35. Forrest ME, Saiakhova A, Beard L, Buchner DA, Scacheri P, LaFramboise T, Markowitz S, Khalil AM*
Colorectal Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
Scientific Reports (Nature Publishing Group), 2018
34. Kenyon J, Sergeeva O, Somoza R, Caplan A, Khalil AM, Lee Z*
Analysis of -5p and -3p strands of miR-145 and miR-140 during mesenchymal stem cell chondrogenic differentiation
Tissue Engineering, 2018
33. Verbus E, Kenyon JD, Sergeeva O, Awadallah A, Yuan L, Weler JF, Caplan AI, Schluchter MD, Khalil AM, and Lee Z.
Expression of miR-145-5p During Chondrogenesis of Mesenchymal Stem Cells
Journal of Stem Cell Research, 2017
32. Mullin NK, Mallipeddi N, Hamburg-Shields E, Khalil AM*, and Atit R*.
Identification and functional analyses of Wnt/β-catenin signaling-responsive lncRNAs and their impact on fibrotic skin.
Frontiers Genetics, 2017
31. Wichman L, Somasundaram S, Briendle C, Valerio D, McCarrey JR, Hodges C and Khalil AM*
Dynamic Expression of Long Non-coding RNAs Reveal their Roles In Spermatogenesis and Fertility.
Biology of Reproduction, 2017
30. Forrest ME and Khalil AM*
Dysregulation of long non-coding RNAs Impacts the Cancer Epigenome.
Cancer Letters, 2017
29. Somoza R, Correa D, Labat I, Sternberg H, Forrest ME, Khalil AM, West M, Tesar P, and Caplan A
Transcriptome-wide analyses of human neonatal articular cartilage and human mesenchymal stem cells (MSCs)-
derived cartilage provide a new molecular target for evaluating engineered cartilage.
Tissue Engineering, 2017
28. Merry CR, McMahon S, Bartel CF, Scacheri P, Thompson C, Jackson M, Harris LN, and Khalil AM*
Transcriptome-wide identification of mRNAs and lincRNAs associated with Trastuzumab-Resistance in HER2-positive breast cancer.
27. Zhao Y, Scott A, Zhang P, Hao Y, Feng X, Somasundaram S, Khalil AM, Willis J, and Wang Z
Regulationof Paxillin-p130-PI3K-AKT Signaling Axis by Src and PTPRT Impacts Colon Tumorigenesis.
26. Merry C, Forrest ME, Sabers J, Beard L, Gao X, Hatzoglu M, Jackson MJ, Wang Z, Markowitz SD, and Khalil AM*
DNMT1-associated long non-coding RNAs Regulate Global Gene Expression and DNA Methylation in Colon Cancer.
Human Molecular Genetics, 2015
25. Merry C, McMahon S, Thompson C, Miskimen K, Harris LN and Khalil AM*
Integrative Transcriptome-wide Analyses Reveal Critical HER2-regulated mRNAs and lincRNAs in HER2-positive Breast Cancer.
Breast Cancer Research and Treatment, 2015
24. Merry C, Niland C and Khalil AM*
Diverse Functions and Mechanisms of Mammalian of Long Non-coding RNAs.
Regulatory Non-coding RNAs (Invited Book Chapter), 2015
23. Morton M, Bai X, Merry CR, Khalil AM, Leidner R, and Thompson CL
Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens.
Lung Cancer, 2014
22. Mazar J, Zhao W, Khalil AM, Lee B, Shelley J, Govindarajan S, Yamamoto F, Ratnam M, Aftab MN, Collins S, Finck BN, Han X, Mattick JS, Dinger ME, Perera RJ
The functional characterization of the long noncoding RNA SPRY4-IT1 in human melanoma cells.
21. Factor D, Tesar PJ, Khalil AM (2013).
Chromatin regulation by long non-coding RNAs.
Book title: Molecular Biology of Long Non-coding RNAs. 2013
20. Mustafi D, Kevany BM, Bai X, Maedda T, Sears JE, Khalil AM, and Palczewski K.
Evolutionary conserved long intergenic non-coding RNAs in the eye.
