WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. - Jens Lichtenberg; Kyle Kurz; Xiaoyu Liang; Rami Al-ouran; Lev Neiman; Lee J. Nau; Joshua D. Welch; Edwin Jacox; Thomas Bitterman; Klaus Ecker; Laura Elnitski; Frank Drews; et al. (BMC Bioinform., 2010)

SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data. - Joshua D. Welch; Ziqing Liu; Li Wang; Junjie Lu; Paul Lerou; Jeremy E. Purvis; Li Qian; Alexander J. Hartemink; Jan F. Prins (RECOMB, 2016)

E Pluribus Unum: United States of Single Cells. - Joshua D. Welch; Alexander J. Hartemink; Jan F. Prins (RECOMB, 2017)

Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning. - Chao Gao; Joshua D. Welch (RECOMB, 2020)

Variational Mixtures of ODEs for Inferring Cellular Gene Expression Dynamics. - Yichen Gu; David T. Blaauw; Joshua D. Welch (ICML, 2022)

Single-Cell Multi-omic Velocity Infers Dynamic and Decoupled Gene Regulation. - Chen Li; Maria Virgilio; Kathleen L. Collins; Joshua D. Welch (RECOMB, 2022)

PyLiger: scalable single-cell multi-omic data integration in Python. - Lu Lu; Joshua D. Welch (Bioinform., 2022)

Mapping Cell Fate Transition in Space and Time. - Yichen Gu; Jialin Liu; Chen Li; Joshua D. Welch (RECOMB, 2024)