Tsung-Yu Lu
A5071525669- Genetic Associations and Epidemiology
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Genetic Mapping and Diversity in Plants and Animals
- CRISPR and Genetic Engineering
- Genomics and Rare Diseases
- Chromosomal and Genetic Variations
- Insurance and Financial Risk Management
- Image Processing and 3D Reconstruction
- RNA modifications and cancer
- Genetic Neurodegenerative Diseases
- Handwritten Text Recognition Techniques
- Vehicle License Plate Recognition
- Genetics, Bioinformatics, and Biomedical Research
- Traffic Prediction and Management Techniques
- Natural Language Processing Techniques
- Facility Location and Emergency Management
- Genetic factors in colorectal cancer
- Evolution and Genetic Dynamics
- Emergency and Acute Care Studies
- Genomics and Chromatin Dynamics
- Forecasting Techniques and Applications
- Evacuation and Crowd Dynamics
- Traffic and Road Safety
- RNA and protein synthesis mechanisms
University of Southern California
2020-2023
Southern California University for Professional Studies
2021-2023
LAC+USC Medical Center
2021
National Tsing Hua University
2021
Ministry of Transportation and Communications
2015
National Taiwan University
2014-2015
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% genome: 26 million base pairs) integrate all forms genetic variation, even across complex loci. identified 107,590 structural variants (SVs), which 68% were not...
Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats extended segmental duplications 1,2 . Although resolution these regions in first complete assembly a genome—the Telomere-to-Telomere Consortium’s CHM13 (T2T-CHM13)—provided model their homology 3 , it remained unclear whether patterns were ancestral or maintained by ongoing recombination exchange. Here we show that contain...
Abstract The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. contains 47 phased, diploid assemblies from cohort of genetically diverse individuals. These cover more than 99% the expected sequence and are accurate at structural base-pair levels. Based on alignments assemblies, we generated that captures known variants haplotypes, reveals novel alleles structurally complex loci, adds 119 million base pairs euchromatic polymorphic 1,529 gene...
Abstract Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations mapping short-read sequencing data 1,2 . Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared pattern SNVs between unique duplicated regions 3,4 We find that are elevated 60% to estimate at least 23% this increase is due interlocus gene conversion (IGC) with up 4.3 megabase pairs SD sequence...
The objective of prehospital emergency medical services (EMSs) is to have a short response time. By increasing the operational efficiency, survival rate patients could potentially be increased. geographic information system (GIS) introduced in this study manage and visualize spatial distribution demand data forecasting results. A flexible model implemented GIS, through which training are prepared with user-desired sizes for grid discretized temporal steps. We applied moving average,...
Abstract Variable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences associations clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach mapping human reference is less effective for divergent sequences. In this work, we solve short reads a repeat-pangenome graph (RPGG), data structure...
Understanding the impact of DNA variation on human traits is a fundamental question in genetics. Variable number tandem repeats (VNTRs) make up ∼3% genome but are often excluded from association analysis owing to poor read mappability or divergent repeat content. Although methods exist estimate VNTR length short-read data, it known that VNTRs vary both and (motif) composition. Here, we use repeat-pangenome graph (RPGG) constructed 35 haplotype-resolved assemblies detect We align...
The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed k-mer indexing strategy for comparative analysis across multiple assemblies, including pangenome reference, GRCh38, and CHM13, telomere-to-telomere assembly. Our approach enabled us to identify valuable collection universally conserved sequences all referred as...
The objective for pre-hospital Emergency Medical Service (EMS) is to reach to, pick up, and deliver patients efficiently. By increasing the operational efficiency, survival rate of major trauma could potentially be improved. In this research, authors applied Moving Average, Artificial Neural Network, Linear Regression, Support Vector Machine forecast emergency medical demand. results from these approaches, as a reference, used pre-allocation ambulances. training models well validation...
Abstract Variable number tandem repeat sequences (VNTR) are composed of consecutive repeats short segments DNA with hypervariable count and composition. They include protein coding associations clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach mapping human reference is less effective for repetitive divergent sequences. We solve reads a repeat-pangenome graph (RPGG), data structure encodes...
Abstract The effectiveness of emergency medical services (EMS) depends on the existing infrastructure and allocation resources. response time for ambulances is in general considered a critical factor to survival EMS patients. challenging task due spatial distribution population geographical layout urban area. configuration ambulance fleets hospitals should be assessed provide an efficient service. Additionally, plays role disaster situations. In this research, effect disasters as disturbance...
<ns3:p>In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics Structural Variation, Pan-genomes, and SARS-CoV-2 research. </ns3:p><ns3:p> The overarching focus was to assess current status field identify remaining challenges. Furthermore, how combine strengths interests drive research method development forward. Over four days, eight groups each designed developed new...
Abstract Understanding the impact of DNA variation on human traits is a fundamental question in genetics. Variable number tandem repeats (VNTRs) make up roughly 3% genome but are often excluded from association analysis due to poor read mappability or divergent repeat content. While methods exist estimate VNTR length short-read data, it known that VNTRs vary both and (motif) composition. Here, we use repeat-pangenome graph (RPGG) constructed 35 haplotype-resolved assemblies detect We align...
This paper presents an off-line handwritten signature verification system based on the Siamese network, where a hybrid architecture is used. The Residual neural Network (ResNet) used to realize powerful feature extraction model such that Writer Independent (WI) features can be effectively learned. A single-layer Neural (NN) Dependent (WD) classifier storage space minimized. For purpose of reducing impact high intraclass variability and ensuring network learn more effectively, we propose...
<ns3:p>In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics Structural Variation, Pan-genomes, and SARS-CoV-2 research. </ns3:p><ns3:p> The overarching focus was to assess current status field identify remaining challenges. Furthermore, how combine strengths interests drive research method development forward. Over four days, eight groups each designed developed new...
This paper focuses on offline writer-dependent signature verification using a Siamese convolutional neural network. A network is comprised of equal-weighted twin networks that can be trained to learn feature space in which similar observations are juxtaposed. To reduce the impact high intra-variability and ensure able more effectively, we propose method selecting Reference (REF). Using proposed reference selection, accuracy increased by 6.4%. By utilizing GPDS-160 data-set, designed system...