A full list of publications can be found on
Justin's Google Scholar page
Pre-Print
Purrington K, Holowatyj AN, Cote ML, Schwartz AG, Chaudry R, Ali-Fehmi R, Dyson G, Colacino JA, Boerner J, Bandyopadhyay S. Novel immune cell subtypes linked to survival among African American women with triple-negative breast cancer. BioRxiv. doi: https://doi.org/10.1101/325951
Wang Y, Thong T, Saligrama V, Colacino JA, Balzano L, Scott C. A gene filter for comparative analysis of single-cell RNA-sequencing trajectory datasets. BioRxiv. doi: https://doi.org/10.1101/637488
You can align your own trajectory based datasets using CoRGI, now implemented in R and available on Github!
Varma U, Colacino JA, Gilbert A. Information Theoretic Feature Selection Methods for Single Cell RNA-Sequencing. BioRxiv. doi: https://doi.org/10.1101/646919
Check out the implementation of information theoretic feature selection methods in the python package PictureRocks on GitHub!
Mahran R^, Pan S, Colacino JA, Hagras M, Sun D, Brenner D. Cellular pharmacology of curcumin with and without piperine. BioRxiv. doi: https://doi.org/10.1101/2021.07.14.452424
Nguyen VK, Middleton LYM, Huang L, Zhao N, Verly E, Kvasnicka J, Sagers L, Patel CJ, Colacino J, Jolliet O. Harmonized US National Health and Nutrition Examination Survey 1988-2018 for high throughput exposome-health discovery. medRxiv. doi: 10.1101/2023.02.06.23284573. The data and some example code to get you started doing your own large scale analyses are available on Kaggle!
Forté CA, Millar JA, Colacino J. Integrating NHANES and Toxicity Forecaster Data to Compare Pesticide Exposure and Bioactivity by Farmwork History and US Citizenship. medRxiv. doi: 10.1101/2023.01.24.23284967
Sala-Hamrick KE*, Tapaswi A*, Polemi KM, Nguyen VK, Colacino JA. High Throughput Transcriptomics to Understand Chemical Drivers of Aggressive Breast Cancer Subtypes. BioRxiv. doi: https://doi.org/10.1101/2022.11.16.516817
Wang K, Kim N, Bagherian M, Li K, Chou E, Colacino JA, Dolinoy DC, Sartor MA. Data Fusion by Matrix Completion for Exposome Target Interaction Prediction. BioRxiv. doi: https://doi.org/10.1101/2022.08.24.505125. To get started predicting the effects of a new chemical exposure, check out the implementation of CMMC on the Sartor Lab’s GitHub!
2023
Elkin ER, Su AL, Dou JF, Colacino JA, Bridges D, Padmanabhan V, Harris SM, Boldenow E, Loch-Caruso R, Bakulski KM. Sexually concordant and dimorphic transcriptional responses to maternal trichloroethylene and/or N-acetyl cysteine exposure in Wistar rat placental tissue. Toxicology. doi: 10.1016/j.tox.2022.153371
Svoboda LK, Wang K, Goorich JM, Jones TR, Colacino JA, Peterson KE, Tellez-Rojo MM, Sartor MA, Dolinoy DC. Perinatal lead exposure promotes sex-specific epigenetic programming of disease-relevant pathways in mouse heart. Toxics. https://doi.org/10.3390/toxics11010085
Campbell KA, Colacino JA, Puttabyatappa M, Dou JF, Elkin ER, Hammoud SS, Domino Se, Dolinoy DC, Goodrich JM, Loch-Caruso R, Padmanabhan V, Bakulski KM. Placental gene expression-based cell type deconvolution: Cell proportions drive preeclampsia gene expression differences. Communications Biology. https://doi.org/10.1038/s42003-023-04623-6
Kim H, Villareal L, Liu Z, Haneef M, Falcon D, Martin D, Lee HJ, Dame M, Attili D, Chen Y, Varani J, Spence J, Kovbasnjuk O, Colacino JA, Lyssiotis C, Lin H, Shah Y, Xue X. Transferrin receptor-mediated iron uptake promotes colon tumorigenesis. Advanced Science. https://doi.org/10.1002/advs.202207693
2022
Harris SM, Colacino JA, Buxton M, Croxton L, Nguyen V^, Loch-Caruso R, Bakulski KM. A data mining approach reveals chemicals detected at higher levels in Non-Hispanic Black women target preterm birth genes and pathways. Reproductive Sciences. doi: 10.1007/s43032-022-00870-w Awarded one of NIEHS’ Papers of the Year for 2022!
