Benjamin Groß
A5026873890- Cancer Genomics and Diagnostics
- Occupational and environmental lung diseases
- Medical Imaging and Pathology Studies
- Bioinformatics and Genomic Networks
- Lung Cancer Treatments and Mutations
- Gastric Cancer Management and Outcomes
- Radiomics and Machine Learning in Medical Imaging
- Esophageal Cancer Research and Treatment
- Ferroptosis and cancer prognosis
- Medical and Biological Sciences
- Epigenetics and DNA Methylation
- Cancer Immunotherapy and Biomarkers
- RNA modifications and cancer
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Genetic factors in colorectal cancer
- Historical Studies and Socio-cultural Analysis
- Genetics, Bioinformatics, and Biomedical Research
- Machine Learning in Healthcare
- Cancer Research and Treatments
- Health and Medical Research Impacts
- Gastrointestinal Tumor Research and Treatment
- Cancer-related Molecular Pathways
- Communism, Protests, Social Movements
- Glioma Diagnosis and Treatment
Memorial Sloan Kettering Cancer Center
2016-2025
Kettering University
2016-2025
Spectrum Research (United States)
2022-2024
Olympic Park Sports Medicine Centre
2023
Institute of Electrical and Electronics Engineers
2022-2023
American College of Clinical Pharmacy
2021-2023
Canadian Standards Association
2022-2023
Seokyeong University
2023
The University of Adelaide
2023
Rutgers, The State University of New Jersey
2023
Abstract The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to from more than 5,000 tumor samples 20 studies. significantly lowers the barriers between complex genomic and researchers who want rapid, intuitive, high-quality molecular profiles clinical attributes large-scale projects empowers translate these rich sets into biologic insights applications....
The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource exploring, visualizing, and analyzing multidimensional cancer genomics data. portal reduces molecular profiling data from tissues cell lines into readily understandable genetic, epigenetic, gene expression, proteomic events. query interface combined with customized storage enables researchers to interactively explore genetic alterations across samples, genes, pathways and, when available in the underlying...
<h2>Summary</h2> Papillary thyroid carcinoma (PTC) is the most common type of cancer. Here, we describe genomic landscape 496 PTCs. We observed a low frequency somatic alterations (relative to other carcinomas) and extended set known PTC driver include <i>EIF1AX</i>, <i>PPM1D</i>, <i>CHEK2</i> diverse gene fusions. These discoveries reduced fraction cases with unknown oncogenic from 25% 3.5%. Combined analyses variants, expression, methylation demonstrated that different groups lead...
Highlights•Alteration map of 10 signaling pathways across 9,125 samples from 33 cancer types•Reusable, curated pathway templates that include a catalogue driver genes•57% tumors have at least one potentially actionable alteration in these pathways•Co-occurrence alterations suggests combination therapy opportunitiesSummaryGenetic control cell-cycle progression, apoptosis, and cell growth are common hallmarks cancer, but the extent, mechanisms, co-occurrence differ between individual tumor...
We conducted comprehensive integrative molecular analyses of the complete set tumors in The Cancer Genome Atlas (TCGA), consisting approximately 10,000 specimens and representing 33 types cancer. performed clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, miRNA expression levels reverse-phase protein arrays, which all, except for revealed primarily organized by histology, tissue type, or anatomic origin. influence cell type was evident...
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition progenitor stem-cell-like features. Here, we provide novel stemness indices for assessing degree oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic epigenetic feature sets derived from non-transformed pluripotent stem cells their progeny. Using OCLR, were able identify previously undiscovered biological mechanisms...
The AACR Project GENIE is an international data-sharing consortium focused on generating evidence base for precision cancer medicine by integrating clinical-grade genomic data with clinical outcome tens of thousands patients treated at multiple institutions worldwide. In conjunction the first public release from approximately 19,000 samples, we describe goals, structure, and standards report conclusions high-level analysis initial phase data. We also provide examples utility data, such as...
Pathway Commons ( http://www.pathwaycommons.org ) is a collection of publicly available pathway data from multiple organisms. provides web-based interface that enables biologists to browse and search comprehensive pathways sources represented in common language, download site integrated bulk sets information standard or convenient formats web service software developers can use conveniently query access all data. Database providers share their via repository. Pathways include biochemical...
