John J. Gosink, PhD.
Bioinformatics Independent Contractor. 9/2014 to present
- General Activities: Sequence analysis, statistics, automated reporting.
- Significant Accomplishments: Designed and created a reporting tool to be used by bench scientists to help analyse sequence data and provide metrics on project completeness.
- Skills: Knitr and markdown, reproducible research, independent contracting.
Scientist, Senior Scientist in Computational Biology, Amgen, Inc. 8/2001 to 4/2011
- General Activities: Genomics, RNA expression profiling, DNA sequence analysis, and flow cytometry data analysis. Biomarker development, qualification, and analysis for efficacy. Biomarker platforms included ELISAs (serum and ex-vivo stimulation panels), qRT-PCR, methylation assays, IHC, Luminex, MSD, flow cytometry, and sequence mutation panels. Cross-department technical presentations.
- Significant Accomplishments: Biomarker development and analysis in 9 Phase 1 & 2 oncology (pancreatic, breast, and colorectal cancer) and inflammation (rheumatoid arthritis, asthma and psoriasis) clinical trials. Managed a project to create a custom in-house microarray. Wrote a specialized data pipeline to control the assembly of data from multiple sources which ensured the quality and accuracy of the final microarray design. Designed, built, and used code libraries to analyze extensive collections of high dimensional flow cytometry data. Collaborated with other researchers to use these libraries in conjunction with an in-house custom application to automate the quality assessment and preliminary analysis of this type of data. Created a multithreaded automated data retrieval system to extract, store, and integrate a large set of diverse sequence and annotation data and integrate them with our internal efforts.
- Skills: R, Perl, Java, SPLUS and UNIX shell programming, SQL and XML manipulation.
Postdoctoral Researcher in Bioinformatics, ZymoGenetics, Inc. 12/1998 to 7/2001
- General Activities: Data mining of genomic, EST and microarray expression databases. DNA sequence analysis.
- Significant Accomplishments: Created a system to mine public microarray data for information relevant to ZymoGenetics’ IP portfolio. Conceived and developed a system to extend genomic contig assembly through sequence alignment with public and private ESTs.
- Skills: Perl and UNIX shell scripting, database construction, sequence analysis.
Postdoctoral Researcher in the Overbaugh Lab, UW 10/1996 to 11/1998
- Skills and General Activities: Molecular investigation of coreceptor usage by temporally evolved SIV strains using virology, tissue culture, molecular biology.
- Significant Accomplishments: Studied the molecular evolution of SIV and HIV to find specific sequence signatures for tissue specificity and heightened virulence.
Doctoral Student in the Staley Lab, UW 9/1990 to 10/1996
- Dissertation: Taxonomy, biogeography, & phylogeny of polar gas vacuolate bacteria.
- Skills: Microbial phenotyping, PCR, cloning, DNA sequence analysis, molecular phylogenetics, bacterial taxonomy, field research in Antarctica, presentation and writing skills, mentoring.
Lecturer, The Institute for Science Training and Research, Inc. 1997 to 1999
- General Activities: Lectured on bioinformatics and phylogenetic inference.
Consultant, Bristol-Myers Squibb 1996 to 1997
- General Activities: DNA sequence analysis and phylogenetic analysis.
Consultant, Pathogenesis Corp. 1995
- General Activities: DNA sequence analysis and phylogenetics software set-up and tutoring.
Laboratory Technician, University of Washington 1988 to 1990
- General Activities: Meiotic pairing, heterochromatization, and sex determination in Drosophila.
- Skills: Drosophila culture and genetics, microinjection, cloning.
Laboratory Technician, University of Alaska 1988 to 1990
- General Activities: Assay atmospheric pollutants in Arctic haze.
- Skills: photospectroscopy, ion exchange chromatography, electrothermal atomic absorption spectroscopy.
2014 M.S. in Statistics (biostatistics emphasis)
Texas A&M, College Station TX
1996 Ph.D. in Microbiology
Department of Microbiology, University of Washington, Seattle WA
1988 B.S. in Natural Science
Department of Biochemistry, University of Wisconsin, Madison WI
Sandan, Shotokan Karate of America. Dojo leader and senior instructor for the University of Washington Shotokan Karate dojo since 1998.
Gosink JJ, Means GD, Rees WA, Su C, Rand HA. Bridging the Divide between Manual Gating and Bioinformatics with the Bioconductor Package flowFlowJo. (2009) Advances in Bioinformatics. doi:10.1155/2009/809469.
Auman AJ, Breezee JL, Gosink JJ, Schumann P, Barnes CR, Kämpfer P, Staley JT. Psychromonas boydii sp. nov., a gas-vacuolate, psychrophilic bacterium isolated from an Arctic sea-ice core. (2010) Int J Syst Evol Microbiol. 60: 84-92.
