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
An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers
Kin Chan,Steven A. Roberts,Steven A. Roberts,Leszek J. Klimczak,Joan F. Sterling,Natalie Saini,Ewa P. Malc,Jaegil Kim,David J. Kwiatkowski,David J. Kwiatkowski,David C. Fargo,Piotr A. Mieczkowski,Gad Getz,Gad Getz,Dmitry A. Gordenin +14 more
TL;DR: It is proposed that APOBEC3A-mediated mutagenesis is much more frequent because APOBec3A itself is highly proficient at generating DNA breaks, whose repair can trigger the formation of single-strand hypermutation substrates.
Journal ArticleDOI
Phosphoproteins in extracellular vesicles as candidate markers for breast cancer
I-Hsuan Chen,Liang Xue,Chuan-Chih Hsu,Juan Sebastian Paez,Li Pan,Hillary Andaluz,Michael K. Wendt,Anton Iliuk,Jian-Kang Zhu,Jian-Kang Zhu,W. Andy Tao +10 more
TL;DR: A general strategy to isolate and identify phosphoproteins in extracellular vesicles from human plasma as potential markers to differentiate disease from healthy states is presented and may transform cancer screening and monitoring.
Journal ArticleDOI
CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria
Seth L. Shipman,Jeff Nivala,Jeff Nivala,Jeffrey D. Macklis,George M. Church,George M. Church +5 more
TL;DR: The underlying principles of the CRISPR–Cas adaptation system are uncovered, including sequence determinants of spacer acquisition that are relevant for understanding both the basic biology of bacterial adaptation and its technological applications.
Journal ArticleDOI
Global Proteome Turnover Analyses of the Yeasts S. cerevisiae and S. pombe
TL;DR: Proteome-wide steady-state protein turnover rate measurements for the evolutionarily distant but ecologically similar yeasts, Saccharomyces cerevisiae and SchizosacCharomyces pombe, find that the half-life of most proteins is much longer than currently thought and determined to a large degree by protein synthesis and dilution due to cell division.
Journal ArticleDOI
Site-specific mapping and quantification of protein S -sulphenylation in cells
TL;DR: A chemoproteomic workflow to map and quantify over 1,000 S-sulfenylation sites on more than 700 proteins in intact cells suggests regulatory crosstalk between redox control and signaling pathways.
References
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Journal ArticleDOI
Linear Motif Atlas for Phosphorylation-Dependent Signaling
Martin L. Miller,Martin L. Miller,Lars Juhl Jensen,Francesca Diella,Claus Jørgensen,Michele Tinti,Lei Li,Marilyn Hsiung,Sirlester A. Parker,Jennifer Bordeaux,Thomas Sicheritz-Pontén,Marina Olhovsky,Adrian Pasculescu,Jes Alexander,Stefan Knapp,Nikolaj Blom,Peer Bork,Peer Bork,Shawn S.-C. Li,Gianni Cesareni,Tony Pawson,Benjamin E. Turk,Michael B. Yaffe,Søren Brunak,Søren Brunak,Rune Linding,Rune Linding,Rune Linding +27 more
TL;DR: The resulting atlas of linear motifs revealed that oncogenic kinases tends to be less specific in the target sequences they phosphorylate than their non-oncogenic counterparts, that autophosphorylation sites tend to be more variable than other substrates of a given kinase, and that coupling interaction domains with kinase domains may allow phosphorylation site specificity to be low while still maintaining substrate specificity.
Journal ArticleDOI
Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments
TL;DR: Two Sample Logo is a web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments.
Journal ArticleDOI
Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini
Sami Mahrus,Jonathan C. Trinidad,David T. Barkan,Andrej Sali,Alma L. Burlingame,James A. Wells +5 more
TL;DR: A general approach for global identification of proteolytic cleavage sites is developed using an engineered enzyme to selectively biotinylate free protein N termini for positive enrichment of corresponding N-terminal peptides to study apoptosis.
Journal ArticleDOI
The CASBAH: a searchable database of caspase substrates.
TL;DR: A comprehensive list of caspase substrates is compiled and a searchable web resource is described which contains information pertaining to all currently known caspases which contains some of the unresolved issues relating to casp enzyme-dependent events in apoptosis and inflammation.
Journal ArticleDOI
Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture
Michael T. Forrester,J. Will Thompson,Matthew W. Foster,Leonardo Nogueira,M. Arthur Moseley,Jonathan S. Stamler +5 more
TL;DR: SNO-RAC revealed that intracellular proteins may undergo rapid denitrosylation on a global scale, and was readily adapted to analyzing diverse cysteine-based protein modifications, including S-acylation.
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