Aleksandar Milosavljevic

Summary

Affiliation: Baylor College of Medicine
Country: USA

Publications

  1. pmc Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood
    Matthew N Davies
    Institute of Psychiatry, King s College London, De Crespigny Park, London, UK
    Genome Biol 13:R43. 2012
  2. pmc The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
    Kevin Riehle
    Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Bioinformatics 13:S11. 2012
  3. pmc Emerging patterns of epigenomic variation
    Aleksandar Milosavljevic
    Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX 77030, USA
    Trends Genet 27:242-50. 2011
  4. doi request reprint Putting epigenome comparison into practice
    Aleksandar Milosavljevic
    NIH Epigenomics Roadmap Data Analysis and Coordination Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, USA
    Nat Biotechnol 28:1053-6. 2010
  5. pmc Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines
    Oliver A Hampton
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    Cancer Genet 204:447-57. 2011
  6. ncbi request reprint The DNA sequence, annotation and analysis of human chromosome 3
    Donna M Muzny
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:1194-8. 2006
  7. pmc A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
    Oliver A Hampton
    Bioinformatics Research Laboratory, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 19:167-77. 2009
  8. pmc Atlas2 Cloud: a framework for personal genome analysis in the cloud
    Uday S Evani
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Genomics 13:S19. 2012
  9. pmc Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome
    Delphine M Saulnier
    Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
    Gastroenterology 141:1782-91. 2011
  10. pmc Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
    BMC Genomics 12:277. 2011

