List of works - Aleksandar Milosavljevic

A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma

scientific article

A high-resolution map of synteny disruptions in gibbon and human genomes

scientific article

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy

scientific article published in 2012

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

scientific article

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

scientific article published on 7 August 2008

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

scientific article published in Science

An integrative variant analysis suite for whole exome next-generation sequencing data

scientific article

Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools

scientific article

Analysis of microRNA expression in the prepubertal testis

scientific article

Atlas2 Cloud: a framework for personal genome analysis in the cloud

scientific article

CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma.

scientific article

CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models

scientific article published on 29 January 2021

Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons.

scientific article published on 16 May 2012

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)

scientific article

ClinGen Allele Registry links information about genetic variants

scientific article published in November 2018

ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants

scientific article published on 12 January 2017

Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments.

scientific article

Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.

scientific article

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

scientific article

Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability

scientific article

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

scientific article

Emerging patterns of epigenomic variation

scientific article

Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types

scientific article

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.

scientific article

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution

scientific article (publication date: June 2009)

Extending gene ontology in the context of extracellular RNA and vesicle communication

scientific article published on 12 April 2016

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

scientific article

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome

scientific article

Histoepigenetic analysis of the mesothelin network within pancreatic ductal adenocarcinoma cells reveals regulation of retinoic acid receptor gamma and AKT by mesothelin

scientific article published on 02 July 2020

Integrating Genomic Resources with Electronic Health Records using the HL7 Infobutton Standard

scientific article published on 31 August 2016

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

scientific article

Intermediate DNA methylation is a conserved signature of genome regulation

scientific article

Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines

scientific article

MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing

scientific article

NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits

scientific article published on 08 May 2013

Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

scientific article

Pash: efficient genome-scale sequence anchoring by Positional Hashing

scientific article published on April 2004

Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium

scientific article published on 2 June 2016

Pooled genomic indexing of rhesus macaque

scientific article

Proinflammatory role for let-7 microRNAS in experimental asthma

scientific article

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

scientific article

Recurrent BCAM-AKT2 fusion gene leads to a constitutively activated AKT2 fusion kinase in high-grade serous ovarian carcinoma

scientific article

Somatic mutations affect key pathways in lung adenocarcinoma

scientific article

Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain

scientific article

Spark: a navigational paradigm for genomic data exploration

scientific article

The DNA sequence, annotation and analysis of human chromosome 3

scientific article (publication date: 27 April 2006)

The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences

scientific article

The NIH Roadmap Epigenomics Mapping Consortium

scientific article (publication date: October 2010)

The finished DNA sequence of human chromosome 12

scientific article

The genome of the sea urchin Strongylocentrotus purpuratus

scientific article

Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE

scientific article

mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities

scientific article

List of works by Aleksandar Milosavljevic

A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma

A high-resolution map of synteny disruptions in gibbon and human genomes

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

An integrative variant analysis suite for whole exome next-generation sequencing data

Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools

Analysis of microRNA expression in the prepubertal testis

Atlas2 Cloud: a framework for personal genome analysis in the cloud

CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma.

CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models

Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)

ClinGen Allele Registry links information about genetic variants

ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants

Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments.

Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

Emerging patterns of epigenomic variation

Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution

Extending gene ontology in the context of extracellular RNA and vesicle communication

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome

Histoepigenetic analysis of the mesothelin network within pancreatic ductal adenocarcinoma cells reveals regulation of retinoic acid receptor gamma and AKT by mesothelin

Integrating Genomic Resources with Electronic Health Records using the HL7 Infobutton Standard

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

Intermediate DNA methylation is a conserved signature of genome regulation

Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines

MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing

NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits

Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

Pash: efficient genome-scale sequence anchoring by Positional Hashing

Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium

Pooled genomic indexing of rhesus macaque

Proinflammatory role for let-7 microRNAS in experimental asthma

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

Recurrent BCAM-AKT2 fusion gene leads to a constitutively activated AKT2 fusion kinase in high-grade serous ovarian carcinoma

Somatic mutations affect key pathways in lung adenocarcinoma

Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain

Spark: a navigational paradigm for genomic data exploration

The DNA sequence, annotation and analysis of human chromosome 3

The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences

The NIH Roadmap Epigenomics Mapping Consortium

The finished DNA sequence of human chromosome 12

The genome of the sea urchin Strongylocentrotus purpuratus

Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE

mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities