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Ronald

Ronald C. Taylor

Computational Biology
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352
509/372-6568

Biography

Dr. Taylor is a research scientist (2003-present) serving in the areas of systems biology and bioinformatics. Dr. Taylor is currently working in the analysis of bacterial communities, in metabolic modeling of bacteria, in analysis of next generation sequencing data (including metatranscriptomics), in inference of biological networks, in the application of high-performance computing techniques to analysis of high-throughput data, and in the construction of scalable databases suitable for data integration and integrated analysis of terabyte-size data sets.

While at PNNL, Dr. Taylor has served as Principal Investigator (PI) for the Complex Queries and Data Structures projects. Also, he was the PI on PNNL's Software Environment for BIological Network Inference (SEBINI) project (Taylor et al., 2006), which provided an interactive environment for the deployment and evaluation of algorithms used to reconstruct the structure of biological regulatory and interaction networks.

Dr. Taylor's 2003 dissertation focused on inference of regulatory networks using information-theoretic methods on correlations in gene expression data, and Dr. Taylor has since have performed substantial work in inference of regulatory networks at PNNL. He has published extensively on the application of computational techniques in network inference in biology as well as the analysis of integrated heterogeneous data sets (Taylor et al., 2013)

Dr. Taylor has served as the architect and administrator of a pilot PNNL project that has implemented a parallel processing/scalable database framework for high volume biological data sets using the open source fault-tolerant Hadoop framework and the HBase NoSQL database, operating on top of Hadoop. This data warehouse now resides on PNNL's Large Scale Analytics Linux cluster. Also, Dr. Taylor published the first general review of Hadoop and HBase use in bioinformatics in 2010 (Taylor, 2010), and has been an invited speaker to talk in this area, as well as a journal reviewer. He is now exploring a Spark-based environment for parallelized distributed graph / topological analysis & querying of large biological networks.

In other current research, Dr. Taylor works closely with the U. S. Department of Energy's systems biology KnowledgeBase (KBase) group, performing gene calling, genome annotation, metabolic model construction, bacterial community analysis and programming in that environment.

Also, Dr. Taylor has helped develop data standards for biological data (e.g., MIAME, MAGE, MISFISHIE, MINSEQE) as an officer and board member since 2000 of the Functional Genomics Data (FGED) Society.

From 2000-2003, Dr. Taylor served as director of gene expression analysis in the Center for Computational Pharmacology at the University of Colorado Health Sciences Center (UCHSC). Before that, he served as a computer scientist at the National Institutes of Health (1991-2000, ending rank GS-14). Dr. Taylor worked first in the BioInformatics & Molecular Analysis Section (BIMAS) at the Division of Computer Research & Technology/NIH and then at the National Cancer Institute/NIH, where he was a senior investigator in the Biometric Research Branch/NCI with responsibility for the design and development of computer systems to handle high-throughput gene expression analysis and analysis of genome and gene expression data to identify and clarify the function of cancer-associated genes.

Dr. Taylor worked on knowledgebase design (automated reasoning, use of ontologies) while at UCHSC, and he created one of the first knowledgebases at NIH, installing the object-oriented Genobase knowledgebase from Argonne National Laboratory while working at BIMAS/DCRT/NIH, adding a web interface and additional public data sets.

Dr. Taylor enjoys building tools and environments that can manage, query, and perform automated reasoning/inference on truly large biological data (e.g., on "Big Data").

