Publications

2022

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

Bazant W, Blevins AS, Crouch K*, Beiting DP*. BioRxiv. Preprint. PDF |

Impact of secondary TCR engagement on the heterogeneity of pathogen-specific CD8+ T cell response during acute and chronic toxoplasmosis

Shallberg LA, Phan AT, Christian DA, Perry JA, Haskins BE, Beiting DP, Harris TH, Koshi AA, Hunter CA PLOS Pathogens . In Press. PDF |

Targeting PARP11 to avert immunosuppression and improve CAR T therapy in solid tumors

Zhang H, Yu P, Tomar VS, Chen X, Atherton MJ, Lu Z, Zhang HG, Li H, Ortiz A, Gui J, Leu NA, Yan F, Blanco A, Meyer-Ficca ML, Meyer RG, Beiting DP, Li J, Nunez-Cruz S, O'Connor RS, Johnson lR, Minn AJ, George SS, Koumenis C, Diehl jA, Milone MC, Zheng H, Fuchs SY Nature Cancer. May 30 2022. PDF |

A genetic screen identifies a protective type III interferon response to Cryptosporidium that requires TLR3 dependent recognition

Gibson AR, Sateriale A, Dumaine JE, Englies JB, Pardy RD, Gullicksrud JA, O'Dea K, Doench JG, Beiting DP, Hunter CA, Striepen B. PLOS Pathogens. May 18 2022. PDF |

Chronic Hypoxemia Induces Mitochondrial Respiratory Complex Gene Expression in the Fetal Sheep Brain

Moon JK, Lawrence KM, Hunt ML, Davey MG, Flake AW, Licht DJ, Chen JM, Kilbaugh TJ, Gaynor JW, Beiting DP The Journal of Thoracic and Cardiovascular Surgery (JCTVS) Open . May 5 2022. PDF |

Re-establishment of spermatogenesis after more than 20 years of cryopreservation of rat spermatogonial stem cells reveals an important impact in differentiation capacity

Whelan EC, Yang F, Avarbock MR, Sullivan MC, Beiting DP, Brinster RL. PLOS Biology. May 10 2022. PDF |

Chapter 121. Parasitic diseases: protozoa

Beiting DP and John AO. Book Chapter: Yamada's Textbook of Gastroenterology, 3 Volume Set, 7th Edition. April 2022 Publisher's website |

2021

Crosstalk between enterocytes and innate lymphoid cells drives early IFN-γ-mediated control of Cryptosporidium

Gullicksrud J, Sateriale A, Englies J, Gibson A, Shaw S, Hutchins Z, Martin L, Christian D, Taylor GA, Yamamoto M, Beiting DP, Striepen B, Hunter CA. Mucosal Immunology. Nov 8 2021. PDF |

The Card19 locus of murine chromosome 13 regulates terminal cell lysis downstream of caspase activation and Gasdermin-D cleavage

Bjanes E, Garcia Sillas R, Matsuda R, Demarco B, Fettrelet T, DeLaney AA, Kronfeld OS, Lee BL, Rodriguez Lopez EM, Grubaugh D, Wynosky-Dolfi MA, Philip NH, Krespan E, Tovar D, Joannas L, Beiting DP, Henao-Mejia J, Schaefer BC, Chen KW, Broz P, Brodsky IE. PLOS Pathogens. October 14 2021. PDF |

An open-source toolkit to expand bioinformatics training in infectious diseases

Berry ASF*, Amorim CF*, Berry CL, Syrett CM, English ED, Beiting DP. mBio. July 6 2021. PDF

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity

Berry ASF, Pierdon MK, Misic AM, Sullivan MC, O’Brien K, Chen Y, Murray SJ, Ramharack LA, Baldassano RN, Parsons RN, Beiting DP. Microbiome. June 27 2021. PDF | Code | Video abstract

Regulation of the intercellular biomolecule transfer-driven tumor angiogenesis, growth, and responses to anti-cancer therapies

Lu Z, Ortiz A, Verginadis I, Peck AR, Zahedi F, Cho C, Yu P, DeRita RM, Sun Y, Yaspan A, Krespan E, Beiting DP, Radaelli E, Ryeom S, Diehl JA, Rui H, Koumenis C, Fuchs SY. Journal of Clinical Investigation. May 17 2021. PDF

Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature

Amorim CF, Novais FO, Nguyen BT, Nascimento MT, Lago J, Lago AS, Carvalho LP, Beiting DP*, Scott P*. PLOS Neglected Tropical Diseases. April 1 2021. PDF

2020

Mutations Affecting HVO_1357 or HVO_2248 Cause Hypermotility in Haloferax volcanii, Suggesting Roles in Motility Regulation

Collins M, Afolayan S, Igiraneza AB, Schiller H, Krespan E, Beiting DP, Dyall-Smith M, Pfeiffer F, Pohlschroder M. Genes. Dec 31 2020. PDF

Natural infection with Giardia is associated with altered community structure of the human and canine gut microbiome

Berry ASF, Johnson K, Martins R, Sullivan MC, Amorim CF, Putre A, Scott A, Wang S, Lindsay B, Baldassano R, Nolan TJ, Beiting DP. mSphere. Aug 05 2020. PDF | Code

Activation of p38α stress-activated protein kinase drives the formation of the pre-metastatic niche in the lungs

Gui J, Zahedi F, Ortiz A, Cho C, Katlinski KV, Alicea-Torres K, Li J, Todd L, Zhang H, Beiting DP, Sander C, Kirkwood JM, Snow BE, Wakeham AC, Mak TW, Diehl JA, Koumenis C, Ryeom SW, Stanger BZ, Puré E, Gabrilovich DI, Fuchs SY. Nature Cancer. May 25 2020. PDF.

Xenosiderophore utilization promotes Bacteroides thetaiotaomicron resilience during colitis

Zhu W, Winter MG, Spiga L, Hughes ER, Chanin R, Mulgaonkar A, Pennington J, Maas M, Behrendt CL, Kim J, Sun X, Beiting DP, Hooper LV, Winter S. Cell Host Microbe. Feb 18 2020. PDF.

The Toxoplasma gondii virulence factor ROP16 acts in cis and trans, and suppresses T cell responses

Chen L*, Christian DA*, Kochanowsky JA, Phan AT, Clark J, Wang S, Berry C, Oh J, Chen X, Roos DS, Beiting DP, Koshy AA, Hunter CA. Journal of Experimental Medicine. Jan 20 2020. PDF.

2019

OHMI: The Ontology of Host-Microbiome Interactions

He Y, Wang H, Zheng J, Beiting DP, Masci AM, Yu H, Curtis JL, Smith B, Alekseyenko AV, Obeid JS. Journal of Biomedical Semantics. Dec 30 2019. PDF.

Variable gene expression and parasite load predict treatment outcome in cutaneous leishmaniasis

Amorim CF, Novais FO, Nguyen B, Misic AM, Carvalho LP, Carvalho EM, Beiting DP*, Scott P*. Science Translational Medicine. Nov 20; 2019. PDF | Code | Cover

Lifecycle progression and sexual development of the apicomplexan parasite Cryptosporidium parvum

Tandel J, English ED, Sateriale A, Gullicksrud JA, Beiting DP, Sullivan MC, Pinkston B, Striepen B. Nature Microbiology. Sept 02; 2019. PDF | Code

Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids

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. Microbiome. Aug 31; 2019. PDF | Code

Gut microbiota features associated with Clostridioides difficile colonization in puppies

Berry ASF, Kelly BJ, Barnhart D, Kelly DJ, Beiting DP, Baldassano RN, Redding LE. PLOS One. Aug 30; 2019. PDF.

Fibroblast activation protein restrains adipogenic differentiation and regulats matrix-mediated mTOR signaling

Blomberg R, Beiting DP, Wabitsch M, Puré E. Matrix Biology. July 17; 2019. PDF.

Infection-Induced Intestinal Dysbiosis Is Mediated by Macrophage Activation and Nitrate Production

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*. MBio. May 28; 2019. PDF.

