Kyle Bittinger

Kyle Bittinger

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Kyle Bittinger

Kyle Bittinger

Publications by authors named "Kyle Bittinger"

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Impact of Steviol Glycosides and Erythritol on the Human and Gut Microbiome.

J Agric Food Chem 2020 Jan 7. Epub 2020 Jan 7.

United States Department of Agriculture , Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center , 600E Mermaid Lane , Wyndmoor , Pennsylvania 19038 , United States.

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http://dx.doi.org/10.1021/acs.jafc.9b06181DOI Listing
January 2020

Metabolic Analysis of Regionally Distinct Gut Microbial Communities Using an Platform.

J Agric Food Chem 2019 Nov 18. Epub 2019 Nov 18.

Proteomics & Mass Spectrometry Facility , Donald Danforth Plant Science Center , St. Louis , Missouri 63132 , United States.

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http://dx.doi.org/10.1021/acs.jafc.9b05202DOI Listing
November 2019

Metagenomic assessment of the Cebus apella gut microbiota.

Am J Primatol 2019 Oct 26;81(10-11):e23023. Epub 2019 Jun 26.

Alpha Genesis Inc, Yemassee, South Carolina.

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http://dx.doi.org/10.1002/ajp.23023DOI Listing
October 2019

Segmented Filamentous Bacteria Prevent and Cure Rotavirus Infection.

Cell 2019 Oct 10;179(3):644-658.e13. Epub 2019 Oct 10.

Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.09.028DOI Listing
October 2019

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam Rivers Michael S Robeson Patrick Rosenthal Nicola Segata Michael Shaffer Arron Shiffer Rashmi Sinha Se Jin Song John R Spear Austin D Swafford Luke R Thompson Pedro J Torres Pauline Trinh Anupriya Tripathi Peter J Turnbaugh Sabah Ul-Hasan Justin J J van der Hooft Fernando Vargas Yoshiki Vázquez-Baeza Emily Vogtmann Max von Hippel William Walters Yunhu Wan Mingxun Wang Jonathan Warren Kyle C Weber Charles H D Williamson Amy D Willis Zhenjiang Zech Xu Jesse R Zaneveld Yilong Zhang Qiyun Zhu Rob Knight J Gregory Caporaso

Nat Biotechnol 2019 Sep;37(9):1091

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0252-6DOI Listing
September 2019

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam Rivers Michael S Robeson Patrick Rosenthal Nicola Segata Michael Shaffer Arron Shiffer Rashmi Sinha Se Jin Song John R Spear Austin D Swafford Luke R Thompson Pedro J Torres Pauline Trinh Anupriya Tripathi Peter J Turnbaugh Sabah Ul-Hasan Justin J J van der Hooft Fernando Vargas Yoshiki Vázquez-Baeza Emily Vogtmann Max von Hippel William Walters Yunhu Wan Mingxun Wang Jonathan Warren Kyle C Weber Charles H D Williamson Amy D Willis Zhenjiang Zech Xu Jesse R Zaneveld Yilong Zhang Qiyun Zhu Rob Knight J Gregory Caporaso

Nat Biotechnol 2019 08;37(8):852-857

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0209-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015180PMC
August 2019

Host mitochondria influence gut microbiome diversity: A role for ROS.

Sci Signal 2019 Jul 2;12(588). Epub 2019 Jul 2.

Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.

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http://dx.doi.org/10.1126/scisignal.aaw3159DOI Listing
July 2019

The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats.

Mol Psychiatry 2019 Mar 4. Epub 2019 Mar 4.

Department of Anesthesiology and Critical Care, Children's Hospital of Philadelphia, Philadelphia, PA, USA.

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http://dx.doi.org/10.1038/s41380-019-0380-xDOI Listing
March 2019

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.

Microbiome 2019 03 22;7(1):46. Epub 2019 Mar 22.

Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s40168-019-0658-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429786PMC
March 2019

Applying Advanced In Vitro Culturing Technology to Study the Human Gut Microbiota.

J Vis Exp 2019 02 15(144). Epub 2019 Feb 15.

Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture.

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http://dx.doi.org/10.3791/59054DOI Listing
February 2019

Microbiota-dependent signals are required to sustain TLR-mediated immune responses.

JCI Insight 2019 Jan 10;4(1). Epub 2019 Jan 10.

Division of Pediatric Rheumatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1172/jci.insight.124370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485364PMC
January 2019

Establishing a mucosal gut microbial community in vitro using an artificial simulator.

PLoS One 2018 17;13(7):e0197692. Epub 2018 Jul 17.

Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197692PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050037PMC
December 2018

Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit.

Infect Control Hosp Epidemiol 2018 Dec 18:1-7. Epub 2018 Dec 18.

1Pulmonary, Allergy and Critical Care Division, Department of Medicine,University of Pennsylvania Perelman School of Medicine,Philadelphia, Pennsylvania.

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https://www.cambridge.org/core/product/identifier/S0899823X1
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http://dx.doi.org/10.1017/ice.2018.319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581638PMC
December 2018

Characterisation of the nasal microbiota in granulomatosis with polyangiitis.

Ann Rheum Dis 2018 10 11;77(10):1448-1453. Epub 2018 Jul 11.

Division of Rheumatology and the Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1136/annrheumdis-2018-213645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463278PMC
October 2018

Microbes vs. chemistry in the origin of the anaerobic gut lumen.

Proc Natl Acad Sci U S A 2018 04 2;115(16):4170-4175. Epub 2018 Apr 2.

Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104;

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http://dx.doi.org/10.1073/pnas.1718635115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5910840PMC
April 2018

A Pilot Characterization of the Human Chronobiome.

Sci Rep 2017 12 7;7(1):17141. Epub 2017 Dec 7.

Department of Systems Pharmacology and Translational Therapeutics, at the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1038/s41598-017-17362-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719427PMC
December 2017

Protective major histocompatibility complex allele prevents type 1 diabetes by shaping the intestinal microbiota early in ontogeny.

Proc Natl Acad Sci U S A 2017 09 22;114(36):9671-9676. Epub 2017 Aug 22.

Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1712280114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5594701PMC
September 2017

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium.

PLoS One 2016 13;11(5):e0155620. Epub 2016 May 13.

Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155620PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866709PMC
July 2017

Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity.

Cell Host Microbe 2017 Jul;22(1):120-128.e4

Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2017.06.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701758PMC
July 2017

Optimizing methods and dodging pitfalls in microbiome research.

Microbiome 2017 05 5;5(1):52. Epub 2017 May 5.

Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.

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http://dx.doi.org/10.1186/s40168-017-0267-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420141PMC
May 2017

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota.

Microbiome 2016 Jun 23;4(1):29. Epub 2016 Jun 23.

Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.

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http://dx.doi.org/10.1186/s40168-016-0172-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917942PMC
June 2016

Composition and dynamics of the respiratory tract microbiome in intubated patients.

Microbiome 2016 Feb 11;4. Epub 2016 Feb 11.

Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s40168-016-0151-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750361PMC
February 2016

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms.

PeerJ 2016 4;4:e1599. Epub 2016 Feb 4.

Department of Clinical Studies, University of Pennsylvania , Kennett Square, PA , United States of America.

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http://dx.doi.org/10.7717/peerj.1599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748696PMC
February 2016

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.

Gut 2016 Jan 26;65(1):63-72. Epub 2014 Nov 26.

Division of Gastroenterology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA Departments of Biostatistics & Epidemiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1136/gutjnl-2014-308209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583329PMC
January 2016

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts.

Inflamm Bowel Dis 2015 Dec;21(12):2797-805

*Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; †Department of Microbiology; and ‡Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1097/MIB.0000000000000557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4950860PMC
December 2015

Bidirectional interactions between indomethacin and the murine intestinal microbiota.

Elife 2015 Dec 23;4:e08973. Epub 2015 Dec 23.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.

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http://dx.doi.org/10.7554/eLife.08973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755745PMC
December 2015

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

Bioinformatics 2015 Aug 29;31(15):2461-8. Epub 2015 Mar 29.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btv183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514928PMC
August 2015

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.

Inflamm Bowel Dis 2015 Aug;21(8):1948-56

*Division of Gastroenterology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania; †Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania; and ‡Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1097/MIB.0000000000000454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509842PMC
August 2015

Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.

Gastroenterology 2014 Nov 18;147(5):1055-63.e8. Epub 2014 Jul 18.

Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2014.07.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252572PMC
November 2014

Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation.

Science 2014 Aug 17;345(6196):578-82. Epub 2014 Jul 17.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1126/science.1256942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548887PMC
August 2014

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts.

PLoS One 2012 6;7(9):e42786. Epub 2012 Sep 6.

Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042786PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435383PMC
May 2013

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.

Am J Respir Crit Care Med 2012 Sep 12;186(6):536-45. Epub 2012 Jul 12.

Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://www.atsjournals.org/doi/abs/10.1164/rccm.201204-0693O
Publisher Site
http://dx.doi.org/10.1164/rccm.201204-0693OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3480531PMC
September 2012

Associating microbiome composition with environmental covariates using generalized UniFrac distances.

Bioinformatics 2012 Aug 17;28(16):2106-13. Epub 2012 Jun 17.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413390PMC
August 2012

Spectral signatures of inter-system crossing mediated by energetically distant doorway levels: examples from the acetylene S1 state.

J Phys Chem A 2011 Nov 29;115(43):11921-43. Epub 2011 Sep 29.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1021/jp2037894DOI Listing
November 2011

Topographical continuity of bacterial populations in the healthy human respiratory tract.

Am J Respir Crit Care Med 2011 Oct 16;184(8):957-63. Epub 2011 Jun 16.

University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1164/rccm.201104-0655OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208663PMC
October 2011

Disordered microbial communities in the upper respiratory tract of cigarette smokers.

PLoS One 2010 Dec 20;5(12):e15216. Epub 2010 Dec 20.

Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015216PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004851PMC
December 2010

Deconvolution of spectral data using a doorway-coupling model Hamiltonian.

J Chem Phys 2010 Apr;132(13):134302

Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1063/1.3357311DOI Listing
April 2010

PyNAST: a flexible tool for aligning sequences to a template alignment.

Bioinformatics 2010 Jan 13;26(2):266-7. Epub 2009 Nov 13.

Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804299PMC
January 2010

Contrasting singlet-triplet dynamical behavior of two vibrational levels of the acetylene S1 2(1)3(1)B2 polyad.

J Phys Chem A 2007 Dec 6;111(49):12534-7. Epub 2007 Oct 6.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1021/jp0760399DOI Listing
December 2007

Angle-energy distributions of Penning ions in crossed molecular beams. IV. He*(21 S,2 3S)+H2-->He+H2+ +e-.

J Chem Phys 2004 May;120(18):8485-93

Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1063/1.1691739DOI Listing
May 2004