Timothy R. Chu
A5035625734- Cancer Genomics and Diagnostics
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Biology Techniques and Applications
- BRCA gene mutations in cancer
- Prostate Cancer Treatment and Research
- Global Cancer Incidence and Screening
- Multiple Myeloma Research and Treatments
- Genetic factors in colorectal cancer
- RNA modifications and cancer
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Cancer-related molecular mechanisms research
- Bladder and Urothelial Cancer Treatments
- Law, AI, and Intellectual Property
- CRISPR and Genetic Engineering
- Takotsubo Cardiomyopathy and Associated Phenomena
- Bacterial Genetics and Biotechnology
- Genomics and Rare Diseases
- Epigenetics and DNA Methylation
- MicroRNA in disease regulation
- Cancer Mechanisms and Therapy
- Biomedical Text Mining and Ontologies
- Urological Disorders and Treatments
- Gene Regulatory Network Analysis
- Drug Transport and Resistance Mechanisms
- Cardiac electrophysiology and arrhythmias
New York Genome Center
2020-2025
University of New Mexico
2017
New York University
2015
Article17 November 2015Open Access An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network Mario L Arrieta-Ortiz Center for Genomics and Systems Biology, Department New York University, York, NY, USA Search more papers by this author Christoph Hafemeister Ashley Rose Bate Timothy Chu Alex Greenfield Bentley Shuster Samantha N Barry Matthew Gallitto Brian Liu Thadeous Kacmarczyk Francis Santoriello Jie Chen Christopher DA Rodrigues Microbiology...
Women of sub-Saharan African descent have disproportionately higher incidence triple-negative breast cancer (TNBC) and TNBC-specific mortality across all populations. Population studies show racial differences in TNBC biology, including prevalence basal-like quadruple-negative subtypes Americans (AA). However, previous investigations relied on self-reported race (SRR) primarily U.S. Due to heterogeneous genetic admixture biological consequences social determinants, the true association...
Advanced urothelial cancer is a frequently lethal disease characterized by marked genetic heterogeneity
Background: Patient-derived cancer models advance therapeutic development and are essential to studies of treatment resistance mechanisms. The Human Cancer Models Initiative (HCMI) has created 665 patient-derived models, including organoids, neurospheres, conditionally reprogrammed cells, all paired with patient tumors clinical annotations. This resource provides an opportunity study genomic conservation divergence during model at scale in a large pan-cancer cohort matched tumor-model pairs....
Here, we present Lancet2, an open-source somatic variant caller designed to improve detection of small variants in short-read sequencing data. Lancet2 introduces significant enhancements, including: 1) Improved discovery and genotyping through partial order multiple sequence alignment assembled haplotype contigs re-alignment sample reads the best supporting allele. 2) Optimized scoring with Explainable Machine Learning models leading better filtering throughout sensitivity scale. 3)...
Aggressive variant and androgen receptor (AR)-independent castration resistant prostate cancers (CRPC) represent the most significant diagnostic therapeutic challenges in cancer. This study examined a case of simultaneous progression both adenocarcinoma squamous tumors from same common origin. Using whole-genome transcriptome sequencing 17 samples collected over >6 years, we established clonal relationship all samples, defined shared complex structural variants, demonstrated divergent...
Abstract Advancing precision oncology requires a diverse and robust repository of patient-derived cancer models that faithfully reflect the clinical, therapeutic, molecular attributes patients’ tumor. Traditional models, while invaluable, often lack sufficient clinical data fail to capture genetic phenotypic complexity human cancers, limiting their translational relevance. To address these challenges, Human Cancer Models Initiative (HCMI) generated 665 next-generation from over 2,500 donors...
Intracranial metastases in prostate cancer are uncommon but clinically aggressive. A detailed molecular characterization of intracranial would improve our understanding their pathogenesis and the search for new treatment strategies. We evaluated clinical characteristics 36 patients with metastatic to either dura or brain parenchyma. performed whole genome sequencing (WGS) 10 metastases, as well WGS primary tumors from men who later developed disease (n = 6) nonbrain 36). This first study led...
Patients with an alcohol use disorder experiencing acute intoxication or withdrawal may be at risk for electrocardiograph (ECG) abnormalities, including prolongation of repolarization (long QTc [corrected QT]) that contribute to arrhythmias and associated a threefold increase in the likelihood sudden cardiac events. coronary syndrome have prolonged as well. To our knowledge, no previous studies compared ACS ethanol (EtOH) syndromes emergency department (ED). The purpose study was compare...
You have accessJournal of UrologyProstate Cancer: Localized: Surgical Therapy II (MP52)1 May 2024MP52-11 EXTENDED PRESERVATION OF THE PROSTATIC URETHRA MITIGATES DISADVANTAGE INNATE SHORT MEMBRANOUS URETHRAL LENGTH Narmina Khanmammadova, Andrei D. Cumpanas, Daniel Jiang, Andrew Shea Afyouni, Mitchell O'Leary, Timothy Chu, Ashley Gao, Jacob Tsai, Tuan Thanh Nguyen, Sohrab Naushad Ali, Mohammed Shahait, and David I. Lee KhanmammadovaNarmina Khanmammadova , CumpanasAndrei Cumpanas JiangDaniel...
Abstract Advanced urothelial cancer is a frequently lethal disease characterized by marked genetic heterogeneity. In this study, we investigate the evolution of genomic signatures caused endogenous and external mutagenic stimuli their interplay with complex structural variants. We superimposed mutational phylogenetic analyses matched serial tumors from patients to define evolutionary patterns these processes. show that APOBEC3-induced mutations are clonal early, whereas bursts comprising...
ABSTRACT Women of sub-Saharan African ancestry have disproportionately higher incidence aggressive, early-onset Triple Negative Breast Cancer (TNBC), and TNBC mortality across all race groups. Population-based comparative studies show racial differences in tumor biology, with prevalence basal-like Quadruple-Negative subtypes Americans (AA). However, most investigations relied on self-reported (SRR) primarily United States (US) populations. given that genetic admixture AAs is extremely...
Abstract Background: Breast cancer (BC) is a leading cause of death in Ghana and around the world. Ghanaian women are diagnosed at younger ages with more aggressive Triple Negative BC (TNBC) subtype where West African ancestry associated advanced diagnosis higher mortality rates compared to age-matched European ancestry. Genomic comparisons tumors from show differences frequencies single nucleotide polymorphisms (SNP) copy number variations. These may contribute disparities disease treatment...
<div>Abstract<p>Women of sub-Saharan African descent have disproportionately higher incidence triple-negative breast cancer (TNBC) and TNBC-specific mortality across all populations. Population studies show racial differences in TNBC biology, including prevalence basal-like quadruple-negative subtypes Americans (AA). However, previous investigations relied on self-reported race (SRR) primarily U.S. Due to heterogeneous genetic admixture biological consequences social...
Supplementary Data from African Ancestry–Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome Women of Descent
Supplementary Figure from African Ancestry–Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome Women of Descent
Supplementary Figure from African Ancestry–Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome Women of Descent
<div>Abstract<p>Women of sub-Saharan African descent have disproportionately higher incidence triple-negative breast cancer (TNBC) and TNBC-specific mortality across all populations. Population studies show racial differences in TNBC biology, including prevalence basal-like quadruple-negative subtypes Americans (AA). However, previous investigations relied on self-reported race (SRR) primarily U.S. Due to heterogeneous genetic admixture biological consequences social...
Supplementary Data from African Ancestry–Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome Women of Descent