Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

Ping Hu's Publications

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Publications

  1. Ping Hu, Sharon Borglin, Nina A. Kamennaya, Liang Chen, Hanwool Park, Laura Mahoney, Aleksandra Kijac, George Shan, Krystle L. Chavarría, Chunmin Zhang, Nigel W.T. Quinn, David Wemmer, Hoi-Ying Holman, Christer Jansson. 2012. Metabolic phenotyping of the cyanobacterium Synechocystis 6803 engineered for production of alkanes and free fatty acids. Applied Energy. In Press.
  2. Anthony A. Fodor, Todd Z. DeSantis, Kristine M. Wylie, Jonathan H. Badger, Yuzhen Ye, Theresa Hepburn, Ping Hu, Erica Sodergren, Konstantinos Liolios, Heather Huot-Creasy, Bruce W. Birren, Ashlee M. Earl. 2012. The Most Wanted Bacteria from the Human Microbiome. PloSOne 7(7):e41294.
  3. P. K H Lee, D. Cheng,  P. Hu, K. A West1, G. J Dick4, E. L Brodie, G. L Andersen, S. H. Zinder, J. He and L. Alvarez-Cohen. 2011. Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. The ISME Journal (2011) 5, 1014–1024.
  4. West, K. A., D. R. Johnson, P. Hu, T. DeSantis, E. L. Brodie, P. K. H. Lee, H. Feil, G. L. Andersen, S. H. Zinder and L. Alvarez-Cohen. 2008. Comparative genomics of Dehalococcoides ethenogenes 195 and an enrichment culture containing unsequenced Dehalococcoides strains.  Appl. Environ. Microbiol. 74:3533-3540.
  5. Hillson, N. J., P. Hu,G. L. Andersen, and L. Shapiro. (2007). Caulobacter crescentus as a Whole-Cell Uranium Biosensor. Applied and Environmental Microbiology. 73:7615-7621. 
  6. Lynch. S. V., L. Dixon, M. R. Benoit, E. L. Brodie, M. Keyhan, P. Hu, D. F. Ackerley, G. L. Andersen, and A. Matin. (2007). Role of the rapA Gene in Controlling Antibiotic Resistance of Escherichia coli Biofilms. Antimicrobial Agents and Chemotherapy. 51: 3650-3658.
  7. McGrath, P. T., L. Zhang, H. Lee, A. A. Iniesta, A. K. Hottes, M. H. Tan, N. J. Hillson, P. Hu, L. Shapiro, and H. H. McAdams. (2007). High-throughput identification of transcription start sites, conserved promoter motifs, and predicted regulons. Nature Biotechnology. 25:584-592. LBNL-63029. 
  8. DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K.  Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench  Compatible with ARB. Appl. Environ. Microbiol. 72:5069-72.
  9. Chain, P. S. G.., P. Hu, S. A. Malfatti, L. Radnedge, F. Larimer, L. M. Vergez, P. Worsham, M. C. Chu, and G. L. Andersen. 2006.  Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J. Bacteriol. 188:4453-4463. LBNL-60248.
  10. Hu,P, E. L. Brodie, Y. Suzuki,   H. H. McAdams and G. L. Andersen. 2005. Whole Genome Transcriptional Analysis of Heavy Metal Stresses in Caulobacter crescentus. J. Bacteriol. 187(24):8437-8449. LBNL-59011.
  11. Motin VL, Georgescu AM, Elliott JM, Hu P, Worsham PL, Ott LL, Slezak TR, Sokhansanj BA, Regala WM, Brubaker RR, Garcia E. 2002. Genetic variability of Yersinia pestis isolates as predicted by PCR-based IS100 genotyping and analysis of structural genes encoding glycerol-3-phosphate dehydrogenase (glpD). J Bacteriology 184(4):1019-27.
  12. Youngren B, L. Radnedge, P. Hu, E. Garcia and S. Austin. 2000. A plasmid partition system of the P1-P7 par family from the pMT1 virulence plasmid of Yersinia pestis. J. Bacteriology 182(14):3924-3928.
