A5003192265- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Chronic Lymphocytic Leukemia Research
- Genetic factors in colorectal cancer
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Biology Techniques and Applications
- Gene expression and cancer classification
- Monoclonal and Polyclonal Antibodies Research
- Pancreatic and Hepatic Oncology Research
- Genetics, Aging, and Longevity in Model Organisms
- Single-cell and spatial transcriptomics
- Lung Cancer Treatments and Mutations
- Computational Drug Discovery Methods
- Cutaneous Melanoma Detection and Management
- Genomics and Phylogenetic Studies
- CAR-T cell therapy research
- Immunotherapy and Immune Responses
- Advanced Breast Cancer Therapies
- Cell Image Analysis Techniques
- Glycosylation and Glycoproteins Research
- Genomics and Rare Diseases
- HER2/EGFR in Cancer Research
- Metabolomics and Mass Spectrometry Studies
- Melanoma and MAPK Pathways
- Glioma Diagnosis and Treatment
IBM (United States)
2013-2024
IBM Research - Thomas J. Watson Research Center
2014-2023
Alliance for Safe Kids
2013-2019
Columbia University Irving Medical Center
2017
Howard Hughes Medical Institute
2017
Memorial Sloan Kettering Cancer Center
2017
New York Genome Center
2017
A.S. Watson (Netherlands)
2016
Clemson University
2014
Hunan Agricultural University
2014
From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation still needed characterize how used help produce functional organism (see Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for Caenorhabditis elegans genome, and The modENCODE Consortium 1787 Drosophila melanogaster full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites,...
Sacituzumab govitecan (SG), the first antibody-drug conjugate (ADC) approved for triple-negative breast cancer, incorporates anti-TROP2 antibody hRS7 conjugated to a topoisomerase-1 (TOP1) inhibitor payload. We sought identify mechanisms of SG resistance through RNA and whole-exome sequencing pretreatment postprogression specimens. One patient exhibiting de novo progression lacked TROP2 expression, in contrast robust expression focal genomic amplification TACSTD2/TROP2 observed with deep,...
Abstract Background Using next-generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data patients caregivers. Specifically, providing current, accurate information on newly approved therapies open clinical trials requires considerable manual curation performed mainly by human “molecular tumor boards” (MTBs). The purpose this study was determine the utility cognitive computing as Watson for Genomics (WfG) compared with...
Abstract Covalent inhibitors of Bruton tyrosine kinase (BTK) have transformed the therapy chronic lymphocytic leukemia (CLL), but continuous has been complicated by development resistance. The most common resistance mechanism in patients whose disease progresses on covalent BTK (BTKis) is a mutation 481 cysteine residue to which bind covalently. Pirtobrutinib highly selective, noncovalent BTKi with substantial clinical activity progressed BTKi, regardless status. Using vitro...
Acral melanoma, the most common melanoma subtype among non-White individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we perform integrative genomic and clinical profiling of acral melanomas from 104 patients treated in North America (n = 37) or China 67). We find that recurrent, late-arising focal amplifications cytoband 22q11.21 are a leading determinant inferior survival, strongly metastasis, linked to downregulation immunomodulatory...
Abstract Background Graphical models of network associations are useful for both visualizing and integrating multiple types association data. Identifying modules, or groups functionally related gene products, is an important challenge in analyzing biological networks. However, existing tools to identify modules insufficient when applied dense networks experimentally derived interaction To address this problem, we have developed agglomerative clustering method that able highly modular sets...
Motivation: Inferring how humans respond to external cues such as drugs, chemicals, viruses or hormones is an essential question in biomedicine. Very often, however, this cannot be addressed because it not possible perform experiments humans. A reasonable alternative consists of generating responses animal models and ‘translating’ those results The limitations translation, are far from clear, systematic assessments its actual potential urgently needed. sbv IMPROVER (systems biology...
Mating triggers physiological and behavioral changes in females. To understand how females effect these changes, we used microarray, proteomic, comparative analyses to characterize gene expression oviducts of mated unmated Drosophila The transition from non-egg laying egg elicits a distinct molecular profile the oviduct. Immune-related transcripts proteins involved muscle polarized epithelial function increase, whereas cell growth differentiation-related genes are down-regulated. Our...
The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine the field of toxicology, cannot be easily studied humans. Thus, biomedical research has continuously relied on animal models for studying impact these compounds attempted 'translate' results In this context, SBV IMPROVER (Systems Biology Verification Industrial Methodology PROcess VErification Research) collaborative initiative, which uses crowd-sourcing...
Cellular responses to carcinogens are typically studied in transformed cell lines, which do not reflect the physiological status of normal tissues. To address this question, we have characterized transcriptional program and cellular human lung WI-38 fibroblasts upon exposure ultimate carcinogen benzo[ a ]pyrene diol epoxide (BPDE). In contrast observations find that BPDE treatment induces strong inflammatory response these fibroblasts. Whole-genome microarrays show induction numerous...
To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each.Tumor DNA was analyzed by commercial targeted panel. In addition, tumor-normal whole-genome sequencing (WGS) RNA (RNA-seq). The WGS RNA-seq data were team of bioinformaticians cancer oncologists, separately IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants identifying drugs.More identified WGS/RNA analysis than panels. WGA completed...
Abstract Although the development of multiple primary tumors in smokers with lung cancer can be attributed to carcinogen-induced field cancerization, occurrence at presentation individuals EGFR -mutant who lack known environmental exposures remains unexplained. In present study, we identified ten patients early stage, resectable, non-small cell presented multiple, anatomically distinct, tumors. We analyzed phylogenetic relationships among from each patient using whole-exome sequencing (WES)...
Biological networks with a structured syntax are powerful way of representing biological information generated from high density data; however, they can become unwieldy to manage as their size and complexity increase. This article presents crowd-verification approach for the visualization expansion networks. Web-based graphical interfaces allow causal correlative relationships represented using Expression Language (BEL). Crowdsourcing principles enable participants communally annotate these...
Sampling circulating tumor DNA (ctDNA) using liquid biopsies offers clinically important benefits for monitoring cancer progression. A single ctDNA sample represents a mixture of shed from all known and unknown lesions within patient. Although shedding levels have been suggested to hold the key identifying targetable uncovering treatment resistance mechanisms, amount by any one specific lesion is still not well characterized. We designed Lesion Shedding Model (LSM) order strongest poorest...
In recent years, there has been tremendous progress in the development of quantum computing hardware, algorithms and services leading to expectation that near future computers will be capable performing simulations for natural science applications, operations research, machine learning at scales mostly inaccessible classical computers. Whereas impact already started recognized fields such as cryptanalysis, simulations, optimization among others, very little is known about full potential...
Abstract Motivation: Using gene expression to infer changes in protein phosphorylation levels induced cells by various stimuli is an outstanding problem. The intra-species challenge organized the IMPROVER consortium provided framework identify best approaches address this issue. Results: Rat lung epithelial were treated with 52 stimuli, and measured. Competing teams used data from 26 develop prediction models ranked based on performance for remaining stimuli. Three tied first place achieving...
Abstract Motivation: Animal models are widely used in biomedical research for reasons ranging from practical to ethical. An important issue is whether rodent predictive of human biology. This has been addressed recently the framework a series challenges designed by systems biology verification Industrial Methodology Process Verification Research (sbv IMPROVER) initiative. In particular, one sub-challenges was devoted prediction protein phosphorylation responses bronchial epithelial cells,...