Human Molecular Genetics, 2013
19. Moran VA, Perera RJ, and Khalil AM*
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs.
Nucleic Acid Research (Invited Review), 2012
18. Moran V, Niland C, Khalil AM*
Co-immunoprecipitation of long non-coding RNAs
Methods in Molecular Biology (PMID: 22907501), 2012
17. Niland C, Merry C, Khalil AM*
Emerging roles for long non-coding RNAs in cancer and neurological disorders
Frontiers in Genetics (PMID: 22375145) Invited review, 2012
16. Geisler S, Lojek L, Khalil AM, Baker KE and Coller J. (2012). “Decapping of Long Non coding RNAs Regulates Inducible Genes”. Molecular Cell (PMID: 22226051)
15. Khalil AM and Rinn JL. (2011). “RNA-protein interactions in human health and disease”. Seminars in Cell and Developmental Biology (PMID: 21333748) Invited Review
14. Huarte M, Guttman M, Feldser D, Garber M, Khalil AM, Zuk O, Amit I, Regev A, Lander ES, Jacks T and Rinn JL. (2010).
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 transcriptional response.
Cell (PMID: 20673990)
13. Getun I, Wu ZK, Khalil AM, and Bois PR. (2010). “The chromatin architecture of mouse recombination hotspots”. Research article, EMBO Reports (PMID: 20508641)
12. Khalil AM and Driscoll, D.J. (2010). “Epigenetic Regulation of Pericentromeric Heterochromatin during Mammalian Meiosis”. Research Article. Cytogenetics and Genome Research (PMID: 20606401)
11. Khalil AM, Huarte M, and Rinn JL (2010). The Emerging Non-coding RNA world. Book Title: MicroRNAs in Development and Cancer. Imperial College Press. Editor: Frank Slack, Yale University.
10. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivera D, Thomas K, Presser A, Bernstein BE, Oudenaarden A, Regev A, Lander ES and Rinn JL. (2009).
Many Human Large Non-coding RNAs Associate with Chromatin Modifying Complexes and Affect Gene Expression. PNAS (PMID: 19571010)
9. Khalil AM. (2009). A geneticist views two theories of X-chromosome inactivation in a broad context. Nature (PMID: 19295563)
8. Khalil AM, Faghihi MA, Modarresi F, Brother SP and Wahlestedt C. (2008). A Novel RNA Transcript with Antiapoptotic Function Is Silenced in Fragile X Syndrome. PLoS ONE (PMID: 18213394)
7. Shan G, Li Y, Zhang J, Szulwach K, Qin Y, Duan R, Faghihi M.A., Khalil AM, Lu L, Chan A, Zhou D, Shi Z, Liu Q, Wahlestedt C, He C and Jin P. (2008). A small molecule enhances RNA interference and promotes microRNA processing. Nature Biotechnology (PMID: 18641635)
6. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St. Laurent III G, Kenny PJ and Wahlestedt C. (2008). Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of b-secretase expression. Nature Medicine (PMID: 18587408)
5. Khalil AM, and Wahlestedt, C. (2008). Epigenetic Mechanisms of Gene Regulation during Mammalian Spermatogenesis. Epigenetics (PMID: 18416029)
4. Khalil AM and Driscoll DJ (2007). Trimethylation of Histone H3 Lysine 4 is an Epigenetic Mark at Regions Escaping Mammalian X Inactivation.
Epigenetics (Cover Article) (PMID: 17965609)
3. Khalil AM and Driscoll DJ (2006). Histone H3 Lysine 4 Dimethylation is Enriched on the Inactive X in Male Meiosis but Absent on the Inactive X in Female Somatic Cells.
Cytogenetics and Genome Research (PMID: 16276085)
2. Khalil AM. (December 2004). Histone Modifications and Chromatin Dynamics of the Mammalian Inactive Sex Chromosomes.
Doctoral Dissertation. University of Florida College of Medicine.
1. Khalil AM, Boyar FZ and Driscoll DJ (2004). Dynamic Histone Modifications Mark Sex Chromosome Inactivation and Reactivation during Mammalian Spermatogenesis.
PNAS (PMID: 15536132).