Sloan-funded MoBE Reference Collection

So one of my projects for the last few months has been to try to create a collection of every peer-reviewed publication that resulted from the Alfred P. Sloan Foundation program of the Microbiology of the Built Environment.  The program has been running for over 10 years and has funded over 100 grants.  To generate this collection we tried many approaches, starting with basic searches for the funded labs and acknowledgement of Sloan funding.  Next we contacted everyone who had ever received a grant through the program and asked them to check their publications… this approach almost doubled the number of publications in the collection.  A last few gaps were filled by begging graduate students to check the lists for non-responsive PIs and a little bit of digging through grant reports at the Sloan Foundation.  After some weeding, and manual addition of metadata we think we have a pretty good collection… but I’m sure we’re still missing publications!

With this collection we hope to do many things including a citation analysis, a network analysis, and other similar approaches that can shed light on the connectivity of labs in the field and the impact of the Sloan program.

We are looking for input on the list!  If you work(ed) in a lab that received Sloan Funding, we would love it if you would ensure that all of your relevant publications are included.  Relevant here meaning they resulted, directly or indirectly, from the Sloan MoBE program.  Please post additions in the comments below.  Thank you for any input!

Abarenkov, K., Adams, R.I., Laszlo, I., Agan, A., Ambrosio, E., Antonelli, A., Bahram, M., Bengtsson-Palme, J., Bok, G., Cangren, P., et al. (2016). Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16, 1–15.

 

Adams, R.I., Amend, A.S., Taylor, J.W., and Bruns, T.D. (2013a). A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: a Case Study of Fungi in Indoor Dust. Microb Ecol 66, 735–741.

 

Adams, R.I., Miletto, M., Taylor, J.W., and Bruns, T.D. (2013b). Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 7, 1262–1273.

 

Adams, R.I., Miletto, M., Taylor, J.W., and Bruns, T.D. (2013c). The Diversity and Distribution of Fungi on Residential Surfaces. PLoS One 8.

 

Adams, R.I., Miletto, M., Lindow, S.E., Taylor, J.W., and Bruns, T.D. (2014). Airborne Bacterial Communities in Residences: Similarities and Differences with Fungi. PLoS One 9.

 

Adams, R.I., Bhangar, S., Pasut, W., Arens, E.A., Taylor, J.W., Lindow, S.E., Nazaroff, W.W., and Bruns, T.D. (2015a). Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes. PLoS One 10.

 

Adams, R.I., Bateman, A.C., Bik, H.M., and Meadow, J.F. (2015b). Microbiota of the indoor environment: a meta-analysis. Microbiome 3.

 

Adams, R.I., Tian, Y., Taylor, J.W., Bruns, T.D., Hyvärinen, A., and Täubel, M. (2015c). Passive dust collectors for assessing airborne microbial material. Microbiome 3.

 

Adams, R.I., Bhangar, S., Dannemiller, K.C., Eisen, J.A., Fierer, N., Gilbert, J.A., Green, J.L., Marr, L.C., Miller, S.L., Siegel, J.A., et al. (2016). Ten questions concerning the microbiomes of buildings. Building and Environment 109, 224–234.

 

Ahrendt, S.R., Medina, E.M., Chang, C.-E.A., and Stajich, J.E. (2017). Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling. PeerJ 5, e3206.

 

Alcaïs, A., Quintana-Murci, L., Thaler, D.S., Schurr, E., Abel, L., and Casanova, J.-L. (2010). Life-threatening infectious diseases of childhood: single-gene inborn errors of immunity?: Genetic architecture of infectious diseases. Annals of the New York Academy of Sciences 1214, 18–33.

 

Al-Hatmi, A.M.S., Van Den Ende, A.H.G.G., Stielow, J.B., Van Diepeningen, A.D., Seifert, K.A., McCormick, W., Assabgui, R., Gräfenhan, T., De Hoog, G.S., and Levesque, C.A. (2016). Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium. Fungal Biol 120, 231–245.

 

Alivisatos, A.P., Blaser, M.J., Brodie, E.L., Chun, M., Dangl, J.L., Donohue, T.J., Dorrestein, P.C., Gilbert, J.A., Green, J.L., Jansson, J.K., et al. (2015). A unified initiative to harness Earth’s microbiomes. Science 350, 507–508.

 

Amend, A.S., Seifert, K.A., Samson, R., and Bruns, T.D. (2010a). Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci U S A 107, 13748–13753.

