Sachdev S Sidhu

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. doi request reprint Antibodies for all: The case for genome-wide affinity reagents
    Sachdev S Sidhu
    Banting and Best Department of Medical Research, University of Toronto, The Donnelly Centre, 160 College Street, Toronto, Ontario, Canada
    FEBS Lett 586:2778-9. 2012
  2. pmc Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps
    Kevin Y Yip
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    BMC Biol 9:53. 2011
  3. pmc MOTIPS: automated motif analysis for predicting targets of modular protein domains
    Hugo Y K Lam
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    BMC Bioinformatics 11:243. 2010
  4. pmc MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets
    TaeHyung Kim
    The Donnelly Centre, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S 3E1
    Nucleic Acids Res 40:e47. 2012
  5. pmc SH3 interactome conserves general function over specific form
    Xiaofeng Xin
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Mol Syst Biol 9:652. 2013
  6. doi request reprint Recombinant genetic libraries and human monoclonal antibodies
    Jarrett J Adams
    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
    Methods Mol Biol 1060:149-70. 2014
  7. doi request reprint Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains
    Joan Teyra
    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada ON M5S 3E1
    FEBS Lett 586:2631-7. 2012
  8. pmc Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes
    Ylva Ivarsson
    Department of Molecular Genetics, Department of Computer Science, Donnelly Centre, University of Toronto, Toronto, ON, Canada M5S 3E1
    Proc Natl Acad Sci U S A 111:2542-7. 2014
  9. pmc The multiple-specificity landscape of modular peptide recognition domains
    David Gfeller
    Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Mol Syst Biol 7:484. 2011
  10. doi request reprint Studying binding specificities of peptide recognition modules by high-throughput phage display selections
    Haiming Huang
    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
    Methods Mol Biol 781:87-97. 2011

