David Van Den Berg
A5085453531- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- Genetic Associations and Epidemiology
- RNA modifications and cancer
- BRCA gene mutations in cancer
- Ovarian cancer diagnosis and treatment
- Genetic factors in colorectal cancer
- Cancer-related molecular mechanisms research
- Cancer-related Molecular Pathways
- Genomics and Chromatin Dynamics
- Medical Imaging and Pathology Studies
- Occupational and environmental lung diseases
- Bladder and Urothelial Cancer Treatments
- Genomic variations and chromosomal abnormalities
- Cancer Risks and Factors
- DNA Repair Mechanisms
- Acute Myeloid Leukemia Research
- Multiple Myeloma Research and Treatments
- Cancer-related gene regulation
- Genomics and Rare Diseases
- Breast Cancer Treatment Studies
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Glioma Diagnosis and Treatment
- Global Cancer Incidence and Screening
Brigham and Women's Hospital
2013-2024
Harvard University
2013-2024
University of Southern California
2014-2023
Cancer Research UK
2009-2023
British Heart Foundation
2023
University of Glasgow
2023
Thrombolysis in Myocardial Infarction Study Group
2022
Utrecht University
1965-2022
Radboud University Medical Center
2013-2018
Radboud University Nijmegen
2013-2018
We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- sequencing-based technologies. Uterine serous tumours ∼25% high-grade endometrioid had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, frequent TP53 mutations. Most alterations or mutations, but mutations in PTEN, CTNNB1, PIK3CA, ARID1A KRAS novel the SWI/SNF chromatin remodelling complex gene ARID5B....
Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents have been approved for treatment disease. As part The Cancer Genome Atlas project, we report here an integrated analysis 131 urothelial carcinomas to provide comprehensive landscape molecular alterations. There were statistically significant recurrent mutations in 32 genes, including multiple genes involved cell-cycle regulation,...
We propose a novel approach to background correction for Infinium HumanMethylation data account technical variation in fluorescence signal. Our capitalizes on new use the I design bead types measure non-specific colour channel opposite of their (Cy3/Cy5). This provides tens thousands features measuring instead much smaller number negative control probes platforms (n = 32 HumanMethylation27 and n 614 HumanMethylation450, respectively). compare performance our methods with existing approaches,...
Significance Brain-inspired computing seeks to develop new technologies that solve real-world problems while remaining grounded in the physical requirements of energy, speed, and size. Meeting these challenges requires high-performing algorithms are capable running on efficient hardware. Here, we adapt deep convolutional neural networks, which today’s state-of-the-art approach for machine perception many domains, perform classification tasks neuromorphic hardware, is most platform networks....
We present the first gesture recognition system implemented end-to-end on event-based hardware, using a TrueNorth neurosynaptic processor to recognize hand gestures in real-time at low power from events streamed live by Dynamic Vision Sensor (DVS). The biologically inspired DVS transmits data only when pixel detects change, unlike traditional frame-based cameras which sample every fixed frame rate. This sparse, asynchronous representation lets operate much lower than cameras. However, of...
Colorectal cancer (CRC) is a heterogeneous disease in which unique subtypes are characterized by distinct genetic and epigenetic alterations. Here we performed comprehensive genome-scale DNA methylation profiling of 125 colorectal tumors 29 adjacent normal tissues. We identified four methylation-based subgroups CRC using model-based cluster analyses. Each subtype shows characteristic clinical features, indicating that they represent biologically subgroups. A CIMP-high (CIMP-H) subgroup,...
Abstract Background Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity mortality. Consequently, identification of genetic environmental contributors to the variation in these measures populations has become a major goal field. Results Leveraging SNP more than 40,000 individuals, we identify 137 genome-wide significant loci, which 113 novel, association study (GWAS) meta-analyses four epigenetic clocks surrogate markers for granulocyte...
Models of visual attention postulate the existence a saliency map whose function is to guide and gaze most conspicuous regions in scene. Although cortical representations have been reported, there mounting evidence for subcortical mechanism, which pre-dates evolution neocortex. Here, we conduct strong test hypothesis by comparing output well-established computational model with activation neurons primate superior colliculus (SC), midbrain structure associated gaze, while monkeys watched...
Abstract Background Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10−8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery additional susceptibility may capture unexplained familial risk. Methods We conducted a GWAS in European descent CRC cases and control subjects using discovery–replication design, followed by examination novel findings multiethnic sample (cumulative n = 163 315). In stage (36 948...
Abstract Substantial experimental evidence indicates that the hormonal form of vitamin D promotes differentiation and inhibits proliferation, invasiveness, metastasis human prostatic cancer cells. Results from epidemiologic studies status and/or receptor (VDR) polymorphisms prostate risk have been mixed. We conducted a population-based, case-control study advanced among men ages 40 to 79 years San Francisco Bay area. Interview data on lifetime sun exposure other factors were collected for...
Studies of related individuals have consistently demonstrated notable familial aggregation cancer. We aim to estimate the heritability and genetic correlation attributable additive effects common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites.
HNF1B is overexpressed in clear cell epithelial ovarian cancer, and we observed epigenetic silencing serous leading us to hypothesize that variation this gene differentially associates with cancer risk according histological subtype. Here comprehensively map respect analyse DNA methylation expression profiles across subtypes. Different single-nucleotide polymorphisms associate invasive (rs7405776 odds ratio (OR)=1.13, P=3.1 × 10−10) (rs11651755 OR=0.77, P=1.6 10−8) cancer. Risk alleles for...
Candidate gene and genome-wide association studies (GWAS) have identified 11 independent susceptibility loci associated with bladder cancer risk. To discover additional risk variants, we conducted a new GWAS of 2422 cases 5751 controls, followed by meta-analysis two independently published GWAS, resulting in combined analysis 6911 814 controls European descent. TaqMan genotyping 13 promising single nucleotide polymorphisms P < 1 × 10−5 was pursued follow-up set 801 1307 controls. Two...
Purpose After curative resection of gastric or gastroesophageal junction adenocarcinoma, Intergroup Trial 0116 (Phase III trial postoperative adjuvant radiochemotherapy for high risk and adenocarcinoma: Demonstrated superior survival patients who received chemoradiotherapy with bolus fluorouracil (FU) leucovorin (LV) compared surgery alone. CALGB 80101 (Alliance; Phase Adjuvant Chemoradiation Resection Gastric Gastroesophageal Adenocarcinoma) assessed whether a regimen that replaced FU plus...