 

Amend, A.S., Seifert, K.A., and Bruns, T.D. (2010b). Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol. Ecol. 19, 5555–5565.

 

Amir, A., McDonald, D., Navas-Molina, J.A., Kopylova, E., Morton, J.T., Zech Xu, Z., Kightley, E.P., Thompson, L.R., Hyde, E.R., Gonzalez, A., et al. (2017). Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems 2, e00191-16.

 

Bálint, M., Bahram, M., Eren, A.M., Faust, K., Fuhrman, J.A., Lindahl, B., O’Hara, R.B., Öpik, M., Sogin, M.L., Unterseher, M., et al. (2016). Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol. Rev.

 

Barberán, A., Ladau, J., Leff, J.W., Pollard, K.S., Menninger, H.L., Dunn, R.R., and Fierer, N. (2015a). Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci U S A 112, 5756–5761.

 

Barberán, A., Dunn, R.R., Reich, B.J., Pacifici, K., Laber, E.B., Menninger, H.L., Morton, J.M., Henley, J.B., Leff, J.W., Miller, S.L., et al. (2015b). The ecology of microscopic life in household dust. Proc. Biol. Sci. 282.

 

Baron, J.L., Vikram, A., Duda, S., Stout, J.E., and Bibby, K. (2014). Shift in the Microbial Ecology of a Hospital Hot Water System following the Introduction of an On-Site Monochloramine Disinfection System. PLoS One 9.

 

Baron, J.L., Harris, J.K., Holinger, E.P., Duda, S., Stevens, M.J., Robertson, C.E., Ross, K.A., Pace, N.R., and Stout, J.E. (2015). Effect of monochloramine treatment on the microbial ecology of Legionella and associated bacterial populations in a hospital hot water system. Syst. Appl. Microbiol. 38, 198–205.

 

Bates, S.T., Ahrendt, S., Bik, H.M., Bruns, T.D., Caporaso, J.G., Cole, J., Dwan, M., Fierer, N., Gu, D., Houston, S., et al. (2013). Meeting Report: Fungal ITS Workshop (October 2012). Stand Genomic Sci 8, 118–123.

 

Benoit, J.B., Adelman, Z.N., Reinhardt, K., Dolan, A., Poelchau, M., Jennings, E.C., Szuter, E.M., Hagan, R.W., Gujar, H., Shukla, J.N., et al. (2016). Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat Commun 7.

 

Betts, M.N., Jospin, G., Eisen, J.A., and Coil, D.A. (2015). Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes ). Genome Announcements 3, e01209-15.

 

Bhangar, S., Huffman, J.A., and Nazaroff, W.W. (2014). Size-resolved fluorescent biological aerosol particle concentrations and occupant emissions in a university classroom. Indoor Air 24, 604–617.

 

Bhangar, S., Adams, R.I., Pasut, W., Huffman, J.A., Arens, E.A., Taylor, J.W., Bruns, T.D., and Nazaroff, W.W. (2016a). Chamber bioaerosol study: human emissions of size-resolved fluorescent biological aerosol particles. Indoor Air 26, 193–206.

 

Bhangar, S., Brooks, B., Firek, B., Licina, D., Tang, X., Morowitz, M.J., Banfield, J.F., and Nazaroff, W.W. (2016b). Pilot study of sources and concentrations of size-resolved airborne particles in a neonatal intensive care unit. Building and Environment 106, 10–19.

 

Bik, H.M., Porazinska, D.L., Creer, S., Caporaso, J.G., Knight, R., and Thomas, W.K. (2012). Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 27, 233–243.

 

Bik, H.M., Coil, D.A., and Eisen, J.A. (2014). microBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere. PLoS Biol 12.

 

Blaser, M.J., Cardon, Z.G., Cho, M.K., Dangl, J.L., Donohue, T.J., Green, J.L., Knight, R., Maxon, M.E., Northen, T.R., Pollard, K.S., et al. (2016). Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. mBio 7.

 

Bokulich, N.A., Lewis, Z.T., Boundy-Mills, K., and Mills, D.A. (2016a). A new perspective on microbial landscapes within food production. Curr Opin Biotechnol 37, 182–189.

 

Bokulich, N.A., Rideout, J.R., Mercurio, W.G., Shiffer, A., Wolfe, B., Maurice, C.F., Dutton, R.J., Turnbaugh, P.J., Knight, R., and Caporaso, J.G. (2016b). mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. mSystems 1.

