-
Article
Open AccesstrioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios
When analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be beneficial when trying to identify certain types of DNA variants. Mendelian inheritance logic c...
-
Article
Open AccessEvaluation of the upregulation and surface expression of hypoxanthine guanine phosphoribosyltransferase in acute lymphoblastic leukemia and Burkitt’s B cell lymphoma
The aim of this study is to determine whether Hypoxanthine Guanine Phosphoribosyltransferase (HPRT) could be used as a biomarker for the diagnosis and treatment of B cell malignancies. With 4.3% of all new can...
-
Article
Open AccessDiverse approaches to predicting drug-induced liver injury using gene-expression profiles
Drug-induced liver injury (DILI) is a serious concern during drug development and the treatment of human disease. The ability to accurately predict DILI risk could yield significant improvements in drug attrit...
-
Article
Open AccessFunctional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line
Ovarian cancer is a significant cancer-related cause of death in women worldwide. The most used chemotherapeutic regimen is based on carboplatin (CBDCA). However, CBDCA resistance is the main obstacle to a bet...
-
Article
Publisher Correction: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
In the version of this article originally published, the color key in Fig. 1a was wrong. In the Cytogenetics key, the box over t(8;21) originally was green. It should have been red, matching the color of the s...
-
Article
Open AccessCorrection to: Membrane expression of thymidine kinase 1 and potential clinical relevance in lung, breast, and colorectal malignancies
Following publication of the original article [1], the authors would like to make an amendment to the Acknowledgements section.
-
Article
Open AccessPotential new biomarkers for endometrial cancer
Incidence of endometrial cancer are rising both in the United States and worldwide. As endometrial cancer becomes more prominent, the need to develop and characterize biomarkers for early stage diagnosis and t...
-
Article
Open AccessMembrane expression of thymidine kinase 1 and potential clinical relevance in lung, breast, and colorectal malignancies
Lung, breast, and colorectal malignancies are the leading cause of cancer-related deaths in the world causing over 2.8 million cancer-related deaths yearly. Despite efforts to improve prevention methods, early...
-
Article
Open AccessCurated compendium of human transcriptional biomarker data
One important use of genome-wide transcriptional profiles is to identify relationships between transcription levels and patient outcomes. These translational insights can guide the development of biomarkers fo...
-
Article
Erratum: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
Nat. Med.; 10.1038/nm.4439; corrected online 1 January 2018 In the version of this article initially published online, Figure 1a has two black boxes in the key that are labeled as 'Unknown'; these boxes should...
-
Article
Open AccessPublisher Correction: Combating subclonal evolution of resistant cancer phenotypes
The originally published version of this Article contained an error in Figure 4. In panel a, grey boxes surrounding the subclones associated with patients #2 and #4 obscured adjacent portions of the heatmap. T...
-
Article
The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
A comprehensive molecular analysis of almost 1,000 pediatric subjects with acute myeloid leukemia (AML) uncovers widespread differences in pediatric AML as compared to adult AML, including a higher frequency o...
-
Article
Open AccessClassifying cancer genome aberrations by their mutually exclusive effects on transcription
Malignant tumors are typically caused by a conglomeration of genomic aberrations—including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemothe...
-
Article
Open AccessCombating subclonal evolution of resistant cancer phenotypes
Metastatic breast cancer remains challenging to treat, and most patients ultimately progress on therapy. This acquired drug resistance is largely due to drug-refractory sub-populations (subclones) within heter...
-
Article
Open AccessActivity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes
The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components,...
-
Article
Open AccessA cloud-based workflow to quantify transcript-expression levels in public cancer compendia
Public compendia of sequencing data are now measured in petabytes. Accordingly, it is infeasible for researchers to transfer these data to local computers. Recently, the National Cancer Institute began explori...
-
Article
Open AccessTools and techniques for computational reproducibility
When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can re...
-
Article
Open AccessGene-expression patterns in peripheral blood classify familial breast cancer susceptibility
Women with a family history of breast cancer face considerable uncertainty about whether to pursue standard screening, intensive screening, or prophylactic surgery. Accurate and individualized risk-estimation ...
-
Article
Open AccessInferring pathway dysregulation in cancers from multiple types of omic data
Although in some cases individual genomic aberrations may drive disease development in isolation, a complex interplay among multiple aberrations is common. Accordingly, we developed Gene Set Omic Analysis (GSO...
-
Article
Robust meta-analysis shows that glioma transcriptional subty** complements traditional approaches
Gliomas traditionally have been sub-classified based on histopathological observations. However, this approach is subject to inter-observer variability, and histopathological features may not reflect the biolo...