IL-27 and TCR Stimulation Promote T Cell Expression of Multiple Inhibitory Receptors

DeLong JH, O’Hara Hall A, Rausch M, Moodley D, Perry J, Park J, Phan AT, Beiting DP, Kedl RM, Hill JA, Hunter CA. ImmunoHorizons. Jan 01; 2019. PDF.

2018

Alarmin S100A11 initiates a chemokine response to the human pathogen Toxoplasma gondii

Safronova A, Araujo A, Camanzo ET, Moon TJ, Elliott MR, Beiting DP, Yarovinsky F. Nature Immunology. Nov 19; 2018. PDF.

Glycolysis is important for optimal asexual growth and formation of mature tissue cysts by Toxoplasma gondii

Shukla A, Olszewski KL, Llinás M, Rommereim LM, Fox BA, Bzik DJ, Xia D, Wastling J, Beiting D, Roos DS, Shanmugam D. International journal for parasitology. Aug 31; 2018. PDF.

Sex-specific gene expression differences are evident in human embryonic stem cells and during in vitro differentiation of human placental progenitor cells

Syrett C, Sierra I, Berry C, Beiting DP, Anguera M. Stem Cells and Development. July 11; 2018. PDF.

The maternal vaginal microbiome partially mediates the effects of prenatal stress on offspring gut and hypothalamus.

Jasarevic E, Howard CD, Morrison KE, Misic AM, Weinkopff T, Scott P, Hunter CA, Beiting DP, Bale TL. Nature Neuroscience. July 9; 2018. PDF.

Culture-independent profiling of the stool microbiome to identify microbial species associated with a diarrheal outbreak in an immunocompromised mouse colony.

Misic AM, Miedel EL, Brice AK, Cole S, Zhang GF, Dyer CD, Secreto A, Smith AL, Danet-Desnoyers G, Beiting DP. Comparative Medicine. June 13; 2018. PDF.

Commensal microbes induce serum IgA responses that protect against polymicrobial sepsis.

Wilmore JR, Gaudette BT, Gomez Atria D, Hashemi T, Jones DD, Gardner CA, Cole SD, Misic A, Beiting DP, Allman D. Cell Host Microbe. Feb 22; 2018. PDF.

CD8+ T cells lack local signals to produce IFN-γ in the skin during leishmania infection.

Novais FO, Wong AC, Villareal DO, Beiting DP, Scott P. Journal of Immunology. Jan 24; 2018. PDF.

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

Oliveira F, Brestelli J, Cade S, Zheng J, Iodice J, Fisher S, Aurrecoechea C, Kissinger JC, Brunk BP, Stoeckert Jr., CJ, Fernandes GR, Roos DS*, Beiting DP*. Nucleic Acids Research. Jan 4; 2018. PDF.

2017

Involvement of Innate Immune System in Late Stages of Inherited Photoreceptor Degeneration.

Sudharsan R, Beiting DP, Aguirre GD, Beltran, WA. Scientific Reports. Dec 20; 2017. PDF.

Replication Defective Viral Genomes Exploit A Cellular Pro-Survival Mechanism To Establish Viral Persistence.

Xu J, Sun Y, Li Y, Ruthel G, Weiss SR, Raj A, Beiting DP, Lopez C. Nature Communications. Oct 6; 2017. PDF.

An oxidative central metabolism enables Salmonella to utilize microbiota-derived succinate.

Spiga L, Winter MG, Furtado de Carvalho T, Zhu W, Hughes ER, Gillis CC, Chanin R, Behrendt CL, Kim J, Chessa D, Andrews-Polymenis H, Beiting DP, Santos RL, Hooper LV, Winter SE. Cell Host and Microbe. Sept 13; 2017. PDF.

Cutaneous leishmaniasis induces a transmissible dysbiotic skin microbiome that promotes increased skin inflammation.

Gimblet C, Meisel JS, Loesche MA, Cole SD, Horwinski J, Novais FO, Misic AM, Bradley CW, Beiting DP, Rankin SC, Carvalho LP, Scott P, Grice EA Cell Host and Microbe. July 12; 2017. PDF.

Stress during pregnancy alters temporal and spatial dynamics of the maternal and offspring microbiome in a sex-specific manner

Jasarevic E, Howard CD, Misic AM, Beiting DP, and Bale TL. Scientific Reports. Mar 7; 2017. PDF.