 

Borrowman, C.K., Zhou, S., Burrow, T.E., and Abbatt, J.P.D. (2015). Formation of environmentally persistent free radicals from the heterogeneous reaction of ozone and polycyclic aromatic compounds. Phys. Chem. Chem. Phys. 18, 205–212.

 

Bowers, R.M., Kyrpides, N.C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T.B.K., Schulz, F., Jarett, J., Rivers, A.R., Eloe-Fadrosh, E.A., et al. (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731.

 

Brooks, B., Firek, B.A., Miller, C.S., Sharon, I., Thomas, B.C., Baker, R., Morowitz, M.J., and Banfield, J.F. (2014). Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome 2, 1.

 

Brown, G.Z., Kline, J., Mhuireach, G., Northcutt, D., and Stenson, J. (2016). Making microbiology of the built environment relevant to design. Microbiome 4.

 

Busby, P.E., Soman, C., Wagner, M.R., Friesen, M.L., Kremer, J., Bennett, A., Morsy, M., Eisen, J.A., Leach, J.E., and Dangl, J.L. (2017). Research priorities for harnessing plant microbiomes in sustainable agriculture. PLOS Biology 15, e2001793.

 

Buse, H.Y., Ji, P., Gomez-Alvarez, V., Pruden, A., Edwards, M.A., and Ashbolt, N.J. (2016). Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms. Microbial Biotechnology.

 

Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336.

 

Caverly, L.J., Carmody, L.A., Haig, S.-J., Kotlarz, N., Kalikin, L.M., Raskin, L., and LiPuma, J.J. (2016). Culture-Independent Identification of Nontuberculous Mycobacteria in Cystic Fibrosis Respiratory Samples. PLoS One 11.

 

Chamberlain, A.T., Lehnert, J.D., and Berkelman, R.L. (2017). The 2015 New York City Legionnaires’ Disease Outbreak: A Case Study on a History-Making Outbreak. J Public Health Manag Pract 23, 410–416.

 

Chase, J., Fouquier, J., Zare, M., Sonderegger, D.L., Knight, R., Kelley, S.T., Siegel, J., and Caporaso, J.G. (2016a). Geography and Location Are the Primary Drivers of Office Microbiome Composition. mSystems 1, e00022-16.

 

Chase, J.H., Bolyen, E., Rideout, J.R., and Caporaso, J.G. (2016b). cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies. mSystems 1.

 

Chen, A.J., Frisvad, J.C., Sun, B.D., Varga, J., Kocsub?, S., Dijksterhuis, J., Kim, D.H., Hong, S.-B., Houbraken, J., and Samson, R.A. (2016a). Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology. Studies in Mycology 84, 1–118.

 

Chen, A.J., Sun, B.D., Houbraken, J., Frisvad, J.C., Yilmaz, N., Zhou, Y.G., and Samson, R.A. (2016b). New Talaromyces species from indoor environments in China. Studies in Mycology 84, 119–144.

 

Chitsaz, H., Yee-Greenbaum, J.L., Tesler, G., Lombardo, M.-J., Dupont, C.L., Badger, J.H., Novotny, M., Rusch, D.B., Fraser, L.J., Gormley, N.A., et al. (2011). Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotechnology 29, 915–921.

 

Coil, D.A. Citizen Microbiology: A Case Study in Space. In The Rightful Place of Science: Citizen Science, (Consortium for Science, Policy & Outcomes), p.

 

Coil, D.A., and Eisen, J.A. (2015). Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado. Genome Announcements 3, e00856-15.

 

Coil, D., Jospin, G., and Darling, A.E. (2015a). A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31, 587–589.

 

Coil, D.A., Doctor, J.I., Lang, J.M., Darling, A.E., and Eisen, J.A. (2013). Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announcements 1, e00172-13-e00172-13.

 

Coil, D.A., Flanagan, J.C., Stump, A., Alexiev, A., Lang, J.M., and Eisen, J.A. (2015b). Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter. PeerJ 3, e1400.

 

Coil, D.A., Benardini, J.N., and Eisen, J.A. (2015c). Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft. Genome Announcements 3, e01360-15.

 

Coil, D.A., Neches, R.Y., Lang, J.M., Brown, W.E., Severance, M., Cavalier, D., and Eisen, J.A. (2016). Growth of 48 built environment bacterial isolates on board the International Space Station (ISS). PeerJ 4, e1842.

