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Biological Sciences Staff information

Ronald 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 staff scientist (2003-present) serving in the areas of systems biology and bioinformatics. Dr. Taylor is currently working in analysis of next generation sequencing data (RNA-Seq), 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.

In earlier work at PNNL, Dr. Taylor created an open source web-based framework for combined use of network inference algorithms on high-throughput data, the Software Environment for Biological Network Inference (SEBINI). 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 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 in order to identify and clarify the function of cancer associated genes. Also, Dr. Taylor has worked on knowledgebase creation (automated reasoning, use of ontologies) while at UCHSC, and helped develop the MIAME and MAGE gene expression data standards.

Research Interests

  • 1) Analysis of high throughput gene expression and protein abundance data; analysis of next generation sequencing data sets.
  • 2) Reconstruction of biological networks, with development of algorithms for inference of regulatory networks focused on information-theoretic and graphical model (Bayesian network) approaches.
  • 3) High performance computing techniques (e.g., Hadoop, HBase platforms on Linux clusters) for large scale data analysis and construction of data warehouses.
  • 4) Automated reasoning and machine learning techniques as applied to analysis of metabolic and signaling pathways and genomic data.
  • 5) Biological database & 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)

Affiliations and Professional Service

  • Secretary 2000-2006, Treasurer 2006-present, Functional Genomics Data (FGED) Society - formerly, Microarray and Gene Expression Data (MGED) Society
  • Member, editorial board of the journal Network Biology
  • Member, International Society for Computational Biology
  • Member, Open Bioinformatics Foundation

Awards and Recognitions

  • Outstanding Mentor Award, US Dept of Energy Office of Science, 2006
  • Navachat Tongvichat Bioinformatics Memorial Scholarship, George Mason University, 2001
  • Member, program committee for the Gene Network & Pathway Generation/Analysis Workshop, August, 2010
  • Member, program committee for the 2010 and 2011 Bioinformatics Open Source Conferences (BOSC)
  • Member, three-person organizing committee for the Second International Emerging Computational Methods for the Life Sciences Workshop (ECMLS-2011)

PNNL Publications

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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