Publications

All publications - Google Scholar Link

Peer-reviewed original contributions :

1. Baygi SF, Barupal DK. IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra. Journal of Cheminformatics. 2024 Jan 18;16(1):8. 

2. Mahajan P, Fiehn O, Barupal D. IDSL. GOA: gene ontology analysis for interpreting metabolomic datasets. Scientific Reports. 2024 Jan 14;14(1):1299. 

3. Barupal, DK, Ramos, ML, Florio, AA, et al. Identification of pre-diagnostic lipid sets associated with liver cancer risk using untargeted lipidomics and chemical set analysis: A nested case-control study within the ATBC cohort. Int J Cancer. 2023; 1-11. doi:10.1002/ijc.34726 

4. Baygi, Sadjad Fakouri, Yashwant Kumar, and Dinesh Kumar Barupal. "IDSL. CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets." Analytical Chemistry (2023).  https://pubs.acs.org/doi/full/10.1021/acs.analchem.3c00376 

5. Chehab, R. F., Ferrara, A., Zheng, S., Barupal, D. K., Ngo, A. L., Chen, L., ... & Zhu, Y. (2023). In utero metabolomic signatures of refined grain intake and risk of gestational diabetes: A metabolome-wide association study. The American Journal of Clinical Nutrition, 117(4), 731-740.  https://www.sciencedirect.com/science/article/pii/S0002916523041564 

6. Baygi, S.F., Banerjee, S.K., Chakraborty, P., Kumar, Y. and Barupal, D.K., 2022. IDSL.UFA assigns high confidence molecular formula annotations for untargeted LC/HRMS datasets in metabolomics and exposomics. Analytical Chemistry. https://pubs.acs.org/doi/10.1021/acs.analchem.2c00563 

7. Fakouri Baygi, S., Kumar, Y., & Barupal, D. K. (2022). IDSL.IPA Characterizes the Organic Chemical Space in Untargeted LC/HRMS Data Sets. Journal of proteome research, 10.1021/acs.jproteome.2c00120. Advance online publication. https://doi.org/10.1021/acs.jproteome.2c00120  

8. Montasser, M.E., Aslibekyan, S., Srinivasasainagendra, V., Tiwari, H.K., Patki, A., Bagheri, M., Kind, T., Barupal, D.K., Fan, S., Perry, J. and Ryan, K.A., 2022. An Amish founder population reveals rare-population genetic determinants of the human lipidome. Communications Biology, 5(1), pp.1-13. 

9. Che X, Brydges CR, Yu Y, Price A, Joshi S, Roy A, Lee B, Barupal DK, Cheng A, Palmer DM, Levine S. Metabolomic Evidence for Peroxisomal Dysfunction in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. International journal of molecular sciences. 2022 Jul 18;23(14):7906. 

10. Zhu, Y., Barupal, D. K., Ngo, A. L., Quesenberry, C. P., Feng, J., Fiehn, O., & Ferrara, A. (2022). Predictive Metabolomic Markers in Early to Mid-Pregnancy for Gestational Diabetes: A Prospective Test and Validation Study. Diabetes. 

11. Barupal, D. K., Mahajan, P., Fakouri-Baygi, S., Wright, R. O., Arora, M., & Teitelbaum, S. L. (2022). CCDB: A database for exploring inter-chemical correlations in metabolomics and exposomics datasets. Environment International, 107240. 

12. Petrick LM, Wolff MS, Barupal D, Teitelbaum SL. Comparison of untargeted and targeted perfluoroalkyl acids measured in adolescent girls. Chemosphere. 2021 Dec 15:133303. 

13. Irvin MR, Montasser ME, Kind T, Fan S, Barupal DK, Patki A, Tanner RM, Armstrong ND, Ryan KA, Claas SA, O’connell JR. Genomics of Postprandial Lipidomics in the Genetics of Lipid-Lowering Drugs and Diet Network Study. Nutrients. 2021 Nov;13(11):4000. 

14. Barupal, D. K., Baygi, S. F., Wright, R. O., & Arora, M. (2021). Data processing thresholds for abundance and sparsity and missed biological insights in an untargeted chemical analysis of blood specimens for exposomics. Frontiers in public health, 9. 

15. Barupal, D. K., Schubauer-Berigan, M. K., Korenjak, M., Zavadil, J., & Guyton, K. Z. (2021). Prioritizing cancer hazard assessments for IARC Monographs using an integrated approach of database fusion and text mining. Environment International, 156, 106624. 

16. Aksenov, Alexander A., Ivan Laponogov, Zheng Zhang, Sophie LF Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux et al. "Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data." Nature Biotechnology 39, no. 2 (2021): 169-173. 

