| Dr Sarah Boyd | ||||||||||||||||||||
| Australian Postdoctoral Research Fellow | ||||||||||||||||||||
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| Research | ||||||||||||||||||||
| I am interested in the application of computers to biological problems (referred to as bioinformatics), particularly in the area of molecular biology. My current research focuses on the ability to use computer programs to predict the behaviour of proteases, enzymes that act on proteins. As part of my research I have written the computational system PoPS (Prediction Of Protease Specificity). Much of this work formed the basis of my PhD thesis. Currently, my research is particularly focussed on cooperativity within the subsites of proteases. I work on problems of how to design and analyse laboratory experiments to find important information in this combinatorial search spaces, making the most of limited (and expensive!) laboratory resources. I collaborate with Australian and international researchers on this work. | ||||||||||||||||||||
| More recently, I have also started working on research for pathway visualisation for systems biology. I am working with Prof Kim Marriott and his Adaptive Diagrams and Documents laboratory researching constrained layout for biological networks, and developing Dunnart for this purpose. I am also interested in the developments of standards for systems biology, including the Systems Biology Graphical Notation, and systems biology file exchange formats such as SBML and BioPax. | ||||||||||||||||||||
| I currently hold an Australian Postdoctoral Fellowship, and an Australian Research Council Discovery Project grant. | ||||||||||||||||||||
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| Publications | ||||||||||||||||||||
| Ng NM, Pike RN, Boyd SE.
Subsite cooperativity in protease specificity. Biol Chem. 2009; vol 390 (5-6): pp 401-7. [PubMed] | ||||||||||||||||||||
| Boyd SE, Kerr FK, Albrecht DW, Garcia de la Banda M, Ng N, Pike RN.
Cooperative effects in the substrate specificity of the complement protease C1s. Biol Chem. 2009; vol 390 (5-6): pp 503-7. [PubMed] | ||||||||||||||||||||
| Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM.
PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res. 2009; vol 37 (Database issue): pp D611-8. [PubMed] | ||||||||||||||||||||
| Kerr FK, Thomas AR, Wijeyewickrema LC, Whisstock JC, Boyd SE, Kaiserman D, Matthews AY, Bird PI, Thielens NM, Rossi V, Pike RN
Elucidation of the substrate specificity of the MASP-2 protease of the lectin complement pathway and identification of the enzyme as a major physiological target of the serpin, C1-inhibitor Mol Immunol. 2008 Feb; vol 45(3): pp 670-7. [PubMed] | ||||||||||||||||||||
| Furmonaviciene R, Ghaemmaghami AM, Boyd SE, Jones NS, Bailey K, Willis AC, Sewell HF, Mitchell DA, Shakib F
The protease allergen Der p 1 cleaves cell surface DC-SIGN and DC-SIGNR: experimental analysis of in silico substrate identification and implications in allergic responses Clin Exp Allergy. 2007 Feb; vol 37 (2): pp 231-42. [PubMed] | ||||||||||||||||||||
| Kerr FK, O'Brien G, Quinsey NS, Whisstock JC, Boyd S, Garcia de la Banda M, Kaiserman D, Matthews AY, Bird PI, Pike RN
Elucidation of the Substrate Specificity of the C1s Protease of the Classical Complement Pathway J. Biol. Chem. 2005 Nov 25; vol 280 (47): pp 39510-39514. [PubMed] | ||||||||||||||||||||
| Golubkov VS, Boyd S, Savinov AY, Chekanov AV, Osterman AL, Remacle A, Rozanov DV, Doxsey SJ, Strongin AY
Membrane Type-1 Matrix Metalloproteinase (MT1-MMP) Exhibits an Important Intracellular Cleavage Function and Causes Chromosome Instability J Biol Chem. 2005 Jul 1; vol 280 (26): pp 25079-86. [PubMed] | ||||||||||||||||||||
| Boyd SE, Garcia de la Banda M, Pike RN, Whisstock JC, Rudy GB
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity J Bioinform Comput Biol. 2005 Jun; vol 3 (3) [Pubmed] | ||||||||||||||||||||
| Boyd SE, Garcia de la Banda M, Pike RN, Whisstock JC, Rudy GB
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity Proc IEEE Comput Syst Bioinform Conf, pp 372-381, Stanford, CA, August 2004. [Paper pdf] [Pubmed] [IEEE Xplore] | ||||||||||||||||||||
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| Grants | ||||||||||||||||||||
| 2007-2009 Australian Research Council Discovery Grant: "Computational techniques for protease research"
Chief Investigator: SE Boyd | ||||||||||||||||||||
| 2004 Monash Small Grant: "A docking approach to model protease specificity"
Chief Investigator: Dr. Maria Garcia de la Banda Partner Investigators: SE Boyd, RN Pike and JC Whisstock | ||||||||||||||||||||
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| Teaching/Supervision | ||||||||||||||||||||
| PhD: Natasha Ng [Associate supervisor, current, Monash Uni] | ||||||||||||||||||||
| Supervision of summer students and advanced undergraduate students | ||||||||||||||||||||
| Teaching: Third year projects, undergraduate tutoring, occasional lecturing and seminars | ||||||||||||||||||||
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