T Regulatory Cells Support Plasma Cell Populations in the Bone Marrow.

Glatman Zaretsky A, Konradt C, Dépis F, Wing JB, Goenka R, Gomez Atria D, Silver JS, Cho S, Wolf AI, Quinn WJ, Engiles JB, Brown DC, Beiting DP, Erikson J, Allman D, Cancro MP, Sakaguchi S, Lu L, Benoist CO, Hunter CA. Cell Reports. Feb 21; 2017. PDF.

CD8 T cell cytotoxicity mediates pathology in the skin by inflammasome activation and IL-1β production.

Novais FO, Carvalho AM, Carvalho LP, Beiting DP, Brodsky IE, Carvalho EM, Scott P. PLOS Pathogens. Feb 13; 2017. PDF.

Inactivation of interferon receptor promotes the establishment of immune privileged tumor microenvironment.

Katlinski KV, Gui J, Katlinskaya KV, Ortiz A, Chakraborty R, Bhattacharya S, Carbone CC, Beiting DP, Girondo MA, Peck AR, Puré E, Chatterji P, Rustgi AK, Diehl JA, Koumenis C, Rui H and Fuchs SY. Cancer Cell. Feb 13; 2017. PDF.

2016

STAT1 signaling in astrocytes is essential for control of Toxoplasma gondii in the central nervous system.

Hidano S, Randall LM, Dawson L, Dietrich HK, Konradt C, Klover PJ, John B, Harris TH, Fang Q, Turek B, Kobayashi T, Hennighausen L, Beiting DP, Koshy A, Hunter CA. MBio. Nov 8; 2016. PDF.

Activity of uncleaved caspase-8 controls anti-bacterial immune defense and TLR-induced cytokine production independent of cell death.

Philip NH, DeLaney A, Santos-Marerro M, Grier J, Sun Y, Wynosky-Dolfi M, Peterson L, Zwack EE, Hu B, Olson TM, Rongvaux A, Pope SD, Lopez CB, Oberst A, Beiting DP, Henao-Mejia J, Brodsky IE. PLOS Pathogens. Oct 13; 2016. PDF.

Divergent isoprenoid biosynthesis pathways in Staphylococcus species constitute a drug target for treating infections in companion animals.

Misic A, Cain C, Morris DO, Rankin S, Beiting DP. mSphere. Sept 28; 2016. PDF | Cover

Meta-transcriptome profiling of the human-Leishmania braziliensis cutaneous lesion.

Christensen S, Dillon LAL, Carvalho LP, Passos S, Novais F, Hughitt K, Beiting DP, Carvalho EM, Scott P, El-Sayed NM and Mosser DM. PLOS Neglected Tropical Diseases. Sept 15; 2016. PDF.

Cutting Edge: IL-4, IL-21, and IFN-g Interact to Govern TBET and CD11c Expression in TLR-Activated B Cells.

Naradikian MS, Myles A, Beiting DP, Roberts KJ, Dawson L, Herati RS, Bengsch B, Linderman SL, Stelekati E, Spolski R, Wherry EJ, Hunter C, Hensley SE, Leonard WJ, Cancro MP. Cutting Edge: Journal of Immunology. July 18; 2016. PDF.

Suppression of type I interferon signaling overcomes the oncogene-induced senescence and mediates melanoma development and progression.

Katlinskaya YV, Katlinski KV, Yu Q, Ortiz A, Beiting DP, Brice A, Davar D, Sanders C, Kirkwood JM, Rui H, Xu X, Koumenis C, Diehl JA, Fuchs SY. Cell Reports. April 5; 2016. PDF.

T Cell Receptor-Induced NF-kB signaling and transcriptional activation are regulated by STIM1- and Orai1-mediated calcium entry.

Liu X, Berry CT, Ruthel G, Madara JJ, MacGillivray K, Gray CM, Madge LA, McCorkell KA, Beiting DP, Hershberg U, May MJ and Freedman BD. J Biol Chem. Jan 29; 2016. <a href="http://hostmicrobe.github.io/pubs/Freedman_JBC_2016.pdf target="_blank">PDF</a>.