Collaborators

Detail Information

Publications25

  1. doi request reprint Antibodies for all: The case for genome-wide affinity reagents
    Sachdev S Sidhu
    Banting and Best Department of Medical Research, University of Toronto, The Donnelly Centre, 160 College Street, Toronto, Ontario, Canada
    FEBS Lett 586:2778-9. 2012
    ..In turn, such a revolution would pay huge dividends by closing the gap between basic research and therapeutic development, thus enabling the development of myriad new therapies for unmet medical needs...
  2. pmc Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps
    Kevin Y Yip
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    BMC Biol 9:53. 2011
    ..They mediate protein-protein interactions by recognizing and binding short motifs in their ligands. Although a great deal is known about PRDs and their interactions, prediction of PRD specificities remains largely an unsolved problem...
  3. pmc MOTIPS: automated motif analysis for predicting targets of modular protein domains
    Hugo Y K Lam
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    BMC Bioinformatics 11:243. 2010
    ..However, predicting domain targets by motif sequence alone without considering other genomic and structural information has been shown to be lacking in accuracy...
  4. pmc MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets
    TaeHyung Kim
    The Donnelly Centre, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S 3E1
    Nucleic Acids Res 40:e47. 2012
    ..We demonstrate the performance of MUSI by analyzing recent phage display data for human SH3 domains as well as microarray data for mouse transcription factors...
  5. pmc SH3 interactome conserves general function over specific form
    Xiaofeng Xin
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Mol Syst Biol 9:652. 2013
    ..Nevertheless, orthologous SH3 domain-mediated interactions are highly rewired. Our results suggest a model of network evolution where general function of the SH3 domain network is conserved over its specific form...
  6. doi request reprint Recombinant genetic libraries and human monoclonal antibodies
    Jarrett J Adams
    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
    Methods Mol Biol 1060:149-70. 2014
    ..Together these methodologies allow us to produce human monoclonal antibodies to manipulate the human proteome. ..
  7. doi request reprint Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains
    Joan Teyra
    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada ON M5S 3E1
    FEBS Lett 586:2631-7. 2012
    ..We discuss SH3 and PDZ domains as well characterized examples, and we explore the feasibility of expanding high-throughput experiments to other peptide-binding domains...
  8. pmc Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes
    Ylva Ivarsson
    Department of Molecular Genetics, Department of Computer Science, Donnelly Centre, University of Toronto, Toronto, ON, Canada M5S 3E1
    Proc Natl Acad Sci U S A 111:2542-7. 2014
    ..The method can be extended to interrogate all potential eukaryotic, bacterial, and viral SLiMs and we suggest it will be a highly valuable approach for studying cellular and pathogen-host protein-protein interactions. ..
  9. pmc The multiple-specificity landscape of modular peptide recognition domains
    David Gfeller
    Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Mol Syst Biol 7:484. 2011
    ..Overall, our results reveal a rich specificity landscape in peptide recognition domains, suggesting new ways of encoding specificity in protein interaction networks...
  10. doi request reprint Studying binding specificities of peptide recognition modules by high-throughput phage display selections
    Haiming Huang
    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
    Methods Mol Biol 781:87-97. 2011
    ..These high-throughput methods greatly expedite the study of PRM families on a genome-wide scale...
  11. ncbi request reprint Engineering and analysis of peptide-recognition domain specificities by phage display and deep sequencing
    Megan E McLaughlin
    Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
    Methods Enzymol 523:327-49. 2013
    ..This approach to studying peptide recognition can be applied to other domains and to a variety of structural and functional models by tailoring the combinatorial library design and selection pressures accordingly...
  12. doi request reprint Synthetic antibody libraries
    Bryce Nelson
    Department of Molecular Genetics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
    Methods Mol Biol 899:27-41. 2012
    ..Since these methods rely entirely upon standard supplies, equipment, and methods, construction of such libraries can be performed by any molecular biology laboratory...
  13. doi request reprint Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing
    Andreas Ernst
    Banting and Best Department of Medical Research, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada
    Mol Biosyst 6:1782-90. 2010
    ..The details of intramolecular cooperativity remain to be elucidated, but nonetheless, we have established a general methodology that can be used to explore protein evolution in a systematic yet rapid manner...
  14. ncbi request reprint Targeting HER2+ breast cancer cells: lysosomal accumulation of anti-HER2 antibodies is influenced by antibody binding site and conjugation to polymeric nanoparticles
    Shawn C Owen
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada Department of Chemistry, University of Toronto, Toronto, Canada
    J Control Release 172:395-404. 2013
    ..Given the importance of lysosomal targeting, these results demonstrate the importance of understanding the influence of the antibody-conjugate on cell trafficking for ultimate optimization of treatment selection. ..
  15. pmc Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs
    David Gfeller
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne, Switzerland
    PLoS ONE 9:e94507. 2014
    ..We confirm these predictions by experimentally validating a selected subset with ELISA. Our work also highlights the importance of better characterizing linear motifs in proteins as many of these can be affected by genetic variations. ..
  16. pmc CDR-H3 diversity is not required for antigen recognition by synthetic antibodies
    Helena Persson
    Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1
    J Mol Biol 425:803-11. 2013
    ....
  17. pmc Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
    Raffi Tonikian
    Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    PLoS Biol 7:e1000218. 2009
    ....
  18. doi request reprint Simplified synthetic antibody libraries
    Saravanan Rajan
    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
    Methods Enzymol 502:3-23. 2012
    ..Most importantly, these simplified methods rely on standard supplies, equipment, and methods that are accessible to any molecular biology laboratory...
  19. doi request reprint Interaction domains of Sos1/Grb2 are finely tuned for cooperative control of embryonic stem cell fate
    Greg M Findlay
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
    Cell 152:1008-20. 2013
    ..This optimized system ensures that PrE lineage commitment occurs in a timely and selective manner during embryogenesis...
  20. doi request reprint Selecting and purifying autonomous human variable heavy (VH) domains
    Raffi Tonikian
    Terrence Donnelly Center for Cellular and Biomolecular Research and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
    Methods Mol Biol 911:327-53. 2012
    ..Subsequently, autonomous VH domains are characterized and chosen using standard biophysical methods...
  21. doi request reprint Synthetic antibodies as tools to probe RNA-binding protein function
    John D Laver
    Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
    Mol Biosyst 8:1650-7. 2012
    ..Given that synthetic antibody selection protocols are amenable to high-throughput antibody production, these results demonstrate that synthetic antibodies can be powerful tools for genome-wide studies of RBP function...
  22. pmc Peptide binding properties of the three PDZ domains of Bazooka (Drosophila Par-3)
    Cao Guo Yu
    Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
    PLoS ONE 9:e86412. 2014
    ..Thus, the peptide binding pockets of each PDZ domain in Baz are not obviously affected by the presence of neighbouring PDZ domains, but act as isolated modules with specific in vitro peptide binding preferences. ..
  23. ncbi request reprint Synthetic antibody technologies
    Jarrett J Adams
    Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Donnelly CCBR, 160 College Street, Toronto, Ontario M5S 3E1, Canada
    Curr Opin Struct Biol 24:1-9. 2014
    ..Here we review recent advances in structural biology facilitated by synthetic antibodies, as well as advances in library designs and selection methods. ..
  24. pmc KIF14 negatively regulates Rap1a-Radil signaling during breast cancer progression
    Syed M Ahmed
    Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A1, Canada
    J Cell Biol 199:951-67. 2012
    ....
  25. doi request reprint Evolving specificity from variability for protein interaction domains
    Tomonori Kaneko
    Department of Biochemistry and the Siebens Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
    Trends Biochem Sci 36:183-90. 2011
    ..Thus, the conformational and sequence variability afforded by surface loops and binding sites provides a general mechanism by which to encode the wide spectrum of specificities observed for modular protein interaction domains...