Education

M.S. Northeastern University – Bioinformatics, 2003
B.S. Cornell University – Biology, 1997

Research and Work Experience

2009-PRESENT, FREELANCE

Bioinformatics, web and database programmer

Clients: Joslin Diabetes Center, MIT (Mark Bathe Lab), Maine Student Film and Video Festival, University of Texas at Austin (Hans Hofmann Lab), Digizyme, Emil Altschuler.
See josiahaltschuler.com for project descriptions.

2008-2009, DANA-FARBER CANCER INSTITUTE

Bioinformatics Engineer

- Cistrome: http://cistrome.dfci.harvard.edu – A database of cis-acting targets of trans-acting factors on a genome scale, accompanied by pipelined tools to analyze ChIP-chip and ChIP-seq data. Involved administering a Linux cluster, database, web server, and integrating various statistical analysis tools using the Django web framework for Python. (Under development.)
- SEQPOS: http://cistrome.dfci.harvard.edu/seqpos.html – Python web interface for a DNA motif discovery algorithm based on tendency for DNA-protein interaction to be centered within ChIPenriched sequences from ChIP-chip data.
- A variety of smaller scripts written in PHP, Perl, Python, Unix

2005-2008, INDEPENDENT MUSICIAN

Solo and freelance accompanist, playing cello, guitar and vocals at many performing arts centers, universities, concert series and clubs, both in the United States, and abroad. Recorded solo CD (http://cdbaby.com/cd/josiahaltschuler) and designed its cover art.

2001-2005, HARVARD UNIVERSITY BAUER CENTER FOR GENOMICS RESEARCH

Computational Biologist

- GeneSets: A web repository of annotation-based, and computationally derived genes. Involved creation of gene sets using statistical analysis software (GeneXPress) on raw microarray data, and Perl/Unix scripting to download and translate many data formats from external databases into GeneSet data.
- Helped users with bioinformatics-related tasks. This included general data management techniques, Perl scripting, setting up MySQL databases, web site design, and using statistical analysis software.
- cichlidBase: A database of all cichlid behavioral, trophic, and phylogenetic information for the scientific community. Set up Apache web server, built MySQL database, coded in Perl. (No longer available.)
- NRDS: Non-Redundant DNA Sequences – Implemented a non-redundant GenBank database on local linux cluster. (No longer available.)
- Designed Hofmann lab website and acted as interim web developer for center. (Sites no longer available.)
- Assisted in planning and building of 5000 gallon fish facility for Hofmann lab
- Small contracts for logo and web design for Bauer Center and MIT

Professional Skills

Computers

- Languages: Python, Perl, PHP, C, C++, Java, JavaScript, Matlab, SQL, Visual Basic, assembly language
- Databases: MySQL, SQLite, Microsoft SQL Server, Access
- Web: CGI scripting, Django web framework, Drupal, Wordpress, HTML, CSS, XML, Apache, Google Analytics
- Graphic design and Animation: Adobe Photoshop, Flash, Maya, Illustrator
- Operating Systems: Unix, Linux, Windows, Mac OS X

Biology

- Polymerase Chain Reaction (PCR), gel electrophoresis, use of X-rays for taxonomy of fishes, field work, behavioral observations

Publications

Discovering Statistically Significant Pathways in Expression Profiling Studies

Lu Tian Steven A. Greenberg, Sek Won, Josiah Altschuler, Isaac S. Kohane, and Peter J. Park
PNAS 2005 102: 13544-13549; September 8 2005
http://pnas.org/cgi/content/full/102/38/13544

A Gene Set Repository for Model Organisms

Poster abstract submission to RECOMB 2005 – PDF

NRDS: Non-Redundant DNA Sequences

Poster presentation at Northeast Bioinformatics Conference, 11/2005

Murder Ballads and Love Songs for Cello and Voice

Solo CD, self-recorded and designed CD cover. Published on ITunes, Amazon, CD Baby.

Other Interests

Cello, guitar, vocals, arrangement of folk/classical music
Drawing, painting, 3D animation, graphic design
Fish keeping (cichlids), animal behavior, neuroscience

Other Languages

Italian, fluent
Spanish, good