A5018308750- Theoretical and Computational Physics
- Quantum Chromodynamics and Particle Interactions
- Cancer Genomics and Diagnostics
- Particle physics theoretical and experimental studies
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Physics of Superconductivity and Magnetism
- Lung Cancer Treatments and Mutations
- Breast Cancer Treatment Studies
- Stochastic processes and statistical mechanics
- Parallel Computing and Optimization Techniques
- Black Holes and Theoretical Physics
- Renal cell carcinoma treatment
- Quantum many-body systems
- Interconnection Networks and Systems
- Ferroptosis and cancer prognosis
- AI in cancer detection
- COVID-19 epidemiological studies
- Cancer Immunotherapy and Biomarkers
- RNA modifications and cancer
- Complex Network Analysis Techniques
- Advanced Breast Cancer Therapies
- High-Energy Particle Collisions Research
- Cancer Cells and Metastasis
- Cancer-related molecular mechanisms research
Rutgers, The State University of New Jersey
2015-2024
Rutgers Cancer Institute of New Jersey
2014-2023
Institute for Advanced Study
2005-2023
Boston University
2006-2023
Center for Systems Biology
2007-2023
Cancer Institute of Florida
2007-2023
University of California, San Diego
1987-2021
Moores Cancer Center
2020
UC San Diego Health System
2020
Rutgers Sexual and Reproductive Health and Rights
2014-2019
Background To improve cancer therapy, it is critical to target metastasizing cells. Circulating tumor cells (CTCs) are rare found in the blood of patients with solid tumors and may play a key role dissemination. Uncovering CTC phenotypes offers potential avenue inform treatment. However, transcriptional profiling limited by leukocyte contamination; an approach surmount this problem single cell analysis. Here we demonstrate feasibility performing high dimensional profiling, providing early...
This paper gives an overview of the BlueGene/L Supercomputer. is a jointly funded research partnership between IBM and Lawrence Livermore National Laboratory as part United States Department Energy ASCI Advanced Architecture Research Program. Application performance scaling studies have recently been initiated with partners at number academic government institutions, including San Diego Supercomputer Center California Institute Technology. massively parallel system 65,536 nodes based on new...
Antibodies that target the immune checkpoint receptor programmed cell death protein 1 (PD-1) have resulted in prolonged and beneficial responses toward a variety of human cancers. However, anti-PD-1 therapy some patients provides no benefit and/or results adverse side effects. The factors determine whether will be drug sensitive or resistant are not fully understood; therefore, genomic assessment exceptional responders can provide important insight into patient response. Here, we identified...
Clear cell renal carcinoma (ccRCC) is the predominant RCC subtype, but even within this classification, natural history heterogeneous and difficult to predict. A sophisticated understanding of molecular features most discriminatory for underlying tumor heterogeneity should be predicated on identifiable biologically meaningful patterns gene expression. Gene expression microarray data were analyzed using software that implements iterative unsupervised consensus clustering algorithms identify...
Human endogenous retroviruses (hERVs) are remnants of exogenous that have integrated into the genome throughout evolution. We developed a computational workflow, hervQuant, which identified more than 3,000 transcriptionally active hERVs within The Cancer Genome Atlas (TCGA) pan-cancer RNA-Seq database. hERV expression was associated with clinical prognosis in several tumor types, most significantly clear cell renal carcinoma (ccRCC). explored two mechanisms by may influence immune...
Abstract Response to immune checkpoint therapy can be associated with a high mutation burden, but other mechanisms are also likely important. We identified patient metastatic gastric cancer meaningful clinical benefit from treatment the anti–programmed death–ligand 1 (PD-L1) antibody avelumab. This tumor showed no evidence of burden or mismatch repair defect was strongly positive for presence Epstein-Barr virus (EBV) encoded RNA. Analysis The Cancer Genome Atlas data (25 EBV+, 80...
It is well known that the dinucleotide CpG under-represented in genomic DNA of many vertebrates. This commonly thought to be due methylation cytosine residues this and corresponding high rate deamination 5-methycytosine, which lowers frequency DNA. Surprisingly, single-stranded RNA viruses replicate these vertebrate hosts also have a very low presence dinucleotides their genomes. Viruses are obligate intracellular parasites evolution virus inexorably linked nature fate its host. One...
