31. Wichman L, Somasundaram S, Briendle C, Valerio D, McCarrey JR, Hodges C and Khalil AM* (Submitted). Dynamic Expression of Long Non-coding RNAs Reveal their Roles In Spermatogenesis and Fertility.
30. Forrest ME and Khalil AM* (2017). Dysregulation of long non-coding RNAs Impacts the Cancer Epigenome.
29. Somoza R, Correa D, Labat I, Sternberg H, Forrest ME, Khalil AM, West M, Tesar P, and Caplan A (in press).
Human mesenchymal stem cells (MSCs) do not make articular cartilage in vitro: Transcriptome-wide analyses of human neonatal cartilage provide a new molecular target for evaluating engineered cartilage. Tissue Engineering
28. Merry CR, McMahon S, Bartel CF, Scacheri P, Thompson C, Jackson M, Harris LN, and Khalil AM* (2016).
Transcriptome-wide identification of mRNAs and lincRNAs associated with Trastuzumab-Resistance in HER2-positive breast cancer. Oncotarget
27. Zhao Y, Scott A, Zhang P, Hao Y, Feng X, Somasundaram S, Khalil AM, Willis J, and Wang Z (2016).
Regulationof Paxillin-p130-PI3K-AKT Signaling Axis by Src and PTPRT Impacts Colon Tumorigenesis. Oncotarget
26. Merry C, Forrest ME, Sabers J, Beard L, Gao X, Hatzoglu M, Jackson MJ, Wang Z, Markowitz SD, and Khalil AM (2015). DNMT1-associated long non-coding RNAs Regulate Global Gene Expression and DNA Methylation in Colon Cancer. Human Molecular Genetics
25. Merry C, McMahon S, Thompson C, Miskimen K, Harris LN and Khalil AM (2015).
Integrative Transcriptome-wide Analyses Reveal Critical HER2-regulated mRNAs and lincRNAs in HER2-positive Breast Cancer. Breast Cancer Research and Treatment
24. Merry C, Niland C and Khalil AM (2015). Diverse Functions and Mechanisms of Mammalian of Long Non-coding RNAs. Regulatory Non-coding RNAs (Invited Book Chapter)
23. Morton M, Bai X, Merry CR, Khalil AM, Leidner R, and Thompson CL (2014). 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
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 (2014).
The functional characterization of the long noncoding RNA SPRY4-IT1 in human melanoma cells. Oncotarget
21. Factor D, Tesar PJ, Khalil AM (2013). Chromatin regulation by long non-coding RNAs. Book title: Molecular Biology of Long Non-coding RNAs. Springer, 2013 Edition
20. Mustafi D, Kevany BM, Bai X, Maedda T, Sears JE, Khalil AM, and Palczewski K. (2013). Evolutionary conserved long intergenic non-coding RNAs in the eye. Research Article, Human Molecular Genetics
19. Moran VA, Perera RJ, and Khalil AM. (2012). Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acid Research (PMID:22492512) Invited Review
18. Moran V, Niland C, Khalil AM. (2012). “Co-immunoprecipitation of long non-coding RNAs”. Methods in Molecular Biology (PMID: 22907501)
17. Niland C, Merry C, Khalil AM. (2012). “Emerging roles for long non-coding RNAs in cancer and neurological disorders”. Frontiers in Genetics (PMID: 22375145) Invited review
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).