All Stories

  1. Draft Genome Sequences of Pseudomonas moraviensis UCD-KL30, Vibrio ostreicida UCD-KL16, Colwellia sp. Strain UCD-KL20, Shewanella sp. Strain UCD-KL12, and Shewanella sp. Strain UCD-KL21, Isolated from Seagrass

    Article • Genome Announcements, March 2017, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  2. Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a Feline Anal Sac

    Article • Genome Announcements, March 2017, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  3. Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria)

    Article • Genome Announcements, February 2017, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  4. Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3

    Article • Genome Announcements, December 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  5. Draft Genome Sequence of Tenacibaculum soleae UCD-KL19

    Article • Genome Announcements, October 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  6. Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria )

    Article • Genome Announcements, October 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  7. Draft Genome Sequence ofKlebsiella pneumoniaeUCD-JA29 Isolated from a Patient with Sepsis

    Article • Genome Announcements, May 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  8. Draft Genome Sequences of Two Pseudoalteromonas porphyrae Strains Isolated from Seagrass Sediment

    Article • Genome Announcements, March 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  9. Draft Genome Sequence of Cobetia sp. UCD-24C, Isolated from Roots and Leaves of the Seagrass Zostera marina

    Article • Genome Announcements, March 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  10. Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina

    Article • Genome Announcements, February 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  11. Draft Genome Sequences of TwoVibrio splendidusStrains, Isolated from Seagrass Sediment

    Article • Genome Announcements, February 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  12. Additional Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients: Table 1 

    Article • Genome Announcements, January 2016, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  13. Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado

    Article • Genome Announcements, November 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  14. Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft

    Article • Genome Announcements, November 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  15. Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes )

    Article • Genome Announcements, November 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  16. Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain UCD-SED8 (Phylum Gammaproteobacteria )

    Article • Genome Announcements, November 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  17. Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes )

    Article • Genome Announcements, October 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  18. Draft Genome Sequences of 26 Porphyromonas Strains Isolated from the Canine Oral Microbiome: Table 1

    Article • Genome Announcements, April 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  19. Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347 T (Phylum Nitrospirae )

    Article • Genome Announcements, January 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  20. Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T(PhylumThermodesulfobacteria)

    Article • Genome Announcements, January 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  21. Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (PhylumProteobacteria)

    Article • Genome Announcements, January 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  22. Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria )

    Article • Genome Announcements, January 2015, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  23. Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients

    Article • Genome Announcements, December 2014, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  24. Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1

    Article • Genome Announcements, August 2014, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  25. Draft Genome Sequence of the Endosymbiont "Candidatus Ruthia magnifica" UCD-CM (Phylum Proteobacteria)

    Article • Genome Announcements, July 2014, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  26. Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265

    Article • Genome Announcements, May 2014, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  27. Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae

    Article • Genome Announcements, April 2014, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  28. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

    Article • Environmental Microbiology, February 2014, Wiley

    Jonathan Eisen, Prof. Jonathan A. Eisen

  29. Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12

    Article • Genome Announcements, February 2014, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  30. PhyloSift: phylogenetic analysis of genomes and metagenomes

    Article • PeerJ, January 2014, PeerJ

    Jonathan Eisen, Prof. Jonathan A. Eisen

  31. Open Science and Reporting Animal Studies: Who's Accountable?

    Article • PLoS Biology, January 2014, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  32. Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

    Article • Standards in Genomic Sciences, December 2013, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen, Prof George M Garrity, Dr Nikos C Kyrpides

  33. Draft Genome Sequence of the Arsenate-Respiring Bacterium Chrysiogenes arsenatis Strain DSM 11915

    Article • Genome Announcements, November 2013, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  34. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment

    Article • The ISME Journal, October 2013, Oxford University Press (OUP)

    Jonathan Eisen, Dr Jason Stajich, Prof. Jonathan A. Eisen

  35. Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

    Article • PLoS ONE, October 2013, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  36. Expert Failure: Re-evaluating Research Assessment

    Article • PLoS Biology, October 2013, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  37. The Impact of Helicobacter pylori Infection on the Gastric Microbiota of the Rhesus Macaque

    Article • PLoS ONE, October 2013, PLOS

    Jonathan Eisen, Professor Jay V Solnick, Prof. Jonathan A. Eisen

  38. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

    Article • Nature Communications, August 2013, Springer Science + Business Media

    Jonathan Eisen, Dr Susannah Green Tringe, Prof. Jonathan A. Eisen

  39. Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria)

    Article • Genome Announcements, June 2013, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  40. Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria)

    Article • Genome Announcements, May 2013, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  41. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria)

    Article • Genome Announcements, May 2013, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  42. Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria)

    Article • Genome Announcements, May 2013, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  43. Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

    Article • PLoS ONE, April 2013, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  44. Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4

    Article • Genome Announcements, March 2013, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  45. Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria)

    Article • Genome Announcements, March 2013, ASM Journals

    Jonathan Eisen, Prof. Jonathan A. Eisen

  46. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence

    Article • BMC Genomics, February 2013, Springer Science + Business Media

    Jonathan Eisen, Dr Arkhat Abzhanov, Dr Richard D Emes, Prof. Jonathan A. Eisen

  47. Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

    Article • PLoS Computational Biology, October 2012, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  48. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

    Article • BMC Bioinformatics, October 2012, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen, Morgan Langille