 

Coil, D.A., Ettinger, C.L., and Eisen, J.A. (2017). Gut Check: The evolution of an educational board game. PLOS Biology 15, e2001984.

 

Collins, R.A., Stajich, J.E., Field, D.J., Olive, J.E., and DeAbreu, D.M. (2015). The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin. RNA 21, 997–1004.

 

Committee on Microbiomes of the Built Environment: From Research to Application, Board on Life Sciences, Board on Environmental Studies and Toxicology, Division on Earth and Life Studies, Health and Medicine Division, Board on Infrastructure and the Constructed Environment, Division on Engineering and Physical Sciences, National Academy of Engineering, and National Academies of Sciences, Engineering, and Medicine (2017). Microbiomes of the Built Environment: A Research Agenda for Indoor Microbiology, Human Health, and Buildings (Washington, D.C.: National Academies Press).

 

Corsi, R.L., Kinney, K.A., and Levin, H. (2012). Microbiomes of built environments: 2011 symposium highlights and workgroup recommendations. Indoor Air 22, 171–172.

 

Craine, J.M., Barberán, A., Lynch, R.C., Menninger, H.L., Dunn, R.R., and Fierer, N. (2017). Molecular analysis of environmental plant DNA in house dust across the United States. Aerobiologia 33, 71–86.

 

Crous, P.W., Wingfield, M.J., Burgess, T.I., Hardy, G.E.S.J., Crane, C., Barrett, S., Cano-Lira, J.F., Leroux, J.J., Thangavel, R., Guarro, J., et al. (2016). Fungal Planet description sheets: 469?557. Persoonia – Molecular Phylogeny and Evolution of Fungi 37, 218–403.

 

Dahlhausen, K., Krebs, B.L., Watters, J.V., and Ganz, H.H. (2016). Crowdfunding Campaigns Help Researchers Launch Projects and Generate Outreach. Journal of Microbiology & Biology Education 17, 32–37.

 

Dahms, P.A., Martin, A.L., Ganz, H.H., Eisen, J.A., and Coil, D.A. (2017). Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a Feline Anal Sac. Genome Announcements 5, e00034-17.

 

Dai, D., Prussin, A.J., Marr, L.C., Vikesland, P.J., Edwards, M.A., and Pruden, A. (2017). Factors Shaping the Human Exposome in the Built Environment: Opportunities for Engineering Control. Environmental Science & Technology 51, 7759–7774.

 

Dannemiller, K.C., Lang-Yona, N., Yamamoto, N., Rudich, Y., and Peccia, J. (2014a). Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations. Atmospheric Environment 84, 113–121.

 

Dannemiller, K.C., Reeves, D., Bibby, K., Yamamoto, N., and Peccia, J. (2014b). Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS). J. Basic Microbiol. 54, 315–321.

 

Dannemiller, K.C., Mendell, M.J., Macher, J.M., Kumagai, K., Bradman, A., Holland, N., Harley, K., Eskenazi, B., and Peccia, J. (2014c). Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development. Indoor Air 24, 236–247.

 

Dannemiller, K.C., Weschler, C.J., and Peccia, J. (2016a). Fungal and bacterial growth in floor dust at elevated relative humidity levels. Indoor Air.

 

Dannemiller, K.C., Gent, J.F., Leaderer, B.P., and Peccia, J. (2016b). Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children. J. Allergy Clin. Immunol. 138, 76–83.e1.

 

Dannemiller, K.C., Gent, J.F., Leaderer, B.P., and Peccia, J. (2016c). Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children. Indoor Air 26, 179–192.

 

Davis, J.C.C., Totten, S.M., Huang, J.O., Nagshbandi, S., Kirmiz, N., Garrido, D.A., Lewis, Z.T., Wu, L.D., Smilowitz, J.T., German, J.B., et al. (2016). Identification of Oligosaccharides in Feces of Breast-fed Infants and Their Correlation with the Gut Microbial Community. Mol. Cell Proteomics 15, 2987–3002.

 

Davis, J.C.C., Lewis, Z.T., Krishnan, S., Bernstein, R.M., Moore, S.E., Prentice, A.M., Mills, D.A., Lebrilla, C.B., and Zivkovic, A.M. (2017). Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota. Scientific Reports 7, 40466.

 

De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J.A., and Ercolini, D. (2016). Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci Rep 6.

