Journal ArticleDOI
pLogo: a probabilistic approach to visualizing sequence motifs
TLDR
The pLogo is described, a motif visualization in which residue heights are scaled relative to their statistical significance, in which real-time conditional probability calculations and visualizations are supported.Abstract:
Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at http://plogo.uconn.edu/ and supports real-time conditional probability calculations and visualizations.read more
Citations
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Journal ArticleDOI
Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction
TL;DR: Hyb4mC as mentioned in this paper adopts the DNA2vec method for sequence embedding, which captures more efficient and comprehensive information compared with the sequence-based feature method, and combines the attention mechanism with a text convolutional neural network for further feature learning.
Book ChapterDOI
Integrated and Quantitative Proteomics of Human Tumors.
TL;DR: To improve the accuracy of the discoveries made using proteomics in human tumors, it is necessary to combine robust and reproducible methods for sample preparation allowing statistical comparison, PTM analyses in addition to global proteomics for additional levels of knowledge, and use of bioinformatics for decrypting protein list.
Journal ArticleDOI
Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics
Tae-Wuk Kim,Chan Ho Park,Chuan-Chih Hsu,Yeong-Woo Kim,Yeong-Woo Ko,Zhenzhen Zhang,Jiachen Zhu,Yu-Chun Hsiao,Tess C. Branon,Krista Kaasik,Evan Saldivar,Kevin Li,Asher Pasha,Nicholas J. Provart,Alma L. Burlingame,Shou-Ling Xu,Alice Y. Ting,Zhi Yong Wang +17 more
TL;DR: In this paper , a TurboID-based proximity labeling (TbPL) was used to identify 400 proximal proteins of Arabidopsis thaliana BRASSINOSTEROID-INSENSITIVE2 (BIN2), a member of the GSK3 kinase kinase family.
Journal ArticleDOI
An Azo Coupling-Based Chemoproteomic Approach to Systematically Profile the Tyrosine Reactivity in the Human Proteome
TL;DR: A novel method integrating azo coupling, bioorthogonal chemistry, and multiplexed proteomics to globally investigate the tyrosine reactivity in the human proteome is reported, which can be extensively applied to advance the understanding of protein functions and facilitate the development of covalent drugs to regulate protein activity.
Journal ArticleDOI
Distinct Hepatic PKA and CDK Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production.
Brandon M. Gassaway,Rebecca L. Cardone,Anil K. Padyana,Max C. Petersen,Evan T. Judd,Sebastian Hayes,Shuilong Tong,Karl W. Barber,Maria Apostolidi,Abudukadier Abulizi,Joshua B. Sheetz,Kshitiz,Hans R. Aerni,Stefan Gross,Charles Kung,Varman T. Samuel,Varman T. Samuel,Gerald I. Shulman,Richard G. Kibbey,Jesse Rinehart +19 more
TL;DR: It is shown that cyclin-dependent kinases (CDKs) are activated by the HFD and responsible for PKL phosphorylation at position S113 in addition to other targets, and these CDKs control PKL nuclear retention, alter cytosolic PKL activity, and ultimately influence glucose production.
References
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Journal ArticleDOI
WebLogo: A Sequence Logo Generator
TL;DR: WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment that provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive.
Journal ArticleDOI
Sequence logos: a new way to display consensus sequences
Thomas D. Schneider,R M Stephens +1 more
TL;DR: From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content at every position in a site or sequence.
Journal ArticleDOI
A C-terminal signal prevents secretion of luminal ER proteins
Sean Munro,Hugh R.B. Pelham +1 more
TL;DR: It is proposed that the KDEL sequence marks proteins that are to be retained in the ER and discuss possible retention mechanisms.
Journal ArticleDOI
The P-loop--a common motif in ATP- and GTP-binding proteins.
TL;DR: Current knowledge of P-loops is discussed with the additional aim of illustrating the fascinating relationship between protein sequence, structure and function.
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