Kunal Poorey

Senior Member of Technical Staff

Author profile picture

Senior Member of Technical Staff

kpoorey@sandia.gov

(925) 294-2244

Sandia National Laboratories, New Mexico
 P.O. Box 5800
 Albuquerque, NM 87185-9292

Biography

Kunal’s work at Sandia is mostly focused on the development of computational tools in biodefense, infectious diseases, microbiome, biomass/biofuel and microbial ecology. Kunal has also built software tools to analyze sequencing data and apply machine-learning techniques for RNA-seq, ChIP-seq, CLK-ChIP-seq, Tiling arrays, expression arrays, Metagenomics and Amplicon sequencing. Kunal’s current area of interests are: Data Science and Machine learning applications in biology, New method development in Genomics, Biofuels and Biomass production, Microbiome, Infectious Diseases, Antibiotic Resistance, Transcription Regulation and Chromatin Structure and Function.

Education

Bachelor’s Degree: Chemical Engineering, IIT-Bombay, Mumbai, India (2000-2004)

Master’s Degrees:

  • Civil Engineering, University of Virginia (2007)
  • Physical and Biosciences, University of Virginia (2007-2011)

Doctoral Degree: Biochemistry and Molecular Genetics, University of Virginia (2011-2014)

Postdoctoral Fellowships: Sandia National Laboratories (2014-2017)

