A5068361263- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Genetic Mapping and Diversity in Plants and Animals
- Chronic Lymphocytic Leukemia Research
- Gut microbiota and health
- Genetic factors in colorectal cancer
- Genetic Associations and Epidemiology
- Genomics and Chromatin Dynamics
- Algorithms and Data Compression
- Molecular Biology Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- Evolution and Genetic Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Fractal and DNA sequence analysis
- Single-cell and spatial transcriptomics
- Pancreatic and Hepatic Oncology Research
- RNA and protein synthesis mechanisms
- Genetic and phenotypic traits in livestock
- Advanced Breast Cancer Therapies
- Data Mining Algorithms and Applications
- Lung Cancer Treatments and Mutations
- CAR-T cell therapy research
IBM (United States)
2015-2024
IBM Research - Thomas J. Watson Research Center
2013-2024
Alliance for Safe Kids
2019-2022
Columbia University Irving Medical Center
2017
New York Genome Center
2017
Memorial Sloan Kettering Cancer Center
2017
Howard Hughes Medical Institute
2017
A.S. Watson (Netherlands)
2016
University of Palermo
2007-2015
Universitat Pompeu Fabra
2011
Abstract Background Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated type. The availability of its genome sequence and methods for identifying genes responsible important traits will aid researchers breeders. Results We describe sequencing assembly 1-6. is 445 Mbp, which significantly larger than a sequenced Criollo cultivar, more typical other cultivars. chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 with contig N50 84.4 kbp, scaffold 34.4...
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,...
The inference of the number clusters in a dataset, fundamental problem Statistics, Data Analysis and Classification, is usually addressed via internal validation measures. stated quite difficult, particular for microarrays, since inferred prediction must be sensible enough to capture inherent biological structure e.g., functionally related genes. Despite rich literature present that area, identification an measure both fast precise has proved elusive. In order partially fill this gap, we...
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...
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)...
Recent advances in sequencing technology have resulted the dramatic increase of data, which, turn, requires efficient management computational resources, such as computing time, memory requirements well prototyping pipelines.We present GenomicTools, a flexible platform, comprising both command-line set tools and C++ API, for analysis manipulation high-throughput data DNA-seq, RNA-seq, ChIP-seq MethylC-seq. GenomicTools implements variety mathematical operations between sets genomic regions...
Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It also question Statistics, Data Analysis and Classification, particular with regard to prediction of number clusters dataset, usually established via internal validation measures. Despite wealth measures available literature, new ones have been recently proposed, some them specifically data. We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure Merit),...
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...
Compiling a comprehensive list of cancer driver genes is imperative for oncology diagnostics and drug development. While are typically discovered by analysis tumor genomes, infrequently mutated often evade detection due to limited sample sizes. Here, we address size limitations integrating genomics data with wide spectrum gene-specific properties search rare drivers, functionally classify them, detect features characteristic genes. We show that our approach, CAnceR geNe similarity-based...
Abstract In response to the ongoing global pandemic, characterizing molecular-level host interactions of new coronavirus SARS-CoV-2 responsible for COVID-19 has been at center unprecedented scientific focus. However, when virus enters body it also interacts with micro-organisms already inhabiting host. Understanding virus-host-microbiome can yield additional insights into biological processes perturbed by viral invasion. Alterations in gut microbiome species and metabolites have noted during...
GWAS focuses on significance loosing false positives; machine learning probes sub-significant features relying predictivity. Yet, these are far from orthogonal. We sought to explore how inform each other in sub-genome-wide significant situations define relevance for predictive features. introduce the SVM-based RubricOE that selects heavily cross-validated feature sets, and LDpred2 PRS as a strong contrast SVM, Our Alzheimer's test case notoriously lacks genetic signals except few very...
Abstract Motivation: Information-theoretic and compositional analysis of biological sequences, in terms k-mer dictionaries, has a well established role genomic proteomic studies. Much less so epigenomics, although the k-mers chromatin organization nucleosome positioning is particularly relevant. Fundamental questions concerning informational content structure favouring disfavoring sequences with respect to their basic building blocks still remain open. Results: We present first on...
Reed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy of the temperate regions world. Despite its economic importance, it lacking in public genomic data. We explore comparative exomics cultivars context response to salt exposure. The limited data set poses challenges computational pipeline. As a prerequisite for study, we generate Phalaris reference transcriptome sequence, one first steps addressing issue paucity processed this species. In addition,...
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...
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...