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

Published date : 29 Aug 2017

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

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

Published date : 29 Aug 2017

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

Genome-wide Analysis of Protein-Coding Variants in Leprosy

Published date : 22 Aug 2017

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
Impact Factor
6.287

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

Published date : 21 Aug 2017

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
Impact Factor
11.991

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

Published date : 15 Aug 2017

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

Published date : 11 Aug 2017

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
Impact Factor
8.329

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

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

Published date : 22 Jul 2017

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
Impact Factor
3.498

The role of apical contractility in determining cell morphology in multilayered epithelial sheets and tubes

Published date : 19 Jul 2017

A multilayered epithelium is made up of individual cells that are stratified in an orderly fashion, layer by layer. In such tissues, individual cells can adopt a wide range of shapes ranging from columnar to squamous. From histological images, we observe that, in flat epithelia such as the skin, the cells in the top layer are squamous while those in the middle and bottom layers are columnar, whereas in tubular epithelia, the cells in all layers are columnar.

type
Journal Paper
journal
Physical Biology, Vol. 14, No. 4, 2017, PMID: 28639563, doi: 10.1088/1478-3975/aa7afc

Benchmarking selected computational gene network growing tools in context of virus-host interactions

Published date : 19 Jul 2017

Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens.

type
Journal Paper
journal
Scientific Reports, 2017 Jul 19;7(1):5805. doi: 10.1038/s41598-017-06020-6
Impact Factor
4.259