Publications, Conferences, and Projects


Publications

·     Jacob Porter.  “Fast NeighborNet: Improving the Speed of the Neighbor-Net Phylogenetic Network Algorithm with Multithreading and a Relaxed Search Strategy.”  BICoB 2016.

·  Jacob Porter, Jonathan Berkhahn, and Liqing Zhang. “A Comparative Analysis of Read Mapping and Indel Calling Pipelines for Next-Generation Sequencing Data.”  Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology.  Chapter 29. 2015. link

    Jacob Porter, Jonathan Berkhahn, and Liqing Zhang.  “A Comparative Analysis of Computational Indel Calling Pipelines for Next Generation Sequencing Data.”  BIOCOMP 2014. link

·    Jacob Porter, Ming-an Sun, Hehuang Xie, and Liqing Zhang. “Investigating Bisulfite Short-Read Mapping Failure with Hairpin Bisulfite Sequencing Data.”  BMC Genomics supplement to ICCABS 2014. Nov 2015. link

    Jacob Porter, Ming-an Sun, Hehuang Xie, and Liqing Zhang. “Improving Bisulfite Short-Read Mapping Efficiency with Hairpin-Bisulfite Data.”  ICCABS 2014. link

·    Tran, Hong, Jacob Porter, Ming-an Sun, Hehuang Xie, and Liqing Zhang. "Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools." Advances in bioinformatics. 2014.  link

Other Conferences Attended

·    Poster: Biomedical Computation at Stanford (BCATS 2009) on statistical modeling for Warfarin dosing link

·    Attended: Joint Math Meetings, Baltimore MD, 2014 and San Francisco, CA 2010 link

Summer Research Experiences

·    Mason Modeling Days (2017): Used conjunctive Bayesian networks (a partially ordered set) to model ordered mutations for the flu virus.  Used MC-CBN software in R.  The model used algebraic statistics.

·    Ding, Lili; et al.  Dosing Predictions for the Anticoagulant Warfarin.  FIFTEENTH MATHEMATICAL AND STATISTICAL MODELING WORKSHOP FOR GRADUATE STUDENTS (2009).  Edited: P. Gremaud, I.C.F. Ipsen, and R.C. Smith, CRSC-TR10-01 (Technical Report)

·    Texas A&M University (2005): Maximized computational results in producing linear phylogenetic invariants for small trees in half the time estimated (Summer Research Experience for Undergraduates).  Website: Small Phylogenetic Trees

Class projects

·    Contributed to implementing a custom Gene Set Enrichment Analysis algorithm in Python

·    Explored a natural language processing model on password security

·    Implemented numerical optimization, linear algebraic, and bioinformatics algorithms in Python and Matlab

·    Made a blog and website with Google App Engine for a Udacity class.

·    Developed a pharmacophore hypothesis for Warfarin/VKORC1 with Open Eye Scientific computer tools

·    Implemented a Javascript compiler with Earley parser in Python

·    Created an Enigma German crypto machine in Scheme