Principal InvestigatorOmics ApproachCitationLink
Chongyuan LuosnmCAT-seq: combined measurement of the transcriptome, DNA methylome, and chromatin accessibilityLuo et al., Cell Genom. 2022
Chongyuan Luosnm3C-seq: DNA methylome and chromatin organizationLee et al., Nat Methods. 2019
Kathrin Plath and Dino Di CarloSEC-seq: Method to simultaneously measure secreted proteins and associated transcriptomes for thousands of individual cellsUdani et al., Nat Nano. 2023
Jasmine ZhoucfMethyl-seq: cost-effective method for DNA methylation profilingStackpole et al., Nat Commun. 2022
Matteo PellegriniTBS: targeted bisufite sequencingMethods. 2021 Mar:187:13-27.doi: 10.1016/j.ymeth.2020.07.006
Principal InvestigatorBioinformatics ApproachCitationLink
Jessica LiscDesign 2: simulates realistic scRNA-seq data for benchmarking scRNA-seq data analysis toolsSun et al., Genome Biol. 2021
Jessica LiscDesign 3:Song et al., Nat Biotech. 2023
Grace XiaoAIDE: improves isoform discoveryLi et al., Genome Res. 2019
Grace XiaomoutainClimber: identifies alternative transcription starts and polyadenylation sitesCass et al., Cell Syst. 2019
Grace XiaoscAllele: detects nucleotide variants in scRNA-seq data and uncovers cancer-enriched variants with alternative splicingQuinones-Valdez et al., Sci Adv. 2022
Grace XiaoL-Giremi: uncovers RNA editing sites in long-read RNA-seq dataLiu et al., Genome Biol., 2023
Jason ErnstConsHMM: produces conservation state annotations of a genome based on a multi-species sequence alignmentArneson et al, NAR Genom Bioinform. 2020https://github.com/ernstlab/ConsHMM
Jason ErnstConsHMM Atlas: a compendium of over 20 conservation state annotations for 8 organisms.Arneson and Ernst, Comm Biology. 2019https://ernstlab.biolchem.ucla.edu/ConsHMMAtlas/
Jason Ernstχ-CNN: integrates 3D-chromatin interactions with epigenomic and TF binding data to fine-map sources of 3D chromatin interactionJaroszewicz et al., Bioinformatics. 2020https://github.com/ernstlab/X-CNN
Jason ErnstLECIF: defines regions with shared functional genomics properties in human and mouseKwon et al., Nat Comm. 2021https://github.com/ernstlab/LECIF
Jason ErnstCSREP: summarizes chromatin states across samples and quantifies differences between samplesVu et al., Bioinformatics. 2023https://github.com/ernstlab/csrep
Jason ErnstChromGene: models epigenetic data at the gene levelJaroszewicz and Ernst, Genome Biol, 2023https://github.com/ernstlab/ChromGene
Jason ErnstCNEP: predicts constrained-non exonic bases from epigenetic dataGrujic et al, Nat Comm 2020https://github.com/ernstlab/CNEP
Jason ErnstHuman universal chromatin state annotations: Chromatin state annotation of the human genome through a large-scale application of stacked ChromHMMVu and Ernst, Genome Biol. 2022https://github.com/ernstlab/full_stack_ChromHMM_annotations
Jason ErnstMouse universal chromatin state annotations: Chromatin state annotation of the human genome through a large-scale application of stacked ChromHMMVu and Ernst, Genome Biol. 2023https://github.com/ernstlab/mouse_fullStack_annotations
Jason ErnstChromHMM: software for chromatin state discovery and characterizationErnst and Kellis, Nat Methods, 2012https://github.com/jernst98/ChromHMM
Jason ErnstDREM: a tool for modeling, analyzing, and visualizing transcriptional gene regulation dynamics.Ernst et al, Mol Syst Biol 2007https://github.com/jernst98/STEM_DREM
Jason ErnstSTEM: a tool for the analysis of short time series gene expression dataErnst and Bar-Joseph, BMC Bioinformatics 2006https://github.com/jernst98/STEM_DREM
Jasmine ZhoucfSNV: detects low frequency mutations from cfDNALi et al., Nat Comm. 2021
Jasmine ZhoucfSort: identifies tissue of originLi et al., PNAS. 2023
Jasmine ZhoucfTrack: monitors cancer treatment outcomes from exome seqsLi et al., Clin Cancer Res. 2022
Matteo PellegriniBSBolt: align bisulfite converted readsGigascience . 2021 May 8;10(5):giab033. doi:10.1093/gigascience/giab033https://github.com/NuttyLogic/BSBolt
Matteo PellegriniBayesAge: maximum likelihood epigenetic clockFront Bioinform. 2024 Apr 4:4:1329144. doi: 10.3389/fbinf.2024.1329144.eCollection 2024.https://github.com/lajoycemboning/BayesAge
Matteo PellegriniEpigenetic Pacemaker: nonlinear epigenetic clockBioinformatics. 2020 Nov 1;36(17):4662-4663. doi: 10.1093/bioinformatics/btaa585.https://github.com/NuttyLogic/EpigeneticPacemaker
Matteo PellegriniACTINN: cell type assignments for scRNA-seqBioinformatics. 2020 Jan 15;36(2):533-538. doi: 10.1093/bioinformatics/btz592.https://github.com/mafeiyang/ACTINN
Grace XiaoBEAPR: ​identifies allele-specific binding of RNA-binding proteins in eCLIP-Seq dataYang et al, Nat Commun. 2019https://github.com/gxiaolab/BEAPR
Grace XiaomoutainClimber: identifies alternative transcription starts and polyadenylation sites in RNA-seqCass et al., Cell Syst. 2019https://github.com/gxiaolab/mountainClimber
Grace XiaoREDITs: identifies differential RNA editing sites in RNA-sequencing dataTran et al, Bioinformatics, 2020https://github.com/gxiaolab/REDITs
Grace XiaoscAllele: detects nucleotide variants in scRNA-seq data and uncovers cancer-enriched variants with alternative splicingQuinones-Valdez et al., Sci Adv. 2022https://github.com/gxiaolab/scAllele
Grace XiaoL-Giremi: uncovers RNA editing sites in long-read RNA-seq dataLiu et al., Genome Biol., 2023https://github.com/gxiaolab/L-GIREMI
Grace XiaodsRID: identifies long dsRNA regions using long-read RNA-seq dataYamamoto et al, Bioinformatics, 2023https://github.com/gxiaolab/dsRID
Grace XiaospliTWAS: identifies splicing-specific transcriptome-wide associationHervoso et al, American Journal of Human Genetics, 2024https://github.com/gxiaolab/SpliTWAS
Grace XiaoisoLASER: variant calling, haplotype phasing and detection of haplotype-specific splicing in long-read RNA-seq dataQuinones-Valdez et al., BioRxiv, 2024https://github.com/gxiaolab/isoLASER