Berkeley Lab

2019 Publications

Jump to: Submitted/In Review Manuscripts | Books/Book Chapters | Legacy and Synergistic External Research

  1. Domingo-Almenara, X.; J. R. Montenegro-Burke, C. Guijas, E. L.-W. Majumder, H. P. Benton and G. Siuzdak (2019) Autonomous METLIN-guided in-source fragmentation detection increases annotation confidence in untargeted metabolomics. ACS Analytical Chemistry. https://pubs.acs.org/doi/10.1021/acs.analchem.8b03126
  2. Mutalik, V.K.; P.S. Novichkov, M.N. Price, T.K. Owens, M. Callaghan, S. Carim, A.M. Deutschbauer, and A.P. Arkin (2019) Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits. Nature Communication. https://doi.org/10.1038/s41467-018-08177-8
  3. Price, M. N.; J. Ray, A. T. Iavarone, H. K. Carlson, E. M. Ryan, R. R. Malmstrom, A. P. Arkin, A. M. Deutschbauer (2019) An Oxidative Pathway of Deoxyribose Catabolism. mSystems. https://msystems.asm.org/content/4/1/e00297-18
  4. Vuono, D.C., R.W. Read, J. Hemp, B.W. Sullivan, A. Arnone, I. Neveux, R.R. Blank, E. Loney, D. Miceli, M-K.H.. Winkler, R. Chakraborty, D.A. Stahl, and J.J. Grzymski.   (2019) Resource concentration modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium. Frontiers in Microbiology.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349771/

Submitted/In Review Manuscripts

  1. Kempher, M.L; A.S. Burns, P.S. Novichkov, K.S. Bender. (2019) Characterization Of A Dual Functioning Small RNA/Riboswitch In Desulfovibrio Vulgaris Hildenborough. mBio. Submitted
  2. Kothari, A.; Y-W. Wu,M. Charrier, L. Rajeev, A. M. Rocha,C. J. Paradis, T. C. Hazen, S. W. Singer, A. Mukhopadhyay (2019) Identification and characterization of a mercury resistance plasmid shows latent functions harbored in pristine groundwater. International Symposium on Microbial Ecology. Accepted
  3. Krantz, GP; K. Lucas, E. L-W. Majumder, L.T Hoang, R. Avci, G. Siuzdak, M.W Fields (2019) Bulk phase resource ratio alters metal corrosion rates and extracellular electron transfer mediators in a sulfate-reducing. Biofouling. Revision
  4. Majumder, E. L.-W.; E.O. Billings, H. P. Benton, A. Palermo, R. L. Martin, C. Guijas, M. M. Rinschen, X. Domingo-Almenara J. R. Montenegro-Burke, G. Siuzdak* (2019) Cognitive Analysis of Metabolomics Data for Systems Biology. Molecular Systems Biology. Submitted
  5. Mutalik, V.K.; P.S. Novichkov, M.N. Price, T.K. Owens, M. Callaghan, S. Carim, A.M. Deutschbauer, and A.P. Arkin (2019) Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits. Nature Communication. Accepted
  6. Paradis, C.J.; W. Reimus, R.H. Johnson, D.M. Mackay, L.D. McKay, T.C. Hazen (2019) Single-well injection-drift test to estimate groundwater velocity. Groundwater. Accepted
  7. N. Price and A.P. Arkin (2019) Curated BLAST for Genomes. bioRxiv. http://biorxiv.org/cgi/content/short/533430v1
  8. Shi, Z.; H Yin, JD Van Nostrand, JW Voordeckers, Q Tu, Y Deng, M Yuan, A Zhou, P Zhang, N Xiao, D Ning, Z He, L Wu, and J Zhou (2019) Functional gene array-based ultra-sensitive and quantitative detection of microbial populations in complex communities. International Society for Microbial Ecology Journal. Submitted
  9. Vuono, D.C., R.W. Read, J. Hemp, B.W. Sullivan, A. Arnone, I. Neveux, R.R. Blank, E. Loney, D. Miceli, M-K.H.. Winkler, R. Chakraborty, D.A. Stahl, and J.J. Grzymski. (2019) Resource concentration modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium. Frontiers in Microbiology. In press
  10. Zelaya A; A. Parker, K. L. Bailey , P. Zhang, J. Van Nostrand, D.A. Elias, J. Zhou, M.W. Fields (2019) High temporal variability in bacterial populations and association networks of an undisturbed, pristine aquifer. ISME Journal. In review

Books/Book Chapters

NA


Legacy and Synergistic External Research

  1. McKay, L.J., M. Dlakić, M.W. Fields, T.O. Delmont, A. Murat Eren, Z.J. Jay, K.B. Klingelsmith, D. Rusch, and W.P. Inskeep. (2019) Co-occurring genomic capacity for anaerobic methane metabolism and dissimilatory sulfite reduction discovered in the Korarchaeota. Nature Microbiology. Accepted