Research Topics
| Aleksandar MilosavljevicSummaryAffiliation: Baylor College of Medicine Country: USA Publications
| Collaborators
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Detail Information
Publications
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequencesKevin 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...
Putting epigenome comparison into practiceAleksandar 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...- Emerging patterns of epigenomic variationAleksandar 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... 
The DNA sequence, annotation and analysis of human chromosome 3Donna M Muzny
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
Nature 440:1194-8. 2006....- A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genomeOliver 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... - Atlas2 Cloud: a framework for personal genome analysis in the cloudUday 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... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard 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... - A metagenomic approach to characterization of the vaginal microbiome signature in pregnancyKjersti 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.... - Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrainPreethi 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... - Pooled genomic indexing of rhesus macaqueAleksandar 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... - Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndromeDelphine 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... - An integrative variant analysis suite for whole exome next-generation sequencing dataDanny 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... - ReadDepth: a parallel R package for detecting copy number alterations from short sequencing readsChristopher 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/... - Abundance and length of simple repeats in vertebrate genomes are determined by their structural propertiesAlbino 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.... - Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell linesOliver 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.... - 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.... - Genomic hypomethylation in the human germline associates with selective structural mutability in the human genomeJian 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... - Analysis of microRNA expression in the prepubertal testisGregory 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... - The finished DNA sequence of human chromosome 12Steven 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... - Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogeneticsLina 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... - Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencingCristian 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... - Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modificationsR Alan Harris
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
Nat Biotechnol 28:1097-105. 2010.... - Pash: efficient genome-scale sequence anchoring by Positional HashingKen 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... - Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard 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 <http://www.hgsc.bcm.tmc.edu
Nature 428:493-521. 2004.... - A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastomaJason 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... - Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumorsChristopher 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... - Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHEPatricia 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...