Rajappa-Titu, Lional Suematsu, Takuma Munoz-Tello, Paola Long, Marius Demir, Özlem Cheng, Kevin J Stagno, Jason R Luecke, Hartmut Amaro, Rommie E Aphasizheva, Inna
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Published in
Nucleic Acids Research
Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei In mitochondria of this pathogen, most mRNAs are in...
Lowe, Todd M Chan, Patricia P
Published in
Nucleic acids research
High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content ...
Tang, Yen-An Chen, Chi-Hsin Sun, H Sunny Cheng, Chun-Pei Tseng, Vincent S Hsu, Han-Shui Su, Wu-Chou Lai, Wu-Wei Wang, Yi-Ching
Published in
Nucleic Acids Research
Overexpression of Oct4, a stemness gene encoding a transcription factor, has been reported in several cancers. However, the mechanism by which Oct4 directs transcriptional program that leads to somatic cancer progression remains unclear. In this study, we provide mechanistic insight into Oct4-driven transcriptional network promoting drug-resistance...
Published in
Nucleic Acids Research
The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for different uses: the UniProt Arc...
Rosenbloom, Kate R Armstrong, Joel Barber, Galt P Casper, Jonathan Clawson, Hiram Diekhans, Mark Dreszer, Timothy R Fujita, Pauline A Guruvadoo, Luvina Haeussler, Maximilian
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Published in
Nucleic acids research
Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new hu...
Goldman, Mary Craft, Brian Swatloski, Teresa Cline, Melissa Morozova, Olena Diekhans, Mark Haussler, David Zhu, Jingchun
Published in
Nucleic acids research
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover and share their research observations. Users can explore the relationship between genomic alterations and phenotypes by visualizing various -omic data alongside cl...
Chelliah, Vijayalakshmi Juty, Nick Ajmera, Ishan Ali, Raza Dumousseau, Marine Glont, Mihai Hucka, Michael Jalowicki, Gaël Keating, Sarah Knight-Schrijver, Vincent
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Published in
Nucleic Acids Research
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models...
Darbari, Vidya C Lawton, Ed Lu, Duo Burrows, Patricia C Wiesler, Simone Nicolas Joly Zhang, Nan Zhang, Xiaodong Buck, Martin
Published in
Nucleic Acids Research
Binding and hydrolysis of ATP is universally required by AAA+ proteins to underpin their mechano-chemical work. Here we explore the roles of the ATPase site in an AAA+ transcriptional activator protein, the phage shock protein F (PspF), by specifically altering the Walker B motif sequence required in catalyzing ATP hydrolysis. One such mutant, the ...
Zhou, Shiguo Wei, Fusheng Nguyen, John Bechner, Mike Potamousis, Konstantinos Goldstein, Steve Pape, Louise Mehan, Michael R Churas, Chris Pasternak, Shiran
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Published in
PLoS genetics
About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence b...
Ramasamy, Adaikalavan Trabzuni, Daniah Gibbs, J Raphael Dillman, Allissa Hernandez, Dena G Arepalli, Sampath Walker, Robert Smith, Colin Ilori, Gigaloluwa Peter Shabalin, Andrey A
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Published in
Nucleic acids research
Polymorphisms in the target mRNA sequence can greatly affect the binding affinity of microarray probe sequences, leading to false-positive and false-negative expression quantitative trait locus (QTL) signals with any other polymorphisms in linkage disequilibrium. We provide the most complete solution to this problem, by using the latest genome and ...
