Publications
  1. Milosavljevic A Emerging patterns of epigenomic variation Trends in Genetics, 19 April 2011

  2. Shohet JM, Ghosh R, Coarfa C, Ludwig A, Benham AL, Chen Z, Patterson DM, Barbieri E, Mestdagh P, Sikorski D, Milosavljevic A, Kim ES, Gunaratne PH A Genome-wide Search for MYCN Binding Sites Reveals Both New Oncogenic and Tumor Suppressor MicroRNAs Associated with Aggressive Neuroblastoma Cancer Res., 2011 Apr 15.
    (PubMed)

  3. Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors BMC Med Genomics, . 2011 Apr 14;4(1):34
    (PubMed)

  4. Miller CA, Hampton O, Coarfa C, Milosavljevic A ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Read Sequencing Data PLoS One, 2011 Jan 31;6(1):e16327

  5. Buchold GM, Coarfa C, Kim J, Milosavljevic A, Gunaratne PH, Matzuk MM Analysis of MicroRNA Expression in the Prepubertal Testis PLoS One, 2010 Dec 29;5(12):e15317 PMC3012074

  6. Coarfa C, Fu Y, Miller C, Chen Z, Harris RA, Milosavljevic A Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing BMC Bioinformatics Epub, Nov. 26 2010 PMC3001746

  7. Milosavljevic A Putting epigenome comparison into practice Nat Biotechnol., 2010 Oct;28(10):1053-6

  8. Bernstein BE, Stamatoyannopoulus JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA The NIH Roadmap Epigenome Mapping Consortium Nat Biotechnol., 2010 Oct;28(10):1045-8

  9. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications Nat Biotechnol., 2010 Oct;28(10):1097-105
    (PubMed)

  10. Shao L, Kang SH, Li J, Hixson P, Taylor J, Yatsenko SA, Shaw CA, Milosavljevic A, Chang CC, Cheung SW, Patel A Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics J Mol Diagn., 2010 Sep;12(5):670-9
    (PubMed)

  11. Polikepahad S, Knight JM, Naghavi AO, Oplt T, Creighton CJ, Shaw C, Benham AL, Kim J, Soibam B, Harris RA, Coarfa C, Zariff A, Milosavljevic A, Batts LM, Kheradmand F, Gunaratne PH, Corry DB Proinflammatory Role for let-7 MicroRNAS in Experimental Asthma Biol Chem., 2010 Sep 24;285(39):30139-49
    (PubMed)

  12. Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A.MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing.. Molecular and Human Reproduction, March 10, 2010.
    (PubMed)

  13. Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ.Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.. PLoS Genetics, June 5, 2009.
    (PubMed) (Journal)

  14. Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic, A. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Research, December 3, 2008.
    (PubMed) (Journal)

  15. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068 (23 October 2008)
    (PubMed) (Journal)

  16. Coarfa, C. and Milosavljevic,A (2008). Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologies.. Pacific Symposium on Biocomputing , 13:102-113.
    (PDF)     (PS)

  17. Harris RA, Rogers J, Milosavljevic A (2007) Human-specific changes of genome structure detected by genomic triangulation. Science, Apr 13;316(5822):235-7.
    (PubMed) (Journal)

  18. Rhesus Macaque Genome Sequencing and Analysis Consortium (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science, Apr 13;316(5822):222-34.
    (PubMed) (Journal)

  19. Milosavljevic A, Harris RA, Sodergren EJ, Jackson AR, Kalafus KJ, Hodgson A, Cree A, Dai W, Csuros M, Zhu B, de Jong PJ, Weinstock GM, Gibbs RA (2005) Pooled Genomic Indexing of Rhesus Macaque. Genome Research , 15:292-301.
    (PubMed) (Journal)

  20. Csuros M, Milosavljevic A (2004). Pooled Genomic Indexing (PGI): Analysis and Design of Experiments. J Comput Biol, 11(2): 1001-1021.
    (PubMed) (Journal)

  21. Kalafus KJ, Jackson AR, and Milosavljevic A (2004). Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing. Genome Res. 14: 672-678.
    (PubMed)     (Journal)

  22. Rat Genome Sequencing Consortium (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428: 493-521.
    (PubMed)     (Journal)

  23. Milosavljevic A, Csuros M, Weinstock G, Gibbs RA (2003). Shotgun sequencing, clone pooling, and comparative stategies for mapping and sequencing. TARGETS, 2(6): 245-252.
    (Journal)

  24. Csuros M, Milosavljevic A (2002). Pooled genomic indexing (PGI): mathematical analysis and experiment design, in Algorithms in Bioinformatics, Second International Workshop, WABI 2002, Guigo R. and Gusfield D. (eds.). Springer Verlag: Heidelberg, Germany. p. 10-28.
    (PDF)     (PS)

  25. Paunesku T, Chang-Liu CM, Shearin-Jones P, Watson C, Milton J, Oryhon J, Salbego D, Milosavljevic A, Woloschak GE (2000). Identification of genes regulated by UV/salicylic acid. Int J Radiat Bio. 76: 189-198.
    (PubMed)

  26. Milosavljevic A (1999). Discovering Patterns in DNA Sequences by the Algorithmic Significance Method. In Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Wang J.T.L., Shapiro B.A. , Shasha D. (eds.). Oxford: Oxford University Press, p. 3-23.