Quang Tran
A5021784087- Genomics and Phylogenetic Studies
- Acute Myeloid Leukemia Research
- Protein Degradation and Inhibitors
- SARS-CoV-2 and COVID-19 Research
- Chromosomal and Genetic Variations
- Algorithms and Data Compression
- RNA and protein synthesis mechanisms
- Mosquito-borne diseases and control
- Gene expression and cancer classification
- Acute Lymphoblastic Leukemia research
- Genomics and Rare Diseases
- CRISPR and Genetic Engineering
- Cancer Genomics and Diagnostics
- Plant nutrient uptake and metabolism
- Computational Drug Discovery Methods
- Legume Nitrogen Fixing Symbiosis
- Advanced biosensing and bioanalysis techniques
- Endoplasmic Reticulum Stress and Disease
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- Genomics and Chromatin Dynamics
- Hippo pathway signaling and YAP/TAZ
- Insect symbiosis and bacterial influences
- Ginger and Zingiberaceae research
- Genomic variations and chromosomal abnormalities
St. Jude Children's Research Hospital
2021-2025
Agency for Science, Technology and Research
2023
Institut Pasteur
2020-2022
Centre National de la Recherche Scientifique
2020-2022
Université Paris Cité
2021-2022
Sorbonne Paris Cité
2021
Délégation Paris 7
2021
University of Memphis
2013-2020
A newly described coronavirus named severe acute respiratory syndrome 2 (SARS-CoV-2), which is the causative agent of disease 2019 (COVID-19), has infected over 2.3 million people, led to death more than 160,000 individuals and caused worldwide social economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for treatment COVID-19, nor there any vaccines that prevent infection SARS-CoV-2, efforts develop hampered by limited knowledge molecular details how SARS-CoV-2...
Small linear motifs targeting protein interacting domains called PSD‐95/Dlg/ZO‐1 (PDZ) have been identified at the C terminus of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) proteins E, 3a, and N. Using a high‐throughput approach affinity‐profiling against full human PDZome, we sixteen PDZ binders SARS‐CoV‐2 3A, N showing significant interactions with dissociation constants values ranging from 3 to 82 μ m . Six them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also...
Interferon restricts SARS-CoV-2 replication in cell culture, but only a handful of Stimulated Genes with antiviral activity against have been identified. Here, we describe functional CRISPR/Cas9 screen aiming at identifying restriction factors. We identify DAXX, scaffold protein residing PML nuclear bodies known to limit the DNA viruses and retroviruses, as potent inhibitor SARS-CoV human cells. Basal expression DAXX is sufficient SARS-CoV-2, over-expression further infection. an early,...
Abstract Arthropod-borne viruses pose a major threat to global public health. Thus, innovative strategies for their control and prevention are urgently needed. Here, we exploit the natural capacity of generate defective viral genomes (DVGs) detriment. While DVGs have been described most viruses, identifying which, if any, can be used as therapeutic agents remains challenge. We present combined experimental evolution computational approach triage DVG sequence space pinpoint fittest deletions,...
The portal venous circulation provides a conduit for pancreatic ductal adenocarcinoma (PDAC) tumor cells to the liver parenchyma sinusoids, frequent site of metastasis. Turbulent flow in promotes retention PDAC shed circulating (CTC) and myeloid-derived immunosuppressor (MDSC). Excessive colony stimulating factor-1 receptor (CSF1R) signaling can induce myeloid differentiation MDSC transformation fibroblasts (M-FB). Interactions between CTC M-FB blood formation immunoresistant clusters that...
Abstract Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define subtype, predict outcome, persist treatment, and can be ideal therapeutic targets. However, mechanistic understanding the etiology oncogenic remains elusive. Here we report a comprehensive detection 272 fusion gene pairs by using tumor transcriptome sequencing data from 5190 patients. We identify diverse factors, including translation frame, protein domain, splicing, length,...
Abstract Despite high cure rates of >90% for newly diagnosed childhood B-ALL, outcomes remain poor relapsed patients. Prior genomics studies have revealed 12 genes with mutations enriched at relapse. However, the resistance mechanisms >50% relapses elusive. Here we performed WGS and RNA sequencing on initial diagnostic, relapse, remission specimens from 183 patients enrolled in AALL1331 trial Children’s Oncology Group. In this cohort, 96 cases did not harbor a known mutation....
Most current approach to metagenomic classification employ short next generation sequencing (NGS) reads that are present in samples identify unique genomic regions. NGS reads, however, might not be long enough differentiate similar genomes. This suggests a potential for using longer improve performance. Presently, tend have higher rate of errors. Thus, given the pros and cons, it remains unclear which types is better classification. We compared two taxonomic protocols: traditional...