17. Bernath, M.M., Bhattacharyya, S., Nho, K., Barupal, D.K., Fiehn, O., Baillie, R., Risacher, S.L., Arnold, M., Jacobson, T., Trojanowski, J.Q. and Shaw, L.M., 2020. Serum triglycerides in Alzheimer disease: Relation to neuroimaging and CSF biomarkers. Neurology. 

18. Germain, A., Barupal, D. K., Levine, S. M., & Hanson, M. R. (2020). Comprehensive Circulatory Metabolomics in ME/CFS Reveals Disrupted Metabolism of Acyl Lipids and Steroids. Metabolites, 10(1), 34. 

19. Bagheri, Minoo, Hemant K. Tiwari, Anarina L. Murillo, Rafet Al-Tobasei, Donna K. Arnett, Tobias Kind, Dinesh Kumar Barupal et al. "A lipidome-wide association study of the lipoprotein insulin resistance index." Lipids in health and disease 19, no. 1 (2020): 1-14. 

20. Baloni, Priyanka, Cory C. Funk, Jingwen Yan, James T. Yurkovich, Alexandra Kueider-Paisley, Kwangsik Nho, Almut Heinken et al. "Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer’s Disease." Cell Reports Medicine 1, no. 8 (2020): 100138. 

21. Gao, B., Duan, Y., Lang, S., Barupal, D., Wu, T. C., Valdiviez, L., ... & Schnabl, B. (2020). Functional microbiomics reveals alterations of the gut microbiome and host co‐metabolism in patients with alcoholic hepatitis. Hepatology communications, 4(8), 1168-1182. 

22. Gao, B., Alonzo-Palma, N., Brooks, B., Jose, A., Barupal, D., Jagadeesan, M., ... & Raj, D. S. (2020). A Pilot Study on the Effect of Prebiotic on Host-Microbial Co-metabolism in Peritoneal Dialysis Patients. Kidney international reports, 5(8), 1309. 

23. Bonini, P., Kind, T., Tsugawa, H., Barupal, D. K., & Fiehn, O. (2020). Retip: retention time prediction for compound annotation in untargeted metabolomics. Analytical chemistry, 92(11), 7515-7522. 

24. Maruvada, P., Lampe, J. W., Wishart, D. S., Barupal, D., Chester, D. N., Dodd, D., ... & Zeisel, S. H. (2020). Perspective: dietary biomarkers of intake and exposure—exploration with omics approaches. Advances in Nutrition, 11(2), 200-215. 

25. Barupal DK and Fiehn O, (2019). Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environmental Health Perspective. 

26. Barupal, DK, Fan, S., & Fiehn, O. (2019). Sets of Co-regulated Serum Lipids are Associated with Alzheimer Disease Pathophysiology, Alzheimer’s and Dementia -Diagnosis, Assessment & Disease Monitoring. 

27. Barupal, DK, et al. "Prioritization of metabolic genes as novel therapeutic targets in estrogen-receptor negative breast tumors using multi-omics data and text mining." Oncotargets (2019) 

28. Fan, S., Kind, T., Cajka, T., Hazen, S.L., Tang, W.W., Kaddurah-Daouk, R., Irvin, M.R., Arnett, D.K., Barupal, D.K. and Fiehn, O., 2019. Systematic error removal using random forest for normalizing large-scale untargeted lipidomics data. Analytical chemistry, 91(5), pp.3590-3596.\

29. Barupal, DK, et al. "A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium." Metabolites 9.5 (2019): 101. 

30. McKirnan, M.D., Ichikawa, Y., Zhang, Z., Zemljic-Harpf, A.E., Fan, S., Barupal, D.K., Patel, H.H., Hammond, H.K. and Roth, D.M., 2019. Metabolomic analysis of serum and myocardium in compensated heart failure after myocardial infarction. Life sciences, 221, pp.212-223.

31. Trott, J.F., Hwang, V.J., Ishimaru, T., Chmiel, K.J., Zhou, J.X., Shim, K., Stewart, B.J., Mahjoub, M.R., Jen, K.Y., Barupal, D.K. and Li, X., 2018. Arginine reprogramming in ADPKD results in arginine-dependent cystogenesis. American Journal of Physiology-Renal Physiology, 315(6), pp.F1855-F1868.

32. Barupal, DK, Fan, S., Wancewicz, B., Cajka, T., Sa, M., Showalter, M. R., ... & Fiehn, O. (2018). Generation and quality control of lipidomics data for the alzheimer’s disease neuroimaging initiative cohort. Scientific data, 5, 180263. 

