Publications

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor

Bioconductor’s SummarizedExperiment class unites numerical assay quantifications with sample- and experiment-level metadata. …

Orchestrating a community-developed computational workshop and accompanying training materials

The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for …

Orchestrating a community-developed computational workshop and accompanying training materials

The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for …

Resources for Interpreting Variants in Precision Genomic Oncology Applications

Precision genomic oncology–applying high throughput sequencing (HTS) at the point-of-care to inform clinical decisions–is a …

Resources for Interpreting Variants in Precision Genomic Oncology Applications

Precision genomic oncology–applying high throughput sequencing (HTS) at the point-of-care to inform clinical decisions–is a …

Public data and open source tools for multi-assay genomic investigation of disease

Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the …

Public data and open source tools for multi-assay genomic investigation of disease

Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the …

Statistical Genomics

This volume expands on statistical analysis ofgenomic data by discussing cross-cutting groundworkmaterial, public data repositories, …

On the Selective Packaging of Genomic RNA by HIV-1

Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. …

caOmicsV: an R package for visualizing multidimensional cancer genomic data

Translational genomics research in cancers, e.g., International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), has …

On the Selective Packaging of Genomic RNA by HIV-1

Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. …

caOmicsV: an R package for visualizing multidimensional cancer genomic data

Translational genomics research in cancers, e.g., International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), has …

Inhibition of Survivin with YM155 Induces Durable Tumor Response in Anaplastic Thyroid Cancer

Anaplastic thyroid cancer (ATC) is a rare but lethal malignancy without any effective therapy. The aim of this study is to use a …

Inhibition of Survivin with YM155 Induces Durable Tumor Response in Anaplastic Thyroid Cancer

Anaplastic thyroid cancer (ATC) is a rare but lethal malignancy without any effective therapy. The aim of this study is to use a …

Super-enhancers delineate disease-associated regulatory nodes in T cells

Enhancers regulate spatiotemporal gene expression and impart cell-specific transcriptional outputs that drive cell identity. …

Super-enhancers delineate disease-associated regulatory nodes in T cells

Enhancers regulate spatiotemporal gene expression and impart cell-specific transcriptional outputs that drive cell identity. …

The Bioconductor channel in F1000Research

Bioconductor ( bioconductor.org) is a rich source of software and know-how for the integrative analysis of genomic data. The …

miR30a inhibits LOX expression and anaplastic thyroid cancer progression

Anaplastic thyroid cancer (ATC) is one of the most lethal human malignancies, but its genetic drivers remain little understood. In this …

The Bioconductor channel in F1000Research

Bioconductor ( bioconductor.org) is a rich source of software and know-how for the integrative analysis of genomic data. The …

miR30a inhibits LOX expression and anaplastic thyroid cancer progression

Anaplastic thyroid cancer (ATC) is one of the most lethal human malignancies, but its genetic drivers remain little understood. In this …

Downregulation of IGFBP2 is associated with resistance to IGF1R therapy in rhabdomyosarcoma

Agents targeting the insulin-like growth factor-1 receptor (IGF1R) are in clinical development, but, despite some initial success of …

Downregulation of IGFBP2 is associated with resistance to IGF1R therapy in rhabdomyosarcoma

Agents targeting the insulin-like growth factor-1 receptor (IGF1R) are in clinical development, but, despite some initial success of …

NCI-60 whole exome sequencing and pharmacological CellMiner analyses

Exome sequencing provides unprecedented insights into cancer biology and pharmacological response. Here we assess these two parameters …

High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias

To understand the genetic mechanisms driving variant and IGHV4-34-expressing hairy-cell leukemias, we performed whole-exome sequencing …

NCI-60 whole exome sequencing and pharmacological CellMiner analyses

Exome sequencing provides unprecedented insights into cancer biology and pharmacological response. Here we assess these two parameters …

High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias

To understand the genetic mechanisms driving variant and IGHV4-34-expressing hairy-cell leukemias, we performed whole-exome sequencing …

Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer

Deregulated E2F transcription factor activity occurs in the vast majority of human tumors and has been solidly implicated in …

Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer

Deregulated E2F transcription factor activity occurs in the vast majority of human tumors and has been solidly implicated in …

Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma

Genetic changes during tumorigenesis are usually acquired sequentially. However, a recent study showed that in 2% to 3% of all cancers …

Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma

Genetic changes during tumorigenesis are usually acquired sequentially. However, a recent study showed that in 2% to 3% of all cancers …

Whole genome and transcriptome sequencing of a B3 thymoma

Molecular pathology of thymomas is poorly understood. Genomic aberrations are frequently identified in tumors but no extensive …

SRAdb: query and use public next-generation sequencing data from within R

The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms …

RCircos: an R package for Circos 2D track plots

Circos is a Perl language based software package for visualizing similarities and differences of genome structure and positional …

Whole genome and transcriptome sequencing of a B3 thymoma

Molecular pathology of thymomas is poorly understood. Genomic aberrations are frequently identified in tumors but no extensive …

