Bilkent University

About: Bilkent University is a education organization based out in Ankara, Turkey. It is known for research contribution in the topics: Metamaterial & Computer science. The organization has 4557 authors who have published 12595 publications receiving 326200 citations. The organization is also known as: Bilkent Üniversitesi & Bilkent.

A global reference for human genetic variation.

Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal

Abstract: The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.

Plasmonics: merging photonics and electronics at nanoscale dimensions.

Abstract: Electronic circuits provide us with the ability to control the transport and storage of electrons. However, the performance of electronic circuits is now becoming rather limited when digital information needs to be sent from one point to another. Photonics offers an effective solution to this problem by implementing optical communication systems based on optical fibers and photonic circuits. Unfortunately, the micrometer-scale bulky components of photonics have limited the integration of these components into electronic chips, which are now measured in nanometers. Surface plasmon-based circuits, which merge electronics and photonics at the nanoscale, may offer a solution to this size-compatibility problem. Here we review the current status and future prospects of plasmonics in various applications including plasmonic chips, light generation, and nanolithography.

Biological properties of extracellular vesicles and their physiological functions

Abstract: In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.

Channel Polarization: A Method for Constructing Capacity-Achieving Codes for Symmetric Binary-Input Memoryless Channels

Abstract: A method is proposed, called channel polarization, to construct code sequences that achieve the symmetric capacity I(W) of any given binary-input discrete memoryless channel (B-DMC) W. The symmetric capacity is the highest rate achievable subject to using the input letters of the channel with equal probability. Channel polarization refers to the fact that it is possible to synthesize, out of N independent copies of a given B-DMC W, a second set of N binary-input channels {WN(i)1 les i les N} such that, as N becomes large, the fraction of indices i for which I(WN(i)) is near 1 approaches I(W) and the fraction for which I(WN(i)) is near 0 approaches 1-I(W). The polarized channels {WN(i)} are well-conditioned for channel coding: one need only send data at rate 1 through those with capacity near 1 and at rate 0 through the remaining. Codes constructed on the basis of this idea are called polar codes. The paper proves that, given any B-DMC W with I(W) > 0 and any target rate R< I(W) there exists a sequence of polar codes {Cfrn;nges1} such that Cfrn has block-length N=2n , rate ges R, and probability of block error under successive cancellation decoding bounded as Pe(N,R) les O(N-1/4) independently of the code rate. This performance is achievable by encoders and decoders with complexity O(N logN) for each.