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Nature Communications|July 2, 2025
Facilitate integrated analysis of single cell multiomic data by binarizing gene expression valuesRohan Misra, Alexander Ferrena, Deyou ZhengPlos One|October 24, 2024
Six3 and Six6 jointly control diverse target genes in multiple cell populations over developmental trajectories of mouse embryonic retinal progenitor cellsAlexander Ferrena, Xusheng Zhang, Rupendra Shrestha, et al.Biorxiv : the Preprint Server for Biology|May 19, 2023
Six3 and Six6 jointly regulate the identities and developmental trajectories of multipotent retinal progenitor cells in the mouse retinaAlexander Ferrena, Xusheng Zhang, Rupendra Shrestha, et al.Biorxiv : the Preprint Server for Biology|September 15, 2025
shinyUMAP: an online tool for promoting understanding of single cell omics data visualizationRohan Misra, Kevin O'Leary, Wenna Chen, et al.Biorxiv : the Preprint Server for Biology|May 20, 2024
scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparisonAlexander Ferrena, Xiang Yu Zheng, Kevyn Jackson, et al.NAR Genomics and Bioinformatics|September 30, 2024
scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparisonAlexander Ferrena, Xiang Yu Zheng, Kevyn Jackson, et al.Nature Communications|March 21, 2023
Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell developmentChristopher De Bono, Yang Liu, Alexander Ferrena, et al.Bioinformatics (Oxford, England)|June 30, 2022
HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elementsVinod Kumar Singh, Rohan Misra, Steven C Almo, et al.Genome Biology|July 5, 2008
Asymmetric histone modifications between the original and derived loci of human segmental duplicationsDeyou ZhengBiorxiv : the Preprint Server for Biology|May 22, 2023
SKP2 knockout in Rb1/p53 deficient mouse models of osteosarcoma induces immune infiltration and drives a transcriptional program with a favorable prognosisAlexander Ferrena, Jichuan Wang, Ranxin Zhang, et al.Pageof 22