Quantification and identification of microbial genomes based on next-generation sequencing data is a challenging problem in metagenomics. Although current methods have mostly focused analyzing bacteria whose been sequenced, such analyses are, however, complicated by the presence unknown or not sequence. We propose method for detecting environmental samples. Our approach unique its utilization short reads only from 16S rRNA genes, entire genomes. show that genes retain sufficient information...
Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort quantify the relationship between complexity of and difficulty short-read alignment. Existing measures sequence seem unsuitable for understanding quantification this relationship. We investigated several found length-sensitive had highest correlation accuracy In particular, rate distinct substrings length k, where k similar read...
Abstract SARS-CoV-2 infection of human cells is initiated by the binding viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen uncover druggable pathways controlling cells. found that BRD2 required for ACE2 transcription in lung epithelial and cardiomyocytes, inhibitors currently evaluated clinical trials potently block endogenous expression cells, including those nasal epithelia. Moreover, pharmacological inhibition with drug ABBV-744 inhibited...
Abstract Small linear motif targeting protein interacting domains called PDZ have been identified at the C-terminus of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins E, 3a, and N. Using a high-throughput approach affinity-profiling against full human PDZome, we sixteen binders SARS-CoV-2 3A N showing significant interactions with dissociation constants values ranging from 3 μM to 82 μM. Six them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also recognized by SARS-CoV...
The alignment of short reads generated by next-generation sequencers to genomes is an important problem in many biomedical and bioinformatics applications. Although proposed methods work very well on narrow ranges read lengths, they tend suffer performance quality for outside these ranges. We introduce RandAL, a novel method that aligns DNA sequences reference genomes. Our approach utilizes two FM indices facilitate efficient bidirectional searching, pruning heuristic speed up the computing...
Efforts such as International HapMap Project and 1000 Genomes resulted in a catalog of millions single nucleotides insertion/deletion (INDEL) variants the human population. Viewed reference existing variants, this resource commonly serves gold standard for studying developing methods to detect genetic variants. Our analysis revealed that contained thousands INDELs were constructed biased manner. This bias occurred at level aligning short reads genomes The is caused by existence many...
Although it is known that aligning short reads to reference genomes becomes harder if such are embedded with complex repeat structures, there has been little effort quantify this intuition. We investigated several measures of complexity, employed 10 popular short-read aligners align a large number diverse genomes, and found unlike existing notions proposed notion length sensitive correlated highly the hardness alignment. This result enables speedy estimation alignment without millions...
Background The effectiveness and accuracy of aligning short reads to genomes have an important impact on many applications that rely next-generation sequencing data. computational requirements material cost for largescale is also expensive. To prevent wasted time resources reads, we investigated the different measures genome complexity [1] correlated best performance alignment propose a linear model each method [2].
Abstract Background: Extensive efforts in the past decade have revolutionized our understanding of genetic underpinnings childhood malignancies and identified numerous driver alterations that can provide potential targets for novel therapy are excellent biomarkers disease monitoring. For these purposes, a whole genome or exome sequencing approach be resource prohibitive. Numerous gene panels developed adult cancers to address challenges. Due dramatic differences landscapes between pediatric...
Real-time visual feedback from catheterization analysis is crucial for enhancing surgical safety and efficiency during endovascular interventions. However, existing datasets are often limited to specific tasks, small scale, lack the comprehensive annotations necessary broader intervention understanding. To tackle these limitations, we introduce CathAction, a large-scale dataset Our CathAction encompasses approximately 500,000 annotated frames action understanding collision detection, 25,000...
Defining the precise location of structural variations (SVs) at single-nucleotide breakpoint resolution is a challenging problem due to large gaps in alignment. Previously, Alignment with Gap Excision (AGE) enabled us define breakpoints SVs resolution; however, AGE requires vast amount memory when aligning pair long sequences. To address this, we developed memory-efficient implementation-LongAGE-based on classical Hirschberg algorithm. We demonstrate an application LongAGE for resolving...
Abstract Interferon restricts SARS-CoV-2 replication in cell culture, but only a handful of Stimulated Genes with antiviral activity against have been identified. Here, we describe functional CRISPR/Cas9 screen aiming at identifying restriction factors. We identified DAXX, scaffold protein residing PML nuclear bodies known to limit the DNA viruses and retroviruses, as potent inhibitor SARS-CoV human cells. Basal expression DAXX was sufficient SARS-CoV-2, over-expression further restricted...