Wong WC

Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z

Published date : 15 May 2018

Distant homology relationships among proteins with many transmembrane regions (TMs) are difficult to detect as they are clouded by the TMs’ hydrophobic compositional bias and mutational divergence in connecting loops. In the case of several GPI lipid anchor biosynthesis pathway components, the hidden evolutionary signal can be revealed with dissectHMMER, a sequence similarity search tool focusing on fold-critical, high complexity sequence segments.

type
Journal Paper
journal
Cell Cycle, Vol 17, 2018, Issue 7, doi: 10.1080/15384101.2018.1456294
Impact Factor
3.304

Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"

Published date : 24 Jul 2017

BACKGROUND:
Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane's hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein's biological functions.

RESULTS:

type
Journal Paper
journal
BMC Biology 2017 Jul 24;15(1):66. doi: 10.1186/s12915-017-0404-4
Impact Factor
6.779

xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

Published date : 29 Nov 2016

BACKGROUND:
While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis.

RESULTS:

type
Journal Paper
journal
Biology Direct 2016, 11:63, DOI: 10.1186/s13062-016-0163-0
Impact Factor
3.016

The Recipe for Protein-Based Function Predition and its implementation in the ANNOTATOR Software Environment

Published date : 27 Apr 2016

As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction.

type
Book/Book Chapter
journal
Data Mining Techniques for the Life Sciences, Vol. 1415, pg 477-506,2016, ISBN: 978-1-4939-3570-3

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

Published date : 05 Nov 2015

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders.

type
Journal Paper
journal
PLOS Genetics, DOI:10.1371/journal.pgen.1005614 November 5, 2015
Impact Factor
7.528

dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Published date : 01 Aug 2015

Background: Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies.

type
Journal Paper
journal
Biology Direct (2015) 10:39, doi: 10.1186/s13062-015-0068-3
Impact Factor
4.66

A simple shortcut to unsupervised alignment-free phylogenetic genome groupings, even from unassembled sequencing reads

Published date : 02 Dec 2013

We propose an extension to alignment-free approaches that can produce reasonably accurate phylogenetic groupings starting from unaligned genomes, for example, as fast as 1 min on a standard desktop computer for 25 bacterial genomes. A 6-fold speed-up and 11-fold reduction in memory requirements compared to previous alignment-free methods is achieved by reducing the comparison space to a representative sample of k-mers of optimal length and with specific tag motifs.

type
Journal Paper
journal
Journal of Bioinformatics and Computational Biology, Vol. 11, No. 6 (2013), doi: 10.1142/S0219720013430051

Combination Therapy with Gossypol Reveals Synergism against Gemcitabine Resistance in Cancer Cells with High BCL-2 Expression

Published date : 04 Dec 2012

Although gemcitabine is highly active in several cancer types, intrinsic and acquired drug resistance remains a major challenge. Overexpression of Bcl-2 has been associated with gemcitabine resistance. The aim of this study is to determine whether gossypol can overcome gemcitabine resistance in cell lines with high level of Bcl-2 expression in combination drug therapy. Our study demonstrated that in 10 cell lines derived from different cancers, high Bcl-2 baseline expression was observed in cell lines that were resistant to gemcitabine (GEM-R).

type
Journal Paper
journal
PLoS One 2012, 7(12): e50786. doi:10.1371/journal.pone.0050786
Impact Factor
4.411