33. Nagy-Szakal D, Barupal DK, Lee B, Che X, Williams BL, Kahn EJR, Ukaigwe JE, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Levin B, Hornig M, Fiehn O, Lipkin WI. Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics. Sci Rep. 2018 Jul 3;8(1):10056. doi: 10.1038/s41598-018-28477-9. PubMed PMID: 29968805; PubMed Central PMCID: PMC6030047. (co-first author)

34. van Veldhoven K, Keski-Rahkonen P, Barupal DK, Villanueva CM, Font-Ribera L, Scalbert A, Bodinier B, Grimalt JO, Zwiener C, Vlaanderen J, Portengen L, Vermeulen R, Vineis P, Chadeau-Hyam M, Kogevinas M. Effects of exposure to water  disinfection by-products in a swimming pool: A metabolome-wide association study. Environ Int. 2018 Feb;111:60-70. doi: 10.1016/j.envint.2017.11.017. Epub 2017 Nov 24. PubMed PMID: 29179034; PubMed Central PMCID: PMC5786667. 

35. Fong LY, Jing R, Smalley KJ, Taccioli C, Fahrmann J, Barupal DK, Alder H, Farber JL, Fiehn O, Croce CM. Integration of metabolomics, transcriptomics, and microRNA expression profiling reveals a miR-143-HK2-glucose network underlying zinc-deficiency-associated esophageal neoplasia. Oncotarget. 2017 Jun 9;8(47):81910-81925. doi: 10.18632/oncotarget.18434. eCollection 2017 Oct 10. PubMed PMID: 29137232; PubMed Central PMCID: PMC5669858.

36. Barupal DK, Fiehn O. Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets. Sci Rep. 2017 Nov 6;7(1):14567. doi: 10.1038/s41598-017-15231-w. PubMed PMID: 29109515; PubMed Central PMCID: PMC5673929. 

37. Vlaanderen JJ, Janssen NA, Hoek G, Keski-Rahkonen P, Barupal DK, Cassee FR, Gosens I, Strak M, Steenhof M, Lan Q, Brunekreef B, Scalbert A, Vermeulen RCH. The impact of ambient air pollution on the human blood metabolome. Environ Res. 2017 Jul;156:341-348. doi: 10.1016/j.envres.2017.03.042. Epub 2017 Apr 6. PubMed  PMID: 28391173.

38. Edmands WM, Petrick L, Barupal DK, Scalbert A, Wilson MJ, Wickliffe JK, Rappaport SM. compMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets. Anal Chem. 2017 Apr 4;89(7):3919-3928. doi: 10.1021/acs.analchem.6b02394. Epub 2017 Mar 27. PubMed PMID: 28225587.

39. Wanichthanarak K, Fan S, Grapov D, Barupal DK, Fiehn O. Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration. PLoS One.  2017 Jan 31;12(1):e0171046. doi: 10.1371/journal.pone.0171046. eCollection 2017.  PubMed PMID: 28141874; PubMed Central PMCID: PMC5283729. 

40. Zamora-Ros R, Barupal DK, Rothwell JA, Jenab M, Fedirko V, Romieu I, Aleksandrova K, Overvad K, Kyrø C, Tjønneland A, Affret A, His M, Boutron-Ruault  MC, Katzke V, Kühn T, Boeing H, Trichopoulou A, Naska A, Kritikou M, Saieva C, Agnoli C, Santucci de Magistris M, Tumino R, Fasanelli F, Weiderpass E, Skeie G,  Merino S, Jakszyn P, Sánchez MJ, Dorronsoro M, Navarro C, Ardanaz E, Sonestedt E, Ericson U, Maria Nilsson L, Bodén S, Bueno-de-Mesquita HB, Peeters PH, Perez-Cornago A, Wareham NJ, Khaw KT, Freisling H, Cross AJ, Riboli E, Scalbert A. Dietary flavonoid intake and colorectal cancer risk in the European prospective investigation into cancer and nutrition (EPIC) cohort. Int J Cancer.  2017 Apr 15;140(8):1836-1844. doi: 10.1002/ijc.30582. Epub 2017 Jan 19. PubMed PMID: 28006847. 

41. Barupal DK, Pinkerton KE, Hood C, Kind T, Fiehn O. Environmental Tobacco Smoke Alters Metabolic Systems in Adult Rats. Chem Res Toxicol. 2016 Nov 21;29(11):1818-1827. Epub 2016 Nov 9. PubMed PMID: 27788581.

