Publications
Pre-print Articles
Gut Competition Dynamics of Live Bacterial Therapeutics Are Shaped by Microbiome Complexity, Diet, and Therapeutic Transgenes
Author(s): Siguenza N, Bailey S, Sadegi M, Gootin H, Tiu M, Price JD, Ramer-Tait A, Zarrinpar A.
Source: bioRxiv [Preprint]. (2025) Jan 21:2025.01.21.634159. doi: 10.1101/2025.01.21.634159
Gut-derived PPAR-γ signaling and risk of bacterial enteric infection: insight from thiazolidinedione users in a US population-based study
Author(s): Birabaharan M, Kaelber DC, Nizet V, Zarrinpar A.
Source: medRxiv [Preprint] (2024) Dec 15:2024.09.24.24313682. doi: 10.1101/2024.09.24.24313682.
Peer-Reviewed Articles
2025
Time-Restricted Feeding Is Not Effective in Modulating
Fibrosis in a Male MASH Model
Author(s): Stephany Flores Ramos, Kelly A. Fogelson, Valentina B. Muti, Wuling Zhong, Jingjing Hu, Mojgan Hosseini, Rohit Loomba, Amir Zarrinpar
Source: Journal of Biological Rhythms
Blood microbial DNA signature differentiates hepatocellular carcinoma from metastatic lesions
Author(s): Guccione C, Dantas Machado AC, Youssef F, Angeli-Pahim I, Duarte S, Warren C, Farmer S, Humphrey G, Richter RA, McDonald D, Weng Y, Burgoyne A, Loomba R, Curtius K, Zarrinpar A, Knight R, Zarrinpar A.
Source: eGastroenterology. 2025;3(3):e100193.
Metatranscriptomics uncovers diurnal functional shifts in bacterial transgenes with profound metabolic effects
Author(s): Flores Ramos S, Siguenza N, Zhong W, Mohanty I, Lingaraju A, Richter RA, Karthikeyan S, Lukowski AL, Zhu Q, Nunes WDG, Zemlin J, Xu ZZ, Hasty J, Dorrestein PC, Panda S, Knight R, Zarrinpar A.
Source: Cell Host Microbe (in press)
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Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences
Author(s): Roos M, Bunga S, Tan A, Maissy E, Skola D, Richter A, Whittaker DS, Desplats P, Zarrinpar A, Conrad R, Kuersten S.
Source: mSystems. 2025 Jun 16:e0016725
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Expression of Fluorescence Reporters and Natural Products in Native Gut Escherichia coli
Author(s): Liu D, Ton PM, Zong D, Zarrinpar A, Ding Y.
Source: ACS Synth Biol. 2025 May 16;14(5):1557-1566
Discovery of metabolites prevails amid in-source fragmentation
Author(s): El Abiead Y, Rutz A, Zuffa S, Amer B, Xing S, Brungs C, Schmid R, Correia MSP, Caraballo-Rodriguez AM, Zarrinpar A, Mannochio-Russo H, Witting M, Mohanty I, Pluskal T, Bittremieux W, Knight R, Patterson AD, van der Hooft JJJ, Böcker S, Dunn WB, Linington RG, Wishart DS, Wolfender JL, Fiehn O, Zamboni N, Dorrestein PC.
Source: Nat Metab. (2025) Mar;7(3):435-437
2024
Engineered bacterial therapeutics for detecting and treating CRC
Author(s): Siguenza N, Brevi A., Zhang J, Pabani A, Bhushan A, Das M, Ding Y, Hasty J, Ghosh P, Zarrinpar A.
Source: Trends Cancer (2024). Jul;10(7):588-597.
Time of sample collection is critical for the replicability of microbiome analyses
Author(s):Allaband C, Lingaraju A, Flores Ramos S, Kumar T, Javaheri H, Tiu MD, Dantas Machado AC, Richter RA, Elijah E, Haddad GG, Leone VA, Dorrestein PC, Knight R, Zarrinpar A.
