Research Topics
| Joshua LabaerSummaryAffiliation: Harvard University Country: USA Publications
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Publications
Protein microarrays as tools for functional proteomicsJoshua Labaer
Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 320 Charles Street, Cambridge, Massachusetts 02141, USA
Curr Opin Chem Biol 9:14-9. 2005..In this review, we discuss some of the promising advances made in the development and use of protein microarrays...- [From genome to proteome--aim of human proteomics]Kazuyuki Nakamura
Department of Biochemistry and Biomolecular Recognition, Fatulty of Medicine, Yamaguchi University, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
Seikagaku 76:1271-4. 2004 - Next-generation high-density self-assembling functional protein arraysNiroshan Ramachandran
Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, Massachusetts 02141, USA
Nat Methods 5:535-8. 2008..This method will enable various experimental approaches to study protein function in high throughput... - A full-genomic sequence-verified protein-coding gene collection for Francisella tularensisTal Murthy
Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, Massachusetts, United States of America
PLoS ONE 2:e577. 2007..These methods and resources represent significant technological steps towards exploiting the genomic information of F. tularensis in discovery applications... - The Pseudomonas aeruginosa PA01 gene collectionJoshua Labaer
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Institute of Proteomics, Cambridge, Massachusetts 02141, USA
Genome Res 14:2190-200. 2004..This gene repository provides a powerful tool for proteome- and genome-scale research of this organism, and the strategies adopted to generate this repository serve as a model for building clone sets for other bacteria... - Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiaeYanhui Hu
Harvard Institute of Proteomics, Harvard Medical School, Cambridge, MA 02141, USA
Genome Res 17:536-43. 2007..Availability of this collection makes possible a wide variety of studies from purified proteins to mutation suppression analysis, which should contribute to a global understanding of yeast protein function... - Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio choleraeAndreas Rolfs
Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology and Dana Farber Harvard Cancer Center DNA Resource Core, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141, USA
Proc Natl Acad Sci U S A 105:4364-9. 2008..These data suggest that the genome-scale, fully sequenced ORF collection reported here will be useful for high-throughput functional proteomic assays, immune response studies, structure biology, and other applications... - A novel approach to sequence validating protein expression clones with automated decision makingElena Taycher
Harvard Institute of Proteomics, Harvard Medical School, Cambridge, MA 02141, USA
BMC Bioinformatics 8:198. 2007..Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation... - A biomedically enriched collection of 7000 human ORF clonesAndreas Rolfs
Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, USA
PLoS ONE 3:e1528. 2008..Thus, this collection is likely to be a powerful resource for researchers who wish to study protein function in a set of genes with documented biomedical significance... - Building a human kinase gene repository: bioinformatics, molecular cloning, and functional validationJaehong Park
Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141, USA
Proc Natl Acad Sci U S A 102:8114-9. 2005..The work described here will facilitate the functional assaying of this important gene family in phenotypic screens and their use in biochemical and structural studies... - Application of protein microarrays for multiplexed detection of antibodies to tumor antigens in breast cancerKaren S Anderson
Cancer Vaccine Center, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
J Proteome Res 7:1490-9. 2008..Here, we present the first demonstration of the application of programmable protein microarray ELISAs for the rapid identification of breast cancer autoantibodies... - PlasmID: a centralized repository for plasmid clone information and distributionDongmei Zuo
Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141, USA
Nucleic Acids Res 35:D680-4. 2007..Researchers interested in requesting clone samples or sharing their own plasmids with the repository can visit the PlasmID website for more information... - Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarraysWagner R Montor
Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Boston Children s Hospital, Boston, MA 02115, USA