Publications

  • Branda, S., Collette, N., Aiosa, N., Garg, N., Mageeney, C.M., Williams, K.P., Phillips, A., Hern, K., Arkin, A., Ricken, B., Wilde, D., Dogra, S., Humphrey, B., Poorey, K., Courtney, C., & Courtney, C. (2022). Reconfiguration of the Respiratory Tract Microbiome to Prevent and Treat Burkholderia Infection. https://doi.org/10.2172/1898252 Publication ID: 80404
  • Timlin, J.A., Reichardt, T.A., Maes, D., Kunstadt, C.G., Katinas, C.M., Hipple, T., Lane, T., Jensen, T., Dempster, T.A., McGowen, J.A., Poorey, K., Curtis, D.J., & Curtis, D.J. (2021). Real-time monitoring of algal pond productivity and pest presence [Conference Presenation]. https://doi.org/10.2172/1873286 Publication ID: 78889
  • Reichardt, T.A., Maes, D., Jensen, T.J., Dempster, T.A., McGowen, J.A., Poorey, K., Curtis, D.J., Lane, T., Timlin, J.A., & Timlin, J.A. (2020). Spectroradiometric detection of competitor diatoms and the grazer Poteriochromonas in algal cultures. Algal Research, 51. https://doi.org/10.1016/j.algal.2020.102020 Publication ID: 106264
  • Branda, S., Poorey, K., & Poorey, K. (2020). COVID-19 biomarkers based on respiratory microbiome content. https://doi.org/10.2172/1673815 Publication ID: 71018
  • Courtney, C.M., Sinha, A., Ray, D., Techel, J., Poorey, K., Collette, N., Phillips, A., el-Etr, S., Franco, M., Branda, S., & Branda, S. (2019). Host-directed CRISPR based countermeasures for Burkholderia [Conference Poster]. https://www.osti.gov/biblio/1643291 Publication ID: 66338
  • Poorey, K. (2019). Deciphering Global Dynamics of Microbial Multidrug Resistance Regulation using Multi-Omics Approach [Conference Poster]. https://www.osti.gov/biblio/1643313 Publication ID: 66372
  • Poorey, K. (2019). iPredictome: A Data Science Toolkit for Predictive Modeling for Health Anomalies [Conference Poster]. https://www.osti.gov/biblio/1643592 Publication ID: 66533
  • Branda, S., Wang, P., Labauve, A., Sinha, A., Poorey, K., Williams, K.P., Michailidis, G., Schoeniger, J.S., Mageeney, C.M., Courtney, C.M., el-Etr, S., Franco, M., Lao, V., D’Haeseleer, P., Pena, J., Segelke, B., & Segelke, B. (2019). Elucidation of Host-Pathogen Interactions via Dual RNA-Seq Analysis to Support Development of Countermeasures Against the Intracellular Bacterial Pathogen Burkholderia pseudomallei [Conference Poster]. https://www.osti.gov/biblio/1643632 Publication ID: 66457
  • Kim, S., Poorey, K., Monroe, E., Davis, R.W., Siccardi, A., & Siccardi, A. (2019). A long-term comprehensive study on environmental and ecological impacts on biomass productivity of periphytic algae flow-way deployed at contaminated US territory [Conference Poster]. https://www.osti.gov/biblio/1642012 Publication ID: 64918
  • Poorey, K. (2019). Current Research Interests [Presentation]. https://www.osti.gov/biblio/1645878 Publication ID: 64666
  • Lane, T., Timlin, J.A., Reichardt, T.A., Poorey, K., Lane, P., Hagerstrand, A., & Hagerstrand, A. (2019). A survey of microalgal resistance to algal pond crashes [Conference Poster]. https://www.osti.gov/biblio/1640882 Publication ID: 69297
  • Jacquet, R., Labauve, A.E., Akoolo, L., Patel, S., Alqarzaee, A.A., Fok Lung, T.W., Poorey, K., Stinear, T.P., Thomas, V.C., Meagher, R.J., Parker, D., & Parker, D. (2019). Dual gene expression analysis identifies factors associated with Staphylococcus aureus virulence in diabetic mice. Infection and Immunity, 87(5), pp. 19-. https://doi.org/10.1128/IAI.00163-19 Publication ID: 67740
  • Courtney, C.M., Sinha, A., Poorey, K., Branda, S., Ray, D., Collette, N., Fergusen, A., el-Etr, S., & el-Etr, S. (2018). Elucidating Genetic Mechanisms of Bacterial Pathogenesis for Host-Directed Protection [Presentation]. https://www.osti.gov/biblio/1594329 Publication ID: 59389
  • Peterson, K., Perego, M., Frederick, J.M., Wheeler, L.B., Bosler, P.A., Ruffing, A.M., Davis, R.W., Whitmore, L.S., Poorey, K., Williams, K.P., Roesler, E.L., Bryan, P.F., Salinger, A.G., Hardesty, J., Tidwell, V.C., Singh, A.K., & Singh, A.K. (2018). SNL/BER Review 2018 [Presentation]. https://www.osti.gov/biblio/1594318 Publication ID: 59367
  • Branda, S., Courtney, C.M., Sinha, A., Poorey, K., Schoeniger, J.S., Labauve, A.E., Williams, K.P., & Williams, K.P. (2018). Elucidation & manipulation of host-pathogen interactions for development of countermeasures against intracellular bacterial pathogen Burkholderiapseudomallei [Presentation]. https://www.osti.gov/biblio/1594641 Publication ID: 59351
  • Fisher, C.L., Lane, P., Poorey, K., Mayali, X., Lane, T., & Lane, T. (2018). Investigating the chemical and biological landscape of microalgae cultures to mitigate pond crashes [Conference Poster]. https://www.osti.gov/biblio/1529474 Publication ID: 62677
  • Maes, D., Reichardt, T.A., Jensen, T.J., Dempster, T.A., McGowen, J.A., Poorey, K., Hipple, T., Lane, T., Timlin, J.A., & Timlin, J.A. (2018). Spectroradiometric Detection of Competitors and Predators in Algal Ponds [Conference Poster]. https://www.osti.gov/biblio/1526346 Publication ID: 62531
  • Fisher, C.L., Lane, P., Poorey, K., & Poorey, K. (2018). Investigating the chemical and biological landscape of microalgae cultures to mitigate pond crashes [Conference Poster]. https://www.osti.gov/biblio/1498617 Publication ID: 60931
  • Fisher, C.L., Lane, P., Poorey, K., Tran-Gyamfi, M., Jaryenneh, J., Beck, N.L., Mahan, K.M., Lane, T., & Lane, T. (2018). Investigating the chemical and biological landscape of microalgae cultures to mitigate pond crashes [Presentation]. https://www.osti.gov/biblio/1498616 Publication ID: 60930
  • Poorey, K. (2018). Deciphering Global Dynamics of Microbial Multidrug Resistance Regulation using Novel method CLK-seq [Conference Poster]. https://www.osti.gov/biblio/1513635 Publication ID: 58569
  • Poorey, K. (2017). Capturing the pond crash signature for algal cultivation optimization [Conference Poster]. https://www.osti.gov/biblio/1483200 Publication ID: 54350
  • Lane, T., Carney, L.T., Lane, P., Poorey, K., Koh, C.Y., Fisher, C.L., Curtis, D.J., Beck, N.L., & Beck, N.L. (2017). Algal crop protection strategies and technologies [Conference Poster]. https://www.osti.gov/biblio/1480677 Publication ID: 53933
