Adam Bazinet

E-mail: adam.bazinet@umiacs.umd.edu

CV

Contents
Research Projects
Professional and Academic Experience
Publications
Conferences, Workshops, and Symposia
Invited Talks
Education


Research Projects
Grid computing — The Lattice Project
     lattice.umiacs.umd.edu | molecularevolution.org
     Publications (Lattice | Research)
        Sequence classification programs — A comparative evaluation
     BMC Bioinformatics (2012)
Lepidopteran molecular phylogenetics — "Leptree"
     Systematic Entomology (November 2016 | September 2016)
     PLOS ONE (December 2013 | March 2013)
     BMC Evolutionary Biology (December 2009)
        Species differentiation — Genealogical Sorting Index
     molecularevolution.org

Professional and Academic Experience

Associate Bioinformatics Principal Investigator, NBACC, Battelle National Biodefense Institute
Frederick, MD. Mar 2016–present.

Post-Doctoral Associate, Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology
Performed molecular data analyses for the Leptree project, which seeks to understand the evolutionary relationships of moths and butterflies.
Lead developer of The Lattice Project, a multi-model grid computing system, which features the GARLI web service hosted at molecularevolution.org.
University of Maryland, College Park, MD. Aug 2015–Mar 2016. Formerly Faculty Research Assistant, Jan 2004–Aug 2015.

Course Instructor, Workshop on Molecular Evolution, Workshop on Genomics, and Workshop on Population and Speciation Genomics
Duties included teaching, setting up the computing environment, providing scientific application support, and administering the workshop web site.
     • Český Krumlov, Czech Republic. 2009–2016.
     • Smithsonian Institution, Washington, DC. 2009, 2011.
     • Colorado State University, Fort Collins, CO. 2011.
     • Marine Biological Laboratory, Woods Hole, MA. 2003, 2004, 2006–2010.
     • Centers for Disease Control and Prevention, Atlanta, GA. 2008.

GRE Test Preparation Instructor
Academic Preparation Center, Transemantics, Inc. 2005–2006.

Co-op, Software and Web Development
Bureau Veritas e-Business, Buffalo, NY. 2001–2003.

Reviewer for:

 [Publons profile]

Publications

[Google Scholar profile]

Book Chapters

  1. Bazinet, A. L. and M. P. Cummings. (2009) The Lattice Project: a Grid research and production environment combining multiple Grid computing models. In Weber, M. H. W. (Ed.) Distributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting Communities. Pages 2–13. Tectum Publishing House, Marburg.
  2. Myers, D. S., Bazinet, A. L., and M. P. Cummings. (2008) Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Pages 71–85. In Talbi, E.-G. and A. Zomaya (Eds.) Grid Computing for Bioinformatics and Computational Biology, Wiley Book Series on Parallel and Distributed Computing. John Wiley & Sons, New York.

Conference Papers

  1. Bazinet, A. L. and M. P. Cummings. (2011) Computing the Tree of Life — Leveraging the Power of Desktop and Service Grids. In Proceedings of the Fifth Workshop on Desktop Grids and Volunteer Computing Systems (PCGrid 2011).