Su AL, Harris SM, Elkin ER, Karnovsky A, Colacino JA, Loch-Caruso R. Trichloroethylene modifies energy metabolites in the amniotic fluid of Wistar rats. Reproductive Toxicology. doi: 10.1016/j.reprotox.2022.03.004
Nguyen VK, Colacino JA, Patel C, Sartor MA, Jolliet O. Identification of occupations susceptible to high exposure and risk associated with multiple toxicants in an observational study: National Health and Nutrition Examination Survey 1999-2014. Exposome. doi: 10.1093/exposome/osac004
Mirabelli C, Santos-Ferreira N, Gilliland MG, Cieza RJ, Colacino JA, Sexton JZ, Neyts J, Taube S, Rocha-Pereira J, Wobus CE. Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids. Journal of Virology. doi: 10.1128/jvi.00855-22
McCabe CF, Goodrich JM, Bakulski KM, Domino SE, Jones TR, Colacino JA, Dolinoy DC, Padmanabhan V. Probing prenatal bisphenol exposure and tissue-specific methylation responses in cord blood, cord tissue, and placenta. Reproductive Toxicology. doi: 10.1016/j.reprotox.2022.11.005
2021
Middleton LY, Dou J, Fisher J, Heiss JA, Nguyen V, Just AC, Faul J, Ware EB, Mitchell C, Colacino JA, Bakulski KM. Saliva cell type DNA methylation reference panel for epidemiology studies in children. Epigenetics. doi: 10.1080/15592294.2021.1890874 Check out these data as a Bioconductor package (“BeadSorted.Saliva.EPIC”) and the implementation in ewastools
Svoboda LK, Wang K, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Sex-specific alterations in cardiac DNA methylation in adult mice by perinatal led exposure. International Journal of Environmental Research and Public Health. doi: 10.3390/ijerph18020577
Elkin ER, Bakulski KM, Colacino JA, Bridges D, Kilburn BA, Armant DR, Loch-Caruso R. Transcriptional profiling of the response to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine revealed activation of the eIF2α/ATF4 integrated stress response in two in vitro placental models. Archives of Toxicology. doi: 10.1007/s00204-021-03011-5
Liu S, Wang K, Svoboda L, Rygiel C^, Jones T, Cavalcante R, Colacino JA, Dolinoy DC, Sartor MA. Perinatal DEHP exposure induces sex- and tissue- specific DNA methylation changes in both juvenile and adult mice. Environmental Epigenetics. doi: 10.1093/eep/dvab004
Forté CA, Colacino JA, Polemi KM, Guytingco A, Peraino NJ, Jindaphong S, Kaviya T, Westrick J, Neitzel R, Nambunmee K. Pesticide exposure and adverse health effects associated with farm work in Northern Thailand. Journal of Occupational Health. doi: 10.1002/1348-9585.12222.