  13. Hu, P., J. Elliott, P. McCready, E. Skowronski, J. Garnes, A. Kobayashi, R. R. Brubaker and E. Garcia. 1998. Structural organization of virulence-associated plasmids of Yersinia pestis.  J. Bacteriology 180(19):5192-202.
  14. Hu, P., T. Leighton, G. Ishkhonova and S. Kustu. 1999. Sensing of Nitrogen Limitation by Bacillus subtilis: Comparison to Enteric Bacteria. J. Bacteriology 181(16):5042-5050.
  15. Chen, S. , D. R. Tomchick, D. Wolle, P. Hu, J. L. Smith, R. L. Switzer, and H. Zalkin. 1997. Mechanism of the synergistic end-product regulation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase by nucleotides. Biochemistry 36:10718-10726.
  16. Hu, P. and R. L. Switzer. 1995. Evidence for substrate stabilization in the degradation of Bacillus subtilis aspartate transcarbamylase in vivo. Archives Biochem. Biophy. 316:260-266.
  17. Hu, P., T. Chase, Jr. and D. E. Eveleigh.  1993. Cloning of a Microbispora bispora cellobiohydrolase gene in Streptomyces lividans. Appl. Microbiol. Biotechnol. 38:631-637.
  18. Hu, P., S. K. Kahrs, T. Chase, Jr. and D. E. Eveleigh. 1992. Cloning of a Microbispora bispora cellobiohydrolase gene in Escherichia coli. J. Indus. Microbiol. 10:103-110.
  19. Ma, J., X. Zhu and P. Hu. 1988. Application of a new method in primary screening mutant strain of fortimicin. Journal of Microbiology, Shanghai.

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Presentations

  1. P. Hu, E. Zhgenti, G. Chanturia, D. Tsereteli, M. Kekelidze, E. Zangaladze, R. Stokowski, G.L. Andersen, and T. Torok. 2012. Application of a SNP-genotyping High Density Microarray to Study Yersinia pestis Isolate from the Caucasus Region. Amer. Soc. for Microbiol. Annual Meeting, San Francisco, CA.
  2. E. A. Dubinsky, P. Hu, Y. M. Piceno, F. C. Reid, L. M. Tom, J. Wong, T. C. Hazen and G. L. Andesen. 2012. Microbial Community Composition in a Deep Water Oil Plume and Dissolved Oxygen Anomalies. Ocean Sciences Meeting. Salt Lake City, UT.
  3. P. Hu, H-Y. Holman, K. Chavarria, L. Mahoney, C. Zhang, N. Quinn, C. Jansson. 2011. Single Cell Metabolic Fingerprinting of the Cyanobacterium Synechocystis PCC6803 Engineered for Production of Free Fatty Acids Using Synchrotron Infrared Spectromicroscopy and Multivariate Analysis. Amer. Soc. for Microbiol. Annual Meeting, New Orleans, LA.
  4. P. Hu, C. Wu, T. DeSantis, P. Jasrotia, H. Woo, K. Kearcher, S. Meiss, T. Torok, D. L. Taylor, W. Overholt, S. Green, G. L. Andersen and T. C. Hazen. 2011. Validation of MycoChip - A Microarray for Fungal Community Stidies. Amer. Soc. for Microbiol. Annual Meeting, New Orleans, LA.
  5. H-Y. Holman, H. A. Bechtel, R. Gomez-Sjoberg, Z. Hao, L. Chen, P. Hu, M.C. Martin, P. S. Nico. 2011. The Berkeleey Synchrontron Infrared structureal Biology (BSISB) Program. Genome Sciences Contractor-Grantee Meeting. Arlington, VA.
  6. Z. Hao, P. Hu, D. Long, R. Chakraborty, A. N. Tauscher, H-Y. Holman. 2011. Towards real time and high throughput molecular characterization of microbial deconstruction of biomass. 2011. Genome Sciences Contractor-Grantee Meeting. Arlington, VA.
  7. Holman, H. N.,  Z. Hao, P. Hu, R. Miles, A. Pisano, I. Park, S. Choi. 2009. Synchrotron Infrared Spectromicroscopy of Cellulose Degradation Strategies of Living Cellulolytic Bacteria. DOE GTL workshop. Washington, DC.
