{"id":279,"date":"2019-11-23T00:19:55","date_gmt":"2019-11-23T05:19:55","guid":{"rendered":"https:\/\/www.eg.bucknell.edu\/~brk009\/?page_id=279"},"modified":"2026-05-02T13:14:14","modified_gmt":"2026-05-02T17:14:14","slug":"pubs","status":"publish","type":"page","link":"https:\/\/www.eg.bucknell.edu\/~brk009\/pubs\/","title":{"rendered":"Publications"},"content":{"rendered":"\n<p>Student collaboration indicated with <span style=\"text-decoration: underline;\">underlined<\/span> authorship<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Journal Publications [Peer-Reviewed]<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><span style=\"text-decoration: underline;\">Murph A<\/span>, Flynt A, <strong>King BR<\/strong> Comparing finite sequences of discrete events with non-uniform time intervals. <em>Sequential Analysis<\/em>, 291-313 (2021) <a href=\"https:\/\/doi.org\/10.1080\/07474946.2021.1940491\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1080\/07474946.2021.1940491<\/a> <\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Kim T<\/span>, <strong>King BR<\/strong>. Time series prediction using deep echo state networks. <em>Neural Computing &amp; Applications<\/em> (2020) <a href=\"https:\/\/doi.org\/10.1007\/s00521-020-04948-x\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1007\/s00521-020-04948-x<\/a> [<a href=\"https:\/\/link.springer.com\/article\/10.1007%2Fs00521-020-04948-x\">link<\/a>]<\/li>\n\n\n\n<li>Hare-Harris AE, Mitchell MW, Meyers SM, Mitchel A, <strong>King BR<\/strong>, Ruocco B, Martin CL, Flax JF, Brzustowicz LM. Within-task variability on standardized language tests predicts autism spectrum disorder: A pilot study of the Response Dispersion Index.\u00a0<em>J Neurodevelop Disord<\/em>\u00a011,\u00a021 (2019) doi:10.1186\/s11689-019-9283-z\u00a0 [<a href=\"https:\/\/doi.org\/10.1186\/s11689-019-9283-z\">link<\/a>]<\/li>\n\n\n\n<li>Lipsky E,\u00a0<strong>King BR<\/strong>, Tromp G. Node-Oriented Workflow (NOW) &#8211; A command template workflow management tool for high throughput data analysis pipelines.\u00a0<em>Journal of Data Mining in Genomics and Proteomics<\/em> 2014; 5(2) [link] [PDF]<\/li>\n\n\n\n<li><strong>King BR<\/strong>, Aburdene M,\u00a0<span style=\"text-decoration: underline;\">Thompson A<\/span>,\u00a0<span style=\"text-decoration: underline;\">Warres Z<\/span>. Application of discrete Fourier inter-coefficient difference for assessing genetic sequence similarity.\u00a0EURASIP Journal on Bioinformatics and Systems Biology; 2014; 8 [link]<\/li>\n\n\n\n<li>Srinivasan SM, Vural S,<strong>\u00a0King BR<\/strong>, Guda C. Mining for class-specific motifs in protein sequence classification.\u00a0BMC Bioinformatics; 2013; 14(96) [link] [PDF]<\/li>\n\n\n\n<li><strong>King BR<\/strong>, Vural S, Pandey S,\u00a0<span style=\"text-decoration: underline;\">Barteau A<\/span>, Guda C. ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes.\u00a0BMC Research Notes; 2012; 5(351) [link] [PDF]<\/li>\n\n\n\n<li>Guda C,\u00a0<strong>King BR<\/strong>, Pal LR, Guda P. A top-down approach to infer and compare domain-domain interactions across eight model organisms.\u00a0<em>PLoS One<\/em>; 2009; 4(3) [<a href=\"http:\/\/www.plosone.org\/article\/info:doi\/10.1371\/journal.pone.0005096\" target=\"_blank\" rel=\"noreferrer noopener\">link<\/a>] [<a href=\"http:\/\/www.plosone.org\/article\/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0005096&amp;representation=PDF\" target=\"_blank\" rel=\"noreferrer noopener\">PDF<\/a>]<\/li>\n\n\n\n<li><strong>King BR<\/strong>, Latham L, Guda C. Estimating the subcellular proteome of prokaryotes.\u00a0<em>The Open Applied Informatics Journal<\/em>\u00a02009; 3(1) [<a href=\"http:\/\/www.bentham.org\/open\/toainfoj\/openaccess2.htm\" target=\"_blank\" rel=\"noreferrer noopener\">link<\/a>] [<a href=\"papers\/1TOAINFOJ.pdf\">PDF<\/a>]<\/li>\n\n\n\n<li><strong>King BR<\/strong>, Guda C. Semi-supervised learning for classification of protein sequence data.