Publications
Our recent publications
2023
1. Rocks D, Jaric I, Bellia F, Cham H, Greally JM, Suzuki M, Kundakovic M. Early-life stress and ovarian hormones alter transcriptional regulation in the nucleus accumbens resulting in sex-specific responses to cocaine. Cell Rep. 2023 Sep 29;42(10):113187. doi: 10.1016/j.celrep.2023.113187, PMID: 37777968
2. Bera BS, Thompson TV, Sosa E, Nomaru H, Reynolds D, Dubin RA, Maqbool SB, Zheng D, Morrow BE, Greally JM, Suzuki M. An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide conjugated antibodies. Epigenetics Chromatin. 2023 Apr 28;16(1):14. PMID: 37118773
3. Chang W, Zhao Y, Rayêe D, Xie Q, Suzuki M, Zheng D, and Cvekl A. Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation. Epigenetics Chromatin. 2023 Jan 25;16(1):4. doi: 10.1186/s13072-023-00478-7. PubMed PMID: 36698218; PubMed Central PMCID: PMC9875507.
2022
1. Ulahannan N, Cutler R, Doña-Termine R, Simões-Pires CA, Wijetunga NA, Croken MM, Johnston AD, Kong Y, Maqbool SB, Suzuki M, and Greally JM. Genomic insights into host and parasite interactions during intracellular infection by Toxoplasma gondii. PLoS One. 2022;17(9):e0275226. doi: 10.1371/journal.pone.0275226. eCollection 2022. PubMed PMID: 36178892; PubMed Central PMCID: PMC9524707.
2. Lundy K, Greally JF, Essilfie-Bondzie G, Olivier JB, Doña-Termine R, Greally JM, and Suzuki M, Vitamin D Deficiency During Development Permanently Alters Liver Cell Composition and Function. Front Endocrinol (Lausanne). 2022;13:860286. doi: 10.3389/fendo.2022.860286.
3. Ma L, Tang Q, Gao X, Lee J, Lei R, Suzuki M, Zheng D., Ito K, Frenette PS, and Dawlaty MM., Tet-mediated DNA demethylation regulates specification of hematopoietic stem and progenitor cells during mammalian embryogenesis. Science Advances. 2022 Mar 4;8(9):eabm3470. doi: 10.1126/sciadv.abm3470.
4. Rocks D, Jaric I, Tesfa L, Greally JM, Suzuki M, Kundakovic M. Cell type-specific chromatin accessibility analysis in the mouse and human brain. Epigenetics. 2022 Jan-Feb;17(2):202-219. doi: 10.1080/15592294.2021.1896983.
2021
1. Rocks D, Jaric I, Tesfa L, Greally JM, Suzuki M, Kundakovic M. Cell type-specific chromatin accessibility analysis in the mouse and human brain. Epigenetics. 2021 Mar 29;:1-18. doi: 10.1080/15592294.2021.1896983. PMID: 33775205.
2. Suzuki M, Wang T, Garretto D, Isasi CR, Cardoso WV, Greally JM, Quadro L. Disproportionate Vitamin A Deficiency in Women of Specific Ethnicities Linked to Differences in Allele Frequencies of Vitamin A-Related Polymorphisms. Nutrients. 2021; 13(6):1743. doi:10.3390/nu13061743. PMID: 34063790
3. Cwiek, A; Suzuki, M; deRonde, K; Conaway, M; Bennett, KM; El Dahr, S; Reidy, K; Charlton, JR*. Premature differentiation of nephron progenitors and dysregulation of gene pathways critical to kidney development in a model of preterm birth. Scientific Reports. 20214;11(1):21667.
doi: 10.1038/s41598-021-00489-y. PMID: 34737344
4. Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol. 2021 Dec 6;22(1):332. doi: 10.1186/s13059-021-02529-2. PMID: 34872606
2020
1. de Torrenté L, Zimmerman S, Suzuki M, Christopeit M, Greally JM, Mar JC. The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data. BMC Bioinformatics. 2020 Dec 28;21(Suppl 21):562. doi: 10.1186/s12859-020-03892-w. PubMed PMID: 33371881; PubMed Central PMCID: PMC7768656.
