Lab Member

ayadlin's picture
Alejandro Wolf-Yadlin
Principal Investigator: PI
ayadlin at uw.edu
Curriculum Vitae:

 

Research interests

Proteomics and Biology: The development and application of novel quantitative proteomics tools, such as mass spectrometry and lysate microarrays. Specifically, cellular signaling dynamics, receptor tyrosine kinase mediated pathways, and the molecular mechanisms of cancer and Alzheimer Disease.

 

Computational Biology: The application of established techniques such as neural networks, statistical models and bayesian inference to mine biological datasets, extract the topology of cellular signaling networks, and understand their role in determining cell phenotype in order to predict potential drug targets.

 

Education

 

2001–2007         Massachusetts Institute of Technology       Cambridge, MA

  • PhD Bioengineering.
  • Dissertation: Development of Mass Spectrometry Based Technologies for Quantitative Cell Signaling Phosphoproteomics: The Epidermal Growth Factor Receptor Family as a Model System

 

1999–2001         Universidad de Chile                                  Santiago, Chile

  • MS Chemical Engineering
  • Awarded six month grant for research done at Lund University, Sweden
  • Thesis: Determination of the Partition Coefficient of Proteins Based on the Aminoacids Exposed on the Protein Surface

 

1995-2001          Universidad de Chile                                  Santiago, Chile

  • BS Engineering and Biotechnology
  • Specialized degree in Biotechnology
  • Graduated Magna Cum Laude

 

 

Research Experience

 

11/2010–Present                    University of Washington           Seattle, WA

Assistant Professor

Description: Development and application of novel mass spectrometry techniques for the high throughtput study of cellular signaling. Current projects:

 

  • Development of antibody based sequential sample enrichement and two dimensional chromatography protocols for proteomics applications.
  • Elucidation of TRKB signaling and its roles in cancer and Alzheimre’s Disease in cell culture and in vivo systems
  • Elucidation of the role of tyrosine phosphorylation in WNT Signaling (with Dr. Randy Moon)
  • Characterization of the human kinome fragmentation patterns for Multiple Reaction Monitoring application (with Dr. Mike MacCoss)

 

2007–2010                      Harvard University                      Cambridge, MA

Post Doctoral Fellow

Advisor: Gavin MacBeath

Description: Conducted systematic data rich studies in order to understand the role of different receptor tyrosine kinases families in controlling cell signaling networks and determining their dynamic topology.

 

  • Cloned six receptor tyrosine kinases and generated six novel cell lines using Invitrogen Flp-In Technology.
  • Designed and applied a large-scale screen of commercially available antibodies for their use in lysate microarray experiments.
  • Validated shRNA reagents for the knockdown of proteins related to cellular signaling.
  • Designed and performed large-scale lysate microarray experiments, collecting over 500,000 independent data points for the elucidation of cellular signaling pathways downstream of six different receptor tyrosine kinases.
  • Designed and performed in vivo studies to elucidate protein expression and signaling along with the induction of tumor growth by cells expressing different receptor tyrosine kinases.

 

 

 

2001–2006         Massachusetts Institute of Technology       Cambridge, MA

Doctoral Candidate

Advisor: Douglas Lauffenburger and Forest White

Description: Develop mass spectrometry based methodologies to identify and quantify cellular phosphorylation events downstream of receptor tyrosine kinase activation. Specifically In particular examined how EGFR family mediated signaling controls cell phenotype.

 

  • Developed and tested antibodies against EGFR ectodomain to inhibit signaling. (Patent Accepted)
  • Designed and applied a novel mass spectrometry technique to quantify tyrosine phosphorylation temporal dynamics of complete pathways. Tested on the EGFR pathway.
  • Coupled mass spectrometry based quantitative phosphorylation studies, phenotypic response experiments and high throughput data analysis studies to better understand intracellular signals leading to different outcomes under different conditions.
  • Expanded mass spectrometry techniques for high throughput proteomics from information dependent acquisition (IDA) mode to multiple reaction monitoring mode (MRM) to obtain more robust data and high reproducibility across many biological conditions.

 

 

1995–2000     Universidad de Santiago/University of Lund      Chile/Sweden

Masters and Undergraduate Research

Advisor: Juan Asenjo  

 

  • Developed a predictive technique to determine the partition coefficient of proteins in low electrolyte aqueous two phase systems based on the protein crystal structure and amino acid hydrophobicity.  
  • Designed a Chimosyn enzyme production plant including devising               building infrastructure, chemical procedures and economic / market strategy

 

 

Publications

 

  • *  Sevecka M, Wolf-Yadlin A, MacBeath, G “Lysate Microarrays Enable High-throughput, Quantitative Investigations of Cellular Signaling”. Mol Cell Proteomics. 2011 Apr; 10(4):M110.005363. Epub 2011 Feb 4.

 

  • Locasale JW, Wolf-Yadlin, A. “Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data”. PLoS One. 2009 Aug 26; 4(8):e6522.

 

  • Wolf-Yadlin A, Sevecka M, MacBeath, G. “Dissecting Protein Function and Signaling Using Protein Microarrays”. Curr. Opin. Chem. Biol. 2009; 13(4):398-405. Epub 2009 Aug 5.

 

  • Gordus A, Krall JA, Beyer EM, Kaushansky A, Wolf-Yadlin A, Sevecka M, Chang BH, Rush J, MacBeath G. “Linear combinations of docking affinities explain quantitative differences in RTK signaling”. Mol Syst Biol. 2009; 5:235. Epub 2009 Jan 20.