\u00a0<em>Scientific Programming<\/em>; 2008; 16(1) [<a href=\"http:\/\/www.hindawi.com\/journals\/sp\/2008\/795010\/abs\/\" target=\"_blank\" rel=\"noreferrer noopener\">link<\/a>][<a href=\"http:\/\/downloads.hindawi.com\/journals\/sp\/2008\/795010.pdf\">PDF<\/a>]<\/li>\n\n\n\n<li><strong>King BR<\/strong>, Guda C. ngLOC: an n-gram based Bayesian method for estimating the subcellular proteomes of eukaryotes.\u00a0<em>Genome Biol<\/em>\u00a02007; 8(5):R68 [<a href=\"http:\/\/genomebiology.com\/2007\/8\/5\/R68\" target=\"_blank\" rel=\"noreferrer noopener\">link<\/a>] [<a href=\"http:\/\/genomebiology.com\/content\/pdf\/gb-2007-8-5-r68.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">PDF<\/a>]<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">International Conferences <br>[Peer Reviewed]<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>King BR<\/strong> and Talmage E. Nifty: DNA Sequence Matching. Presented at ACM SIGCSE Technical Symposium 2026: Nifty Assignments, February 18-21, St. Louis, Missouri, USA [<a href=\"https:\/\/sigcse2026.sigcse.org\/details\/sigcse-ts-2026-nifty-assignments\/4\/Nifty-DNA-Sequence-Matching\">link<\/a>]<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Zeng Z<\/span>, Raymond T, Dutcher D, <strong>King BR: <\/strong>Hygroscopic Tandem Differential Mobility Analyzer (HTDMA) Design for Aerosol Mixture Hygroscopic Behavior Studies. Presented at AIChE 2022 Annual Meeting, Nov 13-18, Phoenix, AZ, USA [<a href=\"https:\/\/aiche.confex.com\/aiche\/2022\/meetingapp.cgi\/Paper\/654296\">link<\/a>]<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Zeng Z<\/span>, <span style=\"text-decoration: underline;\">Hatzinger B<\/span>, <span style=\"text-decoration: underline;\">Torres G<\/span>, Dutcher D, Raymond T and <strong>King BR<\/strong>.  On the Development and Setup of a Hygroscopic Tandem Differential Mobility Analyzer for Aerosol Studies. Presented at <em>AIChE 2021 Annual Meeting, Nov 7-11, Boston MA, USA<\/em> [<a href=\"https:\/\/plan.core-apps.com\/aiche2021\/event\/4042767350f2d05cd1ae2ec8a2232d56\" target=\"_blank\" rel=\"noreferrer noopener\">link<\/a>] <\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Murph A<\/span>, Flynt A, <strong>King BR<\/strong> Comparing finite sequences of discrete events with non-uniform time intervals. Presented at <em>CS2021: The Classificaton Society Annual Meeting, Nov 5-7, Lewisburg, PA, USA<\/em> [<a href=\"https:\/\/www.theclassificationsociety.org\/annual-meeting\/2021\/\" target=\"_blank\" rel=\"noreferrer noopener\">link<\/a>]<\/li>\n\n\n\n<li>Pirmann C, <span style=\"text-decoration: underline;\">Acharya B<\/span>, <strong>King BR<\/strong>, Faull K. Training Algorithms to Read Complex Collections: Handwriting Classification for Improved HTR Models. Presented at <em>DH2020: Digital Humanities, July 22-24, Ottawa, Canada<\/em> [<a href=\"https:\/\/dh2020.adho.org\">link<\/a>]\n<ul class=\"wp-block-list\">\n<li>Due to COVID-19 pandemic, to be presented remotely <\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>King BR<\/strong>, Troiani V. Identifying Scanpath Trends using a Frequent Trajectory Pattern Mining Approach. Journal of Vision September 2019, Vol.19, 307a. Presented at <em>VSS19: Vision Sciences Society 19th Annual Meeting, St. Pete Beach, FL May 17-22, 2019<\/em> [<a href=\"https:\/\/doi.org\/10.1167\/19.10.307a\">link<\/a>]<\/li>\n\n\n\n<li>Hare-Harris AE, Mitchel MW,\u00a0<strong>King BR<\/strong>, Myers SM, Greene B, Martin CL, Flax JF, Brzustowicz LM. Developmental Deviance of Item-Level Responses on Standardized Language Measures Correlates with Autism Spectrum Disorder Diagnosis. Presented at the\u00a0<em>International Meeting for Autism Research, IMFAR 2016<\/em>, May 11-14, Baltimore, MD [<a href=\"https:\/\/insar.confex.com\/insar\/2016\/webprogram\/Paper21281.html\">link<\/a>]<\/li>\n\n\n\n<li>Hare-Harris AE,\u00a0<strong>King BR<\/strong>,\u00a0<span style=\"text-decoration: underline;\">Easse E<\/span>, Ledbetter DH, Martin CL. Building a dosage map of the genome to assist in CNV interpretation. Presented at\u00a0<em>ASHG 2015: American Society of Human Genetics, Oct 6-10, Baltimore, MD<\/em>\u00a0[<a