Faculty

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Daniel P. Beiting, Ph.D.

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1f Graduate Group Affiliations 8

46 Contact information
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University of Pennsylvania
25 School of Veterinary Medicine
22 Department of Pathobiology
1c Rm 314 Hill Pavilion
40 380 S. University Avenue
Philadelphia, PA 19104-4539

2c Office: 2158989247
3c Lab: 2158989247
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Email:
beiting@upenn.edu

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18 Publications
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26 Search PubMed for articles c

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13 Education:
21 a Ph.D. 17 (Immunology) c
2b Cornell University, 2006.
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Links
a2 Search PubMed for articles
d8 Institute for Infectious and Zoonotic Diseases (IIZD)
63 DIYtranscriptomics course
65 MicrobiomeDB web resource
5d GEMINI workshops
4e Lab website
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5 3 3 92 Permanent link
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b6 > Perelman School of Medicine > Faculty > Details a

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Description of Research Expertise

118 The Beiting lab takes an interdisciplinary approach – leveraging immunology, genomics, publicly-available datasets, bioinformatics, and animal models – to identify mechanisms by which the microbiome influences infection and inflammation at barrier surfaces.
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2b8 Our lab operates with an 'open science' philosophy, and has developed tools and methods that help the research community access, analyze, and visualize complex metagenomic datasets. The lab developed and runs an in-person and online course that teaches students how to use the R programming language to interrogate complex transcriptome and metatranscriptome studies. The Beiting lab also leads the MicrobiomeDB project, a web-based systems biology platform that integrates large, publicly-available microbiome studies and provides users with tools for analyzing and visualizing their own data.
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11 KEYWORDS:
14 - Microbiome
18 - Bioinformatics
23 - Host-pathogen interactions
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Selected Publications

100 Berry ASF, Farias Amorim C, Berry CL, Syrett CM, English ED, Beiting DP.: An Open-Source Toolkit To Expand Bioinformatics Training in Infectious Diseases. mBio 12: e0121421, Aug 2021.

137 Berry ASF, Pierdon MK, Misic AM, Sullivan MC, O'Brien K, Chen Y, Murray SJ, Ramharack LA, Baldassano RN, Parsons TD, Beiting DP.: Remodeling of the maternal gut microbiome during pregnancy is shaped by parity. Microbiome 9: 146, Jun 2021.

168 Berry ASF, Johnson K, Martins R, Sullivan MC, Farias Amorim C, Putre A, Scott A, Wang S, Lindsay B, Baldassano RN, Nolan TJ, Beiting DP.: Natural Infection with Giardia Is Associated with Altered Community Structure of the Human and Canine Gut Microbiome. mSphere 5: e00670-20, Aug 2020.

1ae Wang S, Martins R, Sullivan MC, Friedman ES, Misic AM, El-Fahmawi A, De Martinis ECP, O'Brien K, Chen Y, Bradley C, Zhang G, Berry ASF, Hunter CA, Baldassano RN, Rondeau MP, Beiting DP.: Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids. Microbiome 7: 126, Aug 2019.

12b Amorim CF, Novais FO, Nguyen BT, Misic AM, Carvalho LP, Carvalho EM, Beiting DP, Scott P.: Variable gene expression and parasite load predict treatment outcome in cutaneous leishmaniasis. Sci Transl Med 11: eaax4204, Nov 2019.

15a Wang S, El-Fahmawi A, Christian DA, Fang Q, Radaelli E, Chen L, Sullivan MC, Misic AM, Ellringer JA, Zhu XQ, Winter SE, Hunter CA, Beiting DP.: Infection-Induced Intestinal Dysbiosis Is Mediated by Macrophage Activation and Nitrate Production. mBio 10: e00935-19, May 2019.

13d Wilmore JR, Gaudette BT, Gomez Atria D, Hashemi T, Jones DD, Gardner CA, Cole SD, Misic AM, Beiting DP, Allman D.: Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis. Cell Host Microbe 23: 302-311, Mar 2018.

177 Oliveira FS, Brestelli J, Cade S, Zheng J, Iodice J, Fischer S, Aurrecoechea C, Kissinger JC, Brunk BP, Stoeckert CJ Jr, Fernandes GR, Roos DS, Beiting DP.: MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic Acids Res 46: D684-D691, Jan 2018.

178 Gimblet C, Meisel JS, Loesche MA, Cole SD, Horwinski J, Novais FO, Misic AM, Bradley CW, Beiting DP, Rankin SC, Carvalho LP, Carvalho EM, Scott P, Grice EA.: Cutaneous Leishmaniasis Induces a Transmissible Dysbiotic Skin Microbiota that Promotes Skin Inflammation. Cell Host Microbe 22: 13-24, Jul 2017.

12a Misic AM, Cain CL, Morris DO, Rankin SC, Beiting DP.: Divergent Isoprenoid Biosynthesis Pathways in Staphylococcus Species Constitute a Drug Target for Treating Infections in Companion Animals. mSphere 1: e00258-16, Sep 2016.

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