Papers 10000
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#1Yue WuH-Index: 3
#2Michael T. JudgeH-Index: 2
Last. A. Edison
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#1Yahui Long (Hunan University)
#2Min Wu (Agency for Science, Technology and Research)H-Index: 15
Last. Xiaoli Li (Agency for Science, Technology and Research)H-Index: 53
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MOTIVATION: Human microbes play critical roles in drug development and precision medicine. How to systematically understand the complex interaction mechanism between human microbes and drugs remains a challenge nowadays. Identifying microbe-drug associations can not only provide great insights into understanding the mechanism, but also boost the development of drug discovery and repurposing. Considering the high cost and risk of biological experiments, the computational approach is an alternativ...
#1Hongxu Ding (UCSC: University of California, Santa Cruz)
#2Andrew D Bailey (UCSC: University of California, Santa Cruz)
Last. Benedict Paten (UCSC: University of California, Santa Cruz)H-Index: 42
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MOTIVATION Nucleotides modification status can be decoded from the Oxford Nanopore Technologies (ONT) nanopore sequencing ionic current signals. Although various algorithms have been developed for nanopore sequencing-based modification analysis, more detailed characterizations, such as modification numbers, corresponding signal levels and proportions are still lacking. RESULTS We present a framework for the unsupervised determination of the number of nucleotide modifications from nanopore sequen...
#1Nico Borgsmüller (Swiss Institute of Bioinformatics)H-Index: 1
#2Jose BonetH-Index: 1
Last. Niko Beerenwinkel (Swiss Institute of Bioinformatics)H-Index: 44
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Cancer is an evolutionary process characterized by the accumulation of mutations that drive tumor initiation, progression, and treatment resistance.
#1Yi Shi (SJTU: Shanghai Jiao Tong University)H-Index: 9
#2Zehua Guo (SJTU: Shanghai Jiao Tong University)
Last. Xin Zou (SJTU: Shanghai Jiao Tong University)H-Index: 4
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MOTIVATION The mutations of cancers can encode the seeds of their own destruction, in the form of T cell recognizable immunogenic peptides, also known as neoantigens. It is computationally challenging however, to accurately prioritize the potential neoantigen candidates according to their ability of activating the T cell immuno-response, especially when the somatic mutations are abundant. Although a few neoantigen prioritization methods have been proposed to address this issue, advanced machine ...
#1Tim Scherr (KIT: Karlsruhe Institute of Technology)
#2Karolin Streule (KIT: Karlsruhe Institute of Technology)H-Index: 1
Last. Ralf Mikut (KIT: Karlsruhe Institute of Technology)H-Index: 24
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MOTIVATION An automated counting of beads is required for many high-throughput experiments such as studying mimicked bacterial invasion processes. However, state-of-the-art algorithms under- or overestimate the number of beads in low-resolution images. In addition, expert knowledge is needed to adjust parameters. RESULTS In combination with our image labeling tool, BeadNet enables biologists to easily annotate and process their data reducing the expertise required in many existing image analysis...
#1Oriol Canela-Xandri (Western General Hospital)
#2Samira Anbari (Lehigh University)
Last. Javier Buceta (Lehigh University)H-Index: 19
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MOTIVATION Emerging phenomena in developmental biology and tissue engineering are the result of feedbacks between gene expression and cell biomechanics. In that context, in silico experiments are a powerful tool to understand fundamental mechanisms and to formulate and test hypotheses. RESULTS Here we present TiFoSi, a computational tool to simulate the cellular dynamics of planar epithelia. TiFoSi allows to model feedbacks between cellular mechanics and gene expression (either in a deterministi...
#1Hamid Bagheri (Iowa State University)H-Index: 13
#2Andrew J. Severin (Iowa State University)H-Index: 16
Last. Hridesh Rajan (Iowa State University)H-Index: 22
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MOTIVATION As the cost of sequencing decreases, the amount of data being deposited into public repositories is increasing rapidly. Public databases rely on the user to provide metadata for each submission that is prone to user error. Unfortunately, most public databases, such as non-redundant (NR), rely on user input and do not have methods for identifying errors in the provided metadata, leading to the potential for error propagation. Previous research on a small subset of the non-redundant (NR...
#1Weronika Puchała (PAN: Polish Academy of Sciences)
#2Michał Burdukiewicz (Warsaw University of Technology)H-Index: 2
Last. Michal Dadlez (PAN: Polish Academy of Sciences)H-Index: 34
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MOTIVATION Hydrogen-deuterium mass spectrometry (HDX-MS) is a rapidly developing technique for monitoring dynamics and interactions of proteins. The development of new devices has to be followed with new software suites adressing emerging standards in data analysis. RESULTS We propose HaDeX, a novel tool for processing, analysis and vizualisation of HDX-MS experiments. HaDeX supports a reproducible analytical process, including data exploration, quality control and generation of publication-qual...
#1Marianne L. Slaten (MU: University of Missouri)
#2Yen On Chan (MU: University of Missouri)
Last. Ruthie Angelovici (MU: University of Missouri)H-Index: 18
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MOTIVATION Advanced publicly available sequencing data from large populations have enabled informative genome-wide association studies (GWAS) that associate SNPs with phenotypic traits of interest. Many publicly available tools able to perform GWAS have been developed in response to increased demand. However, these tools lack a comprehensive pipeline that includes both pre-GWAS analysis such as outlier removal, data transformation, and calculation of Best Linear Unbiased Predictions (BLUPs) or B...
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