  8. Hu, P., Romy Chakraborty, Eoin L Brodie, Gary L Andersen, Terry C Hazen. 2008. Reduction of Cr(VI) and survival in Cr-contaminated sites by Caulobacter crescentus. The 2008 AGU Fall Meeting, San Francisco, California. 
  9. Hu, P,  J. Zhu, G. L. Andersen, L. Shapiro,   H. H. McAdams, T. Earnest. 2007.High throughput mapping of Caulobacter crescentus protein interactions using tandem affinity purification. American Society for Microbiology Annual Conference. Boston, MA
  10. West, K. A.,  D. R. Johnson, P. Hu, T. Z. DeSantis, E. L. Brodie, H. Feil, G. L. Andersen, S. H. Zinder,   L. Alvarez-Cohen. 2007. Comparative Genomics of Dehalococcoides ethenogenes 195 and a Dehalococcoides-Containing Enrichment Culture Using a Whole-Genome Microarray. American Society for Microbiology Annual Conference. Toronto, Canada.
  11. Belnap, C. P., I. Ball, P. Hu, G. L. Andersen and J. F. Banfield. 2007. Ferroplasma acidarmanus fer1 expression analysis and ecological interactions in co-cultures. American Society for Microbiology Annual Conference. Toronto, Canada
  12. Hillson, N. J., P. Hu, G. L. Andersen and L. Shapiro. 2007. A uranium Biosenser. Department of Energy Genomes-To-Life workshop. Washington D. C.
  13. T. Z. DeSantis1, P. Hugenholtz, N. Larsen, M. Rojas,  E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, Y. M.  Piceno, R. Phan, G. L. Andersen. 2006. Greengenes, The ARB-compatible Chimera-checked 16S rRNA Gene  Database, Introduces New Online Tools Including NAST, A Flexible  Massive Multiple Sequence Alignment Tool. American Society for Microbiology Annual Conference. Orlando, FL.
  14. T. Z. DeSantis1, K. D. Hansen, E. L. Brodie, Y. M.  Piceno, J. Bullard, P. Hu, , G. L. Andersen. 2006.Hybridization efficiency analysis of probes targeting 16S rRNA genes using the Affymetrix Genechip format. American Society for Microbiology Annual Conference. Orlando, FL.
  15. K. West, D. R. Johnson, J. He, P. K. H. Lee, T. Z. DeSantis, P. Hu, G. L. Andersen, S. H. Zinder, L. Alvarez-Cohen. 2006. Comparative Transcriptomics of Dehalococcoides ethenognenes Strain 195 and Dehalococcoides sp. Strain BAV1. American Society for Microbiology Annual Conference. Orlando, FL.
  16. D. R. Johnson, J. He, P. K. H. Lee, E. L. Brodie, P. Hu, G. L. Andersen, S. H. Zinder, L. Alvarez-Cohen. 2006. Effect of Exposure to Cell-Free Spent Media From Different Reductive Dechlorinating Mixed Cultures on Whole-Genome Transcription in Dehalococcoides ethenogenes Strain 195. American Society for Microbiology Annual Conference. Orlando, FL.
  17. D. R. Johnson, J. He, P. Hu, G. L. Andersen, S. H. Zinder, L. Alvarez-Cohen. 2006. Whole-Genome Transcription Analysis of Dehalococcoides ethenogenes Strain 195 Reveals a Cobalamin (Vitamin B12) Regulon. American Society for Microbiology Annual Conference. Orlando, FL.
  18. Hu, P., D. Ballinger, C. Pethiyagoda, K. Pant,T. Torok and G. L. Andersen. Genome-wide Single Nucleotide Polymorphism Analysis of Salmonella enterica. American Society for Microbiology Annual Conference. Orlando, FL.
  19. Andersen, G. L., P. Hu, E. L. Brodie, Y. Suzuki and H. H. McAdams. 2006. Whole Genome Transcriptional Analysis of Toxic Metal Stresses in Caulobacter crescentus. Genomes-To-Life workshop. Washington D. C.
  20. Andersen , G. L., P. Hu,  E. L.. Brodie and H. H. McAdams. 2005. Whole Genome    Transcriptional Analysis of Toxic Metal Stresses in Caulobacter crescentus. Genomes-To-Life workshop. Washington D. C.