Type I Interferons Control Proliferation and Function of Intestinal Epithelium.

Katlinskaya YV, Katlinski KV, Lasri A, Li N, Beiting DP, Durham AC, Yang T, Pikarsky E, lengner CJ, Johnson BF, Ben-Neriah Y, Fuchs SY. Mol Cell Biol. Jan 25; 2016. PDF.

2015

IL-4 dependent, eosinophil-mediated support of nematode growth occurs in the context of an innate response to tissue injury.

Huang L, Beiting DP, Gebreselassie NG, Gagliardo LF, Ruyechan MC, lee NA, lee JJ, Appleton JA. PLOS Pathogens. Dec 31; 2015. PDF | Cover

Genome sequencing reveals clonal dynamics of methicillin-resistant Staphylococcus aureus in the same household in the context of clinical disease in a person and a dog

Davis MF, Misic AM, Morris DO, Moss JT, Tolomeo P, Beiting DP, Nachamkin I, Lautenbach E, Rankin SC. Veterinary Microbiology. Nov 18; 2015. PDF.

Complete genome sequence and methylome of Staphylococcus schleiferi, an important cause of skin and ear infections in veterinary medicine.

Misic A, Cain C, Morris DO, Rankin S, Beiting DP. Genome Announcements. Sept 10; 2015. PDF.

Skin Resident Memory CD4+ T Cells Enhance Protection Against leishmania major Infection.

Glennie ND, Yeramilli VA, Beiting DP, Volk SW, Weaver CT, Scott P. Journal of Experimental Medicine. July 27; 2015. PDF | Synopsis

The Orphan Nuclear Receptor TLX is an Enhancer of STAT1-mediated Transcription and Immunity to Toxoplasma gondii.

Beiting DP, Hidano S, Baggs JE, Geskes JM, Wherry EJ, Fang Q, Hunter CA, Roos DS, Cherry S. PLOS Biology. Jul 21; 2015. PDF | Synopsis

2014

Matrix metalloproteinase 9 production by monocytes is enhanced by TNF-α and participates in the pathology of human cutaneous leishmaniasis.

Campos TM, Passos ST, Novais FO, Beiting DP, Costa RS, Queiroz A, Mosser D, Scott P, Carvalho EM, and Carvalho LP. PLOS Neglected Tropical Diseases. Nov 13; 2014. PDF.

Intermediate monocytes contribute to pathologic immune response during leishmania braziliensis infection.

Passos S, Carvalho LP, Costa RS, Campos TM, Novais FO, Magalhaes A, Machado PRL, Beiting DP, Mosser D, Carvalho EM, Scott P. Journal of Infectious Diseases. Jan 15; 2014. PDF.

Protozoan Parasites and Type I Interferon: A Cold Case Reopened.

Beiting DP. Trends in Parasitology. Oct 30; 2014. PDF.

Genomic Profiling of human leishmania braziliensis lesions identifies transcriptional modules associated with cutaneous immunopathology.

Novais FO, Carvalho LP, Passos S, Roos DS, Carvalho EM, Scott P, Beiting DP. Journal of Investigative Dermatology. May 6; 2014. PDF.

Bystander chronic infection negatively impacts development of CD8+ T cell memory.

Stelekati E, Shin H, Doering TA, Dolfi DV, Ziegler CG, Beiting DP, Dawson L, Liboon J, Wolski D, Ali MA, Katsikis PD, Shen H, Roos DS, Haining WN, Lauer GM, and Wherry EJ. Immunity. May 15; 2014. PDF.

Differential Induction of TLR3-dependent Innate Immune Signaling by Closely Related Parasite Species.

Beiting DP, Peixoto L, Akopyants NS, Beverley SM, Wherry EJ, Christian DA, Hunter CA, Brodsky IE, Roos DS. PLOS One. Feb 5; 2014. PDF.

Human Classical Monocytes Control the Intracellular Stage of leishmania braziliensis by Reactive Oxygen Species.

Novais FO, Nguyen BT, Beiting DP, Carvalho LP, Glennie ND, Passos S, Carvalho EM, Scott P. Journal of Infectious Diseases. Apr 15; 2014. PDF.

