) Metabolomics of cerebrospinal fluid from humans treated for rabies. J. Proteome Res., 12, 481-490.
  • Huang, M. et al. (2013) Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics. J. Proteome Res., 12, 491-504.
  • Zhang, T. et al. (2013) Identification of potential biomarkers for ovarian cancer by urinary metabolomic profiling. J. Proteome Res., 12, 505-512.
  • Tan, Y. et al. (2013) Deciphering the differential toxic responses of Radix aconiti lateralis praeparata in healthy and hydrocortisone-pretreated rats based on serum metabolic profiles. J. Proteome Res., 12, 513-524.
  • Strakova, E. et al. (2013) Systems insight into the spore germination of Streptomyces coelicolor. J. Proteome Res., 12, 525-536.
  • Huang, C. et al. (2013) Metabolic influence of acute cyadox exposure on Kunming mice. J. Proteome Res., 12, 537-545.

• C-HPP Related Papers

  • Ruiz-Romero, C. et al. (2015) The Spanish biology/disease initiative within the human proteome project: Application to rheumatic diseases. J Proteomics, , .
  • Guruceaga, E. et al. (2015) Prediction of a Missing Protein Expression Map in the Context of the Human Proteome Project. J. Proteome Res., , .
  • Lichti, C. F. et al. (2015) Systematic identification of single amino Acid variants in glioma stem-cell-derived chromosome 19 proteins. J. Proteome Res., 14, 778-786. 
  • Nilsson, C. L. et al. (2015) Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome. J. Proteome Res., 14, 603-608.
  • Manda, S. S. et al. (2014) Identification and characterization of proteins encoded by chromosome 12 as part of chromosome-centric human proteome project. J. Proteome Res., 13, 3166-3177.
  • Chaiyarit, S. et al. (2014) Chromosome-centric Human Proteome Project (C-HPP): Chromosome 12. J. Proteome Res., 13, 3160-3165.
  • Gupta, M. K. et al. (2014) Chromosome-centric human proteome project: deciphering proteins associated with glioma and neurodegenerative disorders on chromosome 12. J. Proteome Res., 13, 3178-3190.
  • Pinto, S. M. et al. (2014) Functional annotation of proteome encoded by human chromosome 22. J. Proteome Res., 13, 2749-2760.
  • Lange, P. F. et al. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J. Proteome Res., 13, 2028-2044. 
  • Stadler, C. et al. (2014) RNA- and antibody-based profiling of the human proteome with focus on chromosome 19. J. Proteome Res., 13, 2019-2027. 
  • Alm, T. et al. (2014) A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia. J. Proteome Res., 13, 1669-1676.
  • Ponomarenko, E. et al. (2014) The chromosome-centric human proteome project at FEBS Congress. Proteomics, 14, 147-152.
  • Malm, J. et al. (2013) Blood plasma reference material: a global resource for proteomic research. J. Proteome Res., 12, 3087-3092. 
  • Ranganathan, S. et al. (2013) Functional annotation of the human chromosome 7 "missing" proteins: a bioinformatics approach. J. Proteome Res., 12, 2504-2510. 
  • Lee, H. J. et al. (2013) Comprehensive genome-wide proteomic analysis of human placental tissue for the Chromosome-Centric Human Proteome Project. J. Proteome Res., 12, 2458-2466. 
  • Fagerberg, L. et al. (2013) Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J. Proteome Res., 12, 2439-2448. 
  • Shiromizu, T. et al. (2013) Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-centric Human Proteome Project. J. Proteome Res., 12, 2414-2421. 
  • Fanayan, S. et al. (2013) Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405. J. Proteome Res., 12, 1732-1742. 
  • Paik, Y. K. and Hancock, W. S. (2012) Uniting ENCODE with genome-wide proteomics. Nat. Biotechnol. 30, 1065-1067.
  • Paik,Y. et al. (2012) The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol, 30, 221-3.
  • Archakov, A. et al. (2011) Gene-centric view on the human proteome project: the example of the Russian roadmap for chromosome 18. Proteomics, 11, 1853-1856.
  • Hancock,W. et al. (2011) Proteomics, human proteome project, and chromosomes. J Proteome Res, 10, 210.
  • Editorial (2010) A gene-centric human proteome project: HUPO-the Human Proteome organization. Mol Cell Proteomics, 9, 427-9.
  • Berglund,L. et al. (2008) A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol Cell Proteomics, 7, 2019-27.