Cieza RJ, Golob JL, Colacino JA, Wobus CE. Comparative analysis of public RNA-sequencing data from human intestinal enteroids (HIEs) infected with enteric RNA viruses identifies universal and virus-specific epithelial responses. Viruses. doi: 10.3390/v13061059
Nguyen VK, Colacino JA, Chung MK, Goallec AL, Jolliet O, Patel CJ. Characterizing the relationship between physiological indicators and all-cause mortality. Lancet: Healthy Longevity. doi: 10.1016/s2666-7568(21)00212-9
Polemi K, Nguyen V, Heidt J, Kahana A, Jolliet O, Colacino JA. Identifying the Link Between Chemical Exposures and Breast Cancer in African American Women via ToxCast High Throughput Screening Data. Toxicology. doi: 10.1016/j.tox.2021.152964
2020
Svoboda LK, Neier K, Cavalcante R, Tsai Z, Jones TR, Liu S, Goodrich JM, Lalancette C, Colacino JA, Sartor MA, Dolinoy DC. Tissue and sex-specific programming of DNA methylation by perinatal lead exposure: Implications for environmental epigenetics studies. Epigenetics. doi: 10.1080/15592294.2020.1841872
Bohm MS, Dame MK, Boyd J, Su K, Wu A, Attili D, Chu V, Colacino JA, Spence JR. Low-level mouse DNA in conditioned medium generates false positive cross-species contamination results in human organoid cultures. Frontiers in Genetics. doi:10.3389/fcell.2020.587107
Zick SM, Murphy SL, Colacino JA. Association of Chronic Spinal Pain with Diet Quality. Pain Reports. doi: 10.1097/PR9.0000000000000837
Campbell KA, Colacino JA, Park SK, Bakulski KM. Cell types in environmental epigenetic studies: Biological and epidemiological frameworks. Current Environmental Health Reports. doi: 10.1007/s40572-020-00287-0
Svoboda LK, Wang K, Cavalcante R, Neier K, Colacino JA, Sartor MA, Dolinoy DC. Sex-specific programming of cardiac DNA methylation by developmental phthalate exposure. Epigenetics Insights. doi: 10.1177/2516865720939971
Wang K, Liu S, Svoboda LK, Rygiel C, Neier K, Jones TR, Colacino JA, Dolinoy DC, Sartor MA. Tissue - and sex-specific DNA methylation changes in mice perinatally exposed to lead (Pb). Frontiers in Genetics. doi: 10.3389/fgene.2020.00840
Dame MK, Huang S, Attili D, Spence JR, Colacino JA. Identification and isolation of human LGR5+ cells using an antibody-based strategy. Methods in Molecular Biology: Intestinal Stem Cells. doi: 10.1007/978-1-0716-0747-3_1
Nguyen V, Kahana A, Heidt J, Polemi K, Kvasnicka J, Jolliet O, Colacino JA. A comprehensive analysis of racial disparities in chemical biomarker concentrations in United States women, 1999-2014. Environment International. doi: 10.1016/j.envint.2020.105496
Thong T*, Wang Y*, Brooks MD, Lee C, Scott C, Balzano L, Wicha MS, Colacino JA. Hybrid stem cell states: Insights into the relationship between mammary development and breast cancer using single-cell transcriptomics. Frontiers in Cell and Developmental Biology. doi: 10.3389/fcell.2020.00288
Bakulski KM, Dou JF, Thompson RC, Lee C, Middleton LY, Perera BPU, Ferris SP, Jones TR, Neier K, Zhou X, Sartor MA, Hammoud SS, Dolinoy DC, Colacino JA. Single cell analysis of the effects of developmental lead (Pb) exposure on the hippocampus. Toxicological Sciences. doi: 10.1093/toxsci/kfaa069
2019
Gonzalez T, Rae JM, Colacino JA. Implications of Environmental Estrogens on Breast Cancer Treatment and Progression. Toxicology. https://doi.org/10.1016/j.tox.2019.03.014.
