Applications Abstracts/Posters


Publications



2021


  1. Investigating rare pathogenic/likely pathogenic exonic variation in bipolar disorder.
    Jia X, Goes FS, Locke AE, et. al.
    Mol Psychiatry. 2021 Jan 22. [DOI] [PubMed]

  2. Cell-Free DNA to Detect Heart Allograft Acute Rejection.
    Agbor-Enoh S, Shah P, Tunc I, Hsu S, Russell S, Feller E, Shah K, Rodrigo ME, Najjar SS, Kong H, Pirooznia M, Fideli U, Bikineyeva A, Marishta A, Bhatti K, Yang Y, Mutebi C, Yu K, Jang MK, Marboe C, Berry GJ, Valantine HA; GRAfT Investigators.
    Circulation. 2021 Jan 13. [DOI] [PubMed]

  3. The secretome mouse provides a genetic platform to delineate tissue-specific in vivo secretion.
    Liu J, Jang JY, Pirooznia M, Liu S, Finkel T.
    Proc Natl Acad Sci U S A. 2021 Jan 19;118(3):e2005134118. [DOI] [PubMed]

  4. Effect of Nonuniform Cyst Distribution in LAM on Pulmonary Function: A Cross-Sectional Study.
    Hasani AM, Matthew B, Goljamali M, Chen YC, Stylianou M, Pirooznia M, Taveira-DaSilva A, Chen MY, Wen H, Moss J.
    Eur Respir J. 2021 Jan 8:2003769. [DOI] [PubMed]

  5. Bioinformatics Approaches for Functional Prediction of Long Noncoding RNAs.
    Seifuddin F, Pirooznia M.
    Methods Mol Biol. 2021;2254:1-13. [DOI] [PubMed]

  6. Identification of human long non-coding RNAs associated with nonalcoholic fatty liver disease and metabolic homeostasis.
    Ruan X, Li P, Ma Y, Jiang C, Chen Y, Shi Y, Gupta N, Seifuddin F, Pirooznia M, Ohnishi Y, Yoneda N, Nishiwaki M, Dumbovic G, Rinn JL, Higuchi Y, Kawai K, Suemizu H, Cao H.
    J Clin Invest. 2021 Jan 4:136336. [DOI] [PubMed]


    7. 2020


  7. Genome-Wide Analysis of Off-Target CRISPR/Cas9 Activity in Single-Cell-Derived Human Hematopoietic Stem and Progenitor Cell Clones.
    Smith RH, Chen YC, Seifuddin F, Hupalo D, Alba C, Reger R, Tian X, Araki D, Dalgard CL, Childs RW, Pirooznia M, Larochelle A.
    Genes (Basel). 2020 Dec 13;11(12):E1501. [DOI] [PubMed]

  8. Olfactomedin 4 mediation of prostate stem/progenitor-like cell proliferation and differentiation via MYC.
    Li H, Chaitankar V, Zhu J, Chin K, Liu W, Pirooznia M, Rodgers GP.
    Sci Rep. 2020 Dec 14;10(1):21924. [DOI] [PubMed]

  9. Identification of Genes Contributing to a Long Circadian Period in Drosophila Melanogaster.
    Kumar S, Tunc I, Tansey TR, Pirooznia M, Harbison ST.
    J Biol Rhythms. 2020 Dec 4:748730420975946. [DOI] [PubMed]

  10. Acetylation-mediated remodeling of the nucleolus regulates cellular acetyl-CoA responses.
    Houston R, Sekine S, Calderon MJ, Seifuddin F, Wang G, Kawagishi H, Malide DA, Li Y, Gucek M, Pirooznia M, Nelson AJ, Stokes MP, Stewart-Ornstein J, Mullett SJ, Wendell SG, Watkins SC, Finkel T, Sekine Y.
    PLoS Biol. 2020 Nov 30;18(11):e3000981. [DOI] [PubMed]

  11. lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA.
    Seifuddin F, Singh K, Suresh A, Judy JT, Chen YC, Chaitankar V, Tunc I, Ruan X, Li P, Chen Y, Cao H, Lee RS, Goes FS, Zandi PP, Jafri MS, Pirooznia M.
    Sci Data. 2020 Oct 5;7(1):326. [DOI] [PubMed]

  12. Reducing fatty acid oxidation improves cancer-free survival in a mouse model of Li-Fraumeni syndrome.
    Wang PY, Ma J, Li J, Starost MF, Wolfgang MJ, Singh K, Pirooznia M, Kang JG, Hwang PM.
    Cancer Prev Res (Phila). 2020 Sep 21:canprevres.0368.2020. [DOI] [PubMed]