HPP

• Aebersold, R. et al. (2014) Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan. Proteomics, 14, 975-988.
• Farrah,T. et al. (2011) A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics, , .
• Legrain,P. et al. (2011) The human proteome project: Current state and future direction. Mol Cell Proteomics, , .
• Olsen,J.V. and Mann,M. (2011) Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community. Sci Signal, 4, pe7.
• Omenn,G.S. (2011) Data management and data integration in the HUPO plasma proteome project. Methods Mol Biol, 696, 247-57.
• Sun,A. et al. (2010) Liverbase: a comprehensive view of human liver biology. J Proteome Res, 9, 50-8.
• Vizcaíno,J.A. et al. (2010) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics, 9, 4276-83.
• Omenn,G.S. et al. (2008) 7(th) HUPO World Congress of Proteomics: launching the second phase of the HUPOPlasma Proteome Project (PPP-2) 16-20 August 2008, Amsterdam, The Netherlands. Proteomics, 9, 4-6.
• Yamamoto,T. et al. (2008) Towards standard protocols and guidelines for urine proteomics: a report on the Human Kidney and Urine Proteome Project (HKUPP) symposium and workshop, 6 October 2007, Seoul, Korea and 1 November 2007, San Francisco, CA, USA. Proteomics, 8, 2156-9.
• Hamacher,M. et al. (2008) Maintaining standardization: an update of the HUPO Brain Proteome Project. Expert Rev Proteomics, 5, 165-73.
• Taniguchi,N. (2008) Human disease glycomics/proteome initiative (HGPI). Mol Cell Proteomics, 7, 626-7.
• Mathivanan,S. et al. (2008) Human Proteinpedia enables sharing of human protein data. Nat Biotechnol, 26, 164-7.
• Hamacher,M. et al. (2008) HUPO Brain Proteome Project: toward a code of conduct. Mol Cell Proteomics, 7, 457.
• Hober,S. and Uhlén,M. (2008) Human protein atlas and the use of microarray technologies. Curr Opin Biotechnol, 19, 30-5.
• Martens,L. et al. (2007) Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. Mol Cell Proteomics, 6, 1666-7.
• Miyamoto,M. et al. (2007) In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. J Proteome Res, 6, 3680-90.
• Wada,Y. et al. (2007) Comparison of the methods for profiling glycoprotein glycans--HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study. Glycobiology, 17, 411-22.
• Hamacher,M. et al. (2006) HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy Proteomics, 6, 4890-8.
• Jones,P. et al. (2005) PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res, 34, D659-63.
• He,F. (2005) Human liver proteome project: plan, progress, and perspectives. Mol Cell Proteomics, 4, 1841-8.
• Ping,P. et al. (2005) A functional annotation of subproteomes in human plasma. Proteomics, 5, 3506-19.
• Omenn,G.S. et al. (2005) Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics, 5, 3226-45.
• Orchard,S. et al. (2005) Current status of proteomic standards development. Expert Rev Proteomics, 1, 179-83.
• Uhlen,M. and Ponten,F. (2005) Antibody-based proteomics for human tissue profiling. Mol Cell Proteomics, 4, 384-93.
• Blüggel,M. et al. (2004) Towards data management of the HUPO Human Brain Proteome Project pilot phase. Proteomics, 4, 2361-2.
• Hermjakob,H. et al. (2004) The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol, 22, 177-83.
• Meyer,H.E. et al. (2003) HBPP and the pursuit of standardisation. Lancet Neurol, 2, 657-8.
• Orchard,S. et al. (2003) The proteomics standards initiative. Proteomics, 3, 1374-6.