  • Fisher, C.L., Lane, P., Poorey, K., Beck, N.L., Mahan, K.M., Anthony, S.M., Mowry, C.D., Moorman, M.W., Lane, T., & Lane, T. (2017). Investigating the chemical and biological landscape of microalgae cultures to reduce or mitigate pond crashes [Presentation]. https://www.osti.gov/biblio/1510211 Publication ID: 53451
  • Fisher, C.L., Mowry, C.D., Lane, P., Lane, T., Moorman, M.W., Anthony, S.M., Pimentel, A.S., Beck, N.L., Poorey, K., Curtis, D.J., & Curtis, D.J. (2017). Investigating the chemical landscape of microalgae cultures to mitigate pond crashes [Conference Poster]. https://www.osti.gov/biblio/1466477 Publication ID: 58100
  • Poorey, K. (2017). DISCOVR Project Machine learning [Conference Poster]. https://www.osti.gov/biblio/1456762 Publication ID: 56893
  • Meagher, R.J., Poorey, K., Labauve, A.E., Hamblin, R., Williams, K.P., Bent, Z.W., & Bent, Z.W. (2016). A rapid spin column-based method to enrich pathogen transcripts from eukaryotic host cells prior to sequencing. PLoS ONE, 11(12). https://doi.org/10.1371/journal.pone.0168788 Publication ID: 49972
  • Poorey, K. (2016). Capturing the pond crash signature for algal cultivation optimization [Conference Poster]. https://www.osti.gov/biblio/1420820 Publication ID: 47617
  • Meagher, R.J., Labauve, A.E., Poorey, K., Bent, Z., & Bent, Z. (2016). A Capture-Based Technique for Enhancing RNA-Seq Analyses of Bacterial Transcriptomes During In Vitro and In Vivo Infections [Conference Poster]. https://www.osti.gov/biblio/1410767 Publication ID: 47950
  • Priye, A., Renzi, R.F., Poorey, K., Meagher, R.J., & Meagher, R.J. (2016). INVESTIGATION OF CELL TRAJECTORIES IN CHAOTIC FLOW FIELDS GENERATED BY A HELICAL STATIC MICROMIXER FOR RAPID CROSSLINKING KINETICS [Conference Poster]. https://www.osti.gov/biblio/1399830 Publication ID: 47140
  • Poorey, K. (2016). Dynamics of Ecology during Cultivation of Algae from Waste Water [Conference Poster]. https://www.osti.gov/biblio/1526839 Publication ID: 47566
  • Lane, T., Lane, ., Poorey, K., Geng, H., Curtis, D.J., Carney, L.T., & Carney, L.T. (2016). Algal crop protection strategies and technologies [Conference Poster]. https://www.osti.gov/biblio/1378077 Publication ID: 51867
  • Priye, A., Renzi, R.F., Poorey, K., Meagher, R.J., & Meagher, R.J. (2016). INVESTIGATION OF CELL TRAJECTORIES IN CHAOTIC FLOW FIELDS GENERATED BY A HELICAL STATIC MICROMIXER FOR RAPID CROSSLINKING KINETICS [Conference Poster]. https://www.osti.gov/biblio/1373046 Publication ID: 51237
  • Hess, S., Curtis, D.J., Labauve, A.E., Poorey, K., & Poorey, K. (2016). Deciphering Antibiotic Resistance [Presentation]. https://www.osti.gov/biblio/1373157 Publication ID: 51314
  • Poorey, K. (2016). Deciphering Host Pathogen and Microbiome Interaction [Conference Poster]. https://www.osti.gov/biblio/1505383 Publication ID: 51327
  • Poorey, K. (2016). Capturing Pond Crash Signature in ATP3 sites using Machine Learning [Conference Poster]. https://www.osti.gov/biblio/1368439 Publication ID: 50802
  • Poorey, K., Lane, T., & Lane, T. (2016). Amplicon Sequencing of ATP3 Pond Samples for Pond Crash Forensics [Presentation]. https://www.osti.gov/biblio/1347175 Publication ID: 48839
  • Poorey, K. (2015). Understanding the Spatial and Temporal Dynamics of Pathogenesis [Conference Poster]. https://www.osti.gov/biblio/1530673 Publication ID: 46457
  • Poorey, K. (2015). Amplicon Sequencing of ATP3 Pond Samples for Pond Crash Forensics [Conference Poster]. https://www.osti.gov/biblio/1506771 Publication ID: 46456
  • Hudson, C.M., Schoeniger, J.S., Poorey, K., Ray, D., Williams, K.P., & Williams, K.P. (2015). Sandia?s Web-Based Bioinformatics Tools [Conference Poster]. https://www.osti.gov/biblio/1331543 Publication ID: 44564
  • Poorey, K., Curtis, D.J., Lane, T., Geng, H., & Geng, H. (2015). Genetic Evaluation of Pond Crashes during ATP3 Unified Field Study [Conference Poster]. https://www.osti.gov/biblio/1331587 Publication ID: 44107
  • Meagher, R.J., Poorey, K., Labauve, A.E., Bent, Z., & Bent, Z. (2015). A Capture-Based Technique for Enhancing RNA-Seq Analysis of Bacterial Transcriptomes During in vitro and in vivo Infections [Conference Poster]. https://www.osti.gov/biblio/1255045 Publication ID: 43647
  • Carson, B., Timlin, J.A., Sinclair, M.B., Anthony, S.M., Moorman, M.W., la Bauve, E., Murton, J.K., Williams, K.P., Poorey, K., Jones, H.D., & Jones, H.D. (2015). Identification of Unknown Viral Infections by Hyperspectral Cell Sorting and Deep Sequencing [Conference Poster]. https://www.osti.gov/biblio/1258189 Publication ID: 43537
  • Carson, B., Timlin, J.A., Sinclair, M.B., Anthony, S.M., Moorman, M.W., Murton, J.K., Williams, K.P., Poorey, K., la Bauve, E., & la Bauve, E. (2015). Unknown Pathogen Detection in Clinical Samples: A Novel Hyperspectral Imaging and Single Cell Sequencing Approach [Conference Poster]. https://www.osti.gov/biblio/1258188 Publication ID: 43536
  • Poorey, K., Sinha, A., Curtis, D.J., Williams, K.P., Branda, S., Meagher, R.J., & Meagher, R.J. (2015). A transcriptomic analysis of Yersinia enterocolitica biovar 1B infecting murine macrophages reveals new mechanisms of intracellular survival. Infection and Immunity, 83(7), pp. 2672-2685. https://doi.org/10.1128/IAI.02922-14 Publication ID: 40615
  • Lane, T., Poorey, K., Geng, H., & Geng, H. (2015). Metagenomics of ATP3 Pond Samples [Presentation]. https://www.osti.gov/biblio/1238227 Publication ID: 41515
  • Cui, L., Williams, K.P., Lane, T., Poorey, K., & Poorey, K. (2014). Metagenomics Analysis on Arizona Algae Cultivation System [Presentation]. https://www.osti.gov/biblio/1494259 Publication ID: 37773
  • Carson, B., Sinclair, M.B., Timlin, J.A., Williams, K.P., Poorey, K., Hatch, A., James, C.D., Davis, R.W., la Bauve, E., Jones, H., & Jones, H. (2014). A Novel Approach to Unknown Virus Identification in Clinical Samples [Presentation]. https://www.osti.gov/biblio/1496684 Publication ID: 37598
  • Poorey, K., Sinha, A., Curtis, D.J., Meagher, R.J., & Meagher, R.J. (2014). Using RNA-Seq to Understand the Spatial and Temporal Dynamics of Yersinia enterocolitica Pathogenesis [Presentation]. https://www.osti.gov/biblio/1714453 Publication ID: 40944
Showing 10 of 48 publications.

