SUMMARY:

An interdisciplinary scientist with a background in: solving problems, making innovative discoveries, training future scientists, and leading the pack. I have worked and published papers in microbiology, transcriptomes, genomes, Confidential microarrays, next - gen-sequencing, statistics and bioinformatics.

EXPERTISE:

Molecular biology: next-generation-sequencing (NGS), polymerase chain reaction (PCR), RT-PCR, emPCR, quantitative RT-PCR, nucleic acid extraction and quantification/qualification, gene cloning, library preparation, electrophoresis, assay development, biochemistry, genetics/genomics/transcriptomics, pipetting, SNP and CNV typing

Bioinformatics: machine learning/artificial intelligence modeling, multivariate data analyses, big data analysis, statistics (SAS, SPSS, R-Program, Bioconductor, C++ custom-designed statistical software for faster iterative analyses), matrix algebra, relational data base construction (4th-Dimension, SQL).

Computer Programming: developed C++ standalone software and hundreds of other software programs (e.g., Neuroet, an artificial neural network applications for biologists (see 25 below)).

Leadership: Principal Investigator/collaborator on 7+ international and national science projects involving 50+ scientists; organized and chaired regional, national and international science conferences. Served as panelist expert on national funding review boards NSF, NIH, EPA, USDA. Served as Associate Editor and Board Member for 4 peer-reviewed journals.

Teaching and Communication Skills: taught graduate level university courses in Microbiology, Genomics, Biostatistics, Biotechniques, Microbial Physiology, and Instrumentation, laboratory experience; produced Youtube videos for two science publications.

Supervision/Management: trained and evaluated hundreds of students, several graduate, post-doctoral students, junior faculty members and visiting professors, troubleshoot problems.

Writing: designed, organized and published 50+ peer-reviewed papers (my work has featured in many major science magazines including Science (twice) and New Scientist (twice), technical writing, Designed, organized and wrote about 100 research funding proposals to government agencies (including budgeting and timelines).

WORK EXPERIENCE:

Confidential

Bioinformatic Consultant

Responsibilities:

• Data analyses of microbial communities (16S Confidential genes) collected from spent nuclear reactor water storage basin.
• Compared the data to existing Confidential databases and conducted Principal Component and Hierarchical Clustering analyses in SAS and R-program.
• Made some figures and tables and published a peer-reviewed paper 2 .

Confidential, Seattle

Affiliate Professor

Responsibilities:

• Principal Investigator (PI) on data mining project examining post-transcriptional regulation in response to extreme stress in the zebrafish and mouse.
• Designed massively paralleled C++ programs (+scripts) in Unix environment to manipulate transcriptome sequence data (see sample programs.
• Converted transcriptomic sequences to x- and y- coordinates using ‘Chaos Game Representation’ software 41 to increase computational efficiency. Mined the data for patterns using Machine Learning 25 and performed statistical and network analyses in SAS/JMP, R, Python, and Gephi 0.9. Assembled the tables/figures and wrote the manuscript, which is currently in peer-review 1 .
• PI on international project investigating the effects of extreme stress on gene regulation in the zebrafish and mouse. Annotated the gene transcripts, assembled the databases, performed statistical analyses, made all the figures and tables, wrote the manuscript, obtained consensus among university and institutional collaborators to submit the manuscript to a peer-reviewed journal and published it 3 .
• PI on a project examining microbial signatures (genetic biomarkers) in the oral microbiome.
• Calibrated Confidential microarrays (Gene Meters) to precisely measure microbial abundances in patients with edentulism, periodontitis, caries and health. Made databases and compared results to those obtained by next-generation-sequencing of the same samples.
• Conducted statistical analysis of the data in SAS/JMP and R. Assembled the tables, datasets, figures and wrote manuscripts that are published in peer-reviewed journals 5,10,19 .
• Co-PI on two projects: (i) potential cure for periodontitis by oral microbiome transplant 13 and (ii) preventing microbial corrosion of Ti dental implants 14 . Determined the microbial community composition using next-generation sequencing and performed bioinformatic and statistical analyses. Assembled tables and figures and co-authored the manuscripts.
• Wrote proposals and financial budgets to NIH and various agencies for research funding. Several proposals were awarded and funded the research mentioned above (see Appendix 2).