SEBINI project description

Dr. Taylor's full bibliography of publications - and presentations - at NCBI/NIH, including recent 2015-2017 publications not yet automatically added to this staff page

Dr. Taylor's ResearchGate page

Research Interests

  • Reconstruction of biological networks, with development of algorithms for inference of regulatory networks focused on information-theoretic and graphical model (Bayesian network) approaches.
  • Metabolic modeling of bacteria and bacterial communities, including flux balance analysis and metabolic pathway flux prediction using NMR and mass spectrometry Carbon-13 labeling.
  • Integrated analysis of high-throughput gene expression and protein abundance data; analysis of next-generation sequencing data sets. Most recently, metatranscriptomics analysis of bacterial communities.
  • High-performance computing techniques (e.g., Hadoop, HBase, Spark platforms on Linux clusters) for large-scale data analysis and construction of data warehouses.
  • Automated reasoning and machine learning techniques as applied to joint analysis of regulatory networks, metabolic pathways, and genomic data.
  • Biological database and knowledgebase design.

Education and Credentials

  • Ph.D./ Bioinformatics, George Mason University (dissertation advisor: Lawrence Hunter, University of Colorado School of Medicine), 2003
  • M. S./ Biology, Case Western Reserve University (research-oriented master's; thesis advisor: Ross Overbeek, Argonne National Laboratory (ANL), research performed while holding graduate assistantship at ANL, 1989-1991), 1991
  • M. S./ Computer Science, Case Western Reserve University, 1985
  • B. S./ Physics, Case Western Reserve University, 1979. (National Merit Scholar; CWRU Presidential Scholar)
  • Cloudera certified Hadoop cluster administrator (2011)
  • Cloudera certified CCB-400 HBase specialist (2013)

Affiliations and Professional Service

  • Dr. Taylor has served as a board member and officer in the non-profit Functional Genomics Data (FGED) Society (http://fged.org) - formerly known as the Microarray and Gene Expression Data (MGED) Society - from its inception in November 1999, acting as Secretary (1999-2006) and currently as Treasurer (2006-present). Dr. Taylor has helped set standards for technologies such as high throughput microarrays and next generation sequencing data, and has been a part of the effort to set standards for microarray and NGS data experiment annotation and transfer (MIAME, MAGE-XML, MINSEQE) as well as for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
  • Member, International Society for Computational Biology
  • Member, Open Bioinformatics Foundation

Awards and Recognitions

  • As of December 2016, Dr. Taylor has served on seven NSF grant review panels related to bioinformatics, large-scale data analysis, and biological research infrastructure, the two most recent of such panels being held in 2016.
  • From 2006 to present, Dr. Taylor has served as an ad hoc reviewer for the journals Bioinformatics, Briefings in Bioinformatics, IEEE Transactions on Knowledge and Data Engineering (TKDE), BMC Bioinformatics, PLoS Computational Biology, Database, Nature Chemical Biology, and BMC Medical Informatics. In particular, in recent years Dr. Taylor has server as a reviewer for high performance computing tools (Hadoop and Spark based) for Bioinformatics.
  • Dr. Taylor was an organizing committee member for the 2013 public annual Functional Genomics Data (FGED) Society bioinformatics meeting (FGED-14), program committee member for Sixth International Meeting on Microarray Data Standards, Annotations, Ontologies, and Databases (MGED 6, 2003), organizing committee member (MGED V, 2002), organizing committee member, (MGED IV, 2002), program committee member (MGED III, 2001)
  • Outstanding Mentor Award, US Dept of Energy Office of Science (2006). The Outstanding Mentor award honors U.S. Department of Energy (DOE) Office of Science laboratory staff who have substantially contributed to the practical education of the nation's future scientists by mentoring students who participate in the Science Undergraduate Laboratory Internships (SULI) program at DOE national laboratories.
  • Key Contributor Award - in Next Generation Sequencing (NGS) analysis, Cell Isolation and Systems Analysis Capability (CISA) Capability Group, Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (2011)
  • Navachat Tongvichat Bioinformatics Memorial Scholarship, George Mason University (2001)

PNNL Publications

2016

  • Henry CS, HC Bernstein, P Weisenhorn, RC Taylor, JY Lee, JD Zucker, and HS Song. 2016. "Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction." Journal of Cellular Physiology 231(11):2339-2345.  doi:10.1002/jcp.25428