Journal Articles

  1. Adam L. Bazinet. (2017) Pan-genome and phylogeny of Bacillus cereus sensu lato. BMC Evolutionary Biology 17:176, doi:10.1186/s12862-017-1020-1.
  2. William T. White, Shannon Corrigan, Lei Yang, Aaron C. Henderson, Adam L. Bazinet, David L. Swofford, and Gavin J. P. Naylor. (2017) Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family. Zoological Journal of the Linnean Society, doi:10.1093/zoolinnean/zlx018.
  3. Shannon Corrigan, Pierpaolo Maisano Delser, Corey Eddy, Clinton Duffy, Lei Yang, Chenhong Li, Adam L. Bazinet, Stefano Mona, and Gavin J.P. Naylor. (2017) Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks. Molecular Phylogenetics and Evolution, 110:122-126, doi:10.1016/j.ympev.2017.03.011.
  4. Daniel H. Huson, Rewati Tappu, Adam L. Bazinet, Chao Xie, Michael P. Cummings, Kay Nieselt, and Rohan Williams. (2017) Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads. Microbiome, 5:11, doi:10.1186/s40168-017-0233-2.
  5. Adam L. Bazinet, Kim T. Mitter, Donald R. Davis, Erik J. Van Nieukerken, Michael P. Cummings, and Charles Mitter. (2016) Phylotranscriptomics resolves ancient divergences in the Lepidoptera. Systematic Entomology, doi:10.1111/syen.12217.
  6. Jerome C. Regier, Charles Mitter, Kim Mitter, Michael P. Cummings, Adam L. Bazinet, Winnifred Hallwachs, Daniel H. Janzen, and Andreas Zwick. (2016) Further progress on the phylogeny of Noctuoidea (Insecta: Lepidoptera) using an expanded gene sample. Systematic Entomology, 42(1):82–93, doi:10.1111/syen.12199.
  7. Jessica A. Goodheart, Adam L. Bazinet, Allen G. Collins and Michael P. Cummings. (2015) Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation. Royal Society Open Science, 2(9), doi:10.1098/rsos.150196.
  8. Adam L. Bazinet and Michael P. Cummings. (2015) Subdividing long-running, variable-length analyses into short, fixed-length BOINC workunits. Journal of Grid Computing, 14(3):429–441, doi:10.1007/s10723-015-9348-5.
  9. Adam L. Bazinet, Derrick J. Zwickl, and Michael P. Cummings. (2014) A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0. Systematic Biology, 63(5):812–818, doi:10.1093/sysbio/syu031.
  10. Adam L. Bazinet, Michael P. Cummings, Kim T. Mitter, and Charles W. Mitter. (2013) Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study. PLOS ONE 8(12):e82615.
  11. Regier JC, Mitter C, Zwick A, Bazinet AL, Cummings MP, et al. (2013) A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies). PLOS ONE 8(3):e58568.
  12. Adam L Bazinet and Michael P Cummings. (2012) A comparative evaluation of sequence classification programs. BMC Bioinformatics 13:92.
  13. Regier, J. C., Zwick, A., Cummings, M. P., Kawahara, A. Y., Cho, S., Weller, S. J., Roe, A. D., Baixeras-Almela, J., Brown, J. W., Parr, C. S., Davis, D. R., Epstein, M. E., Hallwachs, W., Hausmann, A., Janzen, D. H., Kitching, I. J., Solis, M. A., Yen, S.-H., Bazinet, A., and Mitter, C. (2009) Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol. Biol. 9:280.
  14. Tue Dao, H., Bazinet, A., Berthier, R., and Shneiderman, B. (2008) NASDAQ Velocity and Forces: An Interactive Visualization of Activity and Change. Journal of Universal Computer Science 14:1391–1410.
  15. Bazinet, A. L., D. S. Myers, J. Fuetsch and M. P. Cummings. (2007) Grid Services Base Library: a high-level, procedural application program interface for writing Globus-based Grid services. Future Generation Computer Systems 22:517–522.

Posters

  1. Adam L. Bazinet. (2017) Pan-genome and phylogeny of Bacillus cereus sensu lato.
  2. Akito Y. Kawahara, Adam L. Bazinet, Michael P. Cummings, and The LepTree Team. (2008) Phylogenetic supermatrix analysis of obtectomeran Lepidoptera: Total evidence from 7 genes and 1796 species.
  3. Bazinet, A. L., and M. P. Cummings. (2004) From GenBank to Multiple Sequence Alignments: Data Mining and Processing for Comparative Genomics.

