| Principal Investigator | Omics Approach | Citation | Link |
|---|---|---|---|
| Chongyuan Luo | snmCAT-seq: combined measurement of the transcriptome, DNA methylome, and chromatin accessibility | Luo et al., Cell Genom. 2022 | |
| Chongyuan Luo | snm3C-seq: DNA methylome and chromatin organization | Lee et al., Nat Methods. 2019 | |
| Kathrin Plath and Dino Di Carlo | SEC-seq: Method to simultaneously measure secreted proteins and associated transcriptomes for thousands of individual cells | Udani et al., Nat Nano. 2023 | |
| Jasmine Zhou | cfMethyl-seq: cost-effective method for DNA methylation profiling | Stackpole et al., Nat Commun. 2022 | |
| Matteo Pellegrini | TBS: targeted bisufite sequencing | Methods. 2021 Mar:187:13-27. | doi: 10.1016/j.ymeth.2020.07.006 |
| Principal Investigator | Bioinformatics Approach | Citation | Link |
|---|---|---|---|
| Jessica Li | scDesign 2: simulates realistic scRNA-seq data for benchmarking scRNA-seq data analysis tools | Sun et al., Genome Biol. 2021 | |
| Jessica Li | scDesign 3: | Song et al., Nat Biotech. 2023 | |
| Grace Xiao | AIDE: improves isoform discovery | Li et al., Genome Res. 2019 | |
| Grace Xiao | moutainClimber: identifies alternative transcription starts and polyadenylation sites | Cass et al., Cell Syst. 2019 | |
| Grace Xiao | scAllele: detects nucleotide variants in scRNA-seq data and uncovers cancer-enriched variants with alternative splicing | Quinones-Valdez et al., Sci Adv. 2022 | |
| Grace Xiao | L-Giremi: uncovers RNA editing sites in long-read RNA-seq data | Liu et al., Genome Biol., 2023 | |
| Jason Ernst | ConsHMM: produces conservation state annotations of a genome based on a multi-species sequence alignment | Arneson et al, NAR Genom Bioinform. 2020 | https://github.com/ernstlab/ConsHMM |
| Jason Ernst | ConsHMM Atlas: a compendium of over 20 conservation state annotations for 8 organisms. | Arneson and Ernst, Comm Biology. 2019 | https://ernstlab.biolchem.ucla.edu/ConsHMMAtlas/ |
| Jason Ernst | χ-CNN: integrates 3D-chromatin interactions with epigenomic and TF binding data to fine-map sources of 3D chromatin interaction | Jaroszewicz et al., Bioinformatics. 2020 | https://github.com/ernstlab/X-CNN |
| Jason Ernst | LECIF: defines regions with shared functional genomics properties in human and mouse | Kwon et al., Nat Comm. 2021 | https://github.com/ernstlab/LECIF |
| Jason Ernst | CSREP: summarizes chromatin states across samples and quantifies differences between samples | Vu et al., Bioinformatics. 2023 | https://github.com/ernstlab/csrep |
| Jason Ernst | ChromGene: models epigenetic data at the gene level | Jaroszewicz and Ernst, Genome Biol, 2023 | https://github.com/ernstlab/ChromGene |
| Jason Ernst | CNEP: predicts constrained-non exonic bases from epigenetic data | Grujic et al, Nat Comm 2020 | https://github.com/ernstlab/CNEP |
| Jason Ernst | Human universal chromatin state annotations: Chromatin state annotation of the human genome through a large-scale application of stacked ChromHMM | Vu and Ernst, Genome Biol. 2022 | https://github.com/ernstlab/full_stack_ChromHMM_annotations |
| Jason Ernst | Mouse universal chromatin state annotations: Chromatin state annotation of the human genome through a large-scale application of stacked ChromHMM | Vu and Ernst, Genome Biol. 2023 | https://github.com/ernstlab/mouse_fullStack_annotations |
| Jason Ernst | ChromHMM: software for chromatin state discovery and characterization | Ernst and Kellis, Nat Methods, 2012 | https://github.com/jernst98/ChromHMM |
| Jason Ernst | DREM: a tool for modeling, analyzing, and visualizing transcriptional gene regulation dynamics. | Ernst et al, Mol Syst Biol 2007 | https://github.com/jernst98/STEM_DREM |
| Jason Ernst | STEM: a tool for the analysis of short time series gene expression data | Ernst and Bar-Joseph, BMC Bioinformatics 2006 | https://github.com/jernst98/STEM_DREM |
| Jasmine Zhou | cfSNV: detects low frequency mutations from cfDNA | Li et al., Nat Comm. 2021 | |
| Jasmine Zhou | cfSort: identifies tissue of origin | Li et al., PNAS. 2023 | |
| Jasmine Zhou | cfTrack: monitors cancer treatment outcomes from exome seqs | Li et al., Clin Cancer Res. 2022 | |
| Matteo Pellegrini | BSBolt: align bisulfite converted reads | Gigascience . 2021 May 8;10(5):giab033. doi:10.1093/gigascience/giab033 | https://github.com/NuttyLogic/BSBolt |
| Matteo Pellegrini | BayesAge: maximum likelihood epigenetic clock | Front Bioinform. 2024 Apr 4:4:1329144. doi: 10.3389/fbinf.2024.1329144.eCollection 2024. | https://github.com/lajoycemboning/BayesAge |
| Matteo Pellegrini | Epigenetic Pacemaker: nonlinear epigenetic clock | Bioinformatics. 2020 Nov 1;36(17):4662-4663. doi: 10.1093/bioinformatics/btaa585. | https://github.com/NuttyLogic/EpigeneticPacemaker |
| Matteo Pellegrini | ACTINN: cell type assignments for scRNA-seq | Bioinformatics. 2020 Jan 15;36(2):533-538. doi: 10.1093/bioinformatics/btz592. | https://github.com/mafeiyang/ACTINN |
| Grace Xiao | BEAPR: identifies allele-specific binding of RNA-binding proteins in eCLIP-Seq data | Yang et al, Nat Commun. 2019 | https://github.com/gxiaolab/BEAPR |
| Grace Xiao | moutainClimber: identifies alternative transcription starts and polyadenylation sites in RNA-seq | Cass et al., Cell Syst. 2019 | https://github.com/gxiaolab/mountainClimber |
| Grace Xiao | REDITs: identifies differential RNA editing sites in RNA-sequencing data | Tran et al, Bioinformatics, 2020 | https://github.com/gxiaolab/REDITs |
| Grace Xiao | scAllele: detects nucleotide variants in scRNA-seq data and uncovers cancer-enriched variants with alternative splicing | Quinones-Valdez et al., Sci Adv. 2022 | https://github.com/gxiaolab/scAllele |
| Grace Xiao | L-Giremi: uncovers RNA editing sites in long-read RNA-seq data | Liu et al., Genome Biol., 2023 | https://github.com/gxiaolab/L-GIREMI |
| Grace Xiao | dsRID: identifies long dsRNA regions using long-read RNA-seq data | Yamamoto et al, Bioinformatics, 2023 | https://github.com/gxiaolab/dsRID |
| Grace Xiao | spliTWAS: identifies splicing-specific transcriptome-wide association | Hervoso et al, American Journal of Human Genetics, 2024 | https://github.com/gxiaolab/SpliTWAS |
| Grace Xiao | isoLASER: variant calling, haplotype phasing and detection of haplotype-specific splicing in long-read RNA-seq data | Quinones-Valdez et al., BioRxiv, 2024 | https://github.com/gxiaolab/isoLASER |