href=\"http:\/\/www.ashg.org\/2015meeting\/\">link<\/a>]<br>Reviewer&#8217;s Choice Abstract winner (top 10% of posters selected &#8211; Congrats to Abby!) <\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Ren C<\/span>,\u00a0<strong>King BR<\/strong>. Predicting Protein Contact Maps by Bagging Decision Trees. Proceedings of\u00a0<em>BCB &#8217;14: ACM International Conference on Bioinformatics, Computational Biology and Health Informatics<\/em>, Sept 20-23, Newport Beach, CA [<a href=\"http:\/\/dl.acm.org\/citation.cfm?id=2649387.2660818&amp;coll=DL&amp;dl=ACM&amp;CFID=675776990&amp;CFTOKEN=64789548\">link<\/a>] [<a href=\"papers\/2014_ACMBCB_Ren.pdf\">PDF<\/a>]<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Hofmeister B<\/span>,\u00a0<strong>King BR<\/strong>. ngPhylo &#8211; N-gram Modeled Proteins with Subsitution Matrices for Phylogenetic Analysis.\u00a0<em>Proceedings of BCB &#8217;13 : ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, Sept 22-25, Washington DC<\/em>\u00a0[<a href=\"http:\/\/dl.acm.org\/citation.cfm?id=2506679\">link<\/a>] [<a href=\"papers\/2013_ACMBCB_Hofmeister.pdf\">PDF<\/a>]<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Cole C<\/span>,\u00a0<strong>King BR<\/strong>. Using Machine Learning to Predict the Health of HIV-Infected Patients.\u00a0<em>Proceedings of BCB &#8217;13 : ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, Sept 22-25, Washington DC<\/em>\u00a0[<a href=\"http:\/\/dl.acm.org\/citation.cfm?id=2506685\">link<\/a>] [<a href=\"papers\/2013_ACMBCB_Cole.pdf\">PDF<\/a>]<\/li>\n\n\n\n<li><strong>King BR<\/strong>, Satyanarayana A. Teaching Data Mining in the Era of Big Data. Presented at\u00a0<em>American Society for Engineering Education, ASEE 2013, June 23-26, Atlanta GA<\/em>\u00a0[<a href=\"http:\/\/www.asee.org\/public\/conferences\/20\/papers\/7580\/view\">link<\/a>] [<a href=\"papers\/ASEE_2013_Final_Paper.pdf\">PDF<\/a>]<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Segar M<\/span>, King BR. An n-gram based probabilistic method for de novo sequence assembly. Presented at\u00a0<em>20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB 2012, July 15-17, Long Beach, CA<\/em>\u00a0[<a href=\"papers\/ngAssem - ISMB 2012 Poster.pdf\">PDF<\/a>]<\/li>\n\n\n\n<li><strong>King BR<\/strong>, Guda C. Semi-supervised learning for protein classification. ROCKY 07 &#8212;\u00a0<em>Presented at 5th Annual Rocky Mountain Bioinformatics Conference, November 30 &#8211; December 2, 2007, Aspen, CO<\/em>\u00a0[<a href=\"http:\/\/www.iscb.org\/cms_addon\/conferences\/rocky07\/presentations\/15%20-%20King.ppt\" target=\"_blank\" rel=\"noreferrer noopener\">PPT<\/a>]<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Local and Regional Conferences<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Sharma, K,\u00a0<strong>King BR<\/strong>. Trajectory Gaze Path Analysis and Isolating Areas of Interest in Eye-Tracking Data for Autism Spectrum Disorder Studies. Presented at <em>21st Annual Kalman Research Symposium,<\/em> April 9, 2022, Bucknell University, Lewisburg, PA (Poster)<\/li>\n\n\n\n<li>Pirrman CM, <strong>King BR<\/strong>, <span style=\"text-decoration: underline;\">Acharya B<\/span>, Faull K: Collaborating on Machine Reading: Training Algorithms to Read Complex Collections. Presented at <em>Bucknell University Digital Scholarship<br>Conference, BUDSC19<\/em>, Oct. 11-13, Bucknell University, Lewisburg, PA (Talk)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Yang T<\/span>, Troiani V,\u00a0<strong>King BR<\/strong>: Using Deep Learning to Analyze Images That Have High Interest from Children with Autism. Presented at<em>\u00a016th Annual Kalman Research Symposium,\u00a0<\/em>April 1, 2017, Bucknell University, Lewisburg, PA (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Eckenroth M<\/span>, Troiani V,\u00a0<strong>King BR<\/strong>: Assessing the Utility of Virtual Reality on Selective Attention Bias in Children with Autism Spectrum Disorder. Presented at\u00a0<em>6th Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2016<\/em>, July 29, Bloomsburg University, Bloomsburg, PA (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Yang T<\/span>, Troiani V,\u00a0<strong>King BR<\/strong>: Using Deep Learning to Analyze Images That Have High Interest from Children with Autism. Presented at<em>\u00a06th Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2016<\/em>, July 29, Bloomsburg University, Bloomsburg, PA (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Yang T<\/span>, Troiani V,\u00a0<strong>King BR<\/strong>: Using Deep Learning to Analyze Images That Have High Interest from Children with Autism. Presented at\u00a0<em>Sigma Xi Summer Research Symposium 2016<\/em>, July 21, Bucknell University, Lewisburg, PA (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Pham S<\/span>,\u00a0<strong>King BR<\/strong>: Using Machine Learning to Automatically Predict Feature Representation on Sequential Data. Presented at<em>\u00a015th Annual Kalman Research Symposium<\/em>, April 2, 2016, Bucknell University, Lewisburg, PA (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Hammett J<\/span>,\u00a0<strong>King BR<\/strong>: Using Data Mining to Construct More Practical Weather Forecasting Models. Presented at\u00a0<em>15th Annual Kalman Research Symposium<\/em>, April 2, 2016, Bucknell University, Lewisburg, PA (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Cowen R<\/span>, Mitchel M, Hare-Harris AE,\u00a0<strong>King BR<\/strong>: Application of n-gram prediction and Brown\u2019s Stages of Syntactic and Morphological Development to design augmentative and alternative communication for children with autism. Presented at\u00a0<em>5th Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2015,<\/em>\u00a0August 4, Bucknell University, Lewisburg, PA. (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Pham S<\/span>,\u00a0<strong>King BR<\/strong>: Using Deep Learning to Automatically Learn Feature Representation and Build a Better Classification Model on Protein Sequential Data. Presented at\u00a0<em>5th Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2015,<\/em>\u00a0August 4, Bucknell University, Lewisburg, PA. (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Hammett J<\/span>,\u00a0<strong>King BR<\/strong>: Using Data Mining to Construct More Practical Weather Forecasting Models. Presented at Sigma Xi Summer Research Symposium 2015, July 23, Bucknell University, Lewisburg, PA (Poster)<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Rogge M<\/span>,\u00a0<strong>King BR<\/strong>. Analysis of Spike Timing Dependent Neural Networks for More Efficient Starting State Learning. Presented at\u00a0<em>14th Annual Kalman Research Symposium<\/em>, March 28, 2015, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Gonthier S<\/span>,\u00a0<strong>King BR<\/strong>. Using statistical learning to improve word prediction for augmentative and alternative communication. Presented at\u00a0<em>14th Annual Kalman Research Symposium<\/em>, March 28, 2015, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Ren C<\/span>,\u00a0<strong>King BR<\/strong>. Predicting a protein contact map from protein sequence. Presented at\u00a0<em>4th Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2014<\/em>, August 5, Geisinger Research, Danville, PA<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Gonthier S<\/span>,\u00a0<strong>King BR<\/strong>. Using statistical learning to improve word prediction for augmentative and alternative communication. Presented at\u00a0<em>4th Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2014<\/em>, August 5, Geisinger Research, Danville PA\n<ul class=\"wp-block-list\">\n<li><strong>Winner\u00a0for oral presentation &#8211; One of three chosen out of 86 submissions<\/strong><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Gonthier S<\/span>, King BR. Using statistical learning to improve word prediction for augmentative and alternative communication. Presented at\u00a0<em>Sigma Xi Summer Research Symposium<\/em>, July 24, 2014, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Ren C<\/span>,\u00a0<strong>King BR<\/strong>. An improved method for protein contact map prediction. Presented at\u00a0<em>13th Annual Kalman Research Symposium 2014<\/em>, March 29, Bucknell University, Lewisburg, PA.