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Todd DeSantis

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Alexander J Probst; Maria Sonnleitner; Kasthuri Venkateswaran; Yvette M Piceno; Gary L Andersen; Hans A Bechtel; Giovanni Birarda; Todd Z DeSantis; Hoi-Ying N Holman; Christine Moissl-Eichinger
Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm.
Nosratola D Vaziri; Jakk Wong; Jun Yuan; Todd Z DeSantis; Tien-Hung Nguyen; Zhenmin Ni; Madeleine Pahl; Yvette M Piceno; Gary L Andersen
Chronic kidney disease alters intestinal microbial flora.
T M Korves; Yvette M Piceno; L M Tom; Gary L Andersen; Todd Z DeSantis; B W Jones; G M Hwang
Bacterial communities in commercial aircraft high-efficiency particulate air (HEPA) filters assessed by PhyloChip analysis.

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2013: Alexander J Probst; Maria Sonnleitner; Kasthuri Venkateswaran; Yvette M Piceno; Gary L Andersen; Hans A Bechtel; Giovanni Birarda; Todd Z DeSantis; Hoi-Ying N Holman; Christine Moissl-Eichinger
Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm.
The ISME journal 2013;7(3):635-51.
2013: Nosratola D Vaziri; Jakk Wong; Jun Yuan; Todd Z DeSantis; Tien-Hung Nguyen; Zhenmin Ni; Madeleine Pahl; Yvette M Piceno; Gary L Andersen
Chronic kidney disease alters intestinal microbial flora.
Kidney international 2013;83(2):308-15.
2013: T M Korves; Yvette M Piceno; L M Tom; Gary L Andersen; Todd Z DeSantis; B W Jones; G M Hwang
Bacterial communities in commercial aircraft high-efficiency particulate air (HEPA) filters assessed by PhyloChip analysis.
Indoor air 2013;23(1):50-61.
2013: Antonietta Mello; Chiara Napoli; Yvette M Piceno; Kornelia Smalla; Lauren M Tom; Gary L Andersen; Todd Z DeSantis; Guo-Chun Ding; Paola Bonfante
Truffle brûlés have an impact on the diversity of soil bacterial communities.
PloS one 2013;8(4):e61945.
2013: Magali Noval Rivas; Hans C Oettgen; Joseph F Petrosino; Janet Warrington; Petra Wise; Yu-qian Zhang; Lynn Bry; Oliver T Burton; Christel Chehoud; Todd Z DeSantis; Maria Garcia Lloret; Georg K Gerber; Suejy A Hobson; Embriette R Hyde; Justin Kuczynski; Sarkis K Mazmanian; Talal A Chatila
A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis.
The Journal of allergy and clinical immunology 2013;131(1):201-12.
2012: Helen L Hayden; Claire Y Allan; Gary L Andersen; Damian S Bougoure; Eoin L Brodie; Todd Z DeSantis; Pauline M Mele; Sorn Norng; Yvette M Piceno; Amity L Williams; Mark J Hovenden
Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil.
Environmental microbiology 2012;14(12):3081-96.
2012: Frank Reith; Carla M Zammit; Jizhong Zhou; Gary L Andersen; Eoin L Brodie; Joel Brugger; Todd Z DeSantis; Katherine C Goldfarb; Adrienne L Gregg; Zhili He; Zhenmei Lu; Yvette M Piceno; Steven A Wakelin
Influence of geogenic factors on microbial communities in metallogenic Australian soils.
The ISME journal 2012;6(11):2107-18.
2012: Kim M Handley; Philip E Long; A Lucie N'Guessan; Aaron Peacock; Yvette M Piceno; Michael J Wilkins; Kenneth H Williams; Kelly C Wrighton; Gary L Andersen; John Bargar; Todd Z DeSantis; Jillian F Banfield
High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment.
FEMS microbiology ecology 2012;81(1):188-204.
2012: Daniel McDonald; Eric P Nawrocki; Morgan N Price; Alexander Probst; Gary L Andersen; Todd Z DeSantis; Julia Goodrich; Rob Knight; Philip Hugenholtz
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
The ISME journal 2012;6(3):610-8.
2012: Anthony A Fodor; Theresa Hepburn; Ping Hu; Heather Huot-Creasy; Konstantinos Liolios; Erica Sodergren; Kristine M Wylie; Yuzhen Ye; Jonathan H Badger; Bruce Birren; Todd Z DeSantis; Ashlee M Earl
The "most wanted" taxa from the human microbiome for whole genome sequencing.
PloS one 2012;7(7):e41294.
2011: Kristen M DeAngelis; Todd Z DeSantis; Julian L Fortney; Terry C Hazen; Shariff R Osman; Mary E Singer; Lauren M Tom; Cindy H Wu; Harry R Beller; Eoin L Brodie; Romy Chakraborty; Gary L Andersen
PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.
Applied and environmental microbiology 2011;77(18):6313-22.