Detail Information

Publications29

  1. pmc Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood
    Matthew N Davies
    Institute of Psychiatry, King s College London, De Crespigny Park, London, UK
    Genome Biol 13:R43. 2012
    ..We characterized intra- and inter-individual methylomic variation across whole blood and multiple regions of the brain from multiple donors...
  2. pmc The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
    Kevin Riehle
    Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Bioinformatics 13:S11. 2012
    ..Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings...
  3. pmc Emerging patterns of epigenomic variation
    Aleksandar Milosavljevic
    Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX 77030, USA
    Trends Genet 27:242-50. 2011
    ..The development of new bioinformatic frameworks for comparative epigenome analysis is putting epigenome maps within the reach of researchers across a wide spectrum of biological disciplines...
  4. doi request reprint Putting epigenome comparison into practice
    Aleksandar Milosavljevic
    NIH Epigenomics Roadmap Data Analysis and Coordination Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, USA
    Nat Biotechnol 28:1053-6. 2010
    ..Comparative analysis of epigenomes offers new opportunities to understand cellular differentiation, mutation effects and disease processes. But the scale and heterogeneity of epigenetic data present numerous computational challenges...
  5. pmc Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines
    Oliver A Hampton
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    Cancer Genet 204:447-57. 2011
    ....
  6. ncbi request reprint The DNA sequence, annotation and analysis of human chromosome 3
    Donna M Muzny
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:1194-8. 2006
    ....
  7. pmc A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
    Oliver A Hampton
    Bioinformatics Research Laboratory, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 19:167-77. 2009
    ..We show that knock-down of SULF2 in cell lines causes tumorigenic phenotypes, including increased proliferation, enhanced survival, and increased anchorage-independent growth...
  8. pmc Atlas2 Cloud: a framework for personal genome analysis in the cloud
    Uday S Evani
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Genomics 13:S19. 2012
    ..To this end, the cloud computing and Software-as-a-Service (SaaS) technologies can help address these issues...
  9. pmc Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome
    Delphine M Saulnier
    Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
    Gastroenterology 141:1782-91. 2011
    ..The intestinal microbiomes of healthy children and pediatric patients with irritable bowel syndrome (IBS) are not well defined. Studies in adults have indicated that the gastrointestinal microbiota could be involved in IBS...
  10. pmc Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
    BMC Genomics 12:277. 2011
    ..To test this, we used massively parallel Illumina sequencing to analyse small RNAs from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence...
  11. pmc An integrative variant analysis suite for whole exome next-generation sequencing data
    Danny Challis
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA
    BMC Bioinformatics 13:8. 2012
    ..Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data...
  12. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  13. pmc Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
    Cristian Coarfa
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA
    BMC Bioinformatics 11:572. 2010
    ..Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing...
  14. pmc ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads
    Christopher A Miller
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 6:e16327. 2011
    ..The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google.com/p/readdepth/...
  15. pmc A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy
    Kjersti Aagaard
    Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Baylor College of Medicine and Texas Children s Hospital, Houston, Texas, United States of America
    PLoS ONE 7:e36466. 2012
    ....
  16. pmc Pooled genomic indexing of rhesus macaque
    Aleksandar Milosavljevic
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 15:292-301. 2005
    ..A further innovation, short-tag pooled genomic indexing (ST-PGI), was also introduced to further improve the economy of mapping by sequencing multiple, short, mapable tags within a single sequencing reaction...
  17. pmc Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome
    Jian Li
    Bioinformatics Research Laboratory, Epigenome Center, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Genet 8:e1002692. 2012
    ..These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease...
  18. pmc Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties
    Albino Bacolla
    Institute of Biosciences and Technology, Center for Genome Research, Texas A and M University Health Science Center, Houston, Texas 77030, USA
    Genome Res 18:1545-53. 2008
    ....
  19. pmc Analysis of microRNA expression in the prepubertal testis
    Gregory M Buchold
    Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 5:e15317. 2010
    ..These studies provide a foundation for interpretation of miRNA changes associated with testicular pathology and identification of novel components of the miRNA editing machinery in the testis...
  20. pmc Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)
    Gloria L Fawcett
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    BMC Genomics 12:311. 2011
    ....
  21. pmc Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    R Alan Harris
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Nat Biotechnol 28:1097-105. 2010
    ....
  22. pmc Pash: efficient genome-scale sequence anchoring by Positional Hashing
    Ken J Kalafus
    Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
    Genome Res 14:672-8. 2004
    ..The results of these comparisons by Pash agree with those computed by other methods that use more than an order of magnitude more computing resources. These results confirm the sensitivity of Positional Hashing...
  23. ncbi request reprint The finished DNA sequence of human chromosome 12
    Steven E Scherer
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:346-51. 2006
    ..The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents...
  24. pmc Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics
    Lina Shao
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77021 2039, USA
    J Mol Diagn 12:670-9. 2010
    ..This pilot study clearly demonstrates high sensitivity of oligonucleotide aCGH for potential use in diagnosis and follow-up in patients with hematological neoplasms...
  25. pmc NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits
    Piotr Dittwald
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 23:1395-409. 2013
    ..2q13, were elucidated in association with novel genomic disorders. Our study quantitates genome architectural features responsible for NAHR-mediated genomic instability and further elucidates the role of NAHR in human disease. ..
  26. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  27. pmc Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE
    Patricia B S Celestino-Soper
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Hum Mol Genet 20:4360-70. 2011
    ..gov/geo/, date last accessed on 30 August 2011). Genboree accession: http://genboree.org/java-bin/gbrowser.jsp?refSeqId=1868&entryPointId=chr17&from=53496072&to=53694382&isPublic=yes, date last accessed on 30 August 2011...
  28. doi request reprint A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma
    Jason M Shohet
    Department of Pediatrics, Section of Hematology Oncology, Baylor College of Medicine, Houston, Texas 77204, USA
    Cancer Res 71:3841-51. 2011
    ..Our data reveal host-gene independent functions of MYCN-target microRNAs and demonstrate that MYCN represses both tumor suppressive and proproliferative microRNAs...
  29. pmc Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors
    Christopher A Miller
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    BMC Med Genomics 4:34. 2011
    ..Analyses that extend beyond single genes are often restricted to examining pathways, interactions and functional modules that are already known...