Morgan N Price

Summary

Publications

  1. doi request reprint Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    MBio 6:e01302-15. 2015
  2. pmc Indirect and suboptimal control of gene expression is widespread in bacteria
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
    Mol Syst Biol 9:660. 2013
  3. pmc Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 977 152, Berkeley, California 94720, USA
    J Bacteriol 193:5716-27. 2011
  4. pmc FastTree 2--approximately maximum-likelihood trees for large alignments
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
    PLoS ONE 5:e9490. 2010
  5. pmc FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, CA, USA
    Mol Biol Evol 26:1641-50. 2009
  6. pmc FastBLAST: homology relationships for millions of proteins
    Morgan N Price
    Physical Biosciences Divison, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS ONE 3:e3589. 2008
  7. pmc Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 9:R4. 2008
  8. pmc Orthologous transcription factors in bacteria have different functions and regulate different genes
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Comput Biol 3:1739-50. 2007
  9. pmc OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments
    Morgan N Price
    Lawrence Berkeley Lab, Mailstop 977 152, Berkeley, CA 94720, USA
    BMC Bioinformatics 7:19. 2006
  10. pmc MicrobesOnline: an integrated portal for comparative and functional genomics
    Paramvir S Dehal
    Virtual Institute for Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:D396-400. 2010

Collaborators

Detail Information

Publications30

  1. doi request reprint Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    MBio 6:e01302-15. 2015
    ..Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force if s is above 10(-7) or so...
  2. pmc Indirect and suboptimal control of gene expression is widespread in bacteria
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
    Mol Syst Biol 9:660. 2013
    ..Because genes that have closely related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory...
  3. pmc Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 977 152, Berkeley, California 94720, USA
    J Bacteriol 193:5716-27. 2011
    ..Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available at http://genomics.lbl.gov/supplemental/DvHtranscripts2011/...
  4. pmc FastTree 2--approximately maximum-likelihood trees for large alignments
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
    PLoS ONE 5:e9490. 2010
    ..We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability...
  5. pmc FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, CA, USA
    Mol Biol Evol 26:1641-50. 2009
    ..In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree...
  6. pmc FastBLAST: homology relationships for millions of proteins
    Morgan N Price
    Physical Biosciences Divison, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS ONE 3:e3589. 2008
    ..As DNA sequencing accelerates and data sets grow, all-versus-all BLAST has become computationally demanding...
  7. pmc Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 9:R4. 2008
    ..To understand how the regulation of these acquired genes evolved, we examined the evolutionary histories of transcription factors and of regulatory interactions from the model bacterium Escherichia coli K12...
  8. pmc Orthologous transcription factors in bacteria have different functions and regulate different genes
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Comput Biol 3:1739-50. 2007
    ..We conclude that the evolution of bacterial regulation should be analyzed with phylogenetic trees, rather than BBHs, and that bacterial regulatory networks evolve more rapidly than previously thought...
  9. pmc OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments
    Morgan N Price
    Lawrence Berkeley Lab, Mailstop 977 152, Berkeley, CA 94720, USA
    BMC Bioinformatics 7:19. 2006
    ..These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known...
  10. pmc MicrobesOnline: an integrated portal for comparative and functional genomics
    Paramvir S Dehal
    Virtual Institute for Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:D396-400. 2010
    ..Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html...
  11. doi request reprint Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria
    Pavel S Novichkov
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
    Environ Microbiol 16:1-8. 2014
    ..The effector-sensing domain in SahR is related to SAM-dependent methylases that are able to tightly bind SAH. SahR represents a novel type of transcriptional regulators for the control of sulphur amino acid metabolism. ..
  12. pmc Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions
    Adam Deutschbauer
    Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Genet 7:e1002385. 2011
    ..The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes...
  13. pmc Towards an informative mutant phenotype for every bacterial gene
    Adam Deutschbauer
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Bacteriol 196:3643-55. 2014
    ..mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness. ..
  14. pmc The life-cycle of operons
    Morgan N Price
    Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Genet 2:e96. 2006
    ..Although operon evolution may be adaptive, it need not be optimal: new operons often comprise functionally unrelated genes that were already in proximity before the operon formed...
  15. pmc Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes
    Alexey E Kazakov
    Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Bacteriol 195:29-38. 2013
    ..The collection of reconstructed regulons is available at the RegPrecise database (http://regprecise.lbl.gov/RegPrecise/Desulfovibrionales.jsp)...
  16. pmc The MicrobesOnline Web site for comparative genomics
    Eric J Alm
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 15:1015-22. 2005
    ..In addition, we provide an interface for genome annotation, which like all of the tools reported here, is freely available to the scientific community...
  17. pmc Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates
    Jeffrey M Skerker
    Energy Biosciences Institute, University of California, Berkeley, CA, USA
    Mol Syst Biol 9:674. 2013
    ..Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance...
  18. pmc Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20
    Jennifer V Kuehl
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    MBio 5:e01041-14. 2014
    ..Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance...
  19. pmc Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium
    Lara Rajeev
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 12:R99. 2011
    ..We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems...
  20. pmc Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication
    Morgan N Price
    Lawrence Berkeley National Lab 1 Cyclotron Road, Mailstop 977 152, Berkeley, CA 94720, USA
    Nucleic Acids Res 33:3224-34. 2005
    ..We find that expression level and phylogenetic ubiquity are correlated with strand bias for both essential and non-essential genes, but only for genes in operons...
  21. pmc A novel method for accurate operon predictions in all sequenced prokaryotes
    Morgan N Price
    Lawrence Berkeley National Lab 1 Cyclotron Road, Mailstop 939R704, Berkeley, CA 94720, USA
    Nucleic Acids Res 33:880-92. 2005
    ....
  22. doi request reprint Metabolic footprinting of mutant libraries to map metabolite utilization to genotype
    Richard Baran
    Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, California 94720, United States
    ACS Chem Biol 8:189-99. 2013
    ..This generally applicable, high-throughput workflow has the potential both to discover novel metabolic capabilities of microorganisms and to identify the corresponding genes...
  23. pmc Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough
    Swapnil R Chhabra
    Virtual Institute of Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 6:e21470. 2011
    ..These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction...
  24. doi request reprint Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase
    Ryan A Melnyk
    Energy Biosciences Institute and Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
    MBio 6:e00233-15. 2015
    ..implying a putative role in immune response evasion in vivo...
  25. doi request reprint Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate
    Hans K Carlson
    Energy Biosciences Institute, UC Berkeley, Berkeley, CA, USA
    ISME J 9:1295-305. 2015
    ..Of these, perchlorate offers better application logistics because of its inhibitory potency, solubility, relative chemical stability, low affinity for mineral cations and high mobility in environmental systems...
  26. pmc Conservation of transcription start sites within genes across a bacterial genus
    Wenjun Shao
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    MBio 5:e01398-14. 2014
    ..Thus, many of these unexpected promoters are likely functional. Fewer promoters that lie within genes on the antisense strand are conserved, but the conserved ones seem to drive the expression of nearby genes...
  27. doi request reprint Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons
    Kelly M Wetmore
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    MBio 6:e00306-15. 2015
    ..RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling...
  28. pmc Operon formation is driven by co-regulation and not by horizontal gene transfer
    Morgan N Price
    Lawrence Berkeley Laboratory, Berkeley California, 94720 USA
    Genome Res 15:809-19. 2005
    ..Consistent with this hypothesis, operons have greater amounts of conserved regulatory sequences than do individually transcribed genes...
  29. ncbi request reprint The histidine operon is ancient
    Morgan N Price
    J Mol Evol 62:807-8. 2006
  30. ncbi request reprint Finding coexpressed genes in counts-based data: an improved measure with validation experiments
    Morgan N Price
    FX Palo Alto Laboratory, 3400 Hillview Avenue Building 4, Palo Alto, CA 94304, USA
    Bioinformatics 20:945-52. 2004
    ..Expressed sequence tag (EST) data reflects variation in gene expression, but previous methods for finding coexpressed genes in EST data are subject to bias and vastly overstate the statistical significance of putatively coexpressed genes...