Proteomics

• Renuse,S. et al. (2011) Proteogenomics. Proteomics, 11, 620-30.
• Menon,R. and Omenn,G.S. (2011) Identification of alternatively spliced transcripts using a proteomic informatics approach. Methods Mol Biol, 696, 319-26.
• Ikami,M. et al. (2011) Immuno-pillar chip: a new platform for rapid and easy-to-use immunoassay. Lab Chip, 10, 3335-40.
• Bradshaw,R.A. and Burlingame,A.L. (2011) Technological innovation revisited. Mol Cell Proteomics, 9, 2335-6.
• Editorial (2010) The call of the human proteome. Nat Methods, 7, 661.
• Walther,T.C. and Mann,M. (2010) Mass spectrometry-based proteomics in cell biology. J Cell Biol, 190, 491-500.
• Duncan,M.W. et al. (2010) The pros and cons of peptide-centric proteomics. Nat Biotechnol, 28, 659-64.
• Vermeulen,M. and Selbach,M. (2010) Quantitative proteomics: a tool to assess cell differentiation. Curr Opin Cell Biol, 21, 761-6.
• Anderson,N.L. et al. (2009) A human proteome detection and quantitation project. Mol Cell Proteomics, 8, 883-6.
• Editorial (2008) The big ome. Nature, 452, 913-4.
• Mueller,M. et al. (2007) Annotating the human proteome: beyond establishing a parts list. Biochim Biophys Acta, 1774, 175-91.
• Bradshaw,R.A. et al. (2006) Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics, 5, 787-8.
• Hamacher,M. et al. (2004) "Does understanding the brain need proteomics and does understanding proteomics need brains?"--Second HUPO HBPP Workshop hosted in Paris. Proteomics, 4, 1932-4.
• Agaton,C. et al. (2003) Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues. Mol Cell Proteomics, 2, 405-14.

Co-expression

• De, S. and Babu, M. M. (2010) Genomic neighbourhood and the regulation of gene expression. Curr. Opin. Cell Biol., 22, 326-333.
• Prieto, C. et al. (2008) Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS ONE, 3, e3911.
• Cohen, B. A. et al. (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet., 26, 183-186.
• Hey, J. and Kliman, R. M. (2002) Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics, 160, 595-608.
• Hurst, L. D. et al. (2004) The evolutionary dynamics of eukaryotic gene order. Nat. Rev. Genet., 5, 299-310.
• Lercher, M. J. et al. (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet., 31, 180-183.
• Gierman, H. J. et al. (2007) Domain-wide regulation of gene expression in the human genome. Genome Res., 17, 1286-1295.
• Goetze, S. et al. (2007) The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Mol. Cell. Biol., 27, 4475-4487.
• Caron, H. et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science, 291, 1289-1292.
• Buness, A. et al. (2007) Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer. Bioinformatics, 23, 2273-2280.
• Myllykangas, S. and Knuutila, S. (2006) Manifestation, mechanisms and mysteries of gene amplifications. Cancer Lett., 232, 79-89.
• Zhou, Y. et al. (2003) Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis. Cancer Res., 63, 5781-5784.
• Kallioniemi, A. et al. (1994) Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization. Proc. Natl. Acad. Sci. U.S.A., 91, 2156-2160.
• Liao, B. Y. and Zhang, J. (2008) Coexpression of linked genes in Mammalian genomes is generally disadvantageous. Mol. Biol. Evol., 25, 1555-1565.
• Sémon, M. and Duret, L. (2006) Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol. Biol. Evol., 23, 1715-1723.
• Singer, G. A. et al. (2005) Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol. Biol. Evol., 22, 767-775.
• Korbel, J. O. et al. (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat. Biotechnol., 22, 911-917.
• Boutanaev, A. M. et al. (2002) Large clusters of co-expressed genes in the Drosophila genome. Nature, 420, 666-669.
• Cohen, B. A. et al. (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet., 26, 183-186.

Transcriptome

• Wu, J. Q. et al. (2010) Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc. Natl. Acad. Sci. U.S.A., 107, 5254-5259.
• Chen, R. et al. (2012) Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell, 148, 1293-1307.