42. Guha N, Guyton KZ, Loomis D, Barupal DK. Prioritizing Chemicals for Risk Assessment Using Chemoinformatics: Examples from the IARC Monographs on Pesticides. Environ Health Perspect. 2016 Dec;124(12):1823-1829. Epub 2016 May 10. PubMed PMID: 27164621; PubMed Central PMCID: PMC5132635.

43. Rothwell JA, Urpi-Sarda M, Boto-Ordoñez M, Llorach R, Farran-Codina A, Barupal DK, Neveu V, Manach C, Andres-Lacueva C, Scalbert A. Systematic analysis  of the polyphenol metabolome using the Phenol-Explorer database. Mol Nutr Food Res. 2016 Jan;60(1):203-11. doi: 10.1002/mnfr.201500435. Epub 2015 Oct 15. PubMed PMID: 26310602; PubMed Central PMCID: PMC5057353. 

44. Edmands WM, Ferrari P, Rothwell JA, Rinaldi S, Slimani N, Barupal DK, Biessy  C, Jenab M, Clavel-Chapelon F, Fagherazzi G, Boutron-Ruault MC, Katzke VA, Kühn T, Boeing H, Trichopoulou A, Lagiou P, Trichopoulos D, Palli D, Grioni S, Tumino  R, Vineis P, Mattiello A, Romieu I, Scalbert A. Polyphenol metabolome in human urine and its association with intake of polyphenol-rich foods across European countries. Am J Clin Nutr. 2015 Oct;102(4):905-13. doi: 10.3945/ajcn.114.101881.  Epub 2015 Aug 12. PubMed PMID: 26269369. 

45. Stepien M, Duarte-Salles T, Fedirko V, Floegel A, Barupal DK, Rinaldi S, Achaintre D, Assi N, Tjønneland A, Overvad K, Bastide N, Boutron-Ruault MC, Severi G, Kühn T, Kaaks R, Aleksandrova K, Boeing H, Trichopoulou A, Bamia C, Lagiou P, Saieva C, Agnoli C, Panico S, Tumino R, Naccarati A, Bueno-de-Mesquita  HB, Peeters PH, Weiderpass E, Quirós JR, Agudo A, Sánchez MJ, Dorronsoro M, Gavrila D, Barricarte A, Ohlsson B, Sjöberg K, Werner M, Sund M, Wareham N, Khaw  KT, Travis RC, Schmidt JA, Gunter M, Cross A, Vineis P, Romieu I, Scalbert A, Jenab M. Alteration of amino acid and biogenic amine metabolism in hepatobiliary  cancers: Findings from a prospective cohort study. Int J Cancer. 2016 Jan 15;138(2):348-60. doi: 10.1002/ijc.29718. Epub 2015 Aug 21. PubMed PMID: 26238458. 

46. Miyamoto S, Taylor SL, Barupal DK, Taguchi A, Wohlgemuth G, Wikoff WR, Yoneda KY, Gandara DR, Hanash SM, Kim K, Fiehn O. Systemic Metabolomic Changes in Blood  Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry. Metabolites. 2015 Apr 9;5(2):192-210. doi: 10.3390/metabo5020192. PubMed PMID: 25859693; PubMed Central PMCID: PMC4495369. 

47. Edmands WM, Barupal DK, Scalbert A. MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets. Bioinformatics. 2015 Mar 1;31(5):788-90. doi: 10.1093/bioinformatics/btu705. Epub 2014 Oct 27. PubMed PMID: 25348215; PubMed Central PMCID: PMC4341062. 

48. Barupal DK, Lee SJ, Karoly ED, Adhya S. Inactivation of metabolic genes causes short- and long-range dys-regulation in Escherichia coli metabolic network. PLoS One. 2013 Dec 5;8(12):e78360. doi: 10.1371/journal.pone.0078360. eCollection 2013. PubMed PMID: 24363806; PubMed Central PMCID: PMC3868466. 

49. Budczies J, Brockmöller SF, Müller BM, Barupal DK, Richter-Ehrenstein C, Kleine-Tebbe A, Griffin JL, Orešic M, Dietel M, Denkert C, Fiehn O. Comparative metabolomics of estrogen receptor positive and estrogen receptor negative breast  cancer: alterations in glutamine and beta-alanine metabolism. J Proteomics. 2013  Dec 6;94:279-88. doi: 10.1016/j.jprot.2013.10.002. Epub 2013 Oct 11. PubMed PMID: 24125731. 

50. Perroud B, Jafar-Nejad P, Wikoff WR, Gatchel JR, Wang L, Barupal DK, Crespo-Barreto J, Fiehn O, Zoghbi HY, Kaddurah-Daouk R. Pharmacometabolomic signature of ataxia SCA1 mouse model and lithium effects. PLoS One. 2013 Aug 2;8(8):e70610. doi: 10.1371/journal.pone.0070610. Print 2013. PubMed PMID: 23936457; PubMed Central PMCID: PMC3732229. 