The identification of phenotypic changes in breast cancer (BC) histopathology on account corresponding molecular is significant clinical importance predicting disease outcome. One such example the presence lymphocytic infiltration (LI) histopathology, which has been correlated with nodal metastasis and distant recurrence HER2+ BC patients. In this paper, we present a computer-aided diagnosis (CADx) scheme to automatically detect grade extent LI digitized histopathology. Lymphocytes are first...
Abstract Background MicroRNA regulate mRNA levels in a tissue specific way, either by inducing degradation of the transcript or inhibiting translation transcription. Putative targets microRNA identified from seed sequence matches are available many databases. However, such have high false positive rate and cannot identify specificity regulation. Results We describe simple method to direct dysregulated cancers expression level measurements patient matched tumor/normal samples. The word...
<i>Caenorhabditis elegans</i> is a powerful model for analysis of the conserved mechanisms that modulate healthy aging. In aging nematode nervous system, neuronal death and/or detectable loss processes are not readily apparent, but because dendrite restructuring and synaptic integrity hypothesized to contribute human brain decline dysfunction, we combined fluorescence microscopy electron (EM) screen at high resolution system changes. We report two major components morphological change in...
Abstract Gene expression analysis has identified biologically relevant subclasses of breast cancer. However, most classification schemes do not robustly cluster all HER2+ cancers, in part due to limitations and bias clustering techniques used. In this article, we propose an alternative approach that first separates the tumors using a gene amplification signal for Her2/neu amplicon genes then applies consensus ensemble separately HER2− clusters look further substructure. We applied procedure...
The presence of lymphocytic infiltration (LI) has been correlated with nodal metastasis and tumor recurrence in HER2+ breast cancer (BC). ability to automatically detect quantify extent LI on histopathology imagery could potentially result the development an image based prognostic tool for human epidermal growth factor receptor-2 (HER2+) BC patients. Lymphocyte segmentation hematoxylin eosin (H&E) stained images is complicated by similarity appearance between lymphocyte nuclei other...
Although a subset of clear cell renal carcinoma (ccRCC) patients respond to immune checkpoint blockade (ICB), predictors response remain uncertain. We investigated whether abnormal expression endogenous retroviruses (ERVs) in tumors is associated with local activation (ICA) and ICB. Twenty potentially immunogenic ERVs (πERVs) were identified ccRCC The Cancer Genome Atlas data set, stratified into 3 groups based on their levels. πERV-high showed increased infiltration, pathway upregulation,...
We study a simple generalization of Wilson's SU(2) lattice gauge theory. In various limits the model reduces to usual SU(2), SO(3), or ${Z}_{2}$ models. Using Monte Carlo techniques on four-dimensional lattice, we follow known SO(3) and first-order transitions into phase diagram. They merge at triple point continue together critical end point. The peak in specific heat is shadow this nearby singularity.
Glutaminase (GLS) isoenzymes GLS1 and GLS2 are key enzymes for glutamine metabolism. Interestingly, display contrasting functions in tumorigenesis with elusive mechanism; promotes tumorigenesis, whereas exhibits a tumor-suppressive function. In this study, we found that but not binds to small GTPase Rac1 inhibits its interaction activators guanine-nucleotide exchange factors, which turn suppress cancer metastasis. This function of is independent glutaminase activity. Furthermore, decreased...
This paper gives an overview of the BlueGene/L Supercomputer. is a jointly funded research partnership between IBM and Lawrence Livermore National Laboratory as part United States Department Energy ASCI Advanced Architecture Research Program. Application performance scaling studies have recently been initiated with partners at number academic government institutions,including San Diego Supercomputer Center California Institute Technology. massively parallel system 65,536 nodes based on new...
We consider 1+1-dimensional QCD coupled to Majorana fermions in the adjoint representation of gauge group $SU(N)$. Pair creation partons (fermion quanta) is not suppressed large-$N$ limit, where glueball-like bound states become free. In this limit spectrum given by a linear \lc\ Schr\" odinger equation, which we study numerically using discretized \lcq. find discrete states, with logarithm level density growing approximately linearly mass. The wave function typical excited state complicated...
We have created a stand-alone software tool, ConsensusCluster, for the analysis of high-dimensional single nucleotide polymorphism (SNP) and gene expression microarray data. Our implements consensus clustering algorithm principal component to stratify data into given number robust clusters. The robustness is achieved by combining results from sample resampling as well averaging over various algorithms parameter settings achieve accurate, stable results. implemented several different in...