A5101764034- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Mosquito-borne diseases and control
- Chromosomal and Genetic Variations
- Epigenetics and DNA Methylation
- Immunotherapy and Immune Responses
- Viral Infections and Vectors
- Bioinformatics and Genomic Networks
- Genome Rearrangement Algorithms
- Malaria Research and Control
- Immune Cell Function and Interaction
- Evolution and Paleontology Studies
- Glycosylation and Glycoproteins Research
- RNA and protein synthesis mechanisms
- Mycorrhizal Fungi and Plant Interactions
- Immune cells in cancer
- RNA modifications and cancer
- T-cell and B-cell Immunology
- Innovative Energy Harvesting Technologies
- Cancer Immunotherapy and Biomarkers
- Insect symbiosis and bacterial influences
- Banana Cultivation and Research
- Evolution and Genetic Dynamics
- Genomics and Chromatin Dynamics
- Energy Harvesting in Wireless Networks
National Taiwan University
2019-2025
Harvey Mudd College
2014-2022
Sichuan Agricultural University
2020
Mackay Memorial Hospital
2019
National Taiwan University Hospital
2019
Far Eastern Memorial Hospital
2019
National Taipei University
2019
Institut National des Sciences Appliquées de Lyon
2018
Singapore Institute for Clinical Sciences
2016
Massachusetts Institute of Technology
2011-2015
The reference human genome sequence set the stage for studies of genetic variation and its association with disease, but epigenomic lack a similar reference. To address this need, NIH Roadmap Epigenomics Consortium generated largest collection so far epigenomes primary cells tissues. Here we describe integrative analysis 111 as part programme, profiled histone modification patterns, DNA accessibility, methylation RNA expression. We establish global maps regulatory elements, define modules...
Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here, we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order resolve contentious phylogeny show that lineages leading principal vectors human malaria were among first split. Pervasive autosomal...
Abstract Summary We describe eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences. Availability implementation eMPRess is freely available at http://www.cs.hmc.edu/empress. Supplementary information data are Bioinformatics online.
Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many important applications. However, sequence data alone often lack enough information to confidently support one topology over competing alternatives. Here, we present novel framework for combining and species information, describe an implementation of this TreeFix, new phylogenetic program improving reconstructions. Given (preferably computed using maximum-likelihood program), TreeFix finds "statistically...
The envelope (E) protein of dengue virus (DENV) is the major target neutralizing antibodies (Abs) and vaccine development. Previous studies human dengue-immune sera reported that a significant proportion anti-E Abs, known as group-reactive (GR) were cross-reactive to all four DENV serotypes one or more other flaviviruses. Based on mouse monoclonal (MAbs), GR MAbs nonneutralizing weakly compared with type-specific MAbs; response was thus not regarded important for strategy. We investigated...
Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect tree, many most popular methods consider discordance only due duplication and loss (and sometimes horizontal transfer). Methods do model ILS are either highly parameterized or restricted set histories, thus limiting their applicability...
Background The envelope (E) protein of dengue virus (DENV) is the major target neutralizing antibodies and vaccine development. While previous studies on domain III or I/II alone have reported several epitopes monoclonal (mAbs) against DENV E protein, possibility interdomain relationship between potency remain largely unexplored. Methodology/Principal Findings We developed a dot blot assay by using 67 alanine mutants predicted surface-exposed residues as systematic approach to identify...
Dengue virus (DENV) is the leading cause of arboviral diseases in humans worldwide. The envelope (E) protein DENV major target neutralizing antibodies (Abs). Previous studies have shown that a significant proportion anti-E Abs human serum after infection recognize highly conserved fusion loop (FL) E protein. role anti-FL protection against subsequent versus pathogenesis remains unclear. A monoclonal Ab was used as standard virion-capture ELISA to measure concentration Abs, [anti-E Abs],...
Abstract Motivation: The accurate inference of gene trees is a necessary step in many evolutionary studies. Although the problem tree has received considerable attention, most existing methods are only applicable to families unaffected by horizontal transfer. As result, affected transfer remains largely unaddressed problem. Results: In this study, we introduce new and highly effective method for error correction presence Our efficiently models transfers, duplications losses, uses statistical...
Abstract Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts parasites other dependent pairs entities. Reconciliation typically performed using maximum parsimony, in which each event type assigned cost objective to find minimum total cost. It generally understood that reconciliations are sensitive costs, but little about relationship between costs solutions. Moreover, choosing appropriate...
T cell exhaustion, a dysfunctional state caused by prolonged antigen exposure, presents major challenge in cancer immunotherapy. While immune checkpoint inhibitors show therapeutic promise, they fail to rejuvenate cells terminally exhaustion state, potentially due epigenetic barriers. We hypothesized that targeting regulators may provide novel strategies overcome these barriers, thereby rescuing exhausted cells. In this project, we used malignant pleural effusions from advanced lung patients...