2013

Cytotoxic T cells Mediate Pathology and Metastasis in Cutaneous leishmaniasis.

Novais FO, Carvalho LP, Graff JW, Beiting DP, Ruthel G, Roos DS, Betts MR, Goldschmidt MH, Wilson ME, de Oliveira, Scott P. PLOS Pathogens. July 9; 2013. PDF.

2012 and earlier

The cytokines interleukin 27 and interferon-γ promote distinct Treg cell populations required to limit infection-induced pathology.

Hall, AO, Beiting DP, C Tato, B John, G Oldenhove, CG Lombana, GH Pritchard, JS Silver, N Bouladoux, JS Stumhofer, TH Harris, J Grainger, EDT Wojno, S Wagage, DS Roos, P Scott, L A Turka, S Cherry, SL Reiner, D Cua, Y Belkaid, MM Elloso, and CA Hunter. Immunity. Sep 13; 2012. PDF.

Natural resistance-associated macrophage protein is a cellular receptor for sindbis virus in both insect and mammalian hosts.

Rose PP, SL Hanna, A Spiridigliozzi, N Wannissorn, Beiting DP, SR Ross, RW Hardy, SA Bambina, MT Heise, and S Cherry. Cell Host and Microbe. Aug 18; 2011. PDF.

A systems biological view of intracellular pathogens.

Beiting DP, and DS Roos Immunological Reviews. Feb 23; 2011. PDF.

Integrative genomic approaches highlight a family of parasite-specific kinases that regulate host responses.

Peixoto L, F Chen, OS Harb, PH Davis, Beiting DP, CS Brownback, D Ouloguem, and DS Roos. Cell Host and Microbe. Aug 19; 2010. PDF.

Combinatorial effects of interleukin 10 and interleukin 4 determine the progression of hepatic inflammation following murine enteric parasitic infection.

Douglas DB, Beiting DP., JP Loftus, JA Appleton, and SK Bliss Hepatology. May 23; 2010. PDF.

Apicomplexan parasites co-opt host calpains to facilitate their escape from infected cells.

Chandramohanadas R, PH Davis, Beiting DP, MB Harbut, C Darling, G Velmourougane, MY lee, PA Greer, DS Roos, and DC Greenbaum. Science. May 8; 2009. PDF.

Eosinophil deficiency compromises parasite survival in chronic nematode infection.

Fabre V, Beiting DP, SK Bliss, NG Gebreselassie, LF Gagliardo, NA lee, JJ lee, and JA Appleton. The Journal of Immunology. Feb 1; 2009. PDF.

Immunity to Trichinella spiralis muscle infection.

Fabre MV*, Beiting DP*, SK Bliss, and JA Appleton. Veterinary Parasitology. Feb 23; 2009. PDF.

IL-10 regulates movement of intestinally derived CD4+ T cells to the liver.

Bliss SK, SP Bliss, Beiting DP, A Alcaraz, and JA Appleton. The Journal of Immunology. Jun 15; 2007. PDF.

Coordinated control of immunity to muscle stage Trichinella spiralis by IL-10, regulatory T cells, and TGF-beta.

Beiting DP, LF Gagliardo, M Hesse, SK Bliss, D Meskill, and JA Appleton. The Journal of Immunology. Jan 15; 2007. PDF.

Synthesis of syndecan-1 by skeletal muscle cells is an early response to infection with Trichinella spiralis but is not essential for nurse cell development.

Beiting DP, PW Park, and JA Appleton. Infection and Immunity. Feb 22; 2006. PDF.

Interleukin-10 limits local and body cavity inflammation during infection with muscle-stage Trichinella spiralis.

Beiting DP, SK Bliss, DH Schlafer, VL Roberts, and JA Appleton. Infection and Immunity. May 20; 2004. PDF.

A putative serine protease among the excretory-secretory glycoproteins of L1 Trichinella spiralis.

Romaris F, S North, LF Gagliardo, B Butcher, K Ghosh, Beiting DP, M Panico, P Arasu, A Dell, HR Morris, JA Appleton. Mol Biochem Parasitol. April 25; 2002. PDF.