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NAR Genomics and Bioinformatics|January 12, 2024
Brooklyn plots to identify co-expression dysregulation in single cell sequencingArun H Patil, Matthew N McCall, Marc K HalushkaGigascience|August 25, 2022
A curated human cellular microRNAome based on 196 primary cell typesArun H Patil, Andrea Baran, Zachary P Brehm, et al.Biorxiv : the Preprint Server for Biology|July 29, 2024
miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRsAndrea M Baran, Arun H Patil, Ernesto Aparicio-Puerta, et al.NAR Genomics and Bioinformatics|July 26, 2021
miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipelineArun H Patil, Marc K HalushkaGenome Biology|April 23, 2025
miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRsAndrea M Baran, Arun H Patil, Ernesto Aparicio-Puerta, et al.Laboratory Investigation; a Journal of Technical Methods and Pathology|April 26, 2024
Patterns of Unwanted Biological and Technical Expression Variation Among 49 Human TissuesTim O Nieuwenhuis, Hunter H Giles, Jeremy V A Arking, et al.Biostatistics (Oxford, England)|May 26, 2026
NBSR: a Negative Binomial Softmax Regression model for microRNA-seq data analysisSeong-Hwan Jun, Marc K Halushka, Matthew N McCallAmerican Journal of Human Genetics|September 3, 2016
Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung TranscriptomeMatthew N McCall, Peter B Illei, Marc K HalushkaBriefings in Bioinformatics|December 10, 2019
The effect of tissue composition on gene co-expressionYun Zhang, Jonavelle Cuerdo, Marc K Halushka, et al.Trends in Genetics : TIG|January 24, 2018
Big Strides in Cellular MicroRNA ExpressionMarc K Halushka, Bastian Fromm, Kevin J Peterson, et al.Pageof 26