Otto Valladares

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2025 J jnl
BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1000s of omics datasets.
Bioinform.
Pavel P. Kuksa, Matei Ionita, Luke Carter, Jeffrey Cifello, Prabhakaran Gangadharan, Kaylyn Clark, Otto Valladares, Yuk Yee Leung, Li-San Wang
2023 J jnl
hipFG: high-throughput harmonization and integration pipeline for functional genomics data.
Bioinform.
Jeffrey Cifello, Pavel P. Kuksa, Naveensri Saravanan, Otto Valladares, Li-San Wang, Yuk Yee Leung
2020 J jnl
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.
Bioinform.
Pavel P. Kuksa, Chien-Yueh Lee, Alexandre Amlie-Wolf, Prabhakaran Gangadharan, Elizabeth E. Mlynarski, Yi-Fan Chou, Han-Jen Lin, Heather Issen, Emily Greenfest-Allen, Otto Valladares, Yuk Yee Leung, Li-San Wang
2019 J jnl
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products.
Bioinform.
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
2019 J jnl
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.
Bioinform.
Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda Kuzma, Laura Cantwell, Liming Qu, Prabhakaran Gangadharan, William J. Salerno, Gerard D. Schellenberg, Li-San Wang
2019 J jnl
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.
Bioinform.
Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda Kuzma, Laura Cantwell, Liming Qu, William J. Salerno, Gerard D. Schellenberg, Li-San Wang
2018 J jnl
SPAR: small RNA-seq portal for analysis of sequencing experiments.
Nucleic Acids Res.
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
2016 J jnl
DASHR: database of small human noncoding RNAs.
Nucleic Acids Res.
Yuk Yee Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, Li-San Wang
2015 J jnl
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.
Bioinform.
Yih-Chii Hwang, Chiao-Feng Lin, Otto Valladares, John Malamon, Pavel P. Kuksa, Qi Zheng, Brian D. Gregory, Li-San Wang
2013 J jnl
DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments.
Bioinform.
Chiao-Feng Lin, Otto Valladares, Daniel M. Childress, Egor Klevak, Evan T. Geller, Yih-Chii Hwang, Ellen A. Tsai, Gerard D. Schellenberg, Li-San Wang
2012 J jnl
SAVoR: a server for sequencing annotation and visualization of RNA structures.
Nucleic Acids Res.
Fan Li, Paul Ryvkin, Daniel M. Childress, Otto Valladares, Brian D. Gregory, Li-San Wang