 

De Vries, D.R., Martin, A.L., Ganz, H.H., Eisen, J.A., and Coil, D.A. (2016). Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3. Genome Announcements 4, e01386-16.

 

Dedesko, S., and Siegel, J.A. (2015). Moisture parameters and fungal communities associated with gypsum drywall in buildings. Microbiome 3.

 

Dedesko, S., Stephens, B., Gilbert, J.A., and Siegel, J.A. (2015). Methods to assess human occupancy and occupant activity in hospital patient rooms. Building and Environment 90, 136–145.

 

DeVries, Z.C., Mick, R., and Schal, C. (2016). Feel the heat: Activation, orientation, and feeding responses of bed bugs to targets at different temperatures. J. Exp. Biol.

 

Diep, A.L., Lang, J.M., Darling, A.E., Eisen, J.A., and Coil, D.A. (2013). Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria). Genome Announcements 1, e00197-13-e00197-13.

 

Duda, S., Kandiah, S., Stout, J.E., Baron, J.L., Yassin, M., Fabrizio, M., Ferrelli, J., Hariri, R., Wagener, M.M., Goepfert, J., et al. (2014). Evaluation of a new monochloramine generation system for controlling Legionella in building hot water systems. Infect Control Hosp Epidemiol 35, 1356–1363.

 

Dunitz, M.I., Lang, J.M., Jospin, G., Darling, A.E., Eisen, J.A., and Coil, D.A. (2015). Swabs to genomes: a comprehensive workflow. PeerJ 3, e960.

 

Dunn, R.R., Fierer, N., Henley, J.B., Leff, J.W., and Menninger, H.L. (2013). Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes. PLoS One 8.

 

Eisen, J. (2015). What does the term microbiome mean? And where did it come from? A bit of a surprise .. The Winnower.

 

Emerson, J.B., Keady, P.B., Brewer, T.E., Clements, N., Morgan, E.E., Awerbuch, J., Miller, S.L., and Fierer, N. (2015). Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood. Environ. Sci. Technol. 49, 2675–2684.

 

Emerson, J.B., Keady, P.B., Clements, N., Morgan, E.E., Awerbuch, J., Miller, S.L., and Fierer, N. (2017a). High temporal variability in airborne bacterial diversity and abundance inside single-family residences. Indoor Air 27, 576–586.

 

Emerson, J.B., Adams, R.I., Román, C.M.B., Brooks, B., Coil, D.A., Dahlhausen, K., Ganz, H.H., Hartmann, E.M., Hsu, T., Justice, N.B., et al. (2017b). Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome 5, 86.

 

Emerson, J.B., Adams, R.I., Román, C.M.B., Brooks, B., Coil, D.A., Dahlhausen, K., Ganz, H.H., Hartmann, E.M., Hsu, T., Justice, N.B., et al. (2017c). Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome 5.

 

Eren, A.M., Vineis, J.H., Morrison, H.G., and Sogin, M.L. (2013a). A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology. PLoS One 8.

 

Eren, A.M., Maignien, L., Sul, W.J., Murphy, L.G., Grim, S.L., Morrison, H.G., Sogin, M.L., and Freckleton, R. (2013b). Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol 4, 1111–1119.

 

Eren, A.M., Morrison, H.G., Lescault, P.J., Reveillaud, J., Vineis, J.H., and Sogin, M.L. (2015). Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J 9, 968–979.

 

Falkinham, J.O., Pruden, A., and Edwards, M. (2015). Opportunistic Premise Plumbing Pathogens: Increasingly Important Pathogens in Drinking Water. Pathogens 4, 373–386.

 

Feazel, L.M., Baumgartner, L.K., Peterson, K.L., Frank, D.N., Harris, J.K., and Pace, N.R. (2009). Opportunistic pathogens enriched in showerhead biofilms. Proc Natl Acad Sci U S A 106, 16393–16399.

 

Fitzsimons, M.S., Novotny, M., Lo, C.-C., Dichosa, A.E.K., Yee-Greenbaum, J.L., Snook, J.P., Gu, W., Chertkov, O., Davenport, K.W., McMurry, K., et al. (2013). Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Research 23, 878–888.

 

Flanagan, J.C., Lang, J.M., Darling, A.E., Eisen, J.A., and Coil, D.A. (2013). Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria). Genome Announcements 1, e00244-13-e00244-13.

 

Flores, G.E., Bates, S.T., Knights, D., Lauber, C.L., Stombaugh, J., Knight, R., and Fierer, N. (2011). Microbial Biogeography of Public Restroom Surfaces. PLoS One 6.

