Showing papers in "Methods in 2019"

TL;DR: This review provides both the exoteric introduction of deep learning, and concrete examples and implementations of its representative applications in bioinformatics, and introduces deep learning in an easy-to-understand fashion.

TL;DR: The proposed deep cascaded forest model, Deep-Resp-Forest, to classify the anti-cancer drug response as "sensitive" or "resistant", has demonstrated the promising use of deep learning and deep forest approach on the drug response prediction tasks.

TL;DR: A convolutional-recurrent neural network model, called FactorNet, is developed to computationally impute the missing binding data in transcription factors and cell types, ranked among the top teams in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge.

TL;DR: This work reviews the insights gained and how that knowledge has been used to design more potent bispecific T-cell engagers and modifications in existing antibody formats and new experimental molecules designed to mitigate these problems are discussed.

TL;DR: The so-called CrossMab technology that enforces correct light chain association based on the domain crossover of immunoglobulin domains in the Fab region of the bispecific antibody is developed.

TL;DR: Improvements in AID technology are shown, including new plasmids for N-terminal tagging and a detailed protocol for the generation of AID mutants of human HCT116 and DLD1 cells, and the use of an OsTIR1 inhibitor, auxinole, to suppress leaky degradation of degron-fused proteins.

TL;DR: A deeper analysis of Type 2 Diabetes and obesity datasets that have eluded improved results, using a variety of machine learning and feature extraction methods.

TL;DR: Luminex's xMAP technology is the most widely adopted bead-based multiplexing platform with over 35,000 peer-reviewed publications, an installed base of approximately 15,500 instruments, and over 70 Luminex Partners offering more than 1300 research use kits as well as custom assay solutions as mentioned in this paper.

TL;DR: The two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates.

TL;DR: An improved protocol for efficient biallelic engineering of single nucleotide variants in human iPS cells is developed using a fluorescent BFP->GFP assay to monitor the incorporation of a single base pair change and dramatically shifts the bias of repair in favor of HDR.

TL;DR: RPAD enables the elucidation of circRNA biogenesis, sequence, and function by facilitating the isolation of highly pure circRNAs from total RNA pools.

TL;DR: Some important technical considerations for studying nuclear and cytoplasmic localization are presented, and guidance for quantifying protein levels using fluorescence microscopy and ImageJ software is provided.

TL;DR: This Review will discuss key considerations required in all aspects of screening from initiation to conclusion, which will enable researchers to conduct screens of their own, maximising the potential of this powerful technology.

TL;DR: This work presents the protocol of a Capture-SELEX that specifically allows the in vitro selection of small-molecule binding aptamers, which are essential building blocks for the design process of synthetic riboswitches and biosensors.

TL;DR: Though the precise and efficient re-direction of ADAR activity still remains a challenge, the systems that are being developed lay the foundation for SDRE as a powerful tool for transient genome editing.

TL;DR: The results suggest that exploiting such unlabeled data can be greatly beneficial to improved performance in various biomedical relation extraction, especially when only limited labeled data is available in such tasks.

TL;DR: Efforts to employ FID assays using RNA receptors are summarized and significant contributions of the method are described towards the development of chemical probes to reveal unknown RNA functions are described.

TL;DR: Attempts to enhance CRISPR-Cas9 specificity by selection of Cas9 orthologs from various bacterial species and their further refinement by introduction of beneficial mutations are reviewed.

TL;DR: Unsupervised DL is shown to be a promising analytical approach for integrative analysis of temporal multi-omics in cardiovascular diseases and results in the highest number of enriched pathways, suggesting the strength of its unified framework based on visual similarities.

TL;DR: A robust heterodimeric Fc platform is presented, engineered for efficient development of bispecific antibodies and Fc fusions of multiple formats, and manufacturing data is presented reinforcing the robustness of the heterodIMC platform at scale.

TL;DR: Good practices for performing benchmarks forRNA secondary structure prediction are discussed, including the choice of benchmarking structures, metrics to quantify accuracy, the importance of allowing flexibility for pairs in the accepted structure, and the significance of statistical testing for significance.

TL;DR: A variety of fluorescent nanoprobes of QDS, CDs, AuNPs and UCNPS, working on the fluorescent sensing mechanisms and applicable for the detection of H2S, CO and NO in biological and environmental samples are discussed.

TL;DR: The outline, prospects, and limitations of the common light chain format, which includes one of Chugai's proprietary technologies, termed ART-Ig technology, are introduced and some tips for de-risking the antibody when engineering a T cell redirecting antibody are described.

TL;DR: This review compares mapping and quantitation studies of ribose methylations from yeast and human culture cells and focuses on ribosomal RNA for which the results can be compared to results from RNA fingerprinting and mass spectrometry.

TL;DR: A practical guide to a novel amplification-free method that provides both single-molecule sensitivity and single-base selectivity by monitoring the repetitive interactions of fluorescent probes to immobilized targets, SiMREPS is provided.

TL;DR: In this article, a formaldehyde crosslinking, immunoprecipitation and sequencing (fCLIP-seq) method was proposed to map DROSHA cleavage sites at single nucleotide resolution.

TL;DR: This review revisits RNA modifications and the related structures from a computational point of view and discusses known substrate structures, their properties such as sub-motifs as well as consequences of modifications on base pairing patterns and possible refolding events.

TL;DR: The many and varied antibody-based building blocks used to achieve multivalency and multispecificity provide opportunities to tailor the design of BsAbs and TsAbs to match the desired applications.

TL;DR: This work finds that IVS2vec has potential capabilities and outperform other state-of-the-art docking tools such as Autodock vina and can identify targets related to adverse drug reactions which is useful to improve medication safety and repurpose drugs.

TL;DR: The results suggest that the faster R-CNN has the potential to augment the prescreening and FP reduction in the CAD system for masses.