John Obenauer Email & Phone Number

Greater Memphis Area

Analyze and curate biomedical data, such as next-generation sequencing experiments, biological pathway databases, and clinically relevant genetic variants. Propose projects to interested clients.

Greater San Diego Area

Analyze and curate biomedical data, such as next-generation sequencing experiments, biological pathway databases, and clinical relevant genetic variants. Propose projects to interested clients. Manage bioinformatics staff.

Greater San Diego Area

Analyze and curate biomedical data, such as next-generation sequencing experiments, biological pathway databases, and clinically relevant genetic variants.

Southaven, Ms

Analyzed biomedical data for clients, including next-generation sequencing experiments and microarrays.1) Detected differentially expressed genes in Affymetrix microarray experiments.2) Detected single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) in Ion Torrent sequencing experments.3) Analyzed ChIP-seq data to detect peaks and novel binding motifs.4) Developed tools for detecting clinically relevant mutations in SNP array data and in next-generation sequencing data.5) Curated database entries for biological pathways.6) Provided bioinformatics training.

Memphis, Tn

Analyzed genome sequencing and genotyping data sets as a member of Jinghui Zhang's research laboratory in Computational Biology.1) Detected influenza mutations involved in adaptation from birds to mammals;2) Identified DNA copy number variants involved in brain tumors and solid tumors;3) Developed methods to detect sample contamination in multiplexed sequencing experiments;4) Adapted human structure variant detection methods to work in other organisms.

Memphis, Tn

Provided bioinformatics services to hospital faculty and managed a staff of 11 scientists and programmers. Assigned research projects, assisted staff with analysis methods, planned group budget, recruited new staff, reviewed manuscripts, gave public presentations, served on advisory committees, and analyzed data.1) Detected peaks and affected genes in chromatin immunoprecipitation sequencing (ChIP-seq) experiments in mice;2) Provided method development and analysis assistance to the Pediatric Cancer Genome Project;3) Mapped genomes for human cell lines and found their sequence differences;4) Profiled miRNA expression from high-throughput sequencing data;5) Identified human transmissibility markers in avian influenza viruses;6) Developed algorithms for assigning genotypes and proteotypes to large sets of aligned sequences;7) Made databases for investigators to store and analyze research results on acute myeloid leukemia, intrinsically unstructured proteins, and T cell receptor sequences, and for the Bioinformatics group to record our projects;8) Arranged joint workshops with the Biostatistics department to share expertise;9) Attended annual meetings of the American Association for Cancer Research to update cancer biology knowledge;10) Conducted strategic planning for the Bioinformatics group and the Information Sciences department.

Memphis, Tn

Assisted faculty members with research needs in bioinformatics.1) Assembled data from public sources for a gene annotation database;2) Developed a parallel-processing version of the protein interaction prediction program Scansite and made it web-accessible;3) Developed a program to convert LC/MS data to a 2D graphical image for peak processing by commercial software;4) Identified genes likely to be translationally regulated by microRNAs;5) Examined promoter regions of genes for SNPs that could disrupt transcription factor binding sites;6) Reorganized all data collected and stored by St. Jude's core facilities to group them by principal investigator;7) Built a database and novel data analysis tools to study DNA and protein sequences for an influenza genome sequencing project.

Cambridge, Ma

Wrote bioinformatics software and provided bioinformatics support for affiliated departments.1) Developed software called Scansite for predicting phosphoprotein interactions important in cancer biology using data derived from oriented peptide library experiments;2) Installed and maintained the Scansite server hardware and software (Red Hat Linux 7.3 on a Dell PowerEdge 8450 8-CPU server);3) Collaborated with the Sharp laboratory to create bioinformatics software for predicting microRNA binding sites on gene transcripts;4) Assisted in the selection and setup of computational tools for analyzing DNA microarray data for the MIT BioMicro Center.

Waltham, Ma

Studied structural features of electron transfer proteins by multidimensional nuclear magnetic resonance (NMR).1) Synthesized the gene for adrenodoxin, a 13 kDa iron-sulfur protein, using molecular biology techniques;2) Taught rotation students and other lab members how to make mutations and purify proteins;3) Grew and purified uniformly 15N-labeled adrenodoxin, as well as its bacterial homologs putidaredoxin and terpredoxin, for heteronuclear 2D NMR studies;4) Grew and purified uniformly 13C,15N-labeled adrenodoxin for 3D NMR sequential assignment experiments;5) Measured the magnetic susceptibilities of all three proteins in their oxidized forms using residual dipolar couplings at multiple magnetic fields;6) Developed a semi-automated batch curve fitting tool using Visual Basic for Applications, Microsoft Excel and Mathcad;7) Wrote programs for text processing of NMR chemical shift lists using Perl;8) Made a toolbar for Microsoft Word with buttons to convert DNA sequences to protein sequences, display the strand complementary to a DNA template, and calculate molecular weights;9) Designed and maintained the lab web page from 1997 to 2000.

Doctor Of Philosophy, Biochemistry

Bachelor Of Arts, Liberal Studies