 

Flores, G.E., Bates, S.T., Caporaso, J.G., Lauber, C.L., Leff, J.W., Knight, R., and Fierer, N. (2013). Diversity, distribution and sources of bacteria in residential kitchens. Environ. Microbiol. 15, 588–596.

 

Fouquier, J., Schwartz, T., and Kelley, S.T. (2015). Rapid assemblage of diverse environmental fungal communities on public restroom floors. Indoor Air.

 

Fouquier, J., Rideout, J.R., Bolyen, E., Chase, J., Shiffer, A., McDonald, D., Knight, R., Caporaso, J.G., and Kelley, S.T. (2016). ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome 4.

 

Fox, K., Fox, A., Elssner, T., Feigley, C., and Salzberg, D. (2010). MALDI-TOF mass spectrometry speciation of staphylococci and their discrimination from micrococci isolated from indoor air of schoolrooms. J Environ Monit 12, 917–923.

 

Fox, K., Fox, A., Rose, J., and Walla, M. (2011). Speciation of coagulase negative staphylococci, isolated from indoor air, using SDS PAGE gel bands of expressed proteins followed by MALDI TOF MS and MALDI TOF-TOF MS-MS analysis of tryptic peptides. J. Microbiol. Methods 84, 243–250.

 

Fujimura, K.E., Demoor, T., Rauch, M., Faruqi, A.A., Jang, S., Johnson, C.C., Boushey, H.A., Zoratti, E., Ownby, D., Lukacs, N.W., et al. (2014). House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proceedings of the National Academy of Sciences 111, 805–810.

 

Fujimura, K.E., Sitarik, A.R., Havstad, S., Lin, D.L., Levan, S., Fadrosh, D., Panzer, A.R., LaMere, B., Rackaityte, E., Lukacs, N.W., et al. (2016). Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nature Medicine 22, 1187–1191.

 

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Nguyen, T.A., Cissé, O.H., Yun Wong, J., Zheng, P., Hewitt, D., Nowrousian, M., Stajich, J.E., and Jedd, G. (2017). Innovation and constraint leading to complex multicellularity in the Ascomycota. Nat Commun 8, 14444.

 

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Peccia, J., and Kwan, S.E. (2016). Buildings, Beneficial Microbes, and Health. Trends in Microbiology 24, 595–597.

 

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Prussin, A.J., Marr, L.C., and Bibby, K.J. (2014). Challenges of studying viral aerosol metagenomics and communities in comparison with bacterial and fungal aerosols. FEMS Microbiol. Lett. 357, 1–9.

 

Prussin, A.J., Garcia, E.B., and Marr, L.C. (2015). Total Virus and Bacteria Concentrations in Indoor and Outdoor Air. Environ Sci Technol Lett 2, 84–88.

 

Prussin, A.J., Vikram, A., Bibby, K.J., and Marr, L.C. (2016). Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center. PLoS One 11.

 

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Raveh-Sadka, T., Thomas, B.C., Singh, A., Firek, B., Brooks, B., Castelle, C.J., Sharon, I., Baker, R., Good, M., Morowitz, M.J., et al. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife 4.

 

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Rhoads, W.J., Pruden, A., and Edwards, M.A. (2016). Convective Mixing in Distal Pipes Exacerbates Legionella pneumophila Growth in Hot Water Plumbing. Pathogens 5.

 

Rhoads, W.J., Pruden, A., and Edwards, M.A. (2017). Interactive Effects of Corrosion, Copper, and Chloramines on Legionella and Mycobacteria in Hot Water Plumbing. Environmental Science & Technology.

 

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4 thoughts on “Sloan-funded MoBE Reference Collection

    1. These did not explicitly acknowledge Sloan funding but were synergistic with our Sloan projects. Prussin was a Sloan post-doc.

      Prussin II, A.J., Schwake, D.O., Marr, L.C., (2017). Ten questions concerning the aerosolization and transmission of Legionella in the built environment, Building and Environment, 123, 684-695.

      Lin, K., Marr, L.C., (2017). Aerosolization of Ebola virus surrogates in wastewater systems, Environmental Science and Technology, 51, 2669–2675.

      Khare, P., Marr, L.C., (2015). Simulation of vertical concentration gradient of influenza viruses in dust resuspended by walking, Indoor Air, 25(4), 428-440.

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