  13. Activation and inhibition of nonsense-mediated mRNA decay control the abundance of alternative polyadenylation products.
    Kishor A, Fritz SE, Haque N, Ge Z, Tunc I, Yang W, Zhu J, Hogg JR.
    Nucleic Acids Res. 2020 Jul 27;48(13):7468-7482. [DOI] [PubMed]

  14. βT87Q-Globin Gene Therapy Reduces Sickle Hemoglobin Production, Allowing for Ex Vivo Anti-sickling Activity in Human Erythroid Cells.
    Demirci S, Gudmundsdottir B, Li Q, Haro-Mora JJ, Nassehi T, Drysdale C, Yapundich M, Gamer J, Seifuddin F, Tisdale JF, Uchida N.
    Mol Ther Methods Clin Dev. 2020 Apr 18;17:912-921. eCollection 2020 Jun 12. [DOI] [PubMed]

  15. Sequential CRISPR-Based Screens Identify LITAF and CDIP1 as the Bacillus cereus Hemolysin BL Toxin Host Receptors.
    Liu J, Zuo Z, Sastalla I, Liu C, Jang JY, Sekine Y, Li Y, Pirooznia M, Leppla SH, Finkel T, Liu S.
    Cell Host Microbe. 2020 Sep 9;28(3):402-410.e5. Epub 2020 Jun 15. [DOI] [PubMed]

  16. Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection.
    Singh K, Chen YC, Judy JT, Seifuddin F, Tunc I, Pirooznia M.
    bioRxiv. 2020 May 14:2020.05.13.092536. [DOI] [PubMed]

  17. Mitochondria regulate intestinal stem cell proliferation and epithelial homeostasis through FOXO.
    Zhang F, Pirooznia M, Xu H.
    Mol Biol Cell. 2020 Jul 1;31(14):1538-1549. [DOI] [PubMed]

  18. Apolipoprotein E Signals via TLR4 to Induce CXCL5 Secretion by Asthmatic Airway Epithelial Cells.
    Kalchiem-Dekel O, Yao X, Barochia AV, Kaler M, Figueroa DM, Karkowsky WB, Gordon EM, Gao M, Fergusson MM, Qu X, Liu P, Li Y, Seifuddin F, Pirooznia M, Levine SJ.
    Am J Respir Cell Mol Biol. 2020 Aug;63(2):185-197. [DOI] [PubMed]

  19. Misregulation of ELK1, AP1, and E12 Transcription Factor Networks is Associated with Melanoma Progression
    Komudi Singh, Michelle Baird, Robert Fischer, Vijender Chaitankar, Fayaz Seifuddin, Yun-Ching Chen, Ilker Tunc, Clare M. Waterman, and Mehdi Pirooznia
    Cancers 2020, 12(2), 458; [DOI] [PubMed]

  20. Discriminating Bipolar Depression From Major Depressive Disorder With Polygenic Risk Scores
    David T Liebers, Mehdi Pirooznia, Andrea Ganna, Bipolar Genome Study (BiGS), Fernando S Goes
    Psychol Med, 1-8 2020 Feb 17, PMID: 32063240 DOI: 10.1017/S003329172000015X [DOI] [PubMed]

  21. Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families.
    Forstner, A.J., Fischer, S.B., Schenk, L.M. et al.
    Transl Psychiatry 10, 57 (2020). [DOI] [PubMed]

  22. Whole genome sequence-based haplotypes reveal a single origin of the 1393 bp HBB deletion
    Wang X, Xu JZ, Conrey A, et al.
    J Med Genet. 2020;jmedgenet-2019-106698. doi:10.1136/jmedgenet-2019-106698 [DOI] [PubMed]

  23. In vivo functional analysis of non-conserved human lncRNAs associated with cardiometabolic traits.
    Ruan X, Li P, Chen Y, et al.
    Nat Commun. 2020;11(1):45. Published 2020 Jan 2. doi:10.1038/s41467-019-13688-z [DOI] [PubMed]

  24. Acetylation-mediated phase control of the nucleolus regulates cellular acetyl-CoA responses
    Ryan Houston, Shiori Sekine, Michael J Calderon, et. al.
    bioRxiv 2020; 10.1101/2020.01.24.918706 [DOI] [bioRxiv]

  25. Multilevel integrative transcriptome analyses in humans and humanized mice define in vivo human lncRNA metabolic regulators
    Xiangbo Ruan, Ping Li, et. al
    bioRxiv 2020; 10.1101/2020.01.01.884023 [DOI] [bioRxiv]