Infect Immun 77:4877-86. 2009..01). The study provides a list of potential candidates for the improvement of serological diagnostics and the development of vaccines... - On-chip protein synthesis for making microarraysNiroshan Ramachandran
Department of Biological Chemistry and Molecular Pharmacology, Harvard Institute of Proteomics, Harvard Medical School, Cambridge, MA, USA
Methods Mol Biol 328:1-14. 2006..Moreover, this approach minimizes concerns about protein stability and integrity, because proteins are produced just in time for assaying. NAPPA has already proven to be a robust tool for protein functional assays... - Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancerAbigail E Witt
Department of Cell Biology, Harvard Medical School, Boston Massachusetts 02115, USA
J Proteome Res 5:599-610. 2006.... - Emerging tools for real-time label-free detection of interactions on functional protein microarraysNiroshan Ramachandran
Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, MA 02141, USA
FEBS J 272:5412-25. 2005..The combination of these technologies will facilitate the large-scale study of protein interactions with proteins as well as with other biomolecules... - Tracking humoral responses using self assembling protein microarraysNiroshan Ramachandran
Harvard Institute of Proteomics, Harvard Medical School, Cambridge, MA, USA
Proteomics Clin Appl 2:1518-27. 2008..This represents a powerful and versatile tool for monitoring the immunome in health and disease... - Vibrio cholerae proteome-wide screen for immunostimulatory proteins identifies phosphatidylserine decarboxylase as a novel Toll-like receptor 4 agonistAnn Thanawastien
Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, USA
PLoS Pathog 5:e1000556. 2009..Taken together, these results provide evidence for the identification of V. cholerae PSD as a novel TLR4 agonist and further demonstrate the potential application of PSD as a vaccine adjuvant... - Recombinational cloningJaehong Park
Harvard Medical School, Cambridge, Massachusetts, USA
Curr Protoc Mol Biol . 2006..This unit summarizes strategies for generating expression-ready clones using two of the most popular recombinational cloning technologies, now commercially available from Invitrogen (Gateway) and BD Clontech (Creator)... - A functional genomic yeast screen to identify pathogenic bacterial proteinsNaomi L Slagowski
Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
PLoS Pathog 4:e9. 2008..In addition, because this assay only requires genomic DNA it is particularly valuable for studying pathogens that are difficult to genetically manipulate or dangerous to culture... - c-IAP1 cooperates with Myc by acting as a ubiquitin ligase for Mad1Lei Xu
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
Mol Cell 28:914-22. 2007..Our results demonstrate that c-IAP1 exerts its oncogenic functions by promoting the degradation of an important negative regulator in the Myc pathway... - Self-assembling protein microarraysNiroshan Ramachandran
Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141, USA
Science 305:86-90. 2004..We used the technology to map pairwise interactions among 29 human DNA replication initiation proteins, recapitulate the regulation of Cdt1 binding to select replication proteins, and map its geminin-binding domain... - Microarray-based method for monitoring yeast overexpression strains reveals small-molecule targets in TOR pathwayRebecca A Butcher
Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
Nat Chem Biol 2:103-9. 2006.... - Many paths to many clones: a comparative look at high-throughput cloning methodsGerald Marsischky
Institute of Proteomics, Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
Genome Res 14:2020-8. 2004..Alternative approaches to creating clones involving mixing of cloning methods, including gap-repair cloning, are also explored... - Tracking gene-disease relationships for high-throughput functional studiesYanhui Hu
Institute of Proteomics, Harvard Medical School, Cambridge, Mass, USA
Surgery 136:504-10. 2004 - The sentinel within: exploiting the immune system for cancer biomarkersKaren S Anderson
Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
J Proteome Res 4:1123-33. 2005..These advances are opening the door for targeted vaccine development, and for using immune response signatures as biomarkers for cancer diagnosis and monitoring... - Proteome-scale purification of human proteins from bacteriaPascal Braun
Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 99:2654-9. 2002..We observed that some domains in the Pfam database were found almost exclusively in proteins that were successfully purified and thus may have predictive character... - The FLEXGene repository: exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic eraLeonardo Brizuela