SRAdb: query and use public next-generation sequencing data from within R

The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms …

RCircos: an R package for Circos 2D track plots

Circos is a Perl language based software package for visualizing similarities and differences of genome structure and positional …

In vivo role of alternative splicing and serine phosphorylation of the microphthalmia-associated transcription factor

The microphthalmia-associated transcription factor (MITF) is a basic helix-loop-helix leucine zipper protein that plays major roles in …

In vivo role of alternative splicing and serine phosphorylation of the microphthalmia-associated transcription factor

The microphthalmia-associated transcription factor (MITF) is a basic helix-loop-helix leucine zipper protein that plays major roles in …

Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples

New technologies allow for genome-scale measurement of DNA methylation. In an effort to increase the clinical utility of DNA …

Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma

Metastasis is characterized by spreading of neoplastic cells to an organ other than where they originated and is the predominant cause …

Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples

New technologies allow for genome-scale measurement of DNA methylation. In an effort to increase the clinical utility of DNA …

Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma

Metastasis is characterized by spreading of neoplastic cells to an organ other than where they originated and is the predominant cause …

Genome-wide depletion of replication initiation events in highly transcribed regions

This report investigates the mechanisms by which mammalian cells coordinate DNA replication with transcription and chromatin assembly. …

Genome-wide depletion of replication initiation events in highly transcribed regions

This report investigates the mechanisms by which mammalian cells coordinate DNA replication with transcription and chromatin assembly. …

Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening

Chromosomal translocations generating oncogenic transcription factors are the hallmark of a variety of tumors, including many sarcomas. …

Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening

Chromosomal translocations generating oncogenic transcription factors are the hallmark of a variety of tumors, including many sarcomas. …

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

The incidence of melanoma is increasing more than any other cancer, and knowledge of its genetic alterations is limited. To …

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

The incidence of melanoma is increasing more than any other cancer, and knowledge of its genetic alterations is limited. To …

Interferon-γlinks ultraviolet radiation to melanomagenesis in mice

Cutaneous malignant melanoma is a highly aggressive and frequently chemoresistant cancer, the incidence of which continues to rise. …

Interferon-γ links ultraviolet radiation to melanomagenesis in mice

Cutaneous malignant melanoma is a highly aggressive and frequently chemoresistant cancer, the incidence of which continues to rise. …

Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate

Limited information is available regarding epigenomic events mediating initiation and progression of tobacco-induced lung cancers. In …

Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate

Limited information is available regarding epigenomic events mediating initiation and progression of tobacco-induced lung cancers. In …

Kinetic complexity of the global response to glucocorticoid receptor action

We have characterized the kinetic response of gene targets throughout the murine genome to transcriptional modulation by the …

Kinetic complexity of the global response to glucocorticoid receptor action

We have characterized the kinetic response of gene targets throughout the murine genome to transcriptional modulation by the …

TRAIL induces apoptosis in triple-negative breast cancer cells with a mesenchymal phenotype

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces apoptosis in some but not all breast cancer cell lines. Breast …

Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression

Pulmonary metastasis continues to be the most common cause of death in osteosarcoma. Indeed, the 5-year survival for newly diagnosed …

A molecular function map of Ewing's sarcoma

EWS-FLI1 is a chimeric ETS transcription factor that is, due to a chromosomal rearrangement, specifically expressed in Ewing’s …

TRAIL induces apoptosis in triple-negative breast cancer cells with a mesenchymal phenotype

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces apoptosis in some but not all breast cancer cell lines. Breast …

Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression

Pulmonary metastasis continues to be the most common cause of death in osteosarcoma. Indeed, the 5-year survival for newly diagnosed …

A molecular function map of Ewing's sarcoma

EWS-FLI1 is a chimeric ETS transcription factor that is, due to a chromosomal rearrangement, specifically expressed in Ewing’s …

Molecular grading of ductal carcinoma in situ of the breast

Increased incidence of ductal carcinoma in situ (DCIS) associated with mammographic screening for breast cancer has emphasized the …

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be …

Molecular grading of ductal carcinoma in situ of the breast

Increased incidence of ductal carcinoma in situ (DCIS) associated with mammographic screening for breast cancer has emphasized the …

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be …

Interaction of the glucocorticoid receptor with the chromatin landscape

The generality and spectrum of chromatin-remodeling requirements for nuclear receptor function are unknown. We have characterized …

Interaction of the glucocorticoid receptor with the chromatin landscape

The generality and spectrum of chromatin-remodeling requirements for nuclear receptor function are unknown. We have characterized …

Suppressor role of activating transcription factor 2 (ATF2) in skin cancer

Activating transcription factor 2 (ATF2) regulates transcription in response to stress and growth factor stimuli. Here, we use a mouse …

Suppressor role of activating transcription factor 2 (ATF2) in skin cancer

Activating transcription factor 2 (ATF2) regulates transcription in response to stress and growth factor stimuli. Here, we use a mouse …

High-resolution mapping and characterization of open chromatin across the genome

Mapping DNase I hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including …

High-resolution mapping and characterization of open chromatin across the genome

Mapping DNase I hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including …

Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells

Constitutively activating internal tandem duplication (ITD) mutations of the receptor tyrosine kinase FLT3 (Fms-like tyrosine kinase 3) …

Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells

Constitutively activating internal tandem duplication (ITD) mutations of the receptor tyrosine kinase FLT3 (Fms-like tyrosine kinase 3) …

GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

Microarray technology has become a standard molecular biology tool. Experimental data have been generated on a huge number of …

GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

Microarray technology has become a standard molecular biology tool. Experimental data have been generated on a huge number of …

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human …

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human …

Modeling synovial sarcoma: timing is everything

Synovial sarcoma is characterized by the presence of a fusion protein involving SYT and SSX2. In this issue of Cancer Cell, Haldar et …

Modeling synovial sarcoma: timing is everything

Synovial sarcoma is characterized by the presence of a fusion protein involving SYT and SSX2. In this issue of Cancer Cell, Haldar et …

DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

Mapping DNase I hypersensitive sites is an accurate method of identifying the location of gene regulatory elements, including …

DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

Mapping DNase I hypersensitive sites is an accurate method of identifying the location of gene regulatory elements, including …

Ewing's sarcoma: general insights from a rare model

Ewing’s sarcoma is characterized by the presence of fusion oncoproteins involving EWSR1 and an ETS gene, most commonly FLI1. In …

Ewing's sarcoma: general insights from a rare model

Ewing’s sarcoma is characterized by the presence of fusion oncoproteins involving EWSR1 and an ETS gene, most commonly FLI1. In …

Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis

Multiple endocrine neoplasia type I (MEN1) is a familial cancer syndrome characterized primarily by tumors of multiple endocrine …

Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis

Multiple endocrine neoplasia type I (MEN1) is a familial cancer syndrome characterized primarily by tumors of multiple endocrine …

Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays

Data obtained from high-density oligonucleotide tiling arrays present new computational challenges for users. This chapter presents …

Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays

Data obtained from high-density oligonucleotide tiling arrays present new computational challenges for users. This chapter presents …

Gene expression profiling of human sarcomas: insights into sarcoma biology

Sarcomas are a biologically complex group of tumors of mesenchymal origin. By using gene expression microarray analysis, we aimed to …

Gene expression profiling of human sarcomas: insights into sarcoma biology

Sarcomas are a biologically complex group of tumors of mesenchymal origin. By using gene expression microarray analysis, we aimed to …

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can …

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can …

Database of mRNA gene expression profiles of multiple human organs

Genome-wide expression profiling of normal tissue may facilitate our understanding of the etiology of diseased organs and augment the …

Database of mRNA gene expression profiles of multiple human organs

Genome-wide expression profiling of normal tissue may facilitate our understanding of the etiology of diseased organs and augment the …

Impact of overlapping recruitment on linkage analysis of complex disorders: simulation studies

Evidence for significant linkage in complexly inherited disorders usually necessitates independent, replicative studies. This study …

Impact of overlapping recruitment on linkage analysis of complex disorders: simulation studies

Evidence for significant linkage in complexly inherited disorders usually necessitates independent, replicative studies. This study …

Linkage and association between inflammatory bowel disease and a locus on chromosome 12

Genetic epidemiological studies have shown that genetic factors are important in the pathogenesis of the idiopathic inflammatory bowel …

Linkage and association between inflammatory bowel disease and a locus on chromosome 12

Genetic epidemiological studies have shown that genetic factors are important in the pathogenesis of the idiopathic inflammatory bowel …

Comparison of nonparametric statistics for detection of linkage in nuclear families: single-marker evaluation

We have evaluated 23 different statistics, from a total of 10 popular software packages for model-free linkage analysis of …

Comparison of nonparametric statistics for detection of linkage in nuclear families: single-marker evaluation

We have evaluated 23 different statistics, from a total of 10 popular software packages for model-free linkage analysis of …

Nonparametric simulation based linkage statistics for general pedigrees

A common strategy for testing for linkage without posing a disease model is to test for increased marker similarity among the affected …

Analysis of bipolar disorder using affected relatives

We have analyzed the GAW10 data from several studies of bipolar affective disorder (BPAD) using the software packages SimIBD and …

Analysis of a complex oligogenic disease

Our analysis of GAW10 problem 2 data set consisted of linear regression analysis followed by linkage analysis. The linear regression …

Nonparametric simulation based linkage statistics for general pedigrees

A common strategy for testing for linkage without posing a disease model is to test for increased marker similarity among the affected …

Analysis of bipolar disorder using affected relatives

We have analyzed the GAW10 data from several studies of bipolar affective disorder (BPAD) using the software packages SimIBD and …

Analysis of a complex oligogenic disease

Our analysis of GAW10 problem 2 data set consisted of linear regression analysis followed by linkage analysis. The linear regression …

Nonparametric simulation-based statistics for detecting linkage in general pedigrees

We present here four nonparametric statistics for linkage analysis that test whether pairs of affected relatives share marker alleles …

Nonparametric simulation-based statistics for detecting linkage in general pedigrees

We present here four nonparametric statistics for linkage analysis that test whether pairs of affected relatives share marker alleles …