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Structural and Computational Biology and Molecular Biophysics

Houston, Texas

A BCM research lab.
Structural and Computational Biology & Molecular Biophysics
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Aleksandar Milosavljevic, Ph.D.

Aleksandar Milosavljevic, Ph.D.

Professor, Department of Molecular and Human Genetics

Professor, Program in Translational Biology and Molecular Medicine

Co-Director of SCBMB Graduate Program

Co-Director, Center for Integrative Biomedical Research (CIBR)

Baylor College of Medicine


Dip. Ing., Electrical Engineering, University of Belgrade, Yugoslavia (1984)
M.S., Computer Science, Santa Clara University, Santa Clara, California (1986)
Ph.D., Computer Science, University of California at Santa Cruz (1990)

Research Interest:

The Bioinformatics Research Laboratory, 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.

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 the 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:

  • Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR and Milosavljevic A. Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability. PLoS Genet, 9(2):e1003333 (2013). PubMed
  • Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J and Milosavljevic A. The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. BMC Bioinformatics, 13:S11 (2012). PubMed
  • 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 and Milosavljevic A. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet, 8(5):e1002692 (2012). PubMed
  • Milosavljevic A. Emerging patterns of epigenomic variation. Trends Genet, 27(6):242-50 (2011). PubMed
  • 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 and Milosavljevic A. 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 (2011). PubMed
  • Miller CA, Settle SH, Shulman EP, Aldape KD and Milosavljevic A. Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC Med Genomics, 4:34 (2011). PubMed
  • Coarfa C, Fu Y, Miller C, Chen Z, Harris RA, and Milosavljevic A. Pash 3.0: A versatile software package for read mapping and integrative analysis of of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics, 11:572 (2010) PubMed

For more publications, see listing on PubMed.

Contact Information:

Department: Molecular and Human Genetics
Address: Baylor College of Medicine
One Baylor Plaza
Room 400D
Houston, Texas 77030
Phone: 713-798-8719
Fax: 713-798-4373
Additional Links: Bioinformatics Research Laboratory, Human Genome Sequencing Center, Genboree Discovery System

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