Publications

  1. Fuller H, Zhu Y, Nicholas J, Chatelaine HA, Drzymalla EM, Sarvestani AK, Julián-Serrano S, Sinnott-Armstrong N, Raffield LM, Rahnavard A, Shutta KH, Hua X, Darst BF
    The Emerging Field of Metabolomic Epidemiology Offers Novel Biological Insights into Disease Etiology
    Nature Metabolism (In Press)

  2. Joshi AD, Rahnavard A, Kachroo P, Mendez KM, Lawrence W, Julián-Serrano S, Hua X, Fuller H, Sinnott-Armstrong N, Tabung FK, Shutta KH
    An epidemiological introduction to human metabolomic investigations
    Trends in Endocrinology & Metabolism (July 2023)

  3. Rahnavard A
    Omics correlation for efficient network construction
    Nature Computational Science (April 2023)

  4. Baghbanzadeh M, Dawson T, Sayoldin B, Oakley T, Crandall K, Rahnavard A
    deepBreaks: a Machine Learning Tool for Identifying and Prioritizing Genotype-phenotype Associations
    Preprint on Research Square (February 2023)

  5. Bustamante J.-M., Dawson T, Loeffler C, Marfori Z, Marchesi J.R, Mullish B.H, Thompson C.C, Crandall K.A, Rahnavard A, Allegretti J.R, Cummings B.P
    Impact of Fecal Microbiota Transplantation on Gut Bacterial Bile Acid Metabolism in Humans
    Nutrients (October 2022)

  6. Rahnavard A, Chatterjee R, Wen H, Gaylord C, Mugusi S, Klatt KC, Smith ER
    Molecular epidemiology of pregnancy using omics data: advances, success stories, and challenges
    Preprint on Research Square (November 2022)

  7. Rahnavard A, Mann B, Giri A, Chatterjee R, Crandall KA
    Metabolite, protein, and tissue dysfunction associated with COVID-19 disease severity
    Scientific Reports (July 2022)

  8. Mallick H, Chatterjee S, Chowdhury S, Chatterjee S, Rahnavard A, Hicks, S.C
    Differential expression of single‐cell RNA‐seq data using Tweedie models Statistics in Medicine (June 2022)

  9. Ghazi AR, Sucipto K, Rahnavad A, et al.
    High-sensitivity pattern discovery in large, paired multiomics datasets
    Bioinformatics (June 2022)

  10. Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA
    Discovery of bioactive microbial gene products in inflammatory bowel disease
    Nature (June 2022)

  11. Chow JH, Rahnavard A, Gomberg-Maitland M, Chatterjee R, Patodi P, Yamane DP, Levine AR, Davison D, Hawkins K, Jackson AM, Quintana MT, Lankford AS, Keneally RJ, Al-Mashat M, Fisher D, Williams J, Berger JS, Mazzeffi MA, Crandall KA.
    Association of Early Aspirin Use With In-Hospital Mortality in Patients With Moderate COVID-19.
    JAMA Network Open (March 2022)

  12. Rahnavard A, Dawson T, Clement R, Stearrett N, Pérez-Losada M, Crandall KA
    Epidemiological associations with genomic variation in SARS-CoV-2.
    Scientific Reports (November 2021)

  13. Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C.
    Multivariable association discovery in population-scale meta-omics studies
    PLoS Computational Biology (November 2021)

  14. Rahnavard A, Chatterjee S, Sayoldin B, Crandall KA, Tekola-Ayele F, Mallick H.
    Omics community detection using multi-resolution clustering
    Bioinformatics (October 2021)

  15. Smith ER, He S, Klatt KC, Barberio MD, Rahnavard A, Azad N, Brandt C, Harker B, Hogan E, Kucherlapaty P, Moradian D, Gernand AD, Ahmadzia HK.
    Limited data exist to inform our basic understanding of micronutrient requirements in pregnancy.
    Sci Adv. (October 2021)

