Lead Support/Systems Analyst 5/97 – 3/99

Christopher Zaleski
503 Brandywine Pkwy ● Guilderland, NY 12084 ● 518-464-1954
http://www.chriszaleski.com/ ● [email protected]
Ten years of professional experience in Information Technology and Bioinformatics.
Extensive genomic database design, creation and integrations.
Detailed experience with genomic data analyses including pattern discovery algorithms, genomic coordinate
correlations, gene-chip & tiling microarrays and biologically relevant control generation.
Numerous bioinformatic algorithm designs with corresponding software implementation.
Full-lifecycle software development including management, design, architecture, and implementation.
Programming Languages: Highly proficient in Java and SQL. Solid experience in Perl, HTML, GWT, JavaScript, C++.
Operating Systems: Proficient with all flavors of Microsoft Windows and Linux variants.
Database Management Systems: MySQL 4.1/5.0, Microsoft SQL Server 6.5/2000.
Bioinformatics tools: NCBI & EBI tools (BLAST, Entrez, FASTA, ClustalW), UCSC Genome Browser,
R/BioConductor, Gibbs sampling, mFold, etc.
Hocus Locus
Rensselaer, NY
Principal Engineer
06/06 – present
Pre-seed startup company developing gene therapies and genomic analysis software. A collaboration among the
University at Albany, Yale University and local entrepreneurs.
 Project: “LIA” – Locus Intersection Analysis. Implemented using Java with a web interface. Performs correlation
analysis of coordinate-based genomic data, identifying common regions.
 Project “COGENT” – Control Set Generator for Genomics. Implemented using Java and MySQL. Creates data sets
of genomic loci and/or sequence for controlling informatic analyses, taken from a database of genomic annotation.
 Project: “HLDBM” - Hocus Locus Database Manager. Implemented using MySQL and Java. A hierarchical schema
with locus-based annotation tables, meta-data tables, and an API utilizing a driver design pattern.
Pathology Dept. Informatics – Yale University
New Haven, CT
Bioinformatics Software Developer
12/05 – present
Genomic data analysis and systems biology.
 Project: “GReg” – Gene Regulation analysis via Transfac and Clover. Implemented in J2EE/GWT, MySQL and Perl.
Pre-processes user data to produce sequences, executes “Match” and “Clover” 3rd party applications for putative
Transcription Factor Binding activity, and parses & loads results to the database allowing for immediate analysis.
 Project: “OmiCube” - Manages locus-based genomic data from tiling microarray or sequencing experiments.
Implemented using MySQL to maintain, organize, and analyze experimental data (TransFrags/TARs) at the level of
individual probes. Accommodates Affymetrix™ and Nimblegen™ tiling array results or deep sequencing data.
Tenenbaum Lab – University at Albany
Rensselaer, NY
Bioinformatics Team Lead
11/03 – present
Post-transcriptional regulation and Ribonomics.
 ENCODE Consortium member providing Protein-RNA regulation profiles (Ribonomics). Responsible for designing
data structures, storage and visualization of RNA binding motifs and cis-regulatory elements.
 Generation of Ribonomic profiling data from microarrays using database mining and correlation analyses.
 Co-creation of TUTR data sets (Training UTR). Aggregated sets of biological sequences containing a well
characterized structural motif, and corresponding annotations. Used as algorithm training data and positive controls.
 Responsible for most aspects of the Bioinformatics lab including web site content, data management, hardware
purchases, system configurations and networking,.
 Project management and mentoring for Graduate students’ thesis projects in the University’s Computer Science
department, as well as 20+ student class projects for Software Engineering coursework.
 Project: “CoMFindR” – Common Motif Finder for RNA. Implemented using Java and MySQL. Finds common
secondary structures across a set of RNA sequences and reports the most over-represented motifs.
Initia Inc.
New City, NY
Software Systems Engineer
3/99 – 9/02
Software based videoconferencing system solutions.
 One of three lead engineers responsible for project design concepts and system architecture. Decisions included
Design Patterns, Inter-process communication and DBMS schema.
 Directly managed a team of four developers with design and implementation of client and server-side modules.
Assisted with design pattern choices, code implementation and integration.
 Designed and coded server-side modules including Session Management, Scheduling, and Asynchronous
Communications protocols. Technologies used included many standard J2SE/J2EE APIs, JMS, JDBC, extensive
Multi-Threading, Reflection, and Socket IO.
 Design and implementation of a web-based client interface for videoconferencing control system. Created using
HTML, Java, JavaScript, VBScript, and Active Server Pages. Drag-and-Drop controllable, reflecting current state of
system sessions and controlled devices using real-time data.
Boehringer Ingelheim Inc.
Ridgefield, CT
Lead Support/Systems Analyst 5/97 – 3/99
Top 20 international pharmaceutical company.
 Lead support of international remote access services, consisting of connectivity from Windows 95 clients to Netware
servers and Windows NT domains. Responsible for all remote access related support that could not be handled by tier
1 support staff.
 Taught training classes on the use of remote access & telecommuting to groups of 10 to 50 clients.
 Traveled nationally for on-site support of software and hardware, as well as installation of Cisco ISDN routers.
 Managed software and hardware rollouts for the company sales force, including shipping & receiving of equipment,
hardware installations, and software installations/upgrades.
University at Albany
Albany, NY Bachelor of Arts, Biology
Western Connecticut State University Danbury, CT Bachelor of Arts, Computer Science
Rockland Community College
Suffern, NY Associate in Science, Business Administration
February 6, 2008 (Serial No.: 12/026,035):
Genomic Data Processing Utilizing Correlation Analysis of Nucleotide Loci
February 5, 2008 (Serial No.: 12/026,042):
Genomic Data Processing Utilizing Correlation Analysis of Nucleotide Loci of Multiple Data sets
February 5, 2008 (Serial No.: 12/026,048):
Segmented Storage and Retrieval of Nucleotide Sequence Information
February 5, 2008 (Serial No.: 12/026,051):
Non-Random Control Data Set Generation for Facilitating Genomic Data Processing
1) Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other
informatic resources. (Methods Mol Biol. 2008;419:39-52.)
Francis Doyle, Christopher Zaleski, Ajish D. George, Erin K. Stenson, Adele Ricciardi and Scott A. Tenenbaum
2) Combining Ribonomic Profiling and Tiling Arrays to analyze the transcribed RNA Activity of Coding and Noncoding Regions of Human Chromosomes 21 and 22. (In Preparation)
Ajish D. George, Philipp Kapranov, Christopher Zaleski, Simon Cawley, Thomas R. Gingeras and Scott A. Tenenbaum
3) LIA – Locus Intersection Analysis of Coordinate-Based Genomic Data. (In Preparation)
Christopher Zaleski, Ajish George, Francis Doyle, Scott A. Tenenbaum
4) COGENT – COntrol Set GENeraTor for Genomics Analysis. (In Preparation)
Francis Doyle, Christopher Zaleski, Ajish George, Scott A. Tenenbaum
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