Editorial Overview : Exploring mechanisms in biology: simulations and experiments come together

type: 
Journal Paper
journal: 
Progress in Biophysics and Molecular Biology, 2017 Sep;128:1-2. doi: 10.1016/j.pbiomolbio.2017.07.005
pubmed: 
28743422
Impact Factor: 
3.227

Thyroid-SPOT for mobile devices: personalised thyroid treatment management app

Thyroid-SPOT is a mobile application that allows users to be able to analyse thyroid function tests laboratory reports by computing the homeostatic euthyroid set point based on regressing thyroid function data according to a patented algorithm to define the parameters that maximize the goodness-of-fit to a negative exponential model for target-centric individualized treatment.

type: 
Journal Paper
journal: 
Scientific Phone Apps and Mobile Devices 2017, 3:4 doi: 10.1186/s41070-017-0016-y
Url: 
https://scientificphoneapps.springeropen.com/articles/10.1186/s41070-017-0016-y
Date of acceptance: 
2017-08-01

Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles

The shape of the experimental frequency distributions (EFD) of diverse molecular interaction events quantifying genome-wide binding is often skewed to the rare but abundant quantities. Such distributions are systematically deviated from standard power-law functions proposed by scale-free network models suggesting that more explanatory and predictive probabilistic model(s) are needed.

type: 
Book/Book Chapter
journal: 
Biological Networks and Pathway Analysis, Methods in Molecular Biology, Vol. 1613, Pg 193-276, doi: 10.1007/978-1-4939-7027-8_9
pubmed: 
28849563
Url: 
https://www.ncbi.nlm.nih.gov/m/pubmed/28849563/
Date of acceptance: 
2017-12-29

Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles

The shape of the experimental frequency distributions (EFD) of diverse molecular interaction events quantifying genome-wide binding is often skewed to the rare but abundant quantities. Such distributions are systematically deviated from standard power-law functions proposed by scale-free network models suggesting that more explanatory and predictive probabilistic model(s) are needed.

type: 
Book/Book Chapter
journal: 
Biological Networks and Pathway Analysis, Methods in Molecular Biology, vol. 1613, Pg 193-276, doi: 10.1007/978-1-4939-7027-8_9
pubmed: 
28849563
Url: 
https://www.ncbi.nlm.nih.gov/m/pubmed/28849563/

Genome-wide Analysis of Protein-Coding Variants in Leprosy

Although genome-wide association studies (GWAS) have greatly advanced our understanding on the contribution of common non-coding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in 7,048 leprosy patients and 14,398 healthy controls of Han Chinese.

type: 
Journal Paper
journal: 
Journal of Investigative Dermatology, 2017, Aug 22, doi: 10.1016/j.jid.2017.08.004
pubmed: 
28842327
Url: 
http://www.jidonline.org/article/S0022-202X(17)32793-8/pdf
Impact Factor: 
6.287

EGF hijacks miR-198/FSTL1 wound-healing switch and steers a two-pronged pathway toward metastasis

Epithelial carcinomas are well known to activate a prolonged wound-healing program that promotes malignant transformation. Wound closure requires the activation of keratinocyte migration via a dual-state molecular switch. This switch involves production of either the anti-migratory microRNA miR-198 or the pro-migratory follistatin-like 1 (FSTL1) protein from a single transcript; miR-198 expression in healthy skin is down-regulated in favor of FSTL1 upon wounding, which enhances keratinocyte migration and promotes re-epithelialization.

type: 
Journal Paper
journal: 
The Journal of Experimental Medicine, 2017,doi: 10.1084/jem.20170354
Url: 
http://jem.rupress.org/content/early/2017/08/18/jem.20170354
Impact Factor: 
11.991
Date of acceptance: 
2017-07-12

In Silico and in Vitro Interactions between Short Chain Fatty Acids and Human Histone Deacetylases

Short chain fatty acids (SCFAs) are postulated to modulate the immune development of neonates via epigenetic regulations such as histone deacetylase (HDAC) inhibition. In the context of atopic diseases, the inhibition of HDAC maintains T-cell homeostasis and induces naïve T-cell differentiation into adaptive Treg, which regulates the production of anti-inflammatory cytokines and suppression of Th2 immune responses.

type: 
Journal Paper
journal: 
Biochemistry, 2017, doi: 10.1021/acs.biochem.7b00508
Impact Factor: 
2.938

Transduction on Directed Graphs via Absorbing Random Walks

In this paper we consider the problem of graph-based transductive classification, and we are particularly interested in the directed graph scenario which is a natural form for many real world applications.Different from existing research efforts that either only deal with undirected graphs or circumvent directionality by means of symmetrization, we propose a novel random walk approach on directed graphs using absorbing Markov chains, which can be regarded as maximizing the accumulated expected number of visits from the unlabeled transient states.

type: 
Journal Paper
journal: 
IEEE Transactions on Pattern Analysis and Machine Intelligence, Issue 99, 2017, doi:10.1109/TPAMI.2017.2730871
pubmed: 
28809671
Url: 
http://ieeexplore.ieee.org/document/8008851/
Impact Factor: 
8.329

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

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
pubmed: 
28738801
Url: 
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0404-4
Impact Factor: 
6.779
Date of acceptance: 
2017-08-07

A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4

Like all members of the Toll-like receptor (TLR) family, TLR4 comprises of a large ectodomain (ECD) involved in ligand recognition at the cell-surface, and a cytosolic Toll/interleukin-1 receptor (TIR) signalling domain, linked by a lipid membrane-anchored transmembrane (TM) domain (TMD).

type: 
Journal Paper
journal: 
Biochimica et Biophysica Acta (BBA) - Biomembranes, 2017 Jul 22;1859(10):2086-2095. doi: 10.1016/j.bbamem.2017.07.010
pubmed: 
28739292
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/?term=28739292
Impact Factor: 
3.498
Date of acceptance: 
2017-07-20
Syndicate content