Joshua Labaer

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. ncbi request reprint [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
  2. ncbi request reprint Protein microarrays as tools for functional proteomics
    Joshua 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
  3. pmc PlasmID: a centralized repository for plasmid clone information and distribution
    Dongmei Zuo
    Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141, USA
    Nucleic Acids Res 35:D680-4. 2007
  4. pmc Next-generation high-density self-assembling functional protein arrays
    Niroshan Ramachandran
    Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nat Methods 5:535-8. 2008
  5. pmc A biomedically enriched collection of 7000 human ORF clones
    Andreas Rolfs
    Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, USA
    PLoS ONE 3:e1528. 2008
  6. pmc Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae
    Yanhui Hu
    Harvard Institute of Proteomics, Harvard Medical School, Cambridge, MA 02141, USA
    Genome Res 17:536-43. 2007
  7. pmc The Pseudomonas aeruginosa PA01 gene collection
    Joshua Labaer
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Institute of Proteomics, Cambridge, Massachusetts 02141, USA
    Genome Res 14:2190-200. 2004
  8. pmc A full-genomic sequence-verified protein-coding gene collection for Francisella tularensis
    Tal 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
  9. pmc Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer
    Karen S Anderson
    Cancer Vaccine Center, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    J Proteome Res 10:85-96. 2011
  10. pmc Building a human kinase gene repository: bioinformatics, molecular cloning, and functional validation
    Jaehong 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

Collaborators

Detail Information

Publications43

  1. ncbi request reprint [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
  2. ncbi request reprint Protein microarrays as tools for functional proteomics
    Joshua 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...
  3. pmc PlasmID: a centralized repository for plasmid clone information and distribution
    Dongmei 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...
  4. pmc Next-generation high-density self-assembling functional protein arrays
    Niroshan 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...
  5. pmc A biomedically enriched collection of 7000 human ORF clones
    Andreas 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...
  6. pmc Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae
    Yanhui 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...
  7. pmc The Pseudomonas aeruginosa PA01 gene collection
    Joshua 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...
  8. pmc A full-genomic sequence-verified protein-coding gene collection for Francisella tularensis
    Tal 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...
  9. pmc Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer
    Karen S Anderson
    Cancer Vaccine Center, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    J Proteome Res 10:85-96. 2011
    ..05). Using all 28 AAb, a classifier was identified with a sensitivity of 80.8% and a specificity of 61.6% (AUC = 0.756). These are potential biomarkers for the early detection of breast cancer...
  10. pmc Building a human kinase gene repository: bioinformatics, molecular cloning, and functional validation
    Jaehong 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...
  11. pmc Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio cholerae
    Andreas 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...
  12. pmc Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer
    Abigail E Witt
    Department of Cell Biology, Harvard Medical School, Boston Massachusetts 02115, USA
    J Proteome Res 5:599-610. 2006
    ....
  13. pmc Application of protein microarrays for multiplexed detection of antibodies to tumor antigens in breast cancer
    Karen 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...
  14. ncbi request reprint On-chip protein synthesis for making microarrays
    Niroshan 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...
  15. pmc A novel approach to sequence validating protein expression clones with automated decision making
    Elena 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...
  16. pmc Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays
    Wagner 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...
  17. ncbi request reprint Many paths to many clones: a comparative look at high-throughput cloning methods
    Gerald 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...
  18. ncbi request reprint Self-assembling protein microarrays
    Niroshan 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...
  19. ncbi request reprint Protein expression clone repositories for functional proteomics
    Joseph 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...
  20. pmc Vibrio cholerae proteome-wide screen for immunostimulatory proteins identifies phosphatidylserine decarboxylase as a novel Toll-like receptor 4 agonist
    Ann 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...
  21. ncbi request reprint Emerging tools for real-time label-free detection of interactions on functional protein microarrays
    Niroshan 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...
  22. pmc Tracking humoral responses using self assembling protein microarrays
    Niroshan 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...
  23. ncbi request reprint The FLEXGene repository: exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic era
    Leonardo 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...
  24. pmc G1/S cell cycle arrest provides anoikis resistance through Erk-mediated Bim suppression
    Nicole 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...
  25. ncbi request reprint Bacterial cell-free system for high-throughput protein expression and a comparative analysis of Escherichia coli cell-free and whole cell expression systems
    T V S Murthy
    Harvard Institute of Proteomics, 320 Charles Street, Cambridge, MA 02141, USA
    Protein Expr Purif 36:217-25. 2004
    ....
  26. ncbi request reprint Tracking gene-disease relationships for high-throughput functional studies
    Yanhui Hu
    Institute of Proteomics, Harvard Medical School, Cambridge, Mass, USA
    Surgery 136:504-10. 2004
  27. pmc A functional genomic yeast screen to identify pathogenic bacterial proteins
    Naomi 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...
  28. doi request reprint Recombinational cloning
    Jaehong 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)...
  29. ncbi request reprint c-IAP1 cooperates with Myc by acting as a ubiquitin ligase for Mad1
    Lei 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...
  30. ncbi request reprint Microarray-based method for monitoring yeast overexpression strains reveals small-molecule targets in TOR pathway
    Rebecca 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
    ....
  31. ncbi request reprint Genomics, proteomics, and the new paradigm in biomedical research
    Joshua 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...
  32. pmc The sentinel within: exploiting the immune system for cancer biomarkers
    Karen 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...
  33. pmc Proteome-scale purification of human proteins from bacteria
    Pascal 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...
  34. pmc Cooperation of the ErbB2 receptor and transforming growth factor beta in induction of migration and invasion in mammary epithelial cells
    Sarah E Seton-Rogers
    Department of Cell Biology and Harvard Institute of Proteomics, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 101:1257-62. 2004
    ....
  35. pmc Applications of protein microarrays for biomarker discovery
    Niroshan 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...
  36. ncbi request reprint 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...
  37. ncbi request reprint DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequences
    Chih Yu Chang
    Chemical Biology Platform, Broad Institute of Harvard and MIT Cambridge, MA 02141 2023, USA
    Bioinformatics 21:2133-5. 2005
    ..If matching DNA sequences are found, DPD verifies that they are from the same gene. The application then reports the discrepancy as a polymorphism along with the corresponding GenBank reference information...
  38. ncbi request reprint Analysis of genomic and proteomic data using advanced literature mining
    Yanhui 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...
  39. ncbi request reprint Mining the literature and large datasets
    Joshua Labaer
    Nat Biotechnol 21:976-7. 2003
  40. pmc A systematic approach for testing expression of human full-length proteins in cell-free expression systems
    Claudia 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...
  41. pmc Alpha-synuclein blocks ER-Golgi traffic and Rab1 rescues neuron loss in Parkinson's models
    Antony 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...
  42. ncbi request reprint A central repository for published plasmids
    Melina Fan
    Science 307:1877. 2005
  43. pmc High-throughput generation of P. falciparum functional molecules by recombinational cloning
    João 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...