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Molecular and Human Genetics

Houston, Texas

Department of Molecular and Human Genetics
Department of Molecular and Human Genetics
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Aleksandar Milosavljevic, Ph.D.

Aleksandar Milosavljevic, Ph.D.

Professor of Molecular and Human Genetics

Other Positions

Co-Director, Program in Structural & Computational Biology and Molecular Biophysics (SCBMB)
Co-Director, Computational and Integrative Biomedical Research Center (CIBR)


Dipl.Ing., Belgrade University, 1984
M.S., Santa Clara University, 1986
Ph.D., University of California, Santa Cruz, 1990

Research Interests

The Bioinformatics Research Laboratory (BRL), directed by Dr. Milosavljevic, develops new computational methods and discovery systems, with ongoing projects in genomics, epigenomics, tumor profiling, and metagenomics. The laboratory develops flexible and scalable informatic frameworks for integration of data and tools and development of web-based collaborative environments for applications of massively parallel sequencing. One recent research initiative is the construction of the Human Epigenome Atlas as part of the NIH Epigenomics Roadmap Initiative and in collaboration with the International Human Epigenome Consortium. BRL serves as the designated Epigenomics Data Analysis and Coordination Center for the Roadmap Initiative. The broad aim is to understand the variation of epigenomes (methylation status, histone marks, chromatin accessibility) across major human tissue types and experimentally relevant human cell lines and to detect and interpret epigenomic variation due to developmental, physiological, and disease processes.

Sites of interchromosomal and intrachromosomal rearrangements in an MCF7 breast cancer cell line

Sites of interchromosomal (red lines) and intrachromosomal (blue lines) rearrangements in an MCF7 breast cancer cell line.

Of particular interest are interactions between genomic and epigenomic variation. Using the reference epigenomes in the Epigenome Atlas, we have recently established an association between selective structural mutability of the human genome and hypomethylation in human germline. We are expanding these studies to better understand interactions between the epigenome and genomic instability not only in human germline but also in human somatic cells and in cancer, with a focus on highly rearranged genomes found in breast, ovarian, and prostate cancer.

The Genboree System is the largest software system developed at BRL. Genboree Workbench contains close to one hundred software tools and utilities organized into toolsets for genome sequencing, transcriptome, cistrome, epigenome, microbiome and metagenome analysis. The Epigenomics Data Analysis and Coordination Center and a number of collaborative epigenomic projects use Genboree as their core informatic infrastructure. Genboree is enabling virtual data integration across the International Human Epigenome Consortium. Other current studies involving Genboree include studies of genome variation in collaboration with HGSC, studies of structural genome variation in human germline and in cancer, comprehensive mapping of genomic and epigenomic aberrations in tumor genomes, disease-focused epigenome analysis projects, and microbiome studies in collaboration with the Microbiome Center at Texas Children’s Hospital and the Alkek Center for Metagenomics and Microbiome Research.

Selected Publications

  1. Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A (2012). Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet. 8(5): e1002692. PubMed PMID: 22615578
  2. Milosavljevic A (2011). Emerging patterns of epigenomic variation. Trends Genet. 27(6): 242-50. PubMed PMID: 21507501
  3. Hampton OA, Koriabine M, Miller CA, Coarfa C, Li J, Den Hollander P, Schoenherr C, Carbone L, Nefedov M, Ten Hallers BF, Lee AV, De Jong PJ, Milosavljevic A (2011). Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines. Cancer Genet. 204(8): 447-57. PubMed PMID: 21962895
  4. Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A (2011). Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC Med. Genomics 4: 34. PubMed PMID: 21489305
  5. Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A (2010). 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 11: 572. PubMed PMID: 21092284
  6. Milosavljevic A (2010). Putting epigenome comparison into practice. Nat. Biotechnol. 28(10): 1053-6. PubMed PMID: 20944597
  7. 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 (2009). 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 Res. 19(2): 167-77. PubMed PMID: 19056696
  8. Harris RA, Rogers J, Milosavljevic A (2007). Human-specific changes of genome structure detected by genomic triangulation. Science 316(5822): 235-7. PubMed PMID: 17431168

Contact Information

Aleksandar Milosavljevic, Ph.D.
Baylor College of Medicine
One Baylor Plaza, BCMD-400D
Houston, TX, 77030, U.S.A.
Mail Stop: BCM225

Phone: 713-798-8719
Fax: 713-798-5556

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