51. Ibáñez C, Simó C, Barupal DK, Fiehn O, Kivipelto M, Cedazo-Mínguez A, Cifuentes A. A new metabolomic workflow for early detection of Alzheimer's disease. J Chromatogr A. 2013 Aug 9;1302:65-71. doi: 10.1016/j.chroma.2013.06.005. Epub 2013 Jun 14. PubMed PMID: 23827464. 

52. Meissen JK, Yuen BT, Kind T, Riggs JW, Barupal DK, Knoepfler PS, Fiehn O. Induced pluripotent stem cells show metabolomic differences to embryonic stem cells in polyunsaturated phosphatidylcholines and primary metabolism. PLoS One. 2012;7(10):e46770. doi: 10.1371/journal.pone.0046770. Epub 2012 Oct 15. PubMed PMID: 23077522; PubMed Central PMCID: PMC3471894. 

53. Lee DY, Park JJ, Barupal DK, Fiehn O. System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium. Mol Cell Proteomics. 2012 Oct;11(10):973-88. Epub 2012 Jul 10. PubMed PMID: 22787274; PubMed Central PMCID: PMC3494149. 

54. Barupal DK, Haldiya PK, Wohlgemuth G, Kind T, Kothari SL, Pinkerton KE, Fiehn O. MetaMapp: mapping and visualizing metabolomic data by integrating information  from biochemical pathways and chemical and mass spectral similarity. BMC Bioinformatics. 2012 May 16;13:99. PubMed PMID: 22591066; PubMed Central PMCID: PMC3495401. 

55. Skogerson K, Wohlgemuth G, Barupal DK, Fiehn O. The volatile compound BinBase mass spectral database. BMC Bioinformatics. 2011 Aug 4;12:321. doi: 10.1186/1471-2105-12-321. PubMed PMID: 21816034; PubMed Central PMCID: PMC3199763.

56. Barupal DK, Kind T, Kothari SL, Lee DY, Fiehn O. Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometry. BMC Biotechnol. 2010 May 21;10:40. doi: 10.1186/1472-6750-10-40. PubMed PMID: 20492649; PubMed Central PMCID: PMC2883956.

57. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17187-92. doi: 10.1073/pnas.0904847106. Epub 2009 Sep 17. PubMed PMID: 19805153; PubMed Central  PMCID: PMC2746123.

Other peer-reviewed publications :

1. Barupal DK, Fan S, Fiehn O. Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets. Curr Opin Biotechnol. 2018 Feb 2;54:1-9. doi: 10.1016/j.copbio.2018.01.010. [Epub ahead of print] Review. PubMed PMID: 29413745.

2. Rappaport SM, Barupal DK, Wishart D, Vineis P, Scalbert A. The blood exposome and its role in discovering causes of disease. Environ Health Perspect. 2014 Aug;122(8):769-74. doi: 10.1289/ehp.1308015. Epub 2014 Mar 21. PubMed PMID: 24659601; PubMed Central PMCID: PMC4123034.

3. Fiehn O, Barupal DK, Kind T. Extending biochemical databases by metabolomic surveys. J Biol Chem. 2011 Jul 8;286(27):23637-43. doi: 10.1074/jbc.R110.173617.  Epub 2011 May 12. Review. Erratum in: J Biol Chem. 2011 Aug 26;286(34):30244. PubMed PMID: 21566124; PubMed Central PMCID: PMC3129143.

4. Maruvada, P., Lampe, J.W., Wishart, D.S., Barupal, D., Chester, D.N., Dodd, D., Djoumbou-Feunang, Y., Dorrestein, P.C., Dragsted, L.O., Draper, J. and Duffy, L.C., 2019. Perspective: dietary biomarkers of intake and exposure—exploration with omics approaches. Advances in Nutrition.

5. Denkert C, Bucher E, Hilvo M, Salek R, Orešic M, Griffin J, Brockmöller S, Klauschen F, Loibl S, Barupal DK, Budczies J, Iljin K, Nekljudova V, Fiehn O. Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery. Genome Med. 2012 Apr 30;4(4):37. PubMed PMID: 22546809; PubMed Central PMCID: PMC3446265.

6. Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O. Identification of small molecules using accurate  mass MS/MS search. Mass Spectrom Rev. 2018 Jul;37(4):513-532. doi: 10.1002/mas.21535. Epub 2017 Apr 24. Review. PubMed PMID: 28436590.