Automated Classification for Pathological Prostate Images using AdaBoost-based

We present an AdaBoost-based Ensemble Learning for supporting automated Gleason grading of prostate adenocarcinoma (PRCA). The method is able to differentiate Gleason patterns 4–5 from patterns 1–3 as the patterns 4-5 are correlated to more aggressive disease while patterns 1-3 tend to reflect more favorable patient outcome. This method is based on various feature descriptors and classifiers for multiple color channels, including color channels of red, green and blue, as well as the optical intensity of hematoxylin and eosin stainings.

type: 
Conference Paper/Poster
journal: 
2016 IEEE Sympsosium Series on Computational Intelligence (IEEE SSCI 2016) Dec 6 to 9, Athens, Greece,

R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes.

type: 
Journal Paper
journal: 
Nucleic Acids Research, 2016, 1, doi: 10.1093/nar/gkw1054
Url: 
http://nar.oxfordjournals.org/cgi/reprint/gkw1054?ijkey=W1rlIk0z5MshLua&keytype=ref
Impact Factor: 
9.202
Date of acceptance: 
2016-10-20

Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins

In addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled inactivation mechanism, making it more resistant to high H2O2 concentrations. During peroxide reduction, the active site alternates between reduced, fully folded (FF), and oxidized, locally unfolded (LU) conformations.

type: 
Journal Paper
journal: 
Scientific Reports 6, 2016, doi: 10.1038/srep37610
Url: 
http://www.nature.com/articles/srep37610
Impact Factor: 
5.228
Date of acceptance: 
2016-10-31

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment

The envelope of Gram-negative bacteria is highly complex, containing separate outer and inner membranes and an intervening periplasmic space encompassing a peptidoglycan (PGN) cell wall. The PGN scaffold is anchored non-covalently to the outer membrane via globular OmpA-like domains of various proteins. We report atomically detailed simulations of PGN bound to OmpA in three different states, including the isolated C-terminal domain (CTD), the full-length monomer, or the complete full-length dimeric form.

type: 
Journal Paper
journal: 
Structure 2016, Nov 8, doi: 10.1016/j.str.2016.10.009
pubmed: 
27866852
Url: 
http://www.cell.com/structure/abstract/S0969-2126(16)30317-3
Impact Factor: 
5.237
Date of acceptance: 
2016-10-14

Big genomics and clinical data analytics strategies for precision cancer prognosis

The field of personalized and precise medicine in the era of big data analytics is growing rapidly. Previously, we proposed our model of patient classification termed Prognostic Signature Vector Matching (PSVM) and identified a 37 variable signature comprising 36 let-7b associated prognostic significant mRNAs and the age risk factor that stratified large high-grade serous ovarian cancer patient cohorts into three survival-significant risk groups.

type: 
Journal Paper
journal: 
Scientific Reports 6, 2016, Article no. 36493 (2016), doi:10.1038/srep36493
Url: 
http://www.nature.com/articles/srep36493
Date of acceptance: 
2016-10-12

Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

Critical regulatory pathways are replete with instances of intra- and interfamily protein-protein interactions due to the pervasiveness of gene duplication throughout evolution. Discerning the specificity determinants within these systems has proven a challenging task. Here, we present an energetic analysis of the specificity determinants within the Bcl-2 family of proteins (key regulators of the intrinsic apoptotic pathway) via a total of ∼20 μs of simulation of 60 distinct protein-protein complexes.

type: 
Journal Paper
journal: 
Structure, Vol 24, Issue 11, pg 2024-2033, 1 Nov 2016, doi: 10.1016/j.str.2016.09.006
pubmed: 
27773689
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27773689
Impact Factor: 
5.237
Date of acceptance: 
2016-09-28

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite a wealth of reported structural and biophysical studies, the structure-function relationships of this protein remain unclear. For example, it is still debated whether it functions as a pore, and the precise molecular role it plays in attachment to the peptidoglycan of the periplasm is unknown. The absence of a consensus view is partly due to the lack of a complete structure of the full-length protein.

type: 
Journal Paper
journal: 
Biophysical Journal, Vol. 111, Issue 8, pg 1692-1702, 18 Oct 2016, doi: 10.1016/j.bpj.2016.09.009
pubmed: 
27760356
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27760356
Impact Factor: 
3.632
Date of acceptance: 
2016-09-06

Multiscale Molecular Dynamics Simulation Approaches to the Structure and Dynamics of Viruses

Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated.

type: 
Journal Paper
journal: 
Progress in Biophysics and Molecular Biology, Oct 17 2016, doi: 10.1016/j.pbiomolbio.2016.09.010
pubmed: 
27765545
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27765545
Impact Factor: 
2.581
Date of acceptance: 
2016-09-27

Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes

With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided.

type: 
Journal Paper
journal: 
Marine Genomics 2016 Oct 9, doi: 10.1016/j.margen.2016.10.00
pubmed: 
27733306
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27733306
Impact Factor: 
1.883
Date of acceptance: 
2016-10-03

Hydrocarbons are essential for optimal cell size, division and growth of cyanobacteria

Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of Synechococcus sp. PCC 7002 and Synechocystis sp.

type: 
Journal Paper
journal: 
Plant Physiology Nov 2016, Vol. 172, No 3, Pg 1928-1940, doi:10.1104/pp.16.01205
pubmed: 
27707888
Url: 
http://www.plantphysiol.org/content/172/3/1928.long
Impact Factor: 
6.28
Date of acceptance: 
2016-10-05
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