| snmCAT-seq: combined measurement of the transcriptome, DNA methylome, and chromatin accessibility. | Luo | Luo et al., Cell Genom. 2022 |
| sn-m3C-seq: DNA methylome and chromatin organization (led to U01HG012079; MPIs: Luo, Plath, Zaitlen) | Luo | Lee et al., Nat Methods. 2019 |
| SEC-seq: method that simultaneously measures secreted proteins and associated transcriptomes across thousands of individual cells | Plath and Dino Di Carlo, PhD (CMINT) | Udani et al., Nat Nano. 2023 |
| scDesign 2, scDesign3: simulate realistic scRNA-seq data for benchmarking scRNA-seq data analysis tools | J Li | Li et al., Genome Res. 2019 |
| AIDE: improves isoform discovery | J Li | Cass et al., Cell Syst. 2019 |
| moutainClimber: identifies alternative transcription start and polyadenylation sites | Xiao | Quinones-Valdez et al., Sci Adv. 2022 |
| scAllele: detects nucleotide variants in scRNA-seq data and uncovers cancer-enriched variants with alternative splicing | Xiao | Liu et al., Genome Biol., 2023 |
| L-Giremi: uncovers RNA editing sites in long-read RNA-seq data | Xiao | Arneson et al., Comm Biology. 2019 |
| ConsHMM Atlas: annotates the genome into conservation states | Ernst | Jaroszewicz et al., Bioinformatics. 2020 |
| χ-CNN: integrates 3D-chromatin interactions with epigenomic and TF binding data to fine-map likely sources of 3D chromatin interaction | Ernst | Kwon et al., Nat Comm. 2021 |
| LECIF: defines regions with shared functional genomics properties in human and mouse | Ernst | Vu et al., Bioinformatics. 2023 |
| CSREP: summarizes chromatin states across samples and quantifies differences between samples | Ernst | Jaroszewicz et al, Genome Biol, 202 |
| Chrom-Gene: models epigenetic data at the gene level | Ernst | Jaroszewicz et al, Genome Biol, 202 |
| Full-stack Chrom-HMM:universal annotation of the human epigenome | Ernst | Vu and Ernst, Genome Biol. 2022 |
| cfSNV detects low frequency mutations from cfDNA, cfSort tissue of origin, cfTrack monitors cancer treatment outcomes from exome seq; cfMethyl-seq, cost-effective method for DNA methylation profiling | Zhou | Li et al.,Nat Comm. 2021 PNAS. 2023, Clin Cancer Res. 2022, Stackpole et al., Nat Commun. 2022. |