    26. 2019


  26. A genomic dating tool for ancient genomes resolves the origins of hundreds of Eurasian genomes
    U. Esposito, G. Holland, G. Alshehab, A. M. Dobre, M. Pirooznia, C. S. Brimacombe, E. Elhaik
    bioRxiv 2019; 10.1101/828962 [DOI] [PubMed]

  27. Affected Sib-pair Analyses Identify Signaling Networks Associated with Social Behavioral Deficits in Autism.
    M Pirooznia, T Niranjan, Y Chen, I Tunc, FS Goes, D Avramopoulos, et. al.
    Frontiers in Genetics, 27 November 2019; 10.3389/fgene.2019.01186 [DOI] [PubMed]

  28. De Novo Variation in Bipolar Disorder.
    Fernando S Goes, Mehdi Pirooznia, Martin Tehan, Peter P Zandi, John McGrath, Paula Wolyniec, Gerald Nestadt, Ann E Pulver
    Mol Psychiatry. 2019;10.1038/s41380-019-0611-1. [DOI] [PubMed]

  29. Electron transport chain biogenesis activated by a JNK-insulin-Myc relay primes mitochondrial inheritance in Drosophila.
    Zong-Heng Wang, Yi Liu, Vijender Chaitankar, Mehdi Pirooznia, Hong Xu
    Elife. 2019;8:e49309. Published 2019 Oct 15. doi:10.7554/eLife.49309 [DOI] [PubMed]

  30. GATA2-deficient mast cells limit IgE-mediated immediate hypersensitivity reactions in humans.
    Desai A, Sowerwine K, Liu Y, et.al.
    J Allergy Clin Immunol. 2019 May 15. pii: S0091-6749(19)30624-4. [DOI] [PubMed]

  31. Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing
    The Somatic Mutation Working Group of the SEQC-II Consortium
    bioRxiv, 2019. [DOI] [BioRxiv]

  32. Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies
    Li Tai Fang, Bin Zhu, Yongmei Zhao, et. al.
    bioRxiv, 2019. [DOI] [BioRxiv]

  33. Circulating lymphangioleiomyomatosis tumor cells with loss of heterozygosity in the Tuberous Sclerosis Complex 2 gene show increased aldehyde dehydrogenase activity.
    Pacheco-Rodriguez G, Steagall WK, Samsel L, Dagur PK, McCoy JP, Tunc I, Pirooznia M, Wang JA, Darling TN, Moss J.
    Chest. 2019 Apr 26. pii: S0012-3692(19)30874-8. [DOI] [PubMed]

  34. IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis
    Yun-Ching Chen, Abhilash Suresh, Chingiz Underbayev, Clare Sun, Komudi Singh, Fayaz Seifuddin, Adrian Wiestner, Mehdi Pirooznia
    Gigascience. 2019;8(10):giz121. [DOI] [PubMed]

  35. Neutrophil Subsets, Platelets, and Vascular Disease in Psoriasis.
    Teague HL, Varghese NJ, Tsoi LC, Dey AK, et. al.,
    JACC Basic Transl Sci. 2019 Feb 25;4(1):1-14. [DOI] [PubMed]

  36. Donor-derived Cell-Free DNA Predicts Allograft Failure and Mortality After Lung Transplantation.
    Sean Agbor-Enoh 1, Yan Wang 2, Ilker Tunc 3, Moon Kyoo Jang, et. al.
    EBioMedicine. 2019 Feb; 40: 541–553. doi: 10.1016/j.ebiom.2018.12.029 [DOI] [PubMed]

  37. Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia.
    Dillon LW, Hayati S, Roloff GW, Tunc I, Pirooznia M, Mitrofanova A, Hourigan CS.
    Haematologica. 2019 Feb;104(2):297-304. [DOI] [PubMed]


    38. 2018


  38. Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians.
    Umberto Esposito, Ranajit Das, Mehdi Pirooznia, Eran Elhaik
    Genes. 2018;9(12):625. Published 2018 Dec 12. doi:10.3390/genes9120625 [DOI] [PubMed]

  39. Effect of Genotype and Maternal Affective Disorder on Intronic Methylation of FK506 Binding Protein 5 in Cord Blood DNA.
    Duis J, Cox OH, Ji Y, Seifuddin F, Lee RS, Wang X.
    Front Genet. 2018 Dec 17;9:648. [DOI] [PubMed]

  40. The transcription factors TFE3 and TFEB amplify p53 dependent transcriptional programs in response to DNA damage.
    Jeong E, Brady OA, Martina JA, Pirooznia M, Tunc I, Puertollano R.
    Elife. 2018 Dec 6;7. pii: e40856. [DOI] [PubMed]

