SAVoR: a server for sequencing annotation and visualization of RNA structures. - Fan Li 002; Paul Ryvkin; Daniel M. Childress; Otto Valladares; Brian D. Gregory; Li-San Wang (Nucleic Acids Res., 2012)

DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments. - 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 (Bioinform., 2013)

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. - Yih-Chii Hwang; Chiao-Feng Lin; Otto Valladares; John Malamon; Pavel P. Kuksa; Qi Zheng; Brian D. Gregory; Li-San Wang (Bioinform., 2015)

DASHR: database of small human noncoding RNAs. - Yuk Yee Leung; Pavel P. Kuksa; Alexandre Amlie-Wolf; Otto Valladares; Lyle H. Ungar; Sampath Kannan; Brian D. Gregory; Li-San Wang (Nucleic Acids Res., 2016)

SPAR: small RNA-seq portal for analysis of sequencing experiments. - Pavel P. Kuksa; Alexandre Amlie-Wolf; Zivadin Katanic; Otto Valladares; Li-San Wang; Yuk Yee Leung (Nucleic Acids Res., 2018)

DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. - Pavel P. Kuksa; Alexandre Amlie-Wolf; Zivadin Katanic; Otto Valladares; Li-San Wang; Yuk Yee Leung (Bioinform., 2019)

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. - 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 (Bioinform., 2019)

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. - 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 (Bioinform., 2019)

SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants. - 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 (Bioinform., 2020)

hipFG: high-throughput harmonization and integration pipeline for functional genomics data. - Jeffrey Cifello; Pavel P. Kuksa; Naveensri Saravanan; Otto Valladares; Li-San Wang; Yuk Yee Leung (Bioinform., 2023)