Joshua D. Welch

12 papers A* 1B 5Journal 6
YearRankTypeTitle / Venue / Authors
2026 J jnl
Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.
PLoS Comput. Biol.
Yichen Gu, Yuxuan Song, David T. Blaauw, Joshua D. Welch
2025 J jnl
CytoSimplex: visualizing single-cell fates and transitions on a simplex.
Bioinform.
Jialin Liu, Yichen Wang, Chen Li, Yichen Gu, Noriaki Ono, Joshua D. Welch
2025 J jnl
Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks.
Bioinform.
Chao Gao, Joshua D. Welch
2024 B conf
Mapping Cell Fate Transition in Space and Time.
RECOMB
Yichen Gu, Jialin Liu, Chen Li, Joshua D. Welch
2022 J jnl
PyLiger: scalable single-cell multi-omic data integration in Python.
Bioinform.
Lu Lu, Joshua D. Welch
2022 B conf
Single-Cell Multi-omic Velocity Infers Dynamic and Decoupled Gene Regulation.
RECOMB
Chen Li, Maria Virgilio, Kathleen L. Collins, Joshua D. Welch
2022 A* conf
Variational Mixtures of ODEs for Inferring Cellular Gene Expression Dynamics.
ICML
Yichen Gu, David T. Blaauw, Joshua D. Welch
2022 J jnl
Variational Mixtures of ODEs for Inferring Cellular Gene Expression Dynamics.
CoRR
Yichen Gu, David T. Blaauw, Joshua D. Welch
2020 B conf
Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning.
RECOMB
Chao Gao, Joshua D. Welch
2017 B conf
E Pluribus Unum: United States of Single Cells.
RECOMB
Joshua D. Welch, Alexander J. Hartemink, Jan F. Prins
2016 B conf
SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data.
RECOMB
Joshua D. Welch, Ziqing Liu, Li Wang, Junjie Lu, Paul Lerou, Jeremy E. Purvis, Li Qian, Alexander J. Hartemink, Jan F. Prins
2010 J jnl
WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures.
BMC Bioinform.
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, Stephen Lee, Lonnie R. Welch