2. Rastogi D, Johnston AD, Nico J, Loh LN, Jorge Y, Suzuki M, Macian F, Greally JM. Functional Genomics of the Pediatric Obese Asthma Phenotype Reveal Enrichment of Rho-GTPase Pathways. Am J Respir Crit Care Med. 2020 Jul 15;202(2):259-274. doi: 10.1164/rccm.201906-1199OC. PubMed PMID: 32255672; PubMed Central PMCID: PMC7365356.
2019
1. Bhagat TD, Von Ahrens D, Dawlaty M, Zou Y, Baddour J, Achreja A, Zhao H, Yang L, Patel B, Kwak C, Choudhary GS, Gordon-Mitchell S, Aluri S, Bhattacharyya S, Sahu S, Bhagat P, Yu Y, Bartenstein M, Giricz O, Suzuki M, Sohal D, Gupta S, Guerrero PA, Batra S, Goggins M, Steidl U, Greally J, Agarwal B, Pradhan K, Banerjee D, Nagrath D, Maitra A, Verma A. Lactate-mediated epigenetic reprogramming regulates formation of human pancreatic cancer-associated fibroblasts. Elife. 2019 Nov 1;8. doi: 10.7554/eLife.50663. PubMed PMID: 31663852; PubMed Central PMCID: PMC6874475.
2. Johnston AD, Simões-Pires CA, Suzuki M, Greally JM. High-efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells using a single-stranded donor oligonucleotide strategy. Commun Biol. 2019;2:312. doi: 10.1038/s42003-019-0559-3. eCollection 2019. PubMed PMID: 31428700; PubMed Central PMCID: PMC6694121.
3. Johnston AD, Simões-Pires CA, Thompson TV, Suzuki M, Greally JM. Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding. Nat Commun. 2019 Aug 2;10(1):3472. doi: 10.1038/s41467-019-11412-5. PubMed PMID: 31375681; PubMed Central PMCID: PMC6677801.
4. Jaric I, Rocks D, Greally JM, Suzuki M, Kundakovic M. Chromatin organization in the female mouse brain fluctuates across the oestrous cycle. Nat Commun. 2019 Jun 28;10(1):2851. doi: 10.1038/s41467-019-10704-0. PubMed PMID: 31253786; PubMed Central PMCID: PMC6598989.
5. Nakahara F, Borger DK, Wei Q, Pinho S, Maryanovich M, Zahalka AH, Suzuki M, Cruz CD, Wang Z, Xu C, Boulais PE, Ma'ayan A, Greally JM, Frenette PS. Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells. Nat Cell Biol. 2019 May;21(5):560-567. doi: 10.1038/s41556-019-0308-3. Epub 2019 Apr 15. PubMed PMID: 30988422; PubMed Central PMCID: PMC6499646.
6. Kong Y, Rastogi D, Seoighe C, Greally JM, Suzuki M. Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data. PLoS One. 2019;14(4):e0215987. doi: 10.1371/journal.pone.0215987. eCollection 2019. PubMed PMID: 31022271; PubMed Central PMCID: PMC6483354.
7. Shenoy N, Bhagat TD, Cheville J, Lohse C, Bhattacharyya S, Tischer A, Machha V, Gordon-Mitchell S, Choudhary G, Wong LF, Gross L, Ressigue E, Leibovich B, Boorjian SA, Steidl U, Wu X, Pradhan K, Gartrell B, Agarwal B, Pagliaro L, Suzuki M, Greally JM, Rakheja D, Thompson RH, Susztak K, Witzig T, Zou Y, Verma A. Ascorbic acid-induced TET activation mitigates adverse hydroxymethylcytosine loss in renal cell carcinoma. J Clin Invest. 2019 Mar 4;129(4):1612-1625. doi: 10.1172/JCI98747. eCollection 2019 Mar 4. PubMed PMID: 30702441; PubMed Central PMCID: PMC6436862.