Exon Array Analyzer: a web interface for Affymetrix exon array analysis. - Pascal Gellert; Shizuka Uchida; Thomas Braun (Bioinform., 2009)

C-It: a knowledge database for tissue-enriched genes. - Pascal Gellert; Katharina Jenniches; Thomas Braun; Shizuka Uchida (Bioinform., 2010)

C-It-Loci: a knowledge database for tissue-enriched loci. - Tyler Weirick; David John; Stefanie Dimmeler; Shizuka Uchida (Bioinform., 2015)

The identification and characterization of novel transcripts from RNA-seq data. - Tyler Weirick; Giuseppe Militello; Raphael Rene Müller; David John; Stefanie Dimmeler; Shizuka Uchida (Briefings Bioinform., 2016)

RNAEditor: easy detection of RNA editing events and the introduction of editing islands. - David John; Tyler Weirick; Stefanie Dimmeler; Shizuka Uchida (Briefings Bioinform., 2017)

Screening and validation of lncRNAs and circRNAs as miRNA sponges. - Giuseppe Militello; Tyler Weirick; David John; Claudia Döring 002; Stefanie Dimmeler; Shizuka Uchida (Briefings Bioinform., 2017)

Resolving the problem of multiple accessions of the same transcript deposited across various public databases. - Tyler Weirick; David John; Shizuka Uchida (Briefings Bioinform., 2017)

Logic programming to infer complex RNA expression patterns from RNA-seq data. - Tyler Weirick; Giuseppe Militello; Yuliya Ponomareva; David John; Claudia Döring 002; Stefanie Dimmeler; Shizuka Uchida (Briefings Bioinform., 2018)

Increasing workflow development speed and reproducibility with Vectools. - Tyler Weirick; Raphael Rene Müller; Shizuka Uchida (F1000Research, 2018)

DRETools: A tool-suite for differential RNA editing detection. - Tyler Weirick; Patrick J. Trainor; Eric C. Rouchka; Andrew P. DeFilippis; Shizuka Uchida (F1000Research, 2018)

CrohnDB: A Web Database for Expression Profiling of Protein-Coding and Long Non-Coding RNA Genes in Crohn Disease. - Rebecca Distefano; Mirolyuba Ilieva; Jens Hedelund Madsen; Shizuka Uchida (Comput., 2023)