2011: Rodrigo Mendes; Marco Kruijt; Irene de Bruijn; Ester Dekkers; Menno van der Voort; Johannes H M Schneider; Yvette M Piceno; Todd Z DeSantis; Gary L Andersen; Peter A H M Bakker; Jos M Raaijmakers
Deciphering the rhizosphere microbiome for disease-suppressive bacteria.
Science (New York, N.Y.) 2011;332(6033):1097-100.
2011: Lisa M Durso; Gregory P Harhay; Timothy P L Smith; James L Bono; Todd Z DeSantis; Michael L Clawson
Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces.
Foodborne pathogens and disease 2011;8(5):647-9.
2011: Dan Knights; Justin Kuczynski; Omry Koren; Ruth E Ley; Dawn Field; Rob Knight; Todd Z DeSantis; Scott T Kelley
Supervised classification of microbiota mitigates mislabeling errors.
The ISME journal 2011;5(4):570-3.
2011: Brian J Haas; Dirk Gevers; Ashlee M Earl; Mike Feldgarden; Doyle V Ward; Georgia Giannoukos; Dawn Ciulla; Diana Tabbaa; Sarah Katherine Highlander; Erica Sodergren; Barbara Methé; Todd Z DeSantis; Joseph F Petrosino; Rob Knight; Bruce Birren
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
Genome research 2011;21(3):494-504.
2011: Yvonne J Huang; Craig E Nelson; Eoin L Brodie; Todd Z DeSantis; Marshall S Baek; J Liu; Tanja Woyke; Martin Allgaier; Jim Bristow; Jeanine P Wiener-Kronish; E Rand Sutherland; Tonya S King; Nikolina Icitovic; Richard J Martin; William J Calhoun; Mario Castro; Loren C Denlinger; Emily DiMango; Monica Kraft; Stephen P Peters; Stephen I Wasserman; Michael E Wechsler; Homer A Boushey; Susan V Lynch
Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma.
The Journal of allergy and clinical immunology 2011;127(2):372-381.e1-3.
2011: Todd Z DeSantis; Keith Keller; Ulas Karaoz; Alexander V Alekseyenko; Navjeet N S Singh; Eoin L Brodie; Zhiheng Pei; Gary L Andersen; Niels Larsen
Simrank: Rapid and sensitive general-purpose k-mer search tool.
BMC ecology 2011;11():11.
2010: Carlos W Nossa; William E Oberdorf; Liying Yang; Jørn A Aas; Bruce J Paster; Todd Z DeSantis; Eoin L Brodie; Daniel Malamud; Michael A Poles; Zhiheng Pei
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome.
World journal of gastroenterology : WJG 2010;16(33):4135-44.
2010: Michael C Schatz; Adam M Phillippy; Pawel Gajer; Todd Z DeSantis; Gary L Andersen; Jacques Ravel
Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray.
Applied and environmental microbiology 2010;76(16):5636-8.
2010: Lisa M Durso; Gregory P Harhay; Timothy P L Smith; James L Bono; Todd Z DeSantis; Dayna M Harhay; Gary L Andersen; James E Keen; William W Laegreid; Michael L Clawson
Animal-to-animal variation in fecal microbial diversity among beef cattle.
Applied and environmental microbiology 2010;76(14):4858-62.
2010: Eiko E Kuramae; Hannes A Gamper; Etienne Yergeau; Yvette M Piceno; Eoin L Brodie; Todd Z DeSantis; Gary L Andersen; Johannes A van Veen; George A Kowalchuk
Microbial secondary succession in a chronosequence of chalk grasslands.
The ISME journal 2010;4(5):711-5.
2010: J Gregory Caporaso; Kyle Bittinger; Frederic D Bushman; Todd Z DeSantis; Gary L Andersen; Rob Knight
PyNAST: a flexible tool for aligning sequences to a template alignment.
Bioinformatics (Oxford, England) 2010;26(2):266-7.
2010: Cindy H Wu; Bram Sercu; Laurie C Van De Werfhorst; Jakk Wong; Todd Z DeSantis; Eoin L Brodie; Terry C Hazen; Patricia A Holden; Gary L Andersen
Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators.
PloS one 2010;5(6):e11285.
2009: Shinichi Sunagawa; Todd Z DeSantis; Yvette M Piceno; Eoin L Brodie; Michael K DeSalvo; Christian R Voolstra; Ernesto Weil; Gary L Andersen; Mónica Medina
Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata.
The ISME journal 2009;3(5):512-21.
2009: Etienne Yergeau; Sung A Schoondermark-Stolk; Eoin L Brodie; Sébastien Déjean; Todd Z DeSantis; Olivier Gonçalves; Yvette M Piceno; Gary L Andersen; George A Kowalchuk
Environmental microarray analyses of Antarctic soil microbial communities.
The ISME journal 2009;3(3):340-51.
2009: Kristen M DeAngelis; Eoin L Brodie; Todd Z DeSantis; Gary L Andersen; Steven E Lindow; Mary K Firestone
Selective progressive response of soil microbial community to wild oat roots.
The ISME journal 2009;3(2):168-78.