Aneuploidy, whole chromosome or arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression proliferation genes. Aneuploidy anti-correlated immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss 3p squamous We applied genome...
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings tumor-infiltrating lymphocytes (TILs) based on H&E from 13 tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches images. Affinity propagation revealed local spatial structure in patterns correlation with overall survival. map...
Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated 9,624 tumors across 33 cancer types using multiple fusion calling tools. identified a total 25,664 fusions, with 63% validation rate. Integration gene expression, copy number, and annotation data revealed that involving oncogenes tend to exhibit increased whereas tumor suppressors have the opposite effect. For kinases, we found 1,275 intact kinase domain, proportion which varied...
We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared distinguishing molecular characteristics gastrointestinal tract (GIACs). Hypermutated tumors were distinct regardless cancer type comprised those enriched for insertions/deletions, representing microsatellite instability cases with epigenetic silencing MLH1 in context CpG island methylator phenotype, plus elevated single-nucleotide variants associated mutations POLE. Tumors chromosomal diverse,...
Hotspot mutations in splicing factor genes have been recently reported at high frequency hematological malignancies, suggesting the importance of RNA cancer. We analyzed whole-exome sequencing data across 33 tumor types The Cancer Genome Atlas (TCGA), and we identified 119 with significant non-silent mutation patterns, including over-representation, recurrent loss function (tumor suppressor-like), or hotspot profile (oncogene-like). Furthermore, analysis revealed altered events associated...
Highlights•MYC paralogs are significantly amplified (28% of all samples)•MYC antagonists mutated (MGA, 4% samples) or deleted (MNT, 10% alterations mutually exclusive with PIK3CA, PTEN, APC, BRAF alterations•Expression analysis reveals pan-cancer and tumor-specific MYC-associated pathwaysSummaryAlthough the MYC oncogene has been implicated in cancer, a systematic assessment MYC, related transcription factors, co-regulatory proteins, forming proximal network (PMN), across human cancers is...
The incidence of esophagogastric cancer is rapidly rising, but only a minority patients derive durable benefit from current therapies. Chemotherapy as well anti-HER2 and PD-1 antibodies are standard treatments. To identify predictive biomarkers drug sensitivity mechanisms resistance, we implemented prospective tumor sequencing with metastatic cancer. There was no association between homologous recombination deficiency defects response to platinum-based chemotherapy. Patients microsatellite...
Abstract Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly biomolecular complexes, transport and catalysis events physical interactions involving proteins, DNA, RNA, small molecules (e.g. metabolites drug compounds). Data collected from multiple providers in standard formats, the Biological Exchange (BioPAX) language Proteomics Standards Initiative Molecular...
The role of enhancers, a key class non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization large number expressed enhancers genome-wide analysis 8928 tumor samples across 33 types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed most cancers. Across types, activity positively associated aneuploidy, but not mutation load, suggesting hypothesis centered...
Highlights•Classification of metabolic expression subtypes in 33 TCGA cancer types•Metabolic show consistent prognostic patterns across types•Analysis master regulators suggesting therapeutic targets•Metabolic associated with sensitivity to drugs clinical useSummaryMetabolic reprogramming provides critical information for oncology. Using molecular data 9,125 patient samples from The Cancer Genome Atlas, we identified tumor types based on mRNA seven major processes and assessed their...
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for large-scale discovery of splice-site-creating (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated clear evidence creating alternative splice junctions. TP53 and GATA3 26 18 SCMs, respectively, ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including...
Abstract Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude large-scale studies were conducted recently that have resulted in unprecedented volume whole transcriptome (RNA-seq) data, such as Genotype Tissue Expression project (GTEx) The Cancer Genome Atlas (TCGA). While these data offer new opportunities identify mechanisms underlying disease, comparison from different sources remains challenging,...
Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases Oncology (ICD-O), Systematized Nomenclature Medicine Clinical Terms (SNOMED-CT), National Institute Thesaurus (NCIt) provide large sets cancer terminologies but they lack a dynamic modernized platform that addresses the fast-evolving needs in clinical reporting genomic sequencing results associated research.To meet these needs, we have developed OncoTree, an...