Department of Biological Chemistry and Molecular Pharmacology, Institute of Proteomics, Harvard Medical School, Boston, MA 02115, USA
Arch Med Res 33:318-24. 2002..Here we describe the rationale and construction of this resource and focus on the data obtained from the Saccharomyces cerevisiae project... - Applications of protein microarrays for biomarker discoveryNiroshan Ramachandran
Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, MA, USA
Proteomics Clin Appl 2:1444-59. 2008..In this review, we will discuss the application of protein microarray technologies that offer unique opportunities to find novel biomarkers... - G1/S cell cycle arrest provides anoikis resistance through Erk-mediated Bim suppressionNicole L Collins
Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
Mol Cell Biol 25:5282-91. 2005..These results provide a novel link between cell cycle arrest and survival, and this mechanism could contribute to the survival of nonreplicating, dormant tumor cells that avert apoptosis during early stages of metastasis... - Protein expression clone repositories for functional proteomicsJoseph Pearlberg
Harvard Institute of Proteomics, and Department of Biochemistry and Molecular Biology, Harvard Medical School, Boston, MA, USA
Curr Opin Chem Biol 8:98-102. 2004..Although still inchoate, these resources are already impacting the manner in which high-throughput functional screens are performed... - So, you want to look for biomarkers (introduction to the special biomarkers issue)Joshua Labaer
Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141, USA
J Proteome Res 4:1053-9. 2005..Central considerations of biomarker discovery and validation, particularly with respect to their intended clinical and research applications, are highlighted... - Bacterial cell-free system for high-throughput protein expression and a comparative analysis of Escherichia coli cell-free and whole cell expression systemsT V S Murthy
Harvard Institute of Proteomics, 320 Charles Street, Cambridge, MA 02141, USA
Protein Expr Purif 36:217-25. 2004.... - Genomics, proteomics, and the new paradigm in biomedical researchJoshua Labaer
Institute of Proteomics, Harvard Medical School, Boston, MA 02115, USA
Genet Med 4:2S-9S. 2002..The author's overview highlighted the recent history of the two fields and laid the foundation for the rest of the symposium presentations... - DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequencesChih-Yu Chang
Chemical Biology Platform, Broad Institute of Harvard and MIT Cambridge, MA 02141-2023, USA
Bioinformatics 21:2133-5. 2005..The application then reports the discrepancy as a polymorphism along with the corresponding GenBank reference information. AVAILABILITY: DPD is currently hosted by the Harvard Institute of Proteomics at http://www.hip.harvard.edu.. - Analysis of genomic and proteomic data using advanced literature miningYanhui Hu
Institute of Proteomics, Harvard Medical School-BCMP, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
J Proteome Res 2:405-12. 2003..Interestingly, this only held true for estrogen receptor (ER) positive tumors, not ER negative. MedGene identified a set of relatively understudied, yet highly expressed genes in ER negative tumors worthy of further examination... - Alpha-synuclein blocks ER-Golgi traffic and Rab1 rescues neuron loss in Parkinson's modelsAntony A Cooper
School of Biological Sciences, University of Missouri Kansas City, Kansas City, MO 64110, USA
Science 313:324-8. 2006..Thus, synucleinopathies may result from disruptions in basic cellular functions that interface with the unique biology of particular neurons to make them especially vulnerable... - A central repository for published plasmidsMelina Fan
Science 307:1877. 2005 - High-throughput generation of P. falciparum functional molecules by recombinational cloningJoão Carlos Aguiar
Malaria Program, Naval Medical Research Center, Silver Spring, Maryland 20910, USA
Genome Res 14:2076-82. 2004..falciparum genome and will provide for a resource for the malaria resource community distributed through public repositories... - A systematic approach for testing expression of human full-length proteins in cell-free expression systemsClaudia Langlais
MRC Toxicology Unit, Protein Profiling Group, Hodgkin Building, Lancaster Road, Leicester, LE1 9HN, UK
BMC Biotechnol 7:64. 2007..Here, we show a systematic approach to successfully express a full-length protein of interest by using cell-free and cell-based expression systems... - Mining the literature and large datasetsJoshua Labaer
Nat Biotechnol 21:976-7. 2003