Confidential, Montgomery, AL

Full Professor

Responsibilities:

• Supervised and trained 30 undergraduate, 5 graduate students and one junior faculty member in ‘hands-on’ molecular biology work (e.g., nucleic acid extraction, cell culture, PCR, electrophoresis, library preparation, Confidential sequencing, bioinformatics). Analyzed Confidential microarray and Next-Generation-Sequencing data (coded in C++; SAS, R-project; R-Bioconductor, SQL; used software to de novo assemble bacterial genomes of Streptococcus sp. and plasmids). Developed massively paralleled C++ programs (operated in Alabama Supercomputer) to search for patterns in Confidential sequences in Craig Venter’s genome projects.
• Maintained and operated high throughput Confidential microarray and Confidential sequencing laboratories.
• Taught graduate level courses in molecular biology, biotechnology, bioinformatics, biostatistics, biochemistry, and microbial physiology.
• Organized and Chaired State-Wide College Research Symposia for undergraduate/ graduates and faculty. Served as Chair for administrative committees (e.g., curriculum development, faculty recruitment).
• Awarded grant research proposals and wrote final reports to funding agencies
• Served as Editorial Board Member and Associate Editor for several peer-reviewed journals (e.g., Journal for Microbiological Methods and Microarrays (now called High Throughput)) and ad hoc reviewer for high impact journals (e.g., Nature and Nucleic Acids Research).
• Organized and co-chaired an international genetics meeting entitled "Physicochemical fundamentals of Confidential hybridizations on surfaces as applied to microarrays and bead-based sequencing technologies " (
• Maintained, organized and chaired meetings with collaborators at the Confidential Irvine, the Confidential Seattle, Confidential -Institute for Evolutionary Biology and Confidential .
• PI on project that discovered an innovated method to accurately and precisely determine the postmortem interval (i.e., time since death) using gene expression data sets. Developed models using a massively paralleled matrix algebra regression algorithm. Tested the models using cross-validation methods. Assembled the tables, datasets, figures and wrote the manuscript which was published in peer-reviewed journal 4 .
• Primary author for invited research and review articles. Designed all the tables and figures and wrote the following peer-reviewed articles: 6-9 .
• PI on project examining biofilms growing on aeration diffusers in wastewater treatment facilities.
• Sequenced raw Confidential and 16S Confidential gene amplicons collected by Confidential Irvine collaborators.
• Conducted bioinformatics analysis of the sequencing output. Assembled the databases and compared raw (metagenomic) sequences to amplicons.
• Designed all the tables and figures and wrote the manuscript.
• Obtained consensus with collaborators to submit the manuscript to a peer-reviewed journal that has been published 12 .
• PI on a project examining the microbiome associated with solid organs of cadavers.
• Designed the study, supervised graduate student, and sequenced the 16S Confidential gene amplicons. Assembled the sequencing dataset and conducted bioinformatic analysis to annotate and count sequences. Made all figures and table and wrote the manuscript which is published 16 .
• Co-PI on a project that calibrated Confidential microarrays for accurate and precise measurements of gene and transcripts in biological samples.
• Analyzed the data (SAS) and made all the figures and tables. Wrote most of the manuscript 15 .

Research Assistant Professor

Confidential, Seattle

Responsibilities:

• Supervised 3 undergraduate, 4 graduate and 3 post-doctoral students.
• Designed experiments and analyzed datasets (C++ programs, SAS, MS Excel).
• Developed software programs in C++ to analyze nucleic acid sequences (melt temperatures; nearest neighbor models) to help molecular biologists predict experimental outcomes.
• Built, tested and used machine intelligence software to analyze biological data 18,24,25,34,39 .
• Extracted equations from the software for integrated software programs (i.e., Deep Learning) 35 .
• Developed pipelines that linked C++/Java analysis software programs to user-friendly web interfaces.
• Studied the physicochemistry of Confidential microarrays and wrote grant proposals, some of which were award to me.
• Served as panelist on national funding committees.
• Designed the figures and tables and wrote the following papers: 20-39 .
• PI on a project studying the physicochemistry of Confidential /RNA hybridization and washing.
• Found the sources of noise in Confidential microarrays.
• Published 4 articles in high impact journal Nucleic Acids Research 17,20,28,31 .
• Developed and tested various methods to mitigate noise problems (e.g., fingerprint approach) 21,23,29 .
• Research lead to a solution for the ‘noise problem’: calibrated Confidential microarrays (i.e., Gene Meters) that is now used in all research 15 .
• PI on project that made machine learning software for biologists 25 . Performed cross-validation approaches to test new software package (Neuroet).

Visiting Professor

Confidential

Responsibilities:

• Learned fundamentals of high-throughput Confidential sequencing.
• Developed the concept of calibrated Confidential microarrays to solve the ‘noise problem’.

Research Assistant Professor

Confidential, Columbia, SC

Responsibilities:

• Supervised one technician, 12 undergraduate students, and one Visiting Professor in research involving genomes, microbial biology, bioinformatics and phytoplankton dynamics.
• Characterized Confidential abundance profiles from marine biofilm samples.
• Studied foundations of complexity research: What makes complex biological systems so complex
• Developed C++ programs to measure objective complexity, dimensionality, Lypanova number, Kolmogorov entropy in time series data.
• Wrote the following papers: 32, 34,38, 41- 46 . Awarded funding.