<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Dwornik L<\/span>,\u00a0<strong>King BR<\/strong>. Regular expressions for named entity recognition. Presented at\u00a0<em>13th Annual Kalman Research Symposium 2014<\/em>, March 29, Bucknell University, Lewisburg, PA.<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Cole C<\/span>,\u00a0<strong>King BR<\/strong>. Using Machine Learning to Predict the Health of HIV-Infected Patients. Presented at\u00a0<em>Third Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2013<\/em>, August 6, Geisinger Research, Danville, PA\n<ul class=\"wp-block-list\">\n<li><strong>Winner\u00a0for oral presentation &#8211; One of three chosen out of 67 submissions<\/strong><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Cole C<\/span>,\u00a0<strong>King BR<\/strong>. Identification of Genetic Variance in HIV Associated with Varying Stages of AIDS to Assess a Patient&#8217;s Prognosis. Presented at\u00a0<em>12th Annual Kalman Research Symposium 2013<\/em>, April 13, Bucknell University, Lewisburg, PA.<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Segar M<\/span>,\u00a0<strong>King BR<\/strong>. Genome Assembly from Next Generation Sequencing Instrumentation, Presented at\u00a0<em>Susquehanna Valley Undergraduate Research Symposium<\/em>, August 9, 2011 Geisinger Research, Danville, PA<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\"><em>S<\/em>tahlfeld P<\/span>, Tromp G,\u00a0<strong>King BR<\/strong>. Installation and deployment of caBIG for cancer research, Presented at\u00a0<em>Sigma Xi Summer Research Symposium<\/em>, July 27, 2011, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li><span style=\"text-decoration: underline;\">Segar M<\/span>,\u00a0<strong>King BR<\/strong>. Genome Assembly from Next Generation Sequencing Instrumentation, Presented at\u00a0<em>Sigma Xi Summer Research Symposium<\/em>, July 27, 2011, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li>King BR,\u00a0<span style=\"text-decoration: underline;\">Barteau A<\/span>, Guda C: ngLOC: software for proteome-wide prediction of subcellular localization, Presented at\u00a0<em>Sigma Xi Summer Research Symposium<\/em>, July 27, 2011, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li>Kagle J,\u00a0<strong>King BR<\/strong>. Identification of a Putative Chlorocatechol Catabolic Pathway in the Triclosan Degrader Sphingomonas sp. RD1. Presented at\u00a0<em>NEMPET 2010<\/em>, June 25-27 2010, Blue Mountain Lake, NY [<a href=\"papers\/NEMPET 2010 Poster.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">PPT<\/a>]<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Honors Theses<\/h2>\n\n\n\n<p>Below is a list of students who completed an undergraduate honors thesis during their senior year under my advisement:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Taehwan Kim &#8217;20<\/strong> &#8211; Chaotic Time Series Prediction using Deep Echo State Networks. Bucknell University Honors Thesis, 2020<\/li>\n\n\n\n<li><strong>Chuqiao Ren &#8217;15<\/strong>\u00a0&#8211; Predicting Protein Contact Maps by Bagging Decision Trees. Bucknell University Honors Thesis, 2015<\/li>\n\n\n\n<li><strong>Charles Cole &#8217;14\u00a0<\/strong>&#8211; Using Machine Learning to Predict the Health of HIV-Infected Patients. Bucknell University Honors Thesis, 2014<\/li>\n\n\n\n<li><strong>Matthew Segar &#8217;12 &#8211;\u00a0<\/strong>Utilization of Probabilistic Models in Short Read Assembly from Second-Generation Sequencing, Bucknell University Honors Thesis, 2012 [<a href=\"papers\/2012 Thesis - Segar.pdf\">PDF<\/a>]\n<ul class=\"wp-block-list\">\n<li><strong>Winner of Harold W. Miller Prize for Outstanding Honor&#8217;s Thesis.<\/strong><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Press<\/h2>\n\n\n\n<p><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Invited Talks and Panels<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>[INVITED TALK]: &#8220;Bioinformatics and Genomics&#8221;, CHEG 470, Spring 2018, Spring 2019.