Publications

Sex-Dependent Efficacy of Dietary Fiber in Pediatric Functional Abdominal Pain.
So SY, Badu S, Wu Q, Yalcinkaya N, Mirabile Y, Castaneda R, Musaad S, Heitkemper M, Savidge TC, Shulman RJ.Gastroenterology. 2024 Apr;166(4):645-657.e14. doi: 10.1053/j.gastro.2023.12.011. Epub 2023 Dec 19.PMID: 38123024

The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease.
Wu Q, Badu S, So SY, Treangen TJ, Savidge TC.J Clin Invest. 2024 Jan 16;134(2):e170859. doi: 10.1172/JCI170859.PMID: 37962956

Donor-recipient specificity and age-dependency in fecal microbiota therapy and probiotic resolution of gastrointestinal symptoms.
Wu Q, Boonma P, Badu S, Yalcinkaya N, So SY, Garey KW, Williams K, Arnold LE, Shulman RJ, Kellermayer R, Savidge TC.NPJ Biofilms Microbiomes. 2023 Aug 3;9(1):54. doi: 10.1038/s41522-023-00421-4.PMID: 37537181

Addressing barriers in FAIR data practices for biomedical data.
Hughes LD, Tsueng G, DiGiovanna J, Horvath TD, Rasmussen LV, Savidge TC, Stoeger T, Turkarslan S, Wu Q, Wu C, Su AI, Pache L; NIAID Systems Biology Data Dissemination Working Group.Sci Data. 2023 Feb 23;10(1):98. doi: 10.1038/s41597-023-01969-8.PMID: 36823198

Neonatal antibiotics have long term sex-dependent effects on the enteric nervous system.
Poon SSB, Hung LY, Wu Q, Parathan P, Yalcinkaya N, Haag A, Luna RA, Bornstein JC, Savidge TC, Foong JPP.J Physiol. 2022 Oct;600(19):4303-4323. doi: 10.1113/JP282939. Epub 2022 Sep 9.PMID: 36082768

Key difference between transition state stabilization and ground state destabilization: increasing atomic charge densities before or during enzyme-substrate binding.
Chen D, Li Y, Li X, Hong X, Fan X, Savidge T. Chem Sci. 2022 Jun 21;13(27):8193-8202. doi: 10.1039/d2sc01994a. eCollection 2022 Jul 13.PMID: 35919436

Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data.
Curry KD, Wang Q, Nute MG, Tyshaieva A, Reeves E, Soriano S, Wu Q, Graeber E, Finzer P, Mendling W, Savidge T, Villapol S, Dilthey A, Treangen TJ.Nat Methods. 2022 Jul;19(7):845-853. doi: 10.1038/s41592-022-01520-4. Epub 2022 Jun 30.PMID: 35773532

Bile acid-independent protection against Clostridioides difficile infection.
Aguirre AM, Yalcinkaya N, Wu Q, Swennes A, Tessier ME, Roberts P, Miyajima F, Savidge T, Sorg JA.PLoS Pathog. 2021 Oct 19;17(10):e1010015. doi: 10.1371/journal.ppat.1010015. eCollection 2021 Oct.PMID: 34665847

New Host-Directed Therapeutics for the Treatment of Clostridioides difficile Infection.
Andersson JA, Peniche AG, Galindo CL, Boonma P, Sha J, Luna RA, Savidge TC, Chopra AK, Dann SM.mBio. 2020 Mar 10;11(2):e00053-20. doi: 10.1128/mBio.00053-20.PMID: 32156806

Next-Generation Probiotics Targeting Clostridium difficile through Precursor-Directed Antimicrobial Biosynthesis.
Spinler JK, Auchtung J, Brown A, Boonma P, Oezguen N, Ross CL, Luna RA, Runge J, Versalovic J, Peniche A, Dann SM, Britton RA, Haag A, Savidge TC.Infect Immun. 2017 Sep 20;85(10):e00303-17. doi: 10.1128/IAI.00303-17. Print 2017 Oct.PMID: 28760934

Regulation of protein-ligand binding affinity by hydrogen bond pairing.
Chen D, Oezguen N, Urvil P, Ferguson C, Dann SM, Savidge TC.Sci Adv. 2016 Mar 25;2(3):e1501240. doi: 10.1126/sciadv.1501240. eCollection 2016 Mar.PMID: 27051863

BIOPHYSICS. Extreme electric fields power catalysis in the active site of ketosteroid isomerase.
Chen D, Savidge T.Science. 2015 Aug 28;349(6251):936. doi: 10.1126/science.aab0095. Epub 2015 Aug 27.PMID: 26315427

Host S-nitrosylation inhibits clostridial small molecule-activated glucosylating toxins.
Savidge TC, Urvil P, Oezguen N, Ali K, Choudhury A, Acharya V, Pinchuk I, Torres AG, English RD, Wiktorowicz JE, Loeffelholz M, Kumar R, Shi L, Nie W, Braun W, Herman B, Hausladen A, Feng H, Stamler JS, Pothoulakis C.Nat Med. 2011 Aug 21;17(9):1136-41. doi: 10.1038/nm.2405.PMID: 21857653