Bakulski KM, Dou J, Lin N, London S, Colacino JA. DNA methylation signature of smoking in lung cancer is enriched for exposure signatures in newborn and adult blood. Scientific Reports. https://www.nature.com/articles/s41598-019-40963-2
Ramakrishnan SK, Zhang H, Ma X, Jung I, Schwartz A, Triner D, Devenport S, Das NK, Xue X, Zeng MY, Hu Y, Mortensen RM, Greenson JK, Cascalho M, Wobus CE, Colacino JA, Nunez G, Rui L, Shah YM. Intestinal non-canonical NFκB signaling shapes the local and systemic immune response. Nature Communications. https://doi.org/10.1038/s41467-019-08581-8
Moynihan M, Tellez-Rojo MM, Colacino JA, Jones AD, Song PX, Cantoral A, Mercado-Garcia A, Peterson K. Prenatal cadmium exposure is negatively associated with adiposity in girls not boys during adolescence. Frontiers in Public Health. doi: 10.3389/fpubh.2019.00061
Hill EM, Esper RM, Simon RB, Aslam MN, Jiang Y, Dame MK, McClintock SD, Colacino JA, Djuric Z, Wicha MS, Smith WL, Brenner DE. Dietary polyunsaturated fatty acids modulate the adipose secretome to influence mammary stem cell self-renewal. Journal of Nutritional Biochemistry. https://doi.org/10.1016/j.jnutbio.2019.05.007
Thong T*, Forté CA*, Hill EM, Colacino JA. Environmental exposures, stem cells, and cancer. Pharmacology and Therapeutics. https://doi.org/10.1016/j.pharmthera.2019.107398
Malloy MA, Kochmanski JJ, Jones TR, Colacino JA, Goodrich JM, Dolinoy DC, Svoboda LK. Perinatal Bisphenol A Exposure and Reprogramming of Imprinted Gene Expression in the Adult Mouse Brain. Frontiers in Genetics. doi: 10.3389/fgene.2019.00951
2018
Triner D, Devenport SM, Ramakrishnan SK, Ma X, Frieler RA, Greenson JK, Inohara N, Nunez G, Colacino JA, Mortensen RM, Shah YM. Neutrophils Restrict Tumor-Associated Microbiota to Reduce Growth and Invasion of Colon Tumors in Mice. Gastroenterology. doi: https://doi.org/10.1053/j.gastro.2018.12.003
Nguyen VK, Colacino JA, Arnot J, Kvasnicka J, Jolliet O. Characterization of age-based trends to identify chemical biomarkers of higher levels in children. Environment International. https://doi.org/10.1016/j.envint.2018.10.042
Gonzalez T, Rae JM, Colacino JA, Richardson R. Homology models of mouse and rat estrogen receptor-α ligand-binding domain created by in silico mutagenesis of a human template: molecular docking with 17ß-estradiol, diethylstilbestrol, and paraben analogs. Computational Toxicology. https://doi.org/10.1016/j.comtox.2018.11.003
Schwartz AJ, Das NK, Ramakrishnan SK, Jain C, Jurkovic M, Wu J, Nemeth E, Lakhal-Littleton S, Colacino JA, Shah YM. Hepatic hepcidin/intestinal HIF-2α axis maintains iron absorption during iron deficiency and overload. Journal of Clinical Investigation. doi: 10.1172/JCI122359 , commentary by Frank Lee available here
Munoz MGI, Colacino JA, Lewis RC, Arthur AE Meeker JD, Ferguson KK. Associations between school lunch consumption and urinary phthalate metabolite concentrations in US children and adolescents: Results from NHANES 2003-2014. Environment International. https://doi.org/10.1016/j.envint.2018.09.009
Triner D, Castillo C, Hakim J, Xue X, Greenson JK, Nunez G, Chen GY, Colacino JA, Shah YM. Myc-Associated zinc finger protein regulates the pro-inflammatory response in colitis and colon cancer by regulating STAT3 signaling. Molecular and Cellular Biology. doi: 10.1128/MCB.00386-18.