  49. Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization

    Article • PLoS ONE, September 2012, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen, Morgan Langille

  50. An Integrated Pipeline for de Novo Assembly of Microbial Genomes

    Article • PLoS ONE, September 2012, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  51. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux

    Article • PLoS ONE, July 2012, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen, Morgan Langille, Dr Robert A Edwards

  52. Badomics words and the power and peril of the ome-meme

    Article • GigaScience, July 2012, Oxford University Press (OUP)

    Jonathan Eisen, Prof. Jonathan A. Eisen

  53. Accounting For Alignment Uncertainty in Phylogenomics

    Article • PLoS ONE, January 2012, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  54. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    Article • PLoS Genetics, September 2011, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  55. The Phylogenetic Diversity of Metagenomes

    Article • PLoS ONE, August 2011, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  56. Aggregating, Tagging and Integrating Biodiversity Research

    Article • PLoS ONE, August 2011, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  57. Towards Automated Phylogenomic Inference

    Article • May 2011, Wiley

    Jonathan Eisen, Prof. Jonathan A. Eisen

  58. Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes

    Article • May 2011, Wiley

    Jonathan Eisen, Prof. Jonathan A. Eisen

  59. Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

    Article • PLoS ONE, March 2011, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  60. PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

    Article • PLoS Computational Biology, January 2011, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  61. Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

    Article • BMC Bioinformatics, June 2010, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  62. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    Article • PLoS ONE, April 2010, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  63. BioTorrents: A File Sharing Service for Scientific Data

    Article • PLoS ONE, April 2010, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen, Morgan Langille

  64. The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon

    Article • PLoS ONE, March 2010, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen, Dr. Mechthild Pohlschroder

  65. Genomics of Emerging Infectious Disease: A PLoS Collection

    Article • PLoS Biology, October 2009, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  66. Assembling the Marine Metagenome, One Cell at a Time

    Article • PLoS ONE, April 2009, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  67. Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola

    Article • PLoS Genetics, February 2009, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  68. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

    Article • PLoS Computational Biology, January 2009, PLOS

    Jonathan Eisen, Dr Christophe Dessimoz

  69. Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

    Article • PLoS ONE, January 2009, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  70. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

    Article • BMC Genomics, December 2008, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen, Dr Raquel Quatrini

  71. A simple, fast, and accurate method of phylogenomic inference

    Article • October 2008, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  72. Correction: An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)

    Article • PLoS ONE, July 2008, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  73. An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)

    Article • PLoS ONE, July 2008, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  74. PLoS Biology 2.0

    Article • PLoS Biology, February 2008, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  75. CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads

    Article • January 2008, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  76. Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii

    Article • PLoS Genetics, May 2007, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  77. Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes

    Article • PLoS Biology, March 2007, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  78. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome

    Article • Genomics, October 2006, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  79. Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters

    Article • PLoS Biology, June 2006, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  80. Genetic and physical mapping of DNA replication origins in Haloferax volcanii

    Article • PLoS Genetics, January 2005, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen

  81. Phylogenetic Analysis and Gene Functional Predictions: Phylogenomics in Action

    Article • Theoretical Population Biology, June 2002, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  82. Brouhaha over the other yeast

    Article • Nature, February 2002, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  83. Unsuspected diversity among marine aerobic anoxygenic phototrophs

    Article • Nature, February 2002, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen, William Nelson

  84. Sequencing and analysis of a 63 kb bacterial artificial chromosome insert from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi

    Article • International Journal for Parasitology, February 2002, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  85. Sequenced strains must be saved from extinction

    Article • Nature, November 2001, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  86. Gastrogenomics

    Article • Nature, January 2001, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  87. Genome of Thermotoga maritima MSB8

    Article • January 2001, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  88. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis

    Article • Current Opinion in Genetics & Development, December 2000, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  89. Assessing evolutionary relationships among microbes from whole-genome analysis

    Article • Current Opinion in Microbiology, October 2000, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  90. Genome data: what do we learn?

    Article • Current Opinion in Structural Biology, June 2000, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  91. Cloning and Characterization of HARP/SMARCAL1: A Prokaryotic HepA-Related SNF2 Helicase Protein from Human and Mouse

    Article • Genomics, May 2000, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  92. Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis

    Article • Research in Microbiology, March 2000, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  93. A phylogenomic study of DNA repair genes, proteins, and processes

    Article • Mutation Research/DNA Repair, December 1999, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  94. Going to extremes

    Article • Trends in Genetics, June 1999, Elsevier

    Jonathan Eisen, Prof. Jonathan A. Eisen

  95. A science renga

    Article • Nature, June 1998, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  96. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences

    Article • FEMS Microbiology Letters, May 1998, Oxford University Press (OUP)

    Jonathan Eisen, Prof. Jonathan A. Eisen

  97. Gastrogenomic delights: A movable feast

    Article • Nature Medicine, October 1997, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  98. The Genetic Data Environment

    Article • January 1997, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen

  99. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions

    Article • Nucleic Acids Research, January 1995, Oxford University Press (OUP)

    Jonathan Eisen, Prof. Jonathan A. Eisen

  100. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences

    Article • Nucleic Acids Research, January 1994, Oxford University Press (OUP)

    Jonathan Eisen, Prof. Jonathan A. Eisen