  41. Pathogenic TERT promoter variants in telomere diseases.
    Gutierrez-Rodrigues F, Donaires FS, Pinto A, Vicente A, et. al,.
    Genet Med. 2018 Dec 7. [DOI] [PubMed]

  42. Human retinoic acid-regulated CD161+ regulatory T cells support wound repair in intestinal mucosa.
    Povoleri GAM, Nova-Lamperti E, Scotta C, Fanelli G, et. al,.
    Nat Immunol. 2018 Dec;19(12):1403-1414. [DOI] [PubMed]

  43. GCN5L1 interacts with αTAT1 and RanBP2 to regulate hepatic α-tubulin acetylation and lysosome trafficking.
    Wu K, Wang L, Chen Y, Pirooznia M, Singh K, Walde S, Kehlenbach RH, Scott I, Gucek M, Sack MN.
    J Cell Sci. 2018 Nov 20;131(22). pii: jcs221036. [DOI] [PubMed]

  44. High density lipoprotein proteome is associated with cardiovascular risk factors and atherosclerosis burden as evaluated by coronary CT angiography. Atherosclerosis.
    Gordon SM, Chung JH, Playford MP, Dey AK, Sviridov D, et al.
    Atherosclerosis. 2018 Nov;278:278-285. [DOI] [PubMed]

  45. Complement receptor CD46 co-stimulates optimal human CD8+ T cell effector function via fatty acid metabolism.
    Arbore G, West EE, Rahman J, Le Friec G, et. al.
    Nat Commun. 2018 Oct 10;9(1):4186. [DOI] [PubMed]

  46. Circulating cell-free DNA as a biomarker of tissue injury: Assessment in a cardiac xenotransplantation model.
    Agbor-Enoh S, Chan JL, Singh A, Tunc I, et. al.
    J Heart Lung Transplant. 2018 Aug;37(8):967-975. [DOI] [PubMed]

  47. Properties of Global- And Local-Ancestry Adjustments in Genetic Association Tests in Admixed Populations.
    Eden R Martin 1 2, Ilker Tunc 3, Zhi Liu 4, Susan H Slifer 1, Ashley H Beecham 2, Gary W Beecham
    Genet Epidemiol, 42 (2), 214-229 Mar 2018 [DOI] [PubMed]

  48. DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt/β-catenin signaling.
    Martin PM, Stanley RE, Ross AP, Freitas AE, et. al.
    Mol Psychiatry. 2018 Feb;23(2):467-475. [DOI] [PubMed]

  49. A Rat Methyl-Seq Platform to Identify Epigenetic Changes Associated with Stress Exposure.
    Carey JL, Cox OH, Seifuddin F, Marque L, et. al.
    J Vis Exp. 2018 Oct 24;(140). [DOI] [PubMed]

  50. Late manifestation of alloantibody-associated injury and clinical pulmonary antibody-mediated rejection: Evidence from cell-free DNA analysis.
    Agbor-Enoh S, Jackson AM, Tunc I, Berry GJ, et. al.
    J Heart Lung Transplant. 2018 Jul;37(7):925-932. [DOI] [PubMed]

  51. Mutations in the pancreatic secretory enzymes CPA1 and CPB1 are associated with pancreatic cancer.
    Tamura K, Yu J, Hata T, Suenaga M, Shindo K, et. al.
    Proc Natl Acad Sci U S A. 2018 May 1;115(18):4767-4772. [DOI] [PubMed]


    52. 2017


  52. The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine.
    Elhaik E, Yusuf L, Anderson AIJ, Pirooznia M, et. al.
    Genome Biol Evol. 2017 Dec 1;9(12):3225-3237. [DOI] [PubMed]

  53. Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort.
    Monson ET, Pirooznia M, Parla J, Kramer M, et. al.
    Mol Neuropsychiatry. 2017 Jul;3(1):1-11. [DOI] [PubMed]

  54. Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
    Daneshjou R, Wang Y, Bromberg Y, Bovo S, et. al.
    Hum Mutat. 2017 Sep;38(9):1182-1192. [DOI] [PubMed]

  55. Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure.
    Seifuddin F, Wand G, Cox O, Pirooznia M, et. al.
    Epigenetics. 2017 Aug;12(8):637-652. [DOI] [PubMed]

  56. Genome-wide DNA hydroxymethylation identifies potassium channels in the nucleus accumbens as discriminators of methamphetamine addiction and abstinence.
    Cadet JL, Brannock C, Krasnova IN, Jayanthi S, et. al.
    Mol Psychiatry. 2017 Aug;22(8):1196-1204. [DOI] [PubMed]