Selected Publications

  • Poorey K, Viswanathan R, Craver MN, Karpova TS, McNelly JG, Bekiranov S, Auble DT. “Measuring Chromatin Interaction Dynamics on the Second-Time Scale at Single-Copy Genes.” Science Oct 2013.
  • Poorey K, Sprouse RO, Wells MN, Viswanathan R, Bekiranov S, Auble DT “RNA synthesis precision is regulated by preinitiation complex turnover.” Genome Res. 2010 Dec; 20(12):1679-88. Epub 2010 Sep 20.
  • Chen X, Poorey K, Wells MN, Muller U, Bekiranov S, Auble DT, Brow DA., Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. PLoS Genetics 2017.
  • Bent ZW, Poorey K, LaBauve AE, Hamblin RY, Williams KP, and Meagher RJ. A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing. PLoS ONE Dec 2016
  • Bent ZW, Poorey K, Brazel DM, LaBauve AE, Sinha A, Curtis DJ, Tew KE, Hamblin RY, Williams KP, Branda SS, Young GM, and Meagher RJ. “A Transcriptomic Analysis of Yersinia enterocolitica biovar 1B Infecting Murine Macrophages Reveals New Mechanisms of Extracellular and Intracellular Survival” Infect Immun. Apr 2015.
  • Li M, Valsakumar V, Poorey K, Bekiranov S, Smith JS. “Genome-wide Analysis of Functional Sirtuin Chromatin Targets in Yeast.” Genome Biol. May 2013.
  • Hyland EM, Molina H, Poorey K, Jie C, Xie Z, Dai J, Qian J, Bekiranov S, Auble DT, Pandey A, Boeke JD. “An evolutionarily ‘young’ lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae.” Genes Dev. June 2011.
  • Wade SL, Poorey K, Bekiranov S, Auble DT “The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression.” EMBO J. 2009 Oct 7;28(19):2919-31