<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Data Science and Analytics, and Bucknell&#8221;. Presented before the Board of Trustees with Abby Flynt and Matt Bailey. October 11, 2018.<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Genomics&#8221;. Foundations Seminar, Fall 2018.<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Agile Design Methodology&#8221;, ENGR 452 \u2013 Interdisciplinary Senior Design, Fall 2018.<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Genomics and Your Future&#8221; \u2013 a talk introducing the movie GATTACA. Campus Theater, March 21, 2018.<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Using eye-tracking to identify gaze behaviors in autistic children&#8221;, Pecha Kucha Night 2019, January 24, 2019<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;SCRUM for Design and Engineering&#8221; ENGR 452 &#8211; Interdisciplinary Senior Design, Fall 2017.<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;IP Course Perspectives&#8221; w\/ Abby Flynt. TLC \/ Faculty Learning Series, Fall 2016.<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Sequential Data Mining&#8221;, September 15, 2016. Mathematics Dept. Student Colloquium Series, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li>[PANEL MEMBER]: &#8220;Conducting research with students&#8221;, November 13, 2014. Teaching and Learning Center, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li>[PANEL MEMBER]: &#8220;Artificial Intelligence: An Interdisciplinary Conversation&#8221;, November 21, 2013, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Bioinformatics: Increasing knowledge in healthcare and medicine.&#8221;\u00a0<em>Presented at Bending the Curve: Innovative Approaches to Controlling Health Care Costs,<\/em>November 2, 2013, Bucknell University, Lewisburg, PA\n<ul class=\"wp-block-list\">\n<li>Included students\u00a0<strong>Charles Cole<\/strong>,\u00a0<strong>Brigitte Hofmeister<\/strong>, and\u00a0<strong>Chuqiao Ren<\/strong>\u00a0in talk to give 5 minute snapshot of their research<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Big Biological Data: The Grand Challenge in Modern Biology and Medicine.&#8221; Presented at\u00a0<em>Grand Challenges Foundation Seminar<\/em>, October 2013, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Analysis of biological sequence data&#8221; Fall 2012, Presented in\u00a0<em>ELEC 402 &#8211; Genomic Signal Processing<\/em>, Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li>[INVITED TALK]: &#8220;Bioinformatics for the Analysis of Biological Data&#8221;, Fall 2011, Presented at the\u00a0<em>Biology Department Seminar Series, Fall 2011,<\/em>\u00a0Bucknell University, Lewisburg, PA<\/li>\n\n\n\n<li>[PANEL MEMBER]: &#8220;What I wish I had known&#8221;,\u00a0 August, 2011. Presented at the\u00a0<em>Teaching and Learning Center discussion for new faculty,\u00a0<\/em>Bucknell University, Lewisburg, PA<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Student collaboration indicated with underlined authorship Journal Publications [Peer-Reviewed] International Conferences [Peer Reviewed] Local and Regional Conferences Honors Theses Below is a list of students who completed an undergraduate honors thesis during their senior year under my advisement: Press Invited Talks and Panels<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"folder":[],"class_list":["post-279","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/pages\/279","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/comments?post=279"}],"version-history":[{"count":26,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/pages\/279\/revisions"}],"predecessor-version":[{"id":523,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/pages\/279\/revisions\/523"}],"wp:attachment":[{"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/media?parent=279"}],"wp:term":[{"taxonomy":"folder","embeddable":true,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/folder?post=279"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}