2015

  • Castelle C, KC Wrighton, BC Thomas, LA Hug, CT Brown, MJ Wilkins, KR Frischkorn, SG Tringe, A Singh, LM Markillie, RC Taylor, KH Williams, and JF Banfield. 2015. "Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling." Current Biology 25(6):690-701.  doi:10.1016/j.cub.2015.01.014

2014

  • Croken M, YF Ma, LM Markillie, RC Taylor, G Orr, LM Weiss, and K Kim. 2014. "Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage." PLoS One 9(11):Article No. e111297.  doi:10.1371/journal.pone.0111297
  • Eraso JM, LM Markillie, HD Mitchell, RC Taylor, G Orr, and W Margolin. 2014. "The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli." Journal of Bacteriology 196(11):2053-2066.  doi:10.1128/JB.01370-13
  • Welkie DG, X Zhang, LM Markillie, RC Taylor, G Orr, JM Jacobs, K Bhide, J Thimmapuram, MA Gritsenko, HD Mitchell, RD Smith, and LA Sherman. 2014. "Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle." BMC Genomics 15:Article No. 1185. 
  • Wilkins MJ, DW Hoyt, MJ Marshall, PA Alderson, AE Plymale, LM Markillie, AE Tucker, ED Walter, BE Linggi, A Dohnalkova, and RC Taylor. 2014. "CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough." Frontiers in Microbiology 5:Article No. 507.  doi:10.3389/fmicb.2014.00507

2013

  • DeAngelis KM, D Sharma, R Varney, BA Simmons, NG Isern, LM Markillie, CD Nicora, AD Norbeck, RC Taylor, JT Aldrich, and EW Robinson. 2013. "Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1." Frontiers in Microbiology 4:Article No. 280. 
  • Hess BM, J Xue, LM Markillie, RC Taylor, HS Wiley, BK Ahring, and BE Linggi. 2013. "Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics." PLoS One 8(6):e66104.  doi:10.1371/journal.pone.0066104
  • Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley. 2013. "Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria." Integrative Biology 5(11):1393-1406.  doi:10.1039/C3IB40120K
  • Tomita T, DJ Bzik, YF Ma, BA Fox, LM Markillie, RC Taylor, K Kim, and LM Weiss. 2013. "The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence." PLoS Pathogens 9(12):e1003823.  doi:10.1371/journal.ppat.1003823

2012

  • Acquaah-Mensah G, RC Taylor, and SV Bhave. 2012. "PACAP Interactions in the Mouse Brain: Implications for Behavioral and Other Disorders." Gene 491(2):224-231.  doi:10.1016/j.gene.2011.09.017
  • McDermott JE, KD Jarman, RC Taylor, MJ Lancaster, H Shankaran, KB Vartanian, SL Stevens, M Stenzel-Poore, and AP Sanfilippo. 2012. "Modeling Dynamic Regulatory Processes in Stroke." PLoS Computational Biology 8(10):e1002722.  doi:10.1371/journal.pcbi.1002722

2011

  • Chervitz SA, EW Deutsch, D Field, HE Parkinson, J Quackenbush, P Rocca-Serra, SA Sansone, CJJ Stoeckert, CF Taylor, RC Taylor, and CA Ball. 2011. "Data Standards for Omics Data: the Basis of Data Sharing and Reuse." Chapter 2 in Bioinformatics for Omics Data: Methods and Protocols, vol. 719, ed. B Mayer, pp. 31-69.  Humana Press, New York, NY. 
  • Perkins E, JK Chipman, S Edwards, T Habib, F Falciani, RC Taylor, G Van Aggelen, C Vulpe, P Antczak, and A Loguinov. 2011. "Reverse Engineering Adverse Outcome Pathways." Environmental Toxicology and Chemistry 30(1):22-38.  doi:10.1002/etc.374
  • Taylor RC, AP Sanfilippo, JE McDermott, RL Baddeley, RM Riensche, RS Jensen, M Verhagen, and J Pustejovsky. 2011. "Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts." International Journal of Computational Biology and Drug Design 4(1):56-82.  doi:10.1504/IJCBDD.2011.038657
  • Verhagen M, J Pustejovsky, RC Taylor, and AP Sanfilippo. 2011. "Modular Semantic Tagging of Medline Abstracts and its Use in Inferring Regulatory Networks." In Proceedings of the 5th IEEE International Conference on Semantic Computing (ICSC 2011), September 18-21, 2011, Palo Alto, California, pp. 498-505.  IEEE Computer Society Press, Los Alamitos, CA.  doi:10.1109/ICSC.2011.78