Dehghani H, Rasmussen B, Fung V, Piper R, Gosink J, Weaver B, Reddy P. Case studies of Mycoplasma contamination in CHO cell cultures. (2007) Proceedings from the PDA workshop on Mycoplasma contamination by plant peptones. p. 53-59.
Auman AJ, Breezee JL, Gosink JJ, Kampfer P, Staley JT. Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice. (2006) Int. J. Sys. Evol. Microbiol. 56: 1001-1007.
Gosink JJ. Genus Polaromonas. (2005) Volume 2, 2nd Edition, Bergey’s Manual of Systematic Bacteriology.
Gosink JJ. Genus Octadecabacter. (2005) Volume 2, 2nd Edition, Bergey’s Manual of Systematic Bacteriology.
Staley JT, and Gosink JJ. Poles apart: biodiversity and biogeography of sea ice bacteria. (1999) Ann. Rev. Microbiol. 53: 189-215.
Bowman JP, Gosink JJ, McCammon SA, Lewis TL, Nichols DS, Skerratt JH, Staley JT, McMeekin TA. Colwellia demingae sp. nov., Colwellia hornerae sp. nov., Colwellia rossensis, and Colwellia psychrotropica sp. sp. nov.: psychrophilic, marine bacteria with the ability to synthesize docosahexaenoic acid (22:6?3). (1998) Int. J. Sys. Bact. 48: 1171-1180.
Kimata JT., Gosink JJ, Kewalramani VN, Rudensey LM, Littman DR, and Overbaugh J. Coreceptor specificity of temporal variants of Simian Immunodeficiency Virus Mne. (1998) J. Virol. 73: 1655-1660.
Poss M, Rodrigo A, Gosink JJ, Learn GH, de Vange Panteleef D, Martin Jr. HL, Bwayo J, Kreiss JK, and Overbaugh J. Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. (1998) J. Virol. 72: 8240-8251.
Junge K, Gosink JJ, Hoppe HG, and Staley JT. Arthrobacter, Brachybacterium, and Planococcus isolates identified from antarctic sea ice brine. Description of Planococcus mcmeekinii, sp. nov. (1998) System. Appl. Microbiol. 21: 306-314.
Gosink JJ, Woese CR, and Staley JT. Polarobacter filamentus gen. nov., sp. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., a gas vesicle producing genus of the Cytophaga/Flavobacteria/Bacteroides phylum. (1998) Int. J. Sys. Bact. 48: 223-235.
Gosink JJ and Staley JT. Octadecabacter arcticus gen. nov., sp. nov., and O. antarctius, sp. nov., nonpigmented, psychrophilic gas vacuolate bacteria from polar sea ice and water. (1997) System. Appl. Microbiol. 20: 357-365.
Hedlund BP, Gosink JJ, and Staley JT. Verrucomicrobia div. nov., a new division of the Bacteria containing three new species of Prosthecobacter. (1997) Antonie van Leeuwenhoek. 72: 29-38.
Poss M, Gosink JJ, Thomas E, Kreiss JK, Ndinyo-Achola J, Mandaliya K, Bwayo J, and Overbaugh J. Phylogenetic evaluation of Kenyan HIV type 1 isolates. (1997) AIDS Res. Human Ret. 13: 493-499.
Hedlund BP, Gosink JJ, and Staley JT. Phylogeny of Prosthecobacter , the fusiform caulobacter: members of a recently discovered division of the Bacteria. (1996) Int. J. Sys. Bact. 46: 960-966.
Irgens RL, Gosink JJ, and Staley JT. Polaromonas vacuolata, gen. et. sp. nov., a psychrophillic, marine gas vacuolate bacterium from Antarctica. (1996) Int. J. Sys. Bact. 46: 822-826
Gosink JJ and Staley JT. Biodiversity of gas vacuolate bacteria from Antarctic sea ice and water. (1995) Appl. Environ. Microbiol. 61: 3486-3489.
Staley JT, Irgens RL, Gosink J, and van Neerven A. Isolation of gas vacuolate heterotrophic bacteria. (1993) Trends in Microbial Ecology. R. Guerrero and C. Pedrós-Alió (eds.). Spanish Society for Microbiology, Barcelona, Spain.
Gosink JJ, Irgens RL, and Staley JT. Vertical distribution of bacteria in arctic sea ice. (1993) FEMS Microbiol. Ecology 102: 85-90.
Surowy CS, Hoganson G, Gosink J, Strunk K, and Spritz RA. The human RD protein is closely related to nuclear RNA-binding proteins and has been highly conserved. (1990) Gene 90: 299-