Source: Nat Metabolism (2024). Jul;6(7):1282-1293.
Harnessing the Power Within: Engineering the Microbiome for Enhanced Gynecologic Health
Author(s): Brennan C, Chan K, Kumar T, Maissy E, Brubaker L, Dothard MI, Gilbert JA, Gilbert KE, Lewis AL, Thackray V, Zarrinpar A, Knight R.
Source: Reprod Fertil. 2024 Mar 1:RAF-23-0060.
Control of Eating Attributes and Weight Loss Outcomes over One Year After Sleeve Gastrectomy
Author(s):Lytvyak E, Zarrinpar A, Dalle Ore C, Lee E, Yazdani-Boset K, Horgan S, Grunvald.
Source: Obes Surg. 2024 Mar 19.
2023
Portosystemic Shunt Placement Reveals Blood Signatures for the Development of Hepatic Encephalopathy Through Mass Spectrometry
Author(s): Dantas Machado, A.C., Flores Ramos S., Gauglitz J.M., Fassler, A.M., Petras D, Aksenov A.A., Kim U.B., Lazarowicz M., Barnard Giustini A., Aryafar H., Vodkin I., Warren C., Dorrestein P.C., Zarrinpar A., Zarrinpar A.
Source: Nature Communications. 2023 14:5303.
Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution
Author(s): Brennan C, Salido RA, Belda-Ferre P, Bryant M, Cowart C, Tiu MD, González A, McDonald D, Tribelhorn C, Zarrinpar A, Knight R.
Source: mSystems. 2023 Jun 23;e0000623
Live Biotherapeutic Products as Cancer Treatments
Author(s): Brevi A, Zarrinpar A.
Source: Cancer Research. 2023 Jun 15;83(12):1929-1932
Obesity, Chronic Stress, and Stress Reduction
Author(s): Goens D, Virzi NE, Jung SE, Rutledge TR, Zarrinpar A.
Source: Gastroenterology Clinics of North America. 2023 Jun;52(2):347-362.
Complete Genome Sequence of an Escherichia coli Strain Isolated from Laboratory Mouse Stool for Use as a Chassis for Transgene Delivery to the Murine Microbiome
Author(s): Siguenza N, Russell BJ, Richter RA, Zarrinpar A.
Source: Microbiology Resource Announcements. 2023 Apr 18;12(4):e0101422
The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases
Author(s): Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R.
Source: Gastroenterology. 2023 Jun;164(7):1069-1085
What is the key challenge in engineering microbiomes?
Author(s): Venturelli OS, Wang HH, Estrela S, Huang KC, Ledesma-Amaro R, Fedorec AJH, Stecher B, Lawson CE, Zarrinpar A, Guo CJ, Soyer OS.
Source: Cell Systems. 2023 Feb 15;14(2):85-90
2022
A high-protein diet prevents weight regain.
Author(s): Zarrinpar A.
Source: Nature Metabolism 2022 Dec;4(12):1616-1617
A self-powered ingestible wireless biosensing system for real-time in situ monitoring of gastrointestinal tract metabolites
Author(s): De la Paz E, Maganti NH, Trifonov A, Jeerapan I, Kuldeep M, Yin L, Sonsa-ard T, Ma N, Jung W, Burns R, Zarrinpar A, Wang J, Mercier PP
Source: Nature Comminucations 2022 Dec 1;13(1):7405
Intestinal Transgene Delivery with Native E. coli Chassis Allows Persistent Physiological Changes
Author(s): Russell BJ, Brown SD, Saran AR, Mai I, Lingaraju A, Siguenza N, Maissy E, Dantas Machado AC, Pinto AFM, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Saghatelian A, Knight R, Zarrinpar A.
Source: Cell 185, 1–15
Complex physiology and clinical implications of time-restricted eating
Author(s): Petersen MC, Gallop MR, Flores Ramos S, Zarrinpar A, Broussard JL, Chondronikola M, Chaix A, Klein S.
Source: Physiol Rev 102: 1991–2034
Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome.
Author(s): Dantas Machado AC, Brown SD, Lingaraju A, Sivaganesh V, Martino C, Chaix A, Zhao P, Pinto AFM, Chang MW, Richter RA, Saghatelian A, Saltiel AR, Knight R, Panda S, Zarrinpar A.
Source: Cell Reports 40, 111008
2021
Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome.
Author(s): Xue J. , Allaband C. , Zhou D. , Poulsen O. , Martino C. , Jiang L. , Tripathi A. , Elijah E. , Dorrestein P. C. , Knight R. , Zarrinpar A. , and Haddad G. G.
Source: Frontiers in Physiology
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Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome.
Author(s):
Source: mSystems Vol. 6
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Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome.
Author(s): Huang S., Jiang S., Huo D., Allaband C., Estaki M., Cantu V., Belda-Ferre P., Vázquez-Baeza Y., Zhu Q., Ma C., Li C., Zarrinpar A., Liu Y., Knight R. and Zhang J.
Source: Microbiome Vol. 9
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2020
Human Skin, Oral, and Gut Microbes Predict Chronological Age.
Author(s): Huang, S., Haiminen, N., Carrieri, A., Hu, R., Jiang, L., Parida, L., Russell, B., Allaband, C., Zarrinpar, A., Vázquez-Baeza, Y., Belda-Ferre, P., Zhou, H., Kim, H., Swafford, A. D., Knight, R., Xu, Z. Z.
Source: mSystems Vol. 5
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Circadian Rhythms in the Pathogenesis and Treatment of Fatty Liver Disease.
Author(s): Saran A. R., Dave S., Zarrinpar A.
Source: Gastroenterology
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2019
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.
Author(s): Allaband, C., McDonald, D., Vázquez-Baeza, Y., Minich, J. J., Tripathi, A., Brenner, D. A., Loomba, R., Smarr, L., Sandborn, W. J., Schnabl, B., Dorrestein, P., Zarrinpar, A., Knight, R.
Source: Clinical Gastroenterology and Hepatology 2019;17:218-230
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Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales.
Author(s): Williams, C. L., Caraballo-Rodríguez, A. M., Allaband, C., Zarrinpar, A., Knight, A., Gauglitz, J.
Source: Drug Discovery Today: Disease Models Vol. 28 2019
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Effect of Obesogenic Medications on Weight-Loss Outcomes in a Behavioral Weight-Management Program.
Author(s): Desalermos, A., Russell, B., Leggett, C., Parnell, A., Ober, K., Hagerich, K., Gerlan, C., Euyhyun-Lee, J. A., Proudfood, E. G., Gupta, S., Ho, S., Zarrinpar, A.
Source: Obesity Vol 27.5
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Aspiration therapy for the treatment of obesity: 4-year results of a multicenter randomized controlled trail.
Author(s): Thompson, C. C., Abu Dayyeh, B. K., Kushnir, V., Kushner, R. F., Jirapinyo, P., Schorr, A. B., Aronne, L. J., Amaro, A., Jaffe, D. L., Schulman, A. R., Early, D., Stein, A. C., Sharaiha, R., Edmundowicz, S. A., Bohning, J. M., Jensen, M. D., Shukla, A. P., Apovian, C., Kim, D. W., Tran, D., Zarrinpar, A., Ryan, M. B., Young, M., Lowe, A., Hass, M., Goldsmith, H., McCrea, J., Sullivan, S.
Source: Surgery for Obesity and Related Diseases 15 (2019)
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2018
The effect of provider-prescribed obesogenic drugs on post-laparoscopic sleeve gastrectomy outcomes: a retrospective cohort study.
Author(s): Leggett, C. B.,* Desalermos, A.*, Brown, S. D., Lee, E., Proudfoot, J. A., Horgan, A., Gupta, S., Grunvald, E., Ho, S. B., Zarrinpar, A.
*These authors contributed equally
Source: International Journal of Obesity 10.1038
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Antibiotic-induced Microbiome Depletion Alters Metabolic Homeostasis by Affecting Gut Signaling and Colonic Metabolism.