Abstract The tumor immune microenvironment reflects a patient's reserve and offers valuable insights for clinical decision-making. It has the potential to stratify late-stage cancer patients, identifying those likely benefit from aggressive therapies better suited palliative care. However, obtaining detailed profiling tissues often requires invasive biopsies poses additional risks. Malignant pleural effusion (MPE), common complication in advanced lung cancer, provides minimally alternative...
Abstract γδ T cells are a distinct subgroup of that bridge the innate and adaptive immune system can attack cancer in an MHC-unrestricted manner. Trials adoptive cell transfer solid tumors have had limited success. Here, we show DNA methyltransferase inhibitors (DNMTis) upregulate surface molecules on related to activation using quantitative proteomics. DNMTi treatment human lung potentiates tumor lysis by ex vivo-expanded Vδ1-enriched cells. Mechanistically, enhances synapse formation...
O1 The metabolomics approach to autism: identification of biomarkers for early detection autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, Wood, F. Luo, Stevenson O2 Phenome-wide association study smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, Hispanic descents Polimanti, J. Gelernter O3 Effects prenatal environment, genotype DNA methylation on birth weight subsequent postnatal outcomes: findings...
Abstract Antibodies are prominent therapeutic agents but costly to develop. Existing approaches predict developability depend on structure, which requires expensive laboratory or computational work obtain. To address this issue, we present a machine learning pipeline from sequence alone using physicochemical and learned embedding features. Our approach achieves high sensitivity specificity dataset of 2400 antibodies. These results suggest that is predictive developability, enabling more...
The immune synapse, a highly organized structure formed at the interface between T lymphocytes and antigen-presenting cells (APCs), is essential for cell activation adaptive response. It has been shown that this shares similarities with primary cilium, sensory organelle in eukaryotic cells, although roles of ciliary proteins on synapse remain elusive. Here, we find inositol polyphosphate-5-phosphatase E (INPP5E), cilium-enriched protein responsible regulating phosphoinositide localization,...
Abstract Model organisms can serve the biological and medical community by enabling study of conserved gene families pathways in experimentally-tractable systems. Their use, however, hinges on ability to reliably identify evolutionary orthologs paralogs with high accuracy, which be a great challenge at both small large distances. Here, we present phylogenomics-based approach for identification orthologous paralogous genes human, mouse, fly, worm, forms foundation comparative analyses...
Gene trees can differ from species due to a variety of biological phenomena, the most prevalent being gene duplication, horizontal transfer, loss, and coalescence. To explain topological incongruence between two trees, researchers apply reconciliation methods, often relying on maximum parsimony framework. However, while several studies have investigated space reconciliations (MPRs) under duplication-loss duplication-transfer-loss models, MPRs duplication-loss-coalescence (DLC) model remains...
Phylogenetic tree reconciliation is widely used in the fields of molecular evolution, cophylogenetics, parasitology, and biogeography to study evolutionary histories pairs entities. In these contexts, often performed using maximum parsimony under Duplication-Transfer-Loss (DTL) event model. general, number reconciliations (MPRs) can grow exponentially with size trees. While a previous efforts have been made count MPRs, find representative compute frequencies events across space little known...
In phylogenetics, we often seek to reconcile gene trees with species within the framework of an evolutionary model. While most popular models for eukaryotic allow only duplication and loss or multispecies coalescence, recent work has combined these phenomena through a reconciliation structure, labeled coalescent tree (LCT), that simultaneously describes duplication-loss history family. However, LCT makes simplifying assumption one individual is sampled per whereas, advances in sequencing,...
Phylogenetic analyses commonly assume that the species history can be represented as a tree. However, in presence of hybridization, is more accurately captured network. Despite several advances modeling phylogenetic networks, there no known polynomial-time algorithm for parsimoniously reconciling gene trees with networks while accounting incomplete lineage sorting. To address this issue, we present case level-1 which hybrid direct ancestor another species. This work enables efficient...
Abstract Background Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type event, which can be difficult estimate. Prior work has explored relationship event in duplication-loss duplication-transfer-loss models, but no studies have addressed this more complicated duplication-loss-coalescence model. Results We provide...
Duck Tembusu virus (DTMuV) is a single-stranded, positive-sense RnA arbovirus, belonging to the genus Flavivirus, family Flaviviridae.As transmembrane protein, non-structural protein 2A (nS2A) plays an important role in virion assembly, replication complex and antagonizing host immune response.Since nS2A contains many hydrophobic amino acids, it hard gain full-length of for prokaryotic expression.Therefore, make deep study, expression polyclonal antibody preparation truncated DTMuV was...