Nucleic Acids Research
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#1Kailin Tang (Tongji University)H-Index: 16
#2Xuejie Ji (Tongji University)
Last. Zhiwei Cao (Tongji University)H-Index: 26
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Though transcriptomics technologies evolve rapidly in the past decades, integrative analysis of mixed data between microarray and RNA-seq remains challenging due to the inherent variability difference between them. Here, Rank-In was proposed to correct the nonbiological effects across the two technologies, enabling freely blended data for consolidated analysis. Rank-In was rigorously validated via the public cell and tissue samples tested by both technologies. On the two reference samples of the...
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#1Melissa F. Adasme (TUD: Dresden University of Technology)H-Index: 5
#2Katja L Linnemann (TUD: Dresden University of Technology)H-Index: 1
Last. Michael Schroeder (TUD: Dresden University of Technology)H-Index: 38
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With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein-ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand-protein complexes. Besides ligand-protein interactions, intera...
3 CitationsSource
#1Weihua Qin (LMU: Ludwig Maximilian University of Munich)H-Index: 11
#2Enes Ugur (LMU: Ludwig Maximilian University of Munich)H-Index: 3
Last. Axel Imhof (LMU: Ludwig Maximilian University of Munich)H-Index: 66
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Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β-/- embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1β is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 ...
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#1Jean Chatain (French Institute of Health and Medical Research)H-Index: 2
#2Alain Blond (CNRS: Centre national de la recherche scientifique)H-Index: 22
Last. Patrizia Alberti (French Institute of Health and Medical Research)H-Index: 23
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Human telomeres are composed of GGGTTA repeats and interspersed with variant repeats. The GGGCTA variant motif was identified in the proximal regions of human telomeres about 10 years ago and was shown to display a length-dependent instability. In parallel, a structural study showed that four GGGCTA repeats folded into a non-canonical G-quadruplex (G4) comprising a Watson-Crick GCGC tetrad. It was proposed that this non-canonical G4 might be an additional obstacle for telomere replication. In th...
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#1Erik Poppleton (ASU: Arizona State University)H-Index: 6
#2Roger Romero (ASU: Arizona State University)H-Index: 1
Last. Petr Šulc (ASU: Arizona State University)H-Index: 19
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OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical sta...
2 CitationsSource
#1Franziska Fritz (Humboldt University of Berlin)
#2Robert Preissner (Humboldt University of Berlin)H-Index: 47
Last. Priyanka Banerjee (Humboldt University of Berlin)H-Index: 10
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Taste is one of the crucial organoleptic properties involved in the perception of food by humans. Taste of a chemical compound present in food stimulates us to take in food and avoid poisons. Bitter taste of drugs presents compliance problems and early flagging of potential bitterness of a drug candidate may help with its further development. Similarly, the taste of chemicals present in food is important for evaluation of food quality in the industry. In this work, we have implemented machine le...
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The isoelectric point is the pH at which a particular molecule is electrically neutral due to the equilibrium of positive and negative charges. In proteins and peptides, this depends on the dissociation constant (pKa) of charged groups of seven amino acids and NH+ and COO- groups at polypeptide termini. Information regarding isoelectric point and pKa is extensively used in two-dimensional gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF), crystallisation, and mass spectrometry...
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#1Dariusz Brzezinski (UVA: University of Virginia)H-Index: 11
#2Przemyslaw J. Porebski (UVA: University of Virginia)H-Index: 15
Last. Wladek Minor (UVA: University of Virginia)H-Index: 56
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Structure-guided drug design depends on the correct identification of ligands in crystal structures of protein complexes. However, the interpretation of the electron density maps is challenging and often burdened with confirmation bias. Ligand identification can be aided by automatic methods such as CheckMyBlob, a machine learning algorithm that learns to generalize ligand descriptions from sets of moieties deposited in the Protein Data Bank. Here, we present the CheckMyBlob web server, a platfo...
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#1Liao Xingyu (CSU: Central South University)
#2Min Li (CSU: Central South University)H-Index: 43
Last. Jianxin Wang (CSU: Central South University)H-Index: 49
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Numerous studies have shown that repetitive regions in genomes play indispensable roles in the evolution, inheritance and variation of living organisms. However, most existing methods cannot achieve satisfactory performance on identifying repeats in terms of both accuracy and size, since NGS reads are too short to identify long repeats whereas SMS (Single Molecule Sequencing) long reads are with high error rates. In this study, we present a novel identification framework, LongRepMarker, based on...
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#1Sergey Knyazev (ORISE: Oak Ridge Institute for Science and Education)H-Index: 7
#2Viachaslau Tsyvina (GSU: Georgia State University)H-Index: 3
Last. Pavel Skums (GSU: Georgia State University)H-Index: 15
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Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient's treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing, but sequencing noise hinders accurate identification. The elimination of sequencing noise i...
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