Author(s): Zarrinpar, A., Chaix, A., Chang, M. W., Marotz, C. A., Saghatelian, A., Knight, R., Panda, S.
Source: Nature Communications 9(1): 2872
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Obesity and Response to Anti-tumor Necrosis Factor-a Agents in Patients with Select Immune-mediated Inflammatory Diseases: A Systemic Review and Meta-Analysis.
Author(s): Singh, S., Facciorusso, A., Singh, A. G., Casteele, N. V., Zarrinpar, A., Prokop, L. J., Grunvald, E. L., Curtis, J. R., Sandborn, W. J.
Source: PLoS One 13(5): e0195123
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High Body Mass Index is Associated with Increased Risk of Treatment Failure and Surgery in Biologic-treated patients with Ulcerative Colitis.
Author(s): Kurnool, S., Nguyen, N. H., Proudfoot, J., Dulai, P. S., Boland, B. S., Vande Casteele, N., Evans, E., Grunvald, E. L., Zarrinpar, A., Sandborn, W. J., Singh, S.
Source: Alimentary Pharmacology and Therapeutics: 47(11): 1472-1479
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2017
High body mass index is associated with increased risk of treatment failure and surgery in biologic-treated patients with ulcerative colitis.
Author(s): Kurnool, S., Nguyen, N.H., Proudfoot, J., Dulai, P.S., Boland, B.S., Vande Casteele, N., Evans, E., Grunvald, E.L., Zarrinpar, A., Sandborn, W.J., Singh, S.
Source: Alimentary Pharmacology and Therapeutics [Epub ahead of print].
Percutaneous Gastrostomy Device for the Treatment of Class II and Class III Obesity: Results of a Randomized Controlled Trial.
Author(s): Thompson, C.C., Abu Dayyeh, B.K., Kushner, R., Sullivan, S., Schorr, A.B., Amaro, A., Apovian, C.M., Fullum, T., Zarrinpar, A., Jensen, M,D., Stein, A.C., Edmundowicz, S., Kahaleh, M., Ryou, M., Bohning, J.M., Ginsberg, G., Huang, C., Tran, D.D., Glaser, J.P., Martin, J.A., Jaffe, D.L., Farraye, F.A., Ho, S.B., Kumar, N., Harakal, D., Young, M., Thomas, C.E., Shukla, A.P., Ryan, M.B., Haas, M., Goldsmith, H., McCrea, J., Aronne, L.J.
Source: American Journal of Gastroenterolgy 112(3):447-457
2016
Obesity in IBD: epidemiology, pathogenesis, disease course and treatment outcomes.
Author(s): Singh, S., Dulai, P.S., Zarrinpar, A., Ramamoorthy, S., Sandborn, W.J.
Source: Nature Reviews Gastroenterology & Hepatology 14:110-121
The circadian coordination of cell biology.
Author(s): Chaix, A., Zarrinpar, A., Panda, S.
Source: Journal of Cell Biology 215:15-25
Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation.
Author(s): Marotz, C.A., Zarrinpar, A.
Source: Yale Journal of Biology and Medicine 89: 383-8
Daily Eating Patterns and Their Impact on Health and Disease.
Author(s): Zarrinpar, A., Chaix, A., and Panda, S.
Source: Trends in endocrinology and metabolism: TEM 27:69-83
Targeting Dysbiosis for the Treatment of Liver Disease.
Author(s): Anand, G., Zarrinpar, A., and Loomba, R.
Source: Seminars in Liver Disease 36: 37-47
Serum microRNAs explain discordance of non-alcoholic fatty liver disease in monozygotic and dizygotic twins: a prospective study.
Author(s): Zarrinpar, A., Gupta, S., Maurya, M.R., Subramaniam, S., and Loomba, R.
Source: Gut 65: 1546-1554
Functional Local Input to Layer 5 Pyramidal Neurons in the Rat Visual Cortex.