2008: Kelly C Wrighton; Peter Agbo; Falk Warnecke; Karrie A Weber; Eoin L Brodie; Todd Z DeSantis; Philip Hugenholtz; Gary L Andersen; John D Coates
A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells.
The ISME journal 2008;2(11):1146-56.
2008: Dylan Chivian; Eoin L Brodie; Eric J Alm; David E Culley; Paramvir S Dehal; Todd Z DeSantis; Thomas M Gihring; Alla Lapidus; Li-Hung Lin; Stephen R Lowry; Duane P Moser; Paul M Richardson; Gordon Southam; Greg Wanger; Lisa M Pratt; Gary L Andersen; Terry C Hazen; Fred J Brockman; Adam P Arkin; Tullis C Onstott
Environmental genomics reveals a single-species ecosystem deep within Earth.
Science (New York, N.Y.) 2008;322(5899):275-8.
2008: Zongzhi Liu; Todd Z DeSantis; Gary L Andersen; Rob Knight
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.
Nucleic acids research 2008;36(18):e120.
2008: Kimberlee A West; David Johnson; Ping Hu; Todd Z DeSantis; Eoin L Brodie; Patrick K H Lee; Helene Feil; Gary L Andersen; Stephen H Zinder; Lisa Alvarez-Cohen
Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains.
Applied and environmental microbiology 2008;74(11):3533-40.
2007: J L Flanagan; E L Brodie; L Weng; Susan V Lynch; Oscar Garcia; R Brown; P Hugenholtz; Todd Z DeSantis; Gary L Andersen; jeanine wiener-kronish; James Bristow
Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa.
Journal of clinical microbiology 2007;45(6):1954-62.
2007: Todd Z DeSantis; Eoin L Brodie; Jordan P Moberg; Ingrid X Zubieta; Yvette M Piceno; Gary L Andersen
High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment.
Microbial ecology 2007;53(3):371-83.
2007: Eoin L Brodie; Todd Z DeSantis; Jordan P Moberg Parker; Ingrid X Zubietta; Yvette M Piceno; Gary L Andersen
Urban aerosols harbor diverse and dynamic bacterial populations.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(1):299-304.
2007: Daniel Dalevi; Todd Z DeSantis; Jakob Fredslund; Gary L Andersen; Victor M Markowitz; Philip Hugenholtz
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool.
BMC bioinformatics 2007;8():402.
2006: Li-Hung Lin; Pei-Ling Wang; Douglas Rumble; Johanna Lippmann-Pipke; Erik Boice; Lisa M Pratt; Barbara Sherwood Lollar; Eoin L Brodie; Terry C Hazen; Gary L Andersen; Todd Z DeSantis; Duane P Moser; Dave Kershaw; Tullis C Onstott
Long-term sustainability of a high-energy, low-diversity crustal biome.
Science (New York, N.Y.) 2006;314(5798):479-82.
2006: Eoin L Brodie; Todd Z DeSantis; Dominique C Joyner; Seung M Baek; Joern T Larsen; Gary L Andersen; Terry C Hazen; Paul M Richardson; Donald J Herman; Tetsu K Tokunaga; Jiamin M Wan; Mary K Firestone
Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation.
Applied and environmental microbiology 2006;72(9):6288-98.
2006: Todd Z DeSantis; Philip Hugenholtz; K Keller; Eoin L Brodie; N Larsen; Yvette M Piceno; R Phan; Gary L Andersen
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes.
Nucleic acids research 2006;34(Web Server issue):W394-9.
2006: Todd Z DeSantis; Philip Hugenholtz; N Larsen; M Rojas; Eoin L Brodie; K Keller; T Huber; Daniel A Dalevi; Ping Hu; Gary L Andersen
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.
Applied and environmental microbiology 2006;72(7):5069-72.
2005: Todd Z DeSantis; Carol E Stone; Sonya R Murray; Jordan P Moberg; Gary L Andersen
Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray.
FEMS microbiology letters 2005;245(2):271-8.
2003: Todd Z DeSantis; I Dubosarskiy; S R Murray; Gary L Andersen
Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA.
Bioinformatics (Oxford, England) 2003;19(12):1461-8.
2002: Kenneth H Wilson; Wendy J Wilson; Jennifer L Radosevich; Todd Z DeSantis; Vijay S Viswanathan; Thomas A Kuczmarski; Gary L Andersen
High-density microarray of small-subunit ribosomal DNA probes.
Applied and environmental microbiology 2002;68(5):2535-41.
2002: Wendy J Wilson; C L Strout; Todd Z DeSantis; J L Stilwell; AV Carrano; Gary L Andersen
Sequence-specific identification of 18 pathogenic microorganisms using microarray technology.
Molecular and cellular probes 2002;16(2):119-27.
2002: J L Radosevich; Wendy J Wilson; J H Shinn; Todd Z DeSantis; Gary L Andersen
Development of a high-volume aerosol collection system for the identification of air-borne micro-organisms.
Letters in applied microbiology 2002;34(3):162-7.