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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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News & Publications
Home › News & Publications › Publications › 2005 Publications

2005 Publications

Alexandrino, J. et al. (2005) Strong selection against hybrids at a hybrid zone in the Ensatina ring species complex and its evolutionary implications. Evolution 59(6), 1334-1347.
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Boore, J. L. et al. (2005) Sequencing and comparing whole mitochondrial genomes of animals. Molecular Evolution: Producing the Biochemical Data, Part B 395, 311-348. Doi 10.1016/S0076-6879(05)95019-2
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Dehal, P. et al. (2005) Two rounds of whole genome duplication in the ancestral vertebrate. Plos Biology 3(10), 1700-1708. ARTN e314 DOI 10.1371/journal.pbio.0030314
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Foster, J. et al. (2005) The Wolbachia genome of Brugia malayi: Endosymbiont evolution within a human pathogenic nematode. Plos Biology 3(4), 599-614. ARTN e121 DOI 10.1371/journal.pbio.0030121
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Francino, M. P. et al. (2005) An adaptive radiation model for the origin of new gene functions. Nature Genetics 37(6), 573-577. Doi 10.1038/Ng1579
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Gatesy, J. et al. (2005) Hidden likelihood support in genomic data: Can forty-five wrongs make a right?. Systematic Biology 54(3), 483-492. Doi 10.1080/10635150590945368
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Jansen, R. K. et al. (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Molecular Evolution: Producing the Biochemical Data, Part B 395, 348-384. Doi 10.1016/S0076-6879(05)95020-9
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Keys, D. N. et al. (2005) A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Proceedings of the National Academy of Sciences of the United States of America 102(3), 679-683. Doi 10.1073/Pnas.0408952102
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Leebens-Mack, J. et al. (2005) Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the felsenstein zone. Molecular Biology and Evolution 22(10), 1948-1963. Doi 10.1093/Molbev/Msi191
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Macey, J. R. et al. (2005) Plethodontid salamander mitochondrial genomics: A parsimony evaluation of character conflict and implications for historical biogeography. Cladistics 21(2), 194-202. Doi 10.1111/J.1096-0031.2005.00054.X
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Macey, J. R. et al. (2005) The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii. Molecular Phylogenetics and Evolution 36(1), 188-193. Doi 10.1016/J.Ympev.2005.03.025
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Medina, M. et al. (2005) Genomes, phylogeny, and evolutionary systems biology. Proceedings of the National Academy of Sciences of the United States of America 102, 6630-6635. Doi 10.1073/Pnas.0501984102
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Medina, M. et al. (2005) Phylogeny of sea hares in the Aplysia clade based on mitochondrial DNA sequence data. Bulletin of Marine Science 76(3), 691-698.
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Mueller, R. L. et al. (2005) Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Molecular Biology and Evolution 22(10), 2104-2112. Doi 10.1093/Molbev/Msi204
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Noonan, J. P. et al. (2005) Genomic sequencing of Pleistocene cave bears. Science 309(5734), 597-9. 10.1126/science.1113485
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Parham, J. F. et al. (2005) A reassessment of the referral of sea turtle skulls to the genus Osteopygis (Late Cretaceous, New Jersey, USA). Journal of Vertebrate Paleontology 25(1), 71-77. Doi 10.1671/0272-4634(2005)025[0071:Arotro]2.0.Co;2
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Place, A. R. et al. (2005) Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation. Journal of Experimental Marine Biology and Ecology 319(1-2), 15-27. Doi 10.1016/J.Jembe.2004.03.024
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Richards, S. et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Research 15(1), 1-18. Doi 10.1101/Gr.3059305
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Rojas, A. et al. (2005) Gata4 expression in lateral mesoderm is downstream of BMP4 and is activated directly by Forkhead and GATA transcription factors through a distal enhancer element. Development 132(15), 3405-3417. Doi 10.1242/Dev.01913
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Tringe, S. G. et al. (2005) Comparative metagenomics of microbial communities. Science 308(5721), 554-557. Doi 10.1126/Science.1107851
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Vrdoljak, G. et al. (2005) Characterization of a diesel sludge microbial consortia for bioremediation. Scanning 27(1), 8-14.
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Weng, L. et al. (2005) Lack of MEF2A mutations in coronary artery disease. Journal of Clinical Investigation 115(4), 1016-1020. Doi 10.1172/Jci24186
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Wolf, P. G. et al. (2005) The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 350(2), 117-128. Doi 10.1016/J.Gene.2005.01.018
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