  21. Hu,P, E. L. Brodie, Y. Suzuki,   H. H. McAdams and G. L. Andersen. 2005. Whole Genome Transcriptional Analysis of Heavy Metal Stresses in Caulobacter crescentus. American Society for Microbiology Annual Conference. Atlanta, GA.
  22. Andersen , G. L., P. Hu and H. H. McAdams. 2004. Whole Genome    Transcriptional Analysis of Toxic Metal Stresses in Caulobacter crescentus. Genomes-To-Life workshop. Washington D. C.
  23. Salceda, S., C. Drumright, A. DiEgidio, B. Liang, P. Hu, Y. Sun, V. V. Hoang, A. Munteanu, H. Recipon, R. Cafferkey and R. A. Macina .  2001.  Identification of differentially expressed genes in breast cancer.   AACR and Nature Genetics meeting: Oncogenomics.
  24. Motin, V. L., A. Georgescu, J. Elliott, P. Hu, P.L. Worsham, A. M. Friedlander, R.R. Brubaker and E. Garcia.  2000.  PCR-IS100-based fingerprinting of a large collection of Yersinia pestis Strains unraveled a putative ancestor isolate to the one that caused the third plague pandemic. Amer. Soc. for Microbiol. Annual Meeting, Los Angeles, CA
  25. Ali, S., S. Salceda, H. Recipon, Y. Sun, P. Hu, C. Drumright, V.V. Hoang, A. Nguyen, N, Dada, M. Iyer, D. Cooper and R. Cafferkey. In Search of New Prostate Cancer Diagnostic Markers. 2000. UCSF Prostate Cancer Center Retreat. San Francisco, CA.
  26. Hu, P., J. Elliott, J. Garnes, A. Kobayashi, P. McCready, E. Skowronski, A. Adamson and E. Garcia. 1998. Sequencing and analysis of the three virulence factor-encoding plasmids in Yersinia pestis. Annual meeting of American Society for microbiology, Atlanta, GA.
  27. Hu, P., J. Elliott, J. Garnes, A. Kobayashi, P. McCready, E. Skowronski, A. Adamson and E. Garcia. 1998. Sequence and analysis of three plasmids encoding virulence determinants in Yersinia pestis     Microbial Genome II, Hiltonhead, SC.
  28. Hu, P., T. Ikeda, A. Shauger and S. Kustu. 1995. Sensing of nitrogen limitation by Bacillus subtilis. The 8th International Conference on Bacilli. Standford, CA.
  29. Hu, P and D. E. Eveleigh. 1992. Cloning and Characterization of a cellobiohydrolase from Microbispora bispora in E. coli and Streptomyces lividans. Amer. Soc. for Microbiol. Annual Meeting, New Orleans, LA.
  30. Goyal, A. K., P. Hu, R. M. Wright, K. O. Elliston and D. E. Eveleigh. 1991. The cellobiohydrolase and beta-glucosidases of Microbispora biospora. Biotechnology Meeting, New York, NY.
  31. Hu, P. and D. E. Eveleigh. 1991. Characterization of a cellobiohydrolase gene from Microbispora bispora. Theobold Smith Society, Annual Meeting, North Brunswick, NJ.
  32. Hu, P., M. Frosco, T. Chase, Jr. and D. E. Eveleigh. 1990. Cloning and characterization of a cellobiohydrlase from Microbispora bispora. Amer. Soc. for Microbiol. Annual Meeting, Anaheim, CA.
  33. Wright, R. M., M. D. Yablonsky, P. Hu, Z. Shalita and D. E. Eveleigh. 1989. Cloning and characterization of a beta-glucosidase from Microbispora bispora in Escherichia coli. Amer. Soc. for Microbiol. Annual Meeting, New Orleans, LA.
  34. Elliston, K. O., M. D. Yablonsky, R. Wright, P. Hu, A. Goyal, M. Szakacs-Dobozi and D. E. Eveleigh. 1990. Cellulase-Insights through recombinant DNA approaches. Amer. Chem. Soc. 199th Meeting, Boston, MA

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