Preprints

  1. Adam L. Bazinet. (2017) Pan-genome and phylogeny of Bacillus cereus sensu lato. bioRxiv preprint, doi:10.1101/119420.

Software

  1. Jill Zapoticznyj, Janine Garnham, Matthew Conte, Adam Bazinet, Paul Craig, David Mix, and Kristen Cotton. (2008) JBioFramework — simulations for biochemistry and bioinformatics: 1D gel electrophoresis, 2D gel electrophoresis and ion exchange chromatography.

Technical Reports

  1. Goodheart, Jessica A., Bazinet, Adam L., Collins, Allen G., and Cummings, Michael P. (2015) Phylogeny of Cladobranchia (Gastropoda: Nudibranchia): a total evidence analysis using DNA sequence data from public databases. Biology Research Works Collection, Digital Repository at the University of Maryland (DRUM).
  2. Tue Dao, H., Bazinet, A., Berthier, R., and Shneiderman, B. (2007) NASDAQ Velocity and Forces: An Interactive Visualization of Activity and Change. HCIL-TR-2007-29, Human-Computer Interaction Lab, Institute for Advanced Computer Studies, University of Maryland.
  3. Myers, D. S., and Bazinet, A. L. (2004) Intercepting Arbitrary Functions on Windows, UNIX, and Macintosh OS X Platforms. Technical Report CS-TR-4585, UMIACS-TR-2004-28, Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland.

Conferences, Workshops, and Symposia

  1.    ISCB DC RSG Bioinformatics, Genomics, and Computational Biology Workshop. College Park, Maryland, USA. 12 July 2017.
  2.    PacBio User Group Meeting. Baltimore, MD, USA. 28 June 2017.
  3. * ASM Microbe. New Orleans, LA, USA. 1–5 June 2017. Pan-genome and phylogeny of Bacillus cereus sensu lato
  4.    Workshop on Deep Learning. College Park, Maryland, USA. 24 May 2017.
  5.    CAMI/M3 Workshop on Metagenomic Software Validation. College Park, Maryland, USA. 7–8 May 2017.
  6.    CAMI Hackathon. College Park, Maryland, USA. 3–5 May 2017.
  7.    M3 Workshop and Conference. College Park, Maryland, USA. 1–2 Nov 2016.
  8.    SMRT Informatics Developers Conference. Gaithersburg, Maryland, USA. 14 Sept 2016.
  9.    ASM Microbe. Boston, Massachusetts, USA. 16–20 June 2016.
  10.    Methods and Analysis of Coevolution Across Scales: From Within Genomes to Disease and Environments. Washington, DC, USA. 15 Sept 2015.
  11.    Genome-Scale Phylogenetics: Analysing the Data. Washington, DC, USA. 15 Sept 2014.
  12.    Trinity and Tuxedo RNA-Seq Workshop. Charlottesville, Virginia, USA. 21 Nov 2013.
  13. * Frontiers in Phylogenetics: "Genome-Scale Phylogenetics". Washington, DC, USA. 20–21 May 2013. Phylo-transcriptomics of Lepidoptera
  14. * 5th Workshop on Desktop Grids and Volunteer Computing Systems (PCGrid 2011). Anchorage, Alaska, USA. 20 May 2011. Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids
  15. * The 6th BOINC Workshop. King's College, London, England. 31 Aug & 1 Sept 2010. The Lattice BOINC Project — Public Computing for the Tree of Life
  16.    GlobusWorld 2010. Argonne National Laboratory, Chicago, Illinois, USA. 2–4 Mar 2010.
  17.    9th Workshop on Algorithms in Bioinformatics (WABI 2009). UPenn, Philadelphia, Pennsylvania, USA. 12–13 Sept 2009.
  18.    GlobusWorld 2008. Austin, Texas, USA. 15–21 Nov 2008.
  19.    GlobusWorld 2006. Washington, District of Columbia, USA. 11–14 Sept 2006.
  20.    GlobusWorld 2005. Boston, Massachusetts, USA. 7–10 Feb 2005.