2010

  • McDermott JE, AP Sanfilippo, RC Taylor, RL Baddeley, RM Riensche, and RS Jensen. 2010. "An Integrated Approach to Predictive Genomic Analytics." In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, pp. 390-393.  Association for Computing Machinery, New York, NY.  doi:10.1145/1854776.1854837
  • Taylor RC. 2010. "An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics." BMC Bioinformatics 11(Suppl 12):S1.  doi:10.1186/1471-2105-11-S12-S1
  • Perkins E, T Habib, X Guan, B Escalon, F Falciani, JK Chipman, P Antczak, S Edwards, RC Taylor, C Vulpe, A Loguinov, G Van Aggelen, DL Villeneuve, and N Garcia-Reyero. 2010. "Discovery of Chemical Toxicity via Biological Networks and Systems Biology ." In Proceedings of the 27th Army Science Meeting, November 29 - December 2, 2010, Orlando, Florida.  US Army, Washington DC. 
  • Taylor RC, AP Sanfilippo, JE McDermott, RL Baddeley, RM Riensche, RS Jensen, and M Verhagen. 2010. "Learning Biological Networks via Bootstrapping with Optimized GO-based Gene Similarity." In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, pp. 515-519.  Association for Computing Machinery, New York, NY.  doi:10.1145/1854776.1854875

2009

  • Cannon WR, BJM Webb-Robertson, AR Willse, M Singhal, LA McCue, JE McDermott, RC Taylor, KM Waters, and CS Oehmen. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." Chapter 4 in Computational and Systems Biology: Methods and Applications, pp. 63-85.  Research Signpost, Trivandrum, India. 
  • McDermott JE, RC Taylor, H Yoon, and F Heffron. 2009. "Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium." Journal of Computational Biology 16(2):169-180.  doi:10.1089/cmb.2008.04TT
  • Sanfilippo AP, RL Baddeley, N Beagley, JE McDermott, RM Riensche, RC Taylor, and B Gopalan. 2009. "Using the Gene Ontology to Enrich Biological Pathways." International Journal of Computational Biology and Drug Design 2(3):221-235.  doi:10.1504/IJCBDD.2009.030114
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Taylor RC, M Singhal, DS Daly, JM Gilmore, WR Cannon, KO Domico, AM White, DL Auberry, KJ Auberry, BS Hooker, GB Hurst, JE McDermott, WH McDonald, DA Pelletier, DA Schmoyer, and HS Wiley. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3(4) (Sp. Iss. SI):409-430. 
  • Taylor RC, M Singhal, JB Weller, S Khoshnevis, L Shi, and JE McDermott. 2009. "A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium ." In Annals of the New York Academy of Sciences, vol. 1158, pp. 143-158.  PubMed, New York, NY. 

