Alexander G. Holman, Ph.D.
23 Cameron Ave #2 Cambridge, MA 02140 508-982-5356 alexander.holman@tufts.edu
Skills and Experience
- Informatics and dataset analysis experience
- Perl, Matlab, R, MySQL, Excel, and Spotfire bioinformatics programming experience
- Statistical proficiency relating to data analysis, data mining and experimental design
- Designed and implemented custom tools for sequence analysis, clustering, hidden Markov modeling, pattern analysis, maximum likelihood, mutual information analysis and genomic clustering
- Designed and implemented an SQL database for sequence and analysis information storage
- Designed scripts for automated interactions with external analysis packages such as BLAT, the UCSC genome server and Random.org
- Molecular biology techniques and experimental design
- PCR and primer design, TaqMan real-time PCR, mutagenic PCR
- Expression array design, spotting, hybridization, data analysis and process troubleshooting
- In vitro enzymatic reactions, retroviral integration reactions, molecular cloning, in vitro sequence selection with multiple round optimization, radioactive and fluorescent molecular tagging
- Polyacrylamide and agarose gel electrophoresis of DNA and protein, affinity purification of DNA
- Tissue and bacterial culture experience and sterile lab technique
Research Experience
- Tufts University: Postdoctoral Associate, Dr. John Coffin’s Laboratory – 2007-present
- Currently mentoring a junior graduate student who is continuing my thesis research.
- Tufts University: Graduate Student, Dr. John Coffin’s Laboratory – 2001-2007
- Investigated the target site selection during retroviral integration in vitro and in vivo. Through statistical analysis, identified novel base preferences exhibiting symmetry correlated to the topology of the integration reaction. Applied a hidden Markov model, clustering and other statistical tools to better characterize structure within the data, in order to describe the relationship between the profile symmetry and the mechanics of the integration reaction.
- Clark University: Undergraduate Researcher, Dr. David Thurlow’s Laboratory – 1999-2000
- Introduced point mutations in the bacterial nucleotidyltransferase gene using mutagenic PCR.
- Millennium Pharmaceuticals: Summer Intern – 1999
- Used transcriptional profiling to identify genes related to ischemic apoptosis. Assisted in troubleshooting micro-array production, array hybridization and data analysis. Designed computer algorithms to further analyze the data produced and search for anomalies relating to array design. Program culminated in a presentation of findings to the neurobiology group and the transcriptional profiling core facility.
- Millennium Pharmaceuticals: Summer Intern – 1998
- Used RT-PCR to determine RNA expression levels in apoptotic cells. Also researched the feasibility of implementing the TaqMan system as a tool for the more precise analysis of RNA expression levels. Wrote an internal report designed to serve as a users guide for implementation of the TaqMan PCR system.
- University of Kansas Medical Center, Wilkenson Cancer Laboratory: Intern – 1995
- Analyzed the effects of lipopolysaccharide on nitric oxide production in mouse macrophages using the Biorad Gene Gun biolistic device.