All Stories

  1. Ten simple rules to increase computational skills among biologists with Code Clubs

    Article • PLoS Computational Biology, August 2020, PLOS

    Professor Patrick D Schloss

  2. Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

    Article • mBio, November 2018, ASM Journals

    Professor Patrick D Schloss

  3. Erratum for Sze and Schloss, “Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors”

    Article • mBio, October 2018, ASM Journals

    Professor Patrick D Schloss

  4. Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization

    Article • mSphere, June 2018, ASM Journals

    Professor Patrick D Schloss

  5. Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research

    Article • mBio, June 2018, ASM Journals

    Professor Patrick D Schloss

  6. Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors

    Article • mBio, June 2018, ASM Journals

    Professor Patrick D Schloss

  7. In Defense of an Academic Career in Microbiology

    Article • mSphere, May 2018, ASM Journals

    Professor Patrick D Schloss

  8. Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients

    Article • mBio, March 2018, ASM Journals

    Professor Patrick D Schloss

  9. Erratum for Sze and Schloss, “Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome”

    Article • mBio, December 2017, ASM Journals

    Professor Patrick D Schloss

  10. Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes

    Article • mSystems, July 2017, ASM Journals

    Professor Patrick D Schloss

  11. Preprinting Microbiology

    Article • mBio, May 2017, ASM Journals

    Professor Patrick D Schloss

  12. OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

    Article • mSphere, March 2017, ASM Journals

    Professor Patrick D Schloss

  13. Microbial Characterization of Qatari Barchan Sand Dunes

    Article • PLoS ONE, September 2016, PLOS

    Professor Patrick D Schloss

  14. Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome

    Article • mBio, August 2016, ASM Journals

    Professor Patrick D Schloss

  15. Status of the Archaeal and Bacterial Census: an Update

    Article • mBio, May 2016, ASM Journals

    Professor Patrick D Schloss, Cameron Thrash

  16. Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer

    Article • mSphere, May 2016, ASM Journals

    Professor Patrick D Schloss

  17. Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods

    Article • mSystems, April 2016, ASM Journals

    Professor Patrick D Schloss

  18. Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions

    Article • Genome Medicine, April 2016, Springer Science + Business Media

    Professor Patrick D Schloss

  19. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

    Article • PeerJ, March 2016, PeerJ

    Professor Patrick D Schloss

  20. De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

    Article • PeerJ, December 2015, PeerJ

    Professor Patrick D Schloss

  21. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals

    Article • American Review of Respiratory Disease, December 2015, American Thoracic Society

    Professor Patrick D Schloss, Professor Thomas M Schmidt

  22. Nurturing the microbiome field

    Article • Science, November 2015, American Association for the Advancement of Science

    Professor Patrick D Schloss

  23. Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis

    Article • mSphere, November 2015, ASM Journals

    Professor Patrick D Schloss

  24. Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

    Article • mBio, July 2015, ASM Journals

    Professor Patrick D Schloss

  25. The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation

    Article • Microbiome, April 2015, Springer Science + Business Media

    Professor Patrick D Schloss, Professor Thomas M Schmidt

  26. Intra- and Interindividual Variations Mask Interspecies Variation in the Microbiota of Sympatric Peromyscus Populations

    Article • Applied and Environmental Microbiology, October 2014, ASM Journals

    Professor Patrick D Schloss

  27. Mathematical modeling of primary succession of murine intestinal microbiota

    Article • Proceedings of the National Academy of Sciences, December 2013, Proceedings of the National Academy of Sciences

    Professor Patrick D Schloss

  28. The Gut Microbiome Modulates Colon Tumorigenesis

    Article • mBio, November 2013, ASM Journals

    Professor Patrick D Schloss

  29. Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

    Article • Applied and Environmental Microbiology, June 2013, ASM Journals

    Professor Patrick D Schloss

  30. Changes in Cystic Fibrosis Airway Microbiota at Pulmonary Exacerbation

    Article • Annals of the American Thoracic Society, June 2013, American Thoracic Society

    Professor Patrick D Schloss

  31. Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

    Article • American Journal of Respiratory and Critical Care Medicine, May 2013, American Thoracic Society

    Professor Elodie Ghedin, Professor Patrick D Schloss, Professor Thomas M Schmidt

  32. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

    Article • Microbiome, March 2013, Springer Science + Business Media

    Professor Patrick D Schloss, Professor Thomas M Schmidt

  33. Bioinformatics for the Human Microbiome Project

    Article • PLoS Computational Biology, November 2012, PLOS

    Professor Patrick D Schloss

  34. Secondary structure improves OTU assignments of 16S rRNA gene sequences

    Article • The ISME Journal, September 2012, Springer Science + Business Media

    Professor Patrick D Schloss

  35. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

    Article • The ISME Journal, June 2012, Springer Science + Business Media

    Professor Patrick D Schloss

  36. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

    Article • PLoS Computational Biology, June 2012, PLOS

    Nicola Segata, Professor Patrick D Schloss, Dr. Jacques Izard

  37. Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

    Article • PLoS ONE, June 2012, PLOS

    Professor Patrick D Schloss

  38. Structure, function and diversity of the healthy human microbiome

    Article • Nature, June 2012, Springer Science + Business Media

    Professor Patrick D Schloss, Dr Tatiana A Vishnivetskaya, Dr. Jacques Izard, Dr Nikos C Kyrpides, Professor Thomas M Schmidt