  16. Bennett TD, Moffitt RA, Hajagos JG, Amor B, Anand A, Bissell MM, Bradwell KR, Bremer C, Byrd JB, Denham A, DeWitt PE, Gabriel D, Garibaldi BT, Girvin AT, Guinney J, Hill EL, Hong SS, Jimenez H, Kavuluru R, Kostka K, Lehmann HP, Levitt E, Mallipattu SK, Manna A, McMurry JA, Morris M, Muschelli J, Neumann AJ, Palchuk MB, Pfaff ER, Qian Z, Qureshi N, Russell S, Spratt H, Walden A, Williams AE, Wooldridge JT, Yoo YJ, Zhang XT, Zhu RL, Austin CP, Saltz JH, Gersing KR, Haendel MA, Chute CG.
    Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort Collaborative.
    JAMA Network Open (July 2021)

  17. Amritphale A, Chatterjee R, Chatterjee S, Amritphale N, Rahnavard A, Awan GM, Omar B, Fonarow GC.
    Predictors of 30-Day Unplanned Readmission After Carotid Artery Stenting Using Artificial Intelligence.
    Adv Ther. (June 2021)

  18. Nikookar E, Naderi E, Rahnavard A.
    Cervical Cancer Prediction by Merging Features of Different Colposcopic Images and Using Ensemble Classifier.
    J Med Signals Sens. (June 2021)

  19. Stearrett N, Dawson T, Rahnavard A, Bachali P, Bendall ML, Zeng C, Caricchio R, Pérez-Losada M, Grammer AC, Lipsky PE, Crandall KA.
    Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression.
    Front Immunol. (April 2021)

  20. Haendel MA, Chute CG, Bennett TD, Eichmann DA, Guinney J, Kibbe WA, Payne PRO, Pfaff ER, Robinson PN, Saltz JH, Spratt H, Suver C, Wilbanks J, Wilcox AB, Williams AE, Wu C, Blacketer C, Bradford RL, Cimino JJ, Clark M, Colmenares EW, Francis PA, Gabriel D, Graves A, Hemadri R, Hong SS, Hripscak G, Jiao D, Klann JG, Kostka K, Lee AM, Lehmann HP, Lingrey L, Miller RT, Morris M, Murphy SN, Natarajan K, Palchuk MB, Sheikh U, Solbrig H, Visweswaran S, Walden A, Walters KM, Weber GM, Zhang XT, Zhu RL, Amor B, Girvin AT, Manna A, Qureshi N, Kurilla MG, Michael SG, Portilla LM, Rutter JL, Austin CP, Gersing KR.
    The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.
    J Am Med Inform Assoc. (March 2021)

  21. He S, Klatt KC, Rahnavard A, Barberio MD, Gernand AD, Smith ER.
    Protocol for meta-research on the evidence informing micronutrient dietary reference intakes for pregnant and lactating women.
    Gates Open Res. (November 2020)

  22. Thingholm LB, Rühlemann MC, Koch M, Fuqua B, Laucke G, Boehm R, Bang C, Franzosa EA, Hübenthal M, Rahnavard A, Frost F, Lloyd-Price J, Schirmer M, Lusis AJ, Vulpe CD, Lerch MM, Homuth G, Kacprowski T, Schmidt CO, Nöthlings U, Karlsen TH, Lieb W, Laudes M, Franke A, Huttenhower C.
    Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.
    Cell Host Microbe. (August 2019)

  23. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA 3rd, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C.
    Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
    Nature (May 2019)

  24. Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C.
    Species-level functional profiling of metagenomes and metatranscriptomes. Nature Methods (November 2018)

  25. McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R.
    American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems (May 2018)

  26. Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C.
    Host genetic variation and its microbiome interactions within the Human Microbiome Project.
    Genome Med. (Jan 2018)

  27. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C.
    Strains, functions and dynamics in the expanded Human Microbiome Project.
    Nature (October 2017)

  28. Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C.
    A reproducible approach to high-throughput biological data acquisition and integration.
    PeerJ (March 2015)