Yu-Feng Huang

Yu-Feng Huang
ACT Genomics Inc. · Bioinformatics

Doctor of Engineering
Manager, Department of Applied Artificial Intelligence, Division of Software Service

About

41
Publications
4,336
Reads
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215
Citations
Introduction
Yu-Feng does research in Evolutionary Biology, Cancer Research and Bioinformatics.
Additional affiliations
July 2021 - present
ACT Genomics
Position
  • Bioinformatician
February 2021 - June 2021
TOP Science Biotechnology Inc.
Position
  • PostDoc Position
October 2011 - January 2021
Academia Sinica
Position
  • PostDoc Position
Education
September 2003 - January 2010
National Taiwan University
Field of study
  • computer science
September 1999 - June 2001
National Chung Cheng University
Field of study
  • computer science
September 1995 - June 1999
Yuan Ze University
Field of study
  • computer science

Publications

Publications (41)
Article
Full-text available
Nosema ceranae is one of the fungal parasites of Apis mellifera. It causes physical and behavioral effects in honey bees. However, only a few studies have reported on gene expression profiling during A. mellifera infection. In this study, the transcriptome profile of mature spores at each time point of infection (5, 10, and 20 days post-infection,...
Article
Full-text available
The complete mitochondrial genome (mitogenome) of Attacus atlas formosanus (Villiard, 1969) is 15,280 bp in length, with the typical gene content and arrangement usually observed in Insecta. It contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one AT-rich region. The overall nucleotide composition of the mitogeno...
Article
Full-text available
Deformed wing virus (DWV) prevalence is high in honey bee (Apis mellifera) populations. The virus infects honey bees through vertical and horizontal transmission, leading to behavioural changes, wing deformity, and early mortality. To better understand the impacts of viral infection in the larval stage of honey bees, artificially reared honey bee l...
Article
Research on gut microbiota of phytophagous insects has shown to be important for the physiological functions of insect hosts; however, little is known about the changes in gut microbiota when they are suffering from environmental stress or pathogen infections. During rearing of Phasmotaenia lanyuhensis (Phasmatodea: Phasmatidae), sluggish locomotio...
Article
Full-text available
Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer prognosis and higher mortality rate compared to breast cancer diagnosed at age 50 or older. EOBC poses a serious threat to public health and requires in-depth investigation. We studied a cohort comprising 90 Taiwanese female patients, aiming to unravel th...
Article
Full-text available
The golden birdwing butterfly (Troides aeacus formosanus) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared T. aeacus larvae. From the previous Kimura-2 parameter (K-2-P) analysis based on the nucleotide sequence of three genes in this isolate, polh, lef-8 and lef-9, the underlying virus...
Article
Full-text available
The baculoviral anti-apoptotic genes, p35 and iap (inhibitor of apoptosis), play important roles in the initiation of viral infection. Recently, a new anti-apoptotic gene (apoptosis suppressor, apsup) was identified in Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV). An apsup homolog gene, Lyxy105 (ly-apsup), was also predicted in the Lyman...
Article
Full-text available
Single cell transcriptome (SCT) analysis provides superior resolution to illustrate tumor cell heterogeneity for clinical implications. We characterized four SCTs of MCF-7 using 143 housekeeping genes (HKGs) as control, of which lactate dehydrogenase B (LDHB) expression is silenced. These SCT libraries mapped to 11,423, 11,486, 10,380, and 11,306 R...
Data
This file shows the results of GO analysis for CE and IE groups. (PDF)
Data
This Excel file lists all expressed genes (including CE, IE and 143 HKGs), their expression levels (in FPKM) in all four single cell transcriptome libraries, their averages, standard deviations and coefficient of variations (CVs). (XLSX)
Data
This file shows the results of BioCarta pathway analysis of CE genes. (Pathway analysis for IE is skipped because they are mainly extracellular proteins). (PDF)
Article
Full-text available
Background Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast can...
Article
Full-text available
Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T...
Article
Full-text available
The Taiwanese (Formosan) macaque ( Macaca cyclopis ) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. W...
Article
Full-text available
Recent studies have demonstrated a potent anticancer potential of medicinal fungus Antrodia cinnamomea, especially against hepatocarcinoma. These studies, however, were performed with prolonged treatments, and the early anticancer events remain missing. To probe the early anticancer mechanisms of A. cinnamomea, we treated SK-Hep-1 liver cancer cell...
Article
Protein structural stability and biological functionality are dictated by the formation of intradomain cores and interdomain interfaces, but the intricate sequence-structure-function interrelationships in the packing of protein cores and interfaces remain difficult to elucidate due to the intractability of enumerating all packing possibilities and...
Article
Full-text available
Background Current next-generation sequencing (NGS) platforms adopt two types of sequencing mechanisms: by synthesis or by ligation. The former is employed by 454 and Solexa systems, while the latter by SOLiD system. Although the pros and cons for each sequencing mechanism have more or less been discussed in a number of occasions, the potential obs...