Genomics

• Li,M. et al. (2011) Widespread RNA and DNA Sequence Differences in the Human Transcriptome. Science, , Epub ahead of print.
• ENCODE Project Consortium,. et al. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol, 9, e1001046.
• Venter,J.C. (2011) Genome-sequencing anniversary. The human genome at 10: successes and challenges. Science, 331, 546-7.
• Lukk,M. et al. (2010) A global map of human gene expression. Nat Biotechnol, 28, 322-4.
• Collins,F.S. (2004) Genome research: the next generation. Cold Spring Harb Symp Quant Biol, 68, 49-54.
• Collins,F.S. et al. (2003) The Human Genome Project: lessons from large-scale biology. Science, 300, 286-90.
• Lander,E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
• Venter,J.C. et al. (2001) The sequence of the human genome. Science, 291, 1304-51.
• Tilghman,S.M. (1996) Lessons learned, promises kept: a biologist's eye view of the Genome Project. Genome Res, 6, 773-80.

Chromosome

• Gregory,S.G. et al. (2006) The DNA sequence and biological annotation of human chromosome 1. Nature, 441, 315-21.
• Muzny,D.M. et al. (2006) The DNA sequence, annotation and analysis of human chromosome 3. Nature, 440, 1194-8.
• Walentinsson,A. et al. (2001) Independent amplification of two gene clusters on chromosome 4 in rat endometrial cancer: identification and molecular characterization. Cancer Res, 61, 8263-73.
• Schmutz,J. et al. (2004) The DNA sequence and comparative analysis of human chromosome 5. Nature, 431, 268-74.
• Mungall,A.J. et al. (2003) The DNA sequence and analysis of human chromosome 6. Nature, 425, 805-11.
• Hillier,L.W. et al. (2003) The DNA sequence of human chromosome 7. Nature, 424, 157-64.
• Nusbaum,C. et al. (2006) DNA sequence and analysis of human chromosome 8. Nature, 439, 331-5.
• Humphray,S.J. et al. (2004) DNA sequence and analysis of human chromosome 9. Nature, 429, 369-74.
• Deloukas,P. et al. (2004) The DNA sequence and comparative analysis of human chromosome 10. Nature, 429, 375-81.
• Taylor,T.D. et al. (2006) Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature, 440, 497-500.
• Scherer,S.E. et al. (2006) The finished DNA sequence of human chromosome 12. Nature, 440, 346-51.
• Montgomery,K.T. et al. (2001) A high-resolution map of human chromosome 12. Nature, 409, 945-6.
• Dunham,A. et al. (2004) The DNA sequence and analysis of human chromosome 13. Nature, 428, 522-8.
• Heilig,R. et al. (2003) The DNA sequence and analysis of human chromosome 14. Nature, 421, 601-7.
• Brüls,T. et al. (2001) A physical map of human chromosome 14. Nature, 409, 947-8.
• Zody,M.C. et al. (2006) Analysis of the DNA sequence and duplication history of human chromosome 15. Nature, 440, 671-5.
• Martin,J. et al. (2004) The sequence and analysis of duplication-rich human chromosome 16. Nature, 432, 988-94.
• Doggett,N.A. et al. (1995) An integrated physical map of human chromosome 16. Nature, 377, 335-65.
• Zody,M.C. et al. (2006) DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature, 440, 1045-9.
• Nusbaum,C. et al. (2005) DNA sequence and analysis of human chromosome 18. Nature, 437, 551-5.
• Grimwood,J. et al. (2004) The DNA sequence and biology of human chromosome 19. Nature, 428, 529-35.
• Deloukas,P. et al. (2002) The DNA sequence and comparative analysis of human chromosome 20. Nature, 414, 865-71.
• Hattori,M. et al. (2000) The DNA sequence of human chromosome 21. Nature, 405, 311-9.
• Dawson,E. et al. (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418, 544-8.
• Mullikin,J.C. et al. (2000) An SNP map of human chromosome 22. Nature, 407, 516-20.
• Dunham,I. et al. (1999) The DNA sequence of human chromosome 22. Nature, 402, 489-95.
• Ross,M.T. et al. (2005) The DNA sequence of the human X chromosome. Nature, 434, 325-37.
• Skaletsky,H. et al. (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature, 423, 825-37.
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