Programmer: data mining, machine learning, anti-spam, bioinformatics
San Francisco Bay Area
- Current
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- Senior Software Engineer at Zvents
- Past
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- Research Engineer at Zvents
- Senior Data Engineer at Proofpoint
- Data Engineer at Proofpoint
- Systems Programmer/Unix Account Manager at Incyte Genomics
- Bioinformatics Programmer at Incyte Genomics
- Senior Bioinformatics Associate at Incyte Pharmaceuticals
- Bioinformatics Associate at National Center for Genome Resources
- GenBank Annotator at Los Alamos National Laboratory
- Education
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- St. John's College
- St. John's College
- Recommended
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4 people have recommended John Markos - Connections
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261
connections
- Industry
- Computer Software
- Websites
John Markos O'Neill’s Summary
Over ten years of experience in data mining and analysis, informatics, and software development, working for public, private, and non-profit firms. Technical application lead of a multi-million dollar project. Experience in machine learning, anti-spam, and distributed computing, working directly with customers and users to make their jobs easier.
John Markos O'Neill’s Specialties:
Machine learning, data mining, data analysis, anti-spam, e-mail, dataflow, bioinformatics, Linux, Ruby on Rails, Perl, distributed computing
John Markos O'Neill’s Experience
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Senior Software Engineer
Zvents
(Privately Held; 11-50 employees; Internet industry)
September 2008 — Present (3 months)
I'm building data mining and content analysis tools to help create the world's most advanced and usable local search.
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Research Engineer
Zvents
(Privately Held; 11-50 employees; Internet industry)
November 2006 — September 2008 (1 year 11 months)
Developed and automated tools for content insertion, analysis, and publication.
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Senior Data Engineer
Proofpoint
(Privately Held; 51-200 employees; Computer Software industry)
January 2005 — November 2006 (1 year 11 months)
Lead new projects to increase effectiveness in fighting spam.
Designed and implemented new classifier features and improvements to data architecture. -
Data Engineer
Proofpoint
(Privately Held; 51-200 employees; Computer Software industry)
January 2004 — January 2005 (1 year 1 month)
Data mining and updates of Proofpoint's anti-spam models.
Generated new features based on emerging spam attacks.
Developed "honeypots," spam-gathering utilities.
Analyzed and captured spam messages for update process.
Worked with customers to stop emerging spam campaigns. -
Systems Programmer/Unix Account Manager
Incyte Genomics
(Public Company; 501-1000 employees; INCY; Research industry)
July 2001 — November 2002 (1 year 5 months)
Managed Unix and Linux accounts for over 100 users in a production bioinformatics, dataflow, and data analysis environment.
Administered production Unix and Linux machines.
Administered and configured a distributed computing cluster (running Platform LSF) of over 1,000 machines.
Wrote programs to automate cluster status reporting and administration. -
Bioinformatics Programmer
Incyte Genomics
(Public Company; 501-1000 employees; INCY; Biotechnology industry)
June 1999 — July 2001 (2 years 2 months)
Technical application lead on Linux farm project, which was both used in-house and sold to outside customers. Co-designed, wrote, documented, and maintained job distribution software, as well as a parallel application launcher, for several clusters of Pentium computers, controlling over 2,000 CPUs.
The project saved Incyte several million dollars in hardware costs by moving the majority of data processing from expensive servers to much cheaper PCs. -
Senior Bioinformatics Associate
Incyte Pharmaceuticals
(Public Company; 501-1000 employees; INCY; Biotechnology industry)
November 1997 — June 1999 (1 year 8 months)
Ran dataflow for Incyte's plant database, defining schedules between sequencing, product science, and legal departments. Screened and annotated several hundred thousand sequences, preparing and analyzing them for release, meeting an aggressive schedule.
Wrote wrapper scripts for dataflow programs to minimize manual processing of data.
Benchmarked different hardware platforms to evaluate cost/performance. This work led to the Linux farm project. -
Bioinformatics Associate
National Center for Genome Resources
(Non-Profit; 11-50 employees; Biotechnology industry)
June 1994 — August 1997 (3 years 3 months)
Annotated and curated Genome Sequence DataBase (GSDB), a public DNA sequence database. GSDB was a major project of the non-profit National Center for Genome Resources.
Served as primary contact for four large genome centers, processing large and multiple sequence submissions into the relational database.
Tested and evaluated GSDB Annotator software. -
GenBank Annotator
Los Alamos National Laboratory
(Government Agency; 10,001 or more employees; Research industry)
August 1993 — June 1994 (11 months)
Trained offsite users in submission file format, answering detailed questions about data insertion.
Assured data quality by checking submissions for correct syntax and accurate biological information.
John Markos O'Neill’s Education
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St. John's College
B.A., Liberal Arts, 1991 — 1993
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St. John's College
Liberal Arts 1989 — 1991
Additional Information
John Markos O'Neill’s Websites:
John Markos O'Neill’s Interests:
programming, scripting, Ruby on Rails, Ruby, Perl, Linux, distributed computing, events, search, bioinformatics, genome, genomics, machine learning, anti-spam, GTD, environment, sustainability, ecological footprint, renewable energy, bicycling, ethics, free speech, free culture
John Markos O'Neill’s Contact Settings
Interested In:
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