Author(s): Zarrinpar, A., and Callaway, E.M.
Source: Cerebral Cortex 26: 991-1003
2015
Differences in Weight Loss Between Persons on Standard Balanced vs Nutrigenetic Diets in a Randomized Controlled Trial.
Author(s): Frankwich, K.A., Egnatios, J., Kenyon, M.L., Rutledge, T.R., Liao, P.S., Gupta, S., Herbst, K.L., and Zarrinpar, A.
Source: Clinical gastroenterology and hepatology: the official clinical practice journal of the American Gastroenterological Association 13: 1625-1632 e1621.
The effects of time-restricted feeding on lipid metabolism and adiposity.
Author(s): Chaix, A., and Zarrinpar, A.
Source: Adipocyte 4: 319-324
Video Capsule Endoscopy in Patients with Chronic Abdominal Pain with or without Associated Symptoms: A Retrospective Study.
Author(s): Egnatios, J., Kaushal, K., Kalmaz, D., and Zarrinpar, A.
Source: PLoS One 10:e1026509
2014
Diet and feeding pattern affect the diurnal dynamics of the gut microbiome.
Author(s): Zarrinpar, A., Chaix, A., Yooseph, S., and Panda, S.
Source: Cell metabolism 20: 1006-1017
Time-restricted feeding is a preventative and therapeutic intervention against diverse nutritional challenges.
Author(s): Chaix, A., Zarrinpar, A., Miu, P., and Panda, S.
Source: Cell metabolism 20: 991-1005
2013 and earlier
A rare cause of an ileocecal fistula in an AIDS patient. Gastrointestinal infection by Histoplasma capsulatum infection identified with internal transcribed spacer primer sets.
Author(s): Zarrinpar, A., Lin, G.Y., and Lonergan, J.T.
Source: Gastroenterology (2103) 144: 697, 857-698
Review article: the emerging interplay among the gastrointestinal tract, bile acids and incretins in the pathogenesis of diabetes and non-alcoholic fatty liver disease.
Author(s): Zarrinpar, A., and Loomba, R.
Source: Alimentary pharmacology & theraputics (2102) 36: 909-921
Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet.
Author(s): Hatori, M., Vollmers, C., Zarrinpar, A., DiTacchio, L., Bushong, E.A., Gill, S., Leblanc, M., Chaix, A., Joens, M., Fitzpatrick, J.A., et al.
Source: Cell metabolism (2012) 15: 848-860
Local connections to specific types of layer 6 neurons in the rat visual cortex.
Author(s): Zarrinpar, A., and Callaway, E.M.
Source: Journal of neurophysiology (2006) 95: 1751-1761
Effects of depression on sensory/motor vs. central processing in visual mental imagery.
Author(s): Zarrinpar, A., Deldin, P., and Kosslyn, S.M.
Source: TrCognition & Emotion (2006) 20: 737-758
Do separate processes identify objects as exemplars versus members of basic-level categories? Evidence from hemispheric specialization.
Author(s): Laeng, B., Zarrinpar, A., and Kosslyn, S.M.
Source: Brain and Cognition (2003) 53: 15-27
Book Chapters
Gut microbiota and their influence on response to food.
Author(s): Marotz, C.A., Brown, S.D, Zarrinpar, A.
Source: Principles of Nutrigenetics and Nutrigenomics. De Caterina, R., Martinez, J.A., Kohlmeier, M. (Eds.)
Editorials
A high-protein diet prevents weight regain
Author(s): Zarrinpar A
Source: Nature Metabolism 2022 Dec 1
Quarantine.
Author(s): Zarrinpar, A.
Source: JAMA: The Journal of the American Medical Association (2003a) 290, 2872
Roles for medical students in the political process.
Author(s): Zarrinpar, A.
Source: JAMA: The Journal of the American Medical Association (2003b) 290, 1774
Psychiatry and stigmatization.
Author(s): Zarrinpar, A.
Source: JAMA: The Journal of the American Medical Association (2002) 287, 1856