 

  • Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. “Multiple Reaction Monitoring for Robust Quantitative Proteomic Analysis of Cellular Signaling Networks”. Proc Natl Acad Sci U S A. 2007; 104(14):5860-5. Epub 2007 Mar 26.

 

  • * Zhang Y, Wolf-Yadlin A, White FM. “Quantitative Proteomic Analysis of Phosphotyrosine-Mediated Cellular Signaling Networks”. Methods Mol Biol. 2007; 359(14):203-212.

 

  • Kumar N, Wolf-Yadlin A, White FM, Lauffenburger DA. “Modeling HER2 Effects on Cell Behavior from Mass Spectrometry Phosphotyrosine Data”. PLoS Comput Biol. 2007; 3(1):e4. Epub 2006 Nov 21.

 

  • Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova V, Lauffenburger DA, White FM. “Effects of HER2 overexpression on cell signaling networks governing proliferation and migration”. Mol Syst Biol. 2006; 2:54. Epub 2006 Oct 3.
  • * Zhang Y, Wolf-Yadlin A, Ross PL, Pappin DJ, Rush J, Lauffenburger DA, White FM. “ Time-resolved mass spectrometry of tyrosine phosphorylation sites in the EGF receptor signaling network reveals dynamic modules”. Mol Cell Proteomics. 2005; 4(9):1240-50. Epub 2005 Jun 11.

 

  • Berggren K, Wolf A, Asenjo JA, Andrews BA, Tjerneld F. “The surface exposed amino acid residues of monomeric proteins determine the partitioning in aqueous two-phase systems”. Biochim Biophys Acta. 2002; 1596(2):253-68.

 

*  In all papers marked with an * Wolf-Yadlin A is co-first author.

 

 

Presentations

 

  • “Lecture Series on Proteomics: Phosphoproteomics and Cellular Signaling Networks”

 

Cold Spring Harbor , NY July 23, 2010

 

  • “Deciphering Receptor Tyrosine Kinase Signaling Networks Conservation and Diversification Using Lysate Microarrays”

 

GeorgiaTech

Atlanta, GA March 1, 2010

 

  • “Developing Lysate Microarrays for Cellular Signaling Networks”

 

Merrimack Pharmaceuticals

    Cambridge, MA October 8, 2009.

 

  • “High Throughput Studies for the Elucidation of Cellular Signaling Networks Downstream of Receptor Tyrosine Kinases”

 

     Lightning Talk.

     Systems Biology of Human Disease

     Boston, MA June 18-19, 2009.

 

  • “Development of Mass Spectrometry Based Technologies for Quantitative Cell Signaling Phosphoproteomics: The Epidermal Growth Factor Receptor Family as a Model System".”

 

    5th International Symposium of the Austrian Proteomics Platform

    Seefeld, Austria January 20-23, 2008.

 

  • “Development of Mass Spectrometry Based Technologies for Quantitative Cell Signaling Phosphoproteomics.”

 

     Cancer Systems Biology Think Tank Seminar Series

     Dana-Faber Cancer Institute

     Boston, MA March 26, 2007.

 

  • “Quantitative Proteomic Analysis of Cellular Signaling Networks”

 

      Cell Circuits Program Meetings.

      Broad Institute (Harvard/MIT),

      Boston, MA: January 23, 2006.

 

  • “Quantitative Proteomic Analysis of Cellular Signaling Networks”

 

       Frontiers in Functional Genomics, Proteomics and Bioinformatics          

       Seminar Series

        Dana-Faber / Harvard Cancer Center

        Boston, MA: May 17, 2005.

 

  • “Comparative Phosphotyrosine Proteomics of the EGFR, HER2 and HER3 Pathways”

 

     Keystone Symposia Proteomics and Bioinformatics.

     Keystone, CO April 9, 2005.

 

 

 

Patents

 

Wolf-Yadlin, A., Chao, G., Olsen, M.J., Lauffenburger, D.A., Wittrup, K.D. “Growth Factor Receptor Polypeptides and Antibodies”. Patent filed February 15, 2006. US. Serial Number: 60/653,423.

 

 

Teaching experience

 

2003-2005          Massachusetts Institute of Technology       Cambridge, MA

Teaching Assistant

  • Courses: Tools for Assessing Biological Function; Laboratory Fundamentals in Biological Engineering
  • Designed and led lectures four times a week on design and applications of bioreactors
  • Collaborated with other teaching assistants to supervise students’ laboratory work
  • Assisted student in final laboratory presentations
  • Advised students through their courses

2003-2005          Universidad de Chile                                  Santiago, Chile

Senior Teaching Assistant

  • Courses: Physical Chemistry; Modern Chemistry; Metabolic Engineering and Fermentation; Enzymology and Protein Structure
  • Led supplementary lectures for courses of 60-160 students
  • Oversaw junior teaching assistants
  • Responsible for monitoring students’ progress

 

 

Awards and honors

 

  • 2009 Awarded Best Poster at System Biology for Human Disease Conference
  • 2006 Daniel K. Ludwig Fellowship recipient for cancer research
  • 2005 Best Poster award GTCbio 2nd International Conference on Tumor Progression & Therapeutic Resistance
  • 2001-2002 Du Pont Fellowship for first year graduate students at MIT
  • 2000 European Community alpha scholarship for graduate students