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Avery Tong

89 Freeman Street,

Quincy, MA 02185

Cell Phone: 832-225-6818

Email: avery_tong2009@yahoo.com

Highlights of Qualifications

• 10 years industrial & academic programming experience in Java, Javascripts,AJAX, GWT, Perl, C++, C#, SQL, and XML, and hibernate

·         Software toolsfor genome annotation and bioinformatics studies published in Bioinformatics Journals.

·         Web site development (http://safegene.hms.harvard.edu/zak and http://dev.safegene.hms.harvard.edu/zak (Harvard Internal ONLY)) from front to back end. Backend work on (http://genotator.hms.harvard.edu/geno/)

• 6 years’ experience in biological data curation, QC, analysis, ranging from single nucleotide polymorphism, whole genome sequence analysis, to microarray data, from raw sequence data to annotated data.
• Certified Programmer for Java 2 Platform since 2001
• Solid experience in RDBMS (MySQL, SQL Server and Oracle), including database design, web based database programming (JSP, ASP), HIBERNATE, database synchronization, database backup and restoration.
• Experience with software development tools, such as Eclipse, IntelliJ,Tomcat, JBoss, Microsoft Visual Studio and .NET 2005, Visual Cafe, IIS, Apache Web Server, Yahoo YUI , and other testing tools ANT, JUnitTest, and Microsoft Interdev
• Working experience of OOA, OOP, bioinformatics software, algorithms and statistics
• Solid experiences in software development, from requirement specification to system testing
• UMLS, SNOMED, Mesh, and Human Disease ontologies.
• US citizen

Professional Experience

Harvard Medical School, CBMI, Boston, MA.  07/2009--Present

Eureka Project:

Created a combined database that merged HGMD, OMIM (text file), GWAS (text file), PharmGKB (text file), and Countsyl (text file) into a searchable database, structured databases.

Created a tool on variants validation and was published on Bioinformatics. (http://www.ncbi.nlm.nih.gov/pubmed/21258063).  In this work, we classified variants disagreement between published works and current genome databases and provided a tool for validating any amino acid changes regarding their consistence with NCBI databases.

Developed a dynamic program with cooperators that dynamically that retrieves information from 11 website on gene annotations with their association with diseases.   This worked is published on BMD Med Genomics (http://www.ncbi.nlm.nih.gov/pubmed/21034472).

Created a website, for searching, editing, viewing, annotating and managing of genetic variants associated with clinical diagnostics (http://devsafegene.hms.harvard.edu/zak). On the search of variants from database by diseases, UMLS, Mesh, Human Disease Ontology and SNOMED terms are used.

Created a database of variants associated with congenital diseases, with allele frequencies, inheritance patterns, incidences, Pubmed ID, and genetic annotations.

Wyeth Pharmaceutical, Cambridge, MA 11/2008-June, 2009

Bioinformatics Consultant

Responsible for the enhancement of Abacus, a web based program for antibody sequence data analysis used by scientists in Wyeth using Java, Java Swing (Tree), RMI, Client/Server, SQL, Hibernate, XML, and GWT . Database is Oracle.

Enhancement -- WyseCat Search

Implemented a software that allows user to search through sample name or request id, tabular display of samples information allowing user to select the samples for structural analysis and frame work identifications.

Enhancement -- FASTA Export

Implemented a program that allow users to export selected antibody protein or nucleotide sequences by antibody structural frame work in FASTA format.

Enhancement -- Analysis Configuration Setup and Management

Implemented functions that allows users to configure their analysis parameters by create, copy/paste from other users for a for antibody structural analysis.

Implemented analysis configuration management program that allows users to management their own setups. Existing setups are displayed in Display in both GWT Tree and tabular forms. Create, copy, delete and editing operations are enabled in both tree node and table row selection.

Seralogix, Austin, TX 02/2008 -- 07/2008

Bioinformatics Developer

Design, coding, and testing of a software program finding transcription factors involved in gene expression using data from microarray analysis Using Java and Java Swing, J2EE(JSP, Client/Server), XML, SQL. Database is MySQL.

Pathway analysis using Seralogix’s X-Manager for protein microarray data

Design, coding, and testing of software finding the location of genes relative to heterochromatin and GC rich region

Web site, database, and software maintenance(Tomcat web server, Mysql database server, and Java servlet template).

Bioinformatics support and data management

Baylor College of Medicine, Houston, TX 5/2005 - 01/2008

Bioinformatics  Programmer

Developed a web based program that displays and downloads user selected sets of genes and attributes in tabular form. Java, J2EE (JSP,Struts), JavaScript,CSS, XML, SQL are used. Database is MySQL.

Developed a web based program that allows user to edit, delete, shift, add, rename, copy, and reassign biological data on individual or group basis.

Enhancement of user data management systems, including user management and user’s data management.

Developed a web-based program that uploads, downloads, and display user selected set of biological samples.

Database optimization. Resolved issues generated from sorting and displaying super large data set in applications of multi-paged view and download.

  

Third Wave Technologies, Madison, WI 10/2003 -- 05/2005

Java programmer

Developed a Java program that accepts gene name and mutation name, find gene information in oracle database, retrieves the DNA sequence from public database, and display the desired sequence with polymorphic site bracketed. Java, POI, JFreeChart are used. Database is Oracle.

Developed a Java program that marks DNA sequence with Single Nucleotide Polymorphisms found from both internal database and internet, mark the polymorphism sites with IUPAC code, and used for assay design and primer design

Developed a Java program that parses Microsoft Excel files. Parsed information is loaded into specific tables in oracle database. Jakarta.apache.POI is used.

Developed several Microsoft Excel templates for Invader lab data processing and display, which import raw data from machine readings, analyze the samples for genotype results, and display individual and summary results. Software is written using VBA.

Bioinformatics support and product design for Cystic Fibrosis, FII, FV, HCV, RETT etc, including assay design and data mining for SNPs, insertion/deletion, and mutation frequencies by disease and population.

Developed a Java program that accepts customer sequences and id, designs probes and invader oligos, and order the designed oligos from third party companies.

Maintained and improved company production software for automated diagnostics probe design.

Massachusetts General Hospital /MIT Broad Institute 03/2002 -- 10/2003

Java Developer

Software Development and Sequence Quality Analysis

Designed and implemented a software pipeline that analyzes genes for DNA sequence quality and project progress. Sequencing files produced from ABI sequencer are read into Perl programs, aligned using Phrap, and the Phred scores of each based are parsed into oracle database. Information from each assay is grouped based on gene name and locations in gene structure. Qualities of each base are summarized based on all the samples sequenced and the nature of the base in gene structure. The results are displayed on the internet and saved as word files with graphics. Tomcat and Struts are used in programming. . Served Mitog and medical population genetics group and report was used for HapMap project. Java, Java Swing are used. Database is Oracl

Publications:

Automated validation of genetic variants from large databases: ensuring that variant references refer tothe same genomic locations.  Tong MY, Cassa CA, Kohane IS.   Bioinformatics. 2011 Mar 15;27(6):891-3. Epub011 Jan 22.

Genotator: a disease-agnostic tool for genetic annotation of disease.Wall DP, Pivovarov R, Tong M, Jung JY, Fusaro VA, DeLuca TF, Tonellato PJ.  BMC Med Genomics. 2010 Oct 29;3:50.

The genome of the sea urchin Strongylocentrotuspurpuratus.  Sea Urchin Genome Sequencing Consortium, et all, Science. 2006 Nov 10;314(5801):941-52.

Education

Ph.D. Genetics, University of California at Davis

MS Computer Science, University of Texas at Dallas; Richardson, Texas

References:

Available on request.

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