  39. A framework for human microbiome research

    Article • Nature, June 2012, Springer Science + Business Media

    Professor Patrick D Schloss, Dr Tatiana A Vishnivetskaya, Dr. Jacques Izard, Dr Nikos C Kyrpides, Professor Thomas M Schmidt

  40. Decade-long bacterial community dynamics in cystic fibrosis airways

    Article • Proceedings of the National Academy of Sciences, March 2012, Proceedings of the National Academy of Sciences

    Professor Patrick D Schloss

  41. Impact of Enhanced Staphylococcus DNA Extraction on Microbial Community Measures in Cystic Fibrosis Sputum

    Article • PLoS ONE, March 2012, PLOS

    Professor Patrick D Schloss

  42. Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

    Article • PLoS ONE, December 2011, PLOS

    Professor Patrick D Schloss

  43. Effect of Sample Storage Conditions on Culture-Independent Bacterial Community Measures in Cystic Fibrosis Sputum Specimens

    Article • Journal of Clinical Microbiology, August 2011, ASM Journals

    Professor Patrick D Schloss

  44. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

    Article • Nature Biotechnology, May 2011, Springer Science + Business Media

    Professor Patrick D Schloss, Dr Nikos C Kyrpides

  45. Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

    Article • Applied and Environmental Microbiology, March 2011, ASM Journals

    Professor Patrick D Schloss

  46. Psychrotrophic Strain of Janthinobacterium lividum from a Cold Alaskan Soil Produces Prodigiosin

    Article • DNA and Cell Biology, September 2010, Mary Ann Liebert Inc

    Professor Patrick D Schloss

  47. The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

    Article • PLoS Computational Biology, July 2010, PLOS

    Professor Patrick D Schloss

  48. A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies

    Article • PLoS ONE, December 2009, PLOS

    Professor Patrick D Schloss

  49. Robustness of the Bacterial Community in the Cabbage White Butterfly Larval Midgut

    Article • Microbial Ecology, November 2009, Springer Science + Business Media

    Professor Patrick D Schloss

  50. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

    Article • Applied and Environmental Microbiology, October 2009, ASM Journals

    Professor Patrick D Schloss

  51. Gut Microbiota of an Invasive Subcortical Beetle, Agrilus planipennis Fairmaire, Across Various Life Stages

    Article • Environmental Entomology, October 2008, Oxford University Press (OUP)

    Professor Patrick D Schloss

  52. Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

    Article • Applied and Environmental Microbiology, July 2008, ASM Journals

    Professor Patrick D Schloss

  53. Evaluating different approaches that test whether microbial communities have the same structure

    Article • The ISME Journal, January 2008, Springer Science + Business Media

    Professor Patrick D Schloss

  54. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Professor Patrick D Schloss

  55. The Last Word: Books as a Statistical Metaphor for Microbial Communities

    Article • Annual Review of Microbiology, October 2007, Annual Reviews

    Professor Patrick D Schloss

  56. What is the extent of prokaryotic diversity?

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, November 2006, Royal Society Publishing

    Professor Patrick D Schloss, Stephen Woodcock

  57. Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures

    Article • Applied and Environmental Microbiology, October 2006, ASM Journals

    Professor Patrick D Schloss

  58. Introducing TreeClimber, a Test To Compare Microbial Community Structures

    Article • Applied and Environmental Microbiology, April 2006, ASM Journals

    Professor Patrick D Schloss

  59. Toward a Census of Bacteria in Soil

    Article • PLoS Computational Biology, January 2006, PLOS

    Professor Patrick D Schloss

  60. Intracellular Screen To Identify Metagenomic Clones That Induce or Inhibit a Quorum-Sensing Biosensor

    Article • Applied and Environmental Microbiology, October 2005, ASM Journals

    Professor Patrick D Schloss

  61. Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

    Article • Applied and Environmental Microbiology, March 2005, ASM Journals

    Professor Patrick D Schloss

  62. Molecular characterization of fungal community dynamics in the initial stages of composting

    Article • FEMS Microbiology Ecology, January 2005, Oxford University Press (OUP)

    Professor Patrick D Schloss

  63. Article • Genome Biology, January 2005, Springer Science + Business Media

    Professor Patrick D Schloss

  64. Status of the Microbial Census

    Article • Microbiology and Molecular Biology Reviews, December 2004, ASM Journals

    Professor Patrick D Schloss

  65. Metagenomics: Genomic Analysis of Microbial Communities

    Article • Annual Review of Genetics, December 2004, Annual Reviews

    Professor Patrick D Schloss

  66. Quantifying bacterial population dynamics in compost using 16S rRNA gene probes

    Article • Applied Microbiology and Biotechnology, September 2004, Springer Science + Business Media

    David Wilson, Professor Patrick D Schloss

  67. Integration of Microbial Ecology and Statistics: a Test To Compare Gene Libraries

    Article • Applied and Environmental Microbiology, September 2004, ASM Journals

    Professor Patrick D Schloss

  68. Tracking temporal changes of bacterial community fingerprints during the initial stages of composting

    Article • FEMS Microbiology Ecology, October 2003, Oxford University Press (OUP)

    David Wilson, Professor Patrick D Schloss

  69. Biotechnological prospects from metagenomics

    Article • Current Opinion in Biotechnology, June 2003, Elsevier

    Professor Patrick D Schloss