Rocco SA, Koneva, L, Middleton LYM, Thong T, Solanki S, Karram S, Nambunmee, K, Harris C, Rozek LS, Sartor MA, Shah YM, Colacino JA. Cadmium exposure inhibits branching morphogenesis and causes alterations consistent with HIF-1α inhibition in human primary breast organoids. Toxicological Sciences. https://doi.org/10.1093/toxsci/kfy112
Tsai YH, Czerwinski M, Wu A, Dame MK, Attili D, Hill E, Colacino JA, Nowacki LM, Shroyer NF, Higgins PDR, Kao JY, Spence JR. A method for establishing organoid cultures from cryogenically-preserved human biopsy tissue. Cellular and Molecular Gastroenterology and Hepatology. https://doi.org/10.1016/j.jcmgh.2018.04.008
McClintock S, Colacino JA, Attili D, Dame M, Richter A, Reddy A, Basrur V, Turgeon DK, Varani J, Aslam M. Calcium-induced differentiation of human colon adenomas in enteroid culture: Calcium versus calcium in conjunction with additional trace elements. Cancer Prevention Research. doi: 10.1158/1940-6207.CAPR-17-0308
Colacino JA, Azizi E, Brooks MD, Fouladdel S, McDermott S, Lee M, Hill D, Sartor MA, Rozek LS, Wicha MS†. Heterogeneity of normal human breast stem and progenitor cells as revealed by transcriptional profiling. Stem Cell Reports. doi: https://doi.org/10.1016/j.stemcr.2018.03.001
Virani S, Wetzel E, Puttawilbul P, Laohawiriyakamol S, Booyaphiphat P, Geater A, Kleer C, Pang J, Rentschler K, Colacino JA, Mendes de Leon CF, Rozek LS, Sriplung H. Religious disparity in breast cancer survival in southern Thai women. Cancer Epidemiology. doi: 10.1016/j.canep.2018.02.007
Dame MK*, Attili D*, McClintock S, Dedhia PH, Ouilette P, Hardt O, Chin AM, Xue X, Laliberte J, Katz EL, Newsome GM, Hill D, Miller A, Agorku D, Tsai YH, Agorku D, Altheim CH, Bosio A, Simon B, Samuelson LC, Stoerker JA, Appelman H, Varani J, Wicha MS, Brenner DE, Shah YM, Spence J, Colacino JA. Identification, isolation, and characterization of human LGR5-positive colon adenoma cells. Development. dev.153049
Wang T, Pehrsson EC, Purushotham D, Li D, Zhang B, Lawson HA, Province MA, Krapp C, Lan Y, Coarfa C, Katz TA, Tang WY, Wang Z, Biswal S, Rajapoalan S, Colacino JA, Sartor MA, Neier K, Dolinoy D, Pinto J, Hamanaka R, Mutlu G, Patisaul HB, Aylor DL, Crawford GE, Chadwick LH, Duncan CG, Garton AE, McAllister KA, The TaRGET II Consortium, Barolomei MS, Walker CL, Tyson FL. The NIEHS TaRGET II Consortium and Environmental Epigenomics. Nature Biotechnology 36, 225–227 doi:10.1038/nbt.4099
2017
Wu Y, Baylin A, Colacino JA. Iron, Oxidative Stress, and Δ9 Stearoyl-CoA Desaturase Index (C16:1/C16:0): An Analysis Applying the National Health and Nutrition Examination Survey 2003-04. Current Developments in Nutrition. doi: https://doi.org/10.3945/cdn.117.001222
Louie KW, Saera-Vila A, Kish PE, Colacino JA, Kahana A. Temporally Distinct Transcriptional Regulation of Myocyte Dedifferentiation and Myofiber Growth During Muscle Regeneration. BMC Genomics. Nov 9;18(1):854. doi: 10.1186/s12864-017-4236-y
Demanelis K, Virani S, Colacino JA, Ruangyuttikarn W, Nishijo M, Swaddiwudhipong W, Nambunmee K, Basu N, Rozek LS. Cadmium exposure and age-associated DNA methylation changes in non-smoking women from northern Thailand. Environmental Epigenetics. Volume 3, Issue 2, 1 January 2017, dvx006. doi: https://doi.org/10.1093/eep/dvx006
Zheng G, Fon GV, Meixner W, Creekmore A, Zong Y, Dame M, Colacino JA, Dedhia PH, Hong S, Wiley JW. Chronic stress and intestinal barrier dysfunction: Glucocorticoid receptor and transcription repressor HES1 regulate tight junction protein Cludin-1 promoter. Scientific Reports. 7, Article number: 4502. doi:10.1038/s41598-017-04755-w
2016
Colacino, JA, Mcdermott, SP, Sartor, MA, Wicha, MS, & Rozek, LS. Transcriptomic profiling of curcumin-treated human breast stem cells identifies a role for stearoyl-coa desaturase in breast cancer prevention. Breast Cancer Research and Treatment, 158(1), 29-41:10.1007/s10549-016-3854-4.
Liu Y, Burness ML, Martin-Trevino R, Guy J, Bai S, Harouaka R, Brooks MD, Shang L, Fox A, Luther TK, Davis A, Baker TL, Colacino JA, Clouthier SG, Shao Z, Wicha MS, Liu S. RAD51 mediates resistance of cancer stem cells to PARP inhibition in triple-negative breast cancer. Clinical Cancer Research. doi: 10.1158/1078-0432.CCR-15-1348.