Data
A collection of 58 active sites This file includes the physicochemical properties of the 58 active site groups collected in this study.
Article
Full-text available
A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with similar reaction chemistries, more and more studies discussing the structural flexibility of the active site have been conducted. Most of the...
Article
Full-text available
RNA-binding proteins (RBPs) play crucial roles in post-transcriptional control of RNA. RBPs are designed to efficiently recognize specific RNA sequences after it is derived from the DNA sequence. To satisfy diverse functional requirements, RNA binding proteins are composed of multiple blocks of RNA-binding domains (RBDs) presented in various struct...
Article
Full-text available
Protein-DNA interactions are essential for fundamental biological activities including DNA transcription, replication, packaging, repair and rearrangement. Proteins interacting with DNA can be classified into two categories of binding mechanisms - sequence-specific and non-specific binding. Protein-DNA specific binding provides a mechanism to recog...
Conference Paper
Full-text available
Protein function is highly correlated with its three dimensional conformation in order to interact with others proteins, ligands, substrates, inhibitors, etc. Studies on binding site and protein function have been investigated to understand the mechanism of protein activity; therefore, protein stability and flexibility play different roles on prote...
Article
Full-text available
This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein–DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur betwe...
Article
Full-text available
Protein function is highly correlated with its three-dimensional conformation in order to interact with others proteins, ligands, substrates, inhibitors, etc. Studies on binding site and protein function have been investigated to understand the mechanism of protein activity. The role of binding site can be characterized by the presence of stable re...
Conference Paper
Full-text available
Sequence conservation related to protein function has been discovered via protein sequence alignment and pattern mining. In contrast, our motivation is to mine structure conservation via frequent itemset mining from the viewpoint of structure. In order to describe local structure, neighborhood residue sphere (NRS) is proposed, which is a sphere wit...
Conference Paper
Full-text available
In order to comprehend residue environment, we use residue environmental sphere which is a sphere with 10 Å of radius, to describe environment information surrounding a residue. For the purpose of detecting residue-residue contacts more quickly and efficiently, we decompose a protein structure into lots of spheres, and it is a great challenge to st...
Conference Paper
Full-text available
Many protein structure comparison methods use secondary structure information to do fast structure similarity search for initial alignment finding and refine the results from possible optimal candidate solutions by iteratively dynamic programming to optimize the final results. In this paper, we develop a method, Ellipsoidal Model Protein Structure...
Conference Paper
Full-text available
Local region conservation has been studied for many years because biologists believe that local conservation could be highly related to protein functions. The concept of local region conservation comes from a motif, a fragment with biological or functional meaning. Besides, structure-based identification of homologues often succeeds where sequence-...
Article
Full-text available
This paper proposes a new method EMPSC for the well-known PSC (Protein Structure Comparison) problem. The proposed method EMPSC is a protein structural alignment algorithm based on ellipsoidal model abstraction. We segment the protein 3D structure into two different kinds of structures, including Secondary Structure Elements recognized by DSSP 1 an...
Article
Full-text available
Local region conservation has been observed in recent years and become more and more important in structure biology. Recent researches point out that local conservation regions are correlated to protein functional sites and functions and studies show that some local conservation on sequence or structure are close to binding area. Hence, in order to...
Article
Full-text available
Search for a tertiary substructure that geometrically matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work, a web server has been built to predict protein-ligand binding sites based on automatically extracted templates. However, a drawback of such templates is th...

Questions

Questions (2)
Question
Currently, I have small population of 7 individuals' mitochondrial genome. The species of these individuals is primate. Previously, I only have experience on mitochondrial genome assembly and evolutionary analysis on mitochondrial. The initial idea for this project is trying to discover the variation among individuals in terms of whole mitogenome, protein-coding genes and D-Loop. Is there any advanced analysis could be applied? Any input is welcome.
Question
I have the finished mitochondrial genome by de novo assembly with next-generation sequencing data. While annotating protein-coding gene in the mitochondrial genome, I use MITOS and DOGMA to predict the regions of protein-coding genes. In addition, I also use blastn and tblastn with reference genome for validation. Unfortunately, there is no consistent result among MITOS, DOGMA, blastn and tblastn. Any input is welcome.

Network

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Projects

Projects (2)
Project
Mitochondrial genome research