2008

  • Deutsch EW, C Ball, JJ Berman, GS Bova, A Brazma, RE Bumgarner, D Campbell, HC Causton, J Christiansen, F Daian, D Dauga, D Davidson, G Gimenez, YA Goo, S Grimmond, T Henrich, BG Herrmann, MH Johnson, M Korb, JC Mills, A Oudes, HE Parkinson, LE Pascal, N Pollet, J Quackenbush, M Ramialison, M Ringwald, D Salgado, SA Sansone, G Sherlock, CJJ Stoeckert, J Swedlow, RC Taylor, L Walashek, A Warford, DG Wilkinson, Y Zhou, LI Zon, AY Liu, and LD True. 2008. "Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)." Nature Biotechnology 26(3):305-312. 
  • Deutsch EW, CA Ball, JJ Berman, GS Bova, A Brazma, RE Bumgarner, D Campbell, HC Causton, J Christiansen, F Daian, D Dauga, D Davidson, G Gimenez, YA Goo, S Grimmond, T Henrich, BG Herrmann, MH Johnson, M Korb, JC Mills, A Oudes, HE Parkinson, LE Pascal, N Pollet, J Quackenbush, M Ramaialison, M Ringwald, D Salgado, SA Sansone, G Sherlock, CJJ Stoeckert, J Swedlow, RC Taylor, L Walasheck, A Warford, DG Wilkinson, Y Zhou, LI Zon, AY Liu, and LD True. 2008. "Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)." Nature Biotechnology 26(3):305-312. 
  • Taylor RC, and M Singhal. 2008. "Biological Network Inference and Analysis using SEBINI and CABIN." Chapter 24 in Computational Systems Biology, vol. 541, pp. 551-576.  Humana Press, New York, NY. 
  • Taylor RC, G Acquaah-Mensah, M Singhal, D Malhotra, and Biswal. 2008. "Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress." PLoS Computational Biology 4(8):Art. no. e1000166. 
  • Tintle N, A Best, M Dejongh, D VanBruggen, F Heffron, S Porwollik, and RC Taylor. 2008. "Gene set analyses for interpreting microarray experiments on prokaryotic organisms. ." BMC Bioinformatics 9:Art. No. 469.  doi:10.1186/1471-2105-9-469

2007

  • Taylor RC, M Singhal, DS Daly, KO Domico, AM White, DL Auberry, KJ Auberry, BS Hooker, GB Hurst, JE McDermott, WH McDonald, DA Pelletier, DD Schmoyer, and WR Cannon. 2007. "SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction ." In Sixth International Conference on Machine Learning and Applications, (ICMLA 2007) , pp. 587-593.  IEEE Computer Society, Washington DC.  doi:10.1109/ICMLA.2007.63

2006

  • Deutsch EW, CA Ball, GS Bova, A Brazma, RE Bumgarner, D Campbell, HC Causton, J Christiansen, D Davidson, LJ Eichner, YA Goo, S Grimmond, T Henrich, MH Johnson, M Korb, JC Mills, A Oudes, HE Parkinson, LE Pascal, J Quackenbush, M Ramialison, M Ringwald, SA Sansone, G Sherlock, CJJ Stoeckert, J Swedlow, RC Taylor, L Walashek, Y Zhou, AY Liu, and LD True. 2006. "Development of the Minimum Information Specification for in situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)." OMICS. A Journal of Integrative Biology 10(2):205-208. 
  • Oehmen CS, TP Straatsma, GA Anderson, G Orr, BJM Webb-Robertson, RC Taylor, RW Mooney, DJ Baxter, DR Jones, and DA Dixon. 2006. "New Challenges Facing Integrative Biological Science in the Post-Genomic Era." Journal of Biological Systems 14(2):275-293. 
  • Stoeckert CJJ, C Ball, A Brazma, R Brinkman, HC Causton, L Fan, J Fostel, G Fragoso, M Heiskanen, F Holstege, N Morrison, HE Parkinson, J Quackenbush, P Rocca-Serra, SA Sansone, U Sarkans, G Sherlock, R Stevens, C Taylor, RC Taylor, P Whetzel, and JC White. 2006. "Letter to the editor in "Wrestling with SUMO and bio-ontologies"." Nature Biotechnology 24(1):21-22. 
  • Taylor RC, A Shah, CC Treatman, and ML Blevins. 2006. "SEBINI: Software Environment for Biological Network Inference." Bioinformatics 22:2706-2708. 

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