Triner D, Xue X, Schwartz AJ, Jung I, Colacino JA, Shah YM. HIF-2a Facilitates the Progression of Colon Tumors through Recruiting CXCL1-Dependent Neutrophils. Molecular and Cellular Biology. Mar 1; 37(5): e00481-16. doi: 10.1128/MCB.00481-16
Zick SM, Colacino JA, Cornellier M, Khabir T, Ren J, Surnow K, Djuric Z. Fatigue reduction diet in breast cancer survivors: A pilot randomized clinical trial. Breast Cancer Research and Treatment. Volume 161, Issue 2, pp 299–310.
Ferguson KK, Colacino JA, Lewis RC, Meeker JD. Personal care product use among adults in NHANES: associations between urinary phthalate metabolites and phenols and use of mouthwash and sunscreen. Journal of Exposure Science and Environmental Epidemiology. doi: 10.1038/jes.2016.27.
Colacino JA†. 3D human tissue culture: modeling environmental effects on the stem cell epigenome. Epigenomics. 8:(11):1453-1457. https://doi.org/10.2217/epi-2016-0107
Selected Papers 2015 and Before
Darr OA*, Colacino JA*, Tang AL, McHugh JB, Bellile EL, Bradford CR, Prince MP, Chepeha DB, Rozek LS, Moyer JS. Epigenetic alterations in metastatic cutaneous carcinoma. Head and Neck. doi: 10.1002/hed.23701 (2015)
Colacino JA, Arthur AE, Ferguson KK, Rozek LS. Dietary antioxidant and anti-inflammatory intake modifies the effect of cadmium exposure on markers of systemic inflammation and oxidative stress. Environmental Research; 131:6-12. doi: 10.1016/j.envres.2014.02.003 (2014)
Colacino JA, Dolinoy DC, Duffy S, Sartor MA, Chepeha DB, Bradford CR, McHugh J, Patel D, Walline HM, Bellile E, Terrell JE, Stoerker JA, Taylor JMG, Carey TE, Wolf G, Rozek LS. Comprehensive analysis of methylation in head and neck squamous cell carcinoma indicates differences by survival and clinicopathologic characteristics. PLoS ONE; 8(1): e54742. Doi:10.1371/journal.pone.0054742 (2013)
Schecter A, Lorber M, Guo Y, Wu Q, Yun SH, Kannan K, Miller J, Hommel M, Imran N, Hynan LS, Cheng D, Colacino JA, Birnbaum LS. Phthalate levels and dietary exposure from Albany, New York, U.S. Food. Environmental Health Perspectives; doi: 10.1289/ehp.1206367 (2013)
Colacino JA*, Arthur AE*, Duffy S, Dolinoy DC, Terrell J, Sartor M, Chepeha D, McHugh J, Wolf G, Carey T, Peterson K, Rozek LS. Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas. Epigenetics; 7(8):883-91 (2012)
Colacino JA, Soliman A, Calafat A, Nahar MS, Van Zomeren-Dohm A, Seifeldin I, Hablas A, Rozek LS, Dolinoy DC. Exposure to phthalates among premenstrual girls from rural and urban, Gharbiah, Egypt: An exposure assessment pilot study. Environmental Health; 10:40. https://doi.org/10.1186/1476-069X-10-40 (2011)
Colacino JA, Harris TR, Schecter A. Dietary intake is associated with phthalate body burden in a nationally representative sample. Environmental Health Perspectives; doi:10.1289/ehp.0901712 (2010)
Schecter A, Colacino JA, Haffner D, Opel M, Päpke O, Birnbaum LS. Perfluorinated compounds, polychlorinated biphenyls, and organochlorine pesticide contamination in composite food samples from the United States. Environmental Health Perspectives; doi:10.1289/ehp.0901347 (2010)
Schecter A, Haffner D, Colacino JA, Patel K, Opel M, Päpke O, Birnbaum LS. Polybrominated diphenyl ethers (PBDEs) and hexabromocyclodecane (HBCD) in U.S. food. Environmental Health Perspectives; 118(3): doi:10.1289/ehp.0901345 (2010)