Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome

CPG Calixto, W Guo, AB James, NA Tzioutziou… - The Plant …, 2018 - academic.oup.com
Plants have adapted to tolerate and survive constantly changing environmental conditions
by reprogramming gene expression The dynamics of the contribution of alternative splicing …

CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within specified regions

M Suzuki, S Sakai, K Ota, Y Bando, C Uchida… - Scientific Reports, 2023 - nature.com
Pairs of sense and antisense transcriptions that are adjacent at their 5′ and 3′ regions are
called divergent and convergent transcription, respectively. However, the structural …

Intergenic disease-associated regions are abundant in novel transcripts

N Bartonicek, MB Clark, XC Quek, JR Torpy… - Genome biology, 2017 - Springer
Background Genotyping of large populations through genome-wide association studies
(GWAS) has successfully identified many genomic variants associated with traits or disease …

You can't always sketch what you want: Understanding Sensemaking in Visual Query Systems

DJL Lee, J Lee, T Siddiqui, J Kim… - IEEE transactions on …, 2019 - ieeexplore.ieee.org
Visual query systems (VQSs) empower users to interactively search for line charts with
desired visual patterns, typically specified using intuitive sketch-based interfaces. Despite …

Time-resolved transcriptomics in neural stem cells identifies a v-ATPase/Notch regulatory loop

S Wissel, H Harzer, F Bonnay, TR Burkard… - Journal of Cell …, 2018 - rupress.org
Drosophila melanogaster neural stem cells (neuroblasts [NBs]) divide asymmetrically by
differentially segregating protein determinants into their daughter cells. Although the …

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics

C Barry, MT Schmitz, C Argus, JM Bolin… - PLOS Computational …, 2019 - journals.plos.org
Pluripotent stem cells retain the developmental timing of their species of origin in vitro, an
observation that suggests the existence of a cell-intrinsic developmental clock, yet the nature …

Deciphering the Nature of Trp73 Isoforms in Mouse Embryonic Stem Cell Models: Generation of Isoform-Specific Deficient Cell Lines Using the CRISPR/Cas9 Gene …

L López-Ferreras, N Martínez-García, L Maeso-Alonso… - Cancers, 2021 - mdpi.com
Simple Summary The Trp73 gene is involved in the regulation of multiple biological
processes such as response to stress, differentiation and tissue architecture. This gene …

MLL3/MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer H3K4me1

G Xie, JE Lee, K McKernan, YK Park, Y Jang, C Liu… - bioRxiv, 2020 - biorxiv.org
Enhancers drive cell-type-specific gene transcription and are marked by H3K4me1. MLL4
(KMT2D), a major H3K4me1 methyltransferase with partial functional redundancy with MLL3 …

Three lessons from accelerating scientific insight discovery via visual querying

DJL Lee, T Siddiqui, K Karahalios, A Parameswaran - Patterns, 2020 - cell.com
Exploratory data analysis is a crucial part of data-driven scientific discovery. Yet, the process
of discovering insights from visualization can be a manual and painstaking process. This …

Experimental design for time-series RNA-Seq analysis of gene expression and alternative splicing

NA Tzioutziou, AB James, W Guo, CPG Calixto… - … Networks: Methods and …, 2022 - Springer
Abstract RNA-sequencing (RNA-seq) is currently the method of choice for analysis of
differential gene expression. To fully exploit the wealth of data generated from genome-wide …