    * – published / presented

Invited Talks

  1. CBCB "Research in Progress" series. 27 Mar 2014. Lepidopteran phylogenomics using RNA-Seq
  2. Hollings Marine Laboratory, Charleston, SC. 21 Feb 2013. Phylo-transcriptomics of Lepidoptera
  3. University of Delaware, Newark, DE. 7 Sept 2012. The Lattice Project: a grid system for phylogenetics
  4. McDaniel College, Westminster, MD. 14 Nov 2011. The Lattice Project: a grid system for phylogenetics
  5. National Institutes of Health, Bethesda, MD. 22 Feb 2011. Applications of next-generation sequencing (NGS) to phylogenomics
  6. Smithsonian Institution, Washington, DC. 12 Nov 2009. The Lattice Project: a multi-model grid computing system
  7. University of Maryland University College, Adelphi, MD. 4 Jan 2007. The Lattice Project: a computational grid system
  8. University System of Maryland, Adelphi, MD. 4 Oct 2006. The Lattice Project: our efforts at grid computing

Education

Ph.D., Computer Science. Aug 2015.
M.S., Computer Science. Dec 2009.
Advanced Special Student, Graduate Program. Sept 2005–May 2007.
University of Maryland, College Park, College Park, MD. Sept 2005–Aug 2015.

Doctoral Dissertation
Title: Computational Methods to Advance Phylogenomic Workflows
Advisor: Dr. Michael Cummings

Master's Thesis
Title: The Lattice Project: A Multi-model Grid Computing System
Advisor: Dr. Michael Cummings

Computer Science Coursework
CMSC858B:Computational Systems Biology and Functional Genomics
     • Class project: An ensemble classifier for metagenomic sequence classification using random forests  [paper]  [presentation]
CMSC828G:Bioinformatics for Metagenomics
     • Class project: Comparing SAP and PhymmBL  [paper]
     • Second presentation: A statistical toolbox for metagenomics  [presentation]
     • First presentation: Assigning sequences to taxa  [presentation]
CMSC858L:Graphs and Networks in Computational Biology
     • Class project: Comparative analysis of metabolic pathways in metagenomics  [paper]  [presentation]
CMSC828T:Applications of GPU and Cloud Computing to Nontraditional Databases, Computer Graphics, Data Mining, and GIS
     • Class project: Infernal-GPU: CUDA-accelerated RNA alignment  [paper]  [presentation]  [code]
CMSC858P:Algorithms for Biosequence Analysis
     • Class project: Genes to trees  [report]  [code]
CMSC714:High Performance Computing
     • Class project: Parallel network motif finding  [paper]  [presentation]
     • Second presentation: Condor and BOINC: distributed and volunteer computing  [presentation]
     • First presentation: Computational and data grids  [presentation]
CMSC734:Information Visualization
     • Class project: NASDAQ velocity and forces: an interactive visualization of activity and change   [paper]   [tech report]
     • Interim project: Analyzing the International HapMap Project and related initiatives like CGEMS   [report]
CMSC828P:Cognitive Science and Artificial Intelligence
CMSC828N:Computational Gene Finding and Genome Assembly
     • Class project: Using random forests for computational gene prediction  [report]  [code]

B.S., Honors Computer Science Program. May 2003.
Rochester Institute of Technology, Rochester, NY. Sept. 2000–May 2003.

Computer Science coursework:

  • Computer Science I, II, III (Java)
  • Computer Science IV (C++)
  • Software Engineering (Java)
  • Computer Graphics I (C++, OpenGL)
  • Operating Systems I
  • Digital Design (Circuit Simulator)
  • Computer Organization (VAX)
  • Data Communications & Networks (Java)
  • Ad hoc Networking
  • Computer Science Theory
  • Artificial Intelligence (Lisp)
  • Abstractions & Practicalities (Lisp)
  • Genetic Algorithms
  • Bioinformatics Independent Study