Full-length transcriptome assembly from RNA-Seq data without a reference genome
…, I Amit, X Adiconis, L Fan, R Raychowdhury… - Nature …, 2011 - nature.com
Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes.
Current approaches for transcript reconstruction from such data often rely on aligning …
Current approaches for transcript reconstruction from such data often rely on aligning …
[HTML][HTML] Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
…, I Amit, X Adiconis, L Fan, R Raychowdhury… - Nature …, 2011 - ncbi.nlm.nih.gov
Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of
transcriptomes. Current approaches for transcript reconstruction from such data often rely on …
transcriptomes. Current approaches for transcript reconstruction from such data often rely on …
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
…, RS Gertner, JT Gaublomme, R Raychowdhury… - Nature, 2013 - nature.com
Recent molecular studies have shown that, even when derived from a seemingly homogenous
population, individual cells can exhibit substantial differences in gene expression, protein …
population, individual cells can exhibit substantial differences in gene expression, protein …
A single-cell survey of the small intestinal epithelium
…, S Beyaz, D Dionne, M Zhang, R Raychowdhury… - Nature, 2017 - nature.com
Intestinal epithelial cells absorb nutrients, respond to microbes, function as a barrier and
help to coordinate immune responses. Here we report profiling of 53,193 individual epithelial …
help to coordinate immune responses. Here we report profiling of 53,193 individual epithelial …
[PDF][PDF] Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens
…, ND Marjanovic, D Dionne, T Burks, R Raychowdhury… - cell, 2016 - cell.com
Genetic screens help infer gene function in mammalian cells, but it has remained difficult to
assay complex phenotypes—such as transcriptional profiles—at scale. Here, we develop …
assay complex phenotypes—such as transcriptional profiles—at scale. Here, we develop …
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
…, S Weaver, J Wang, X Wang, R Ding, R Raychowdhury… - Nature, 2014 - nature.com
High-throughput single-cell transcriptomics offers an unbiased approach for understanding
the extent, basis and function of gene expression variation between seemingly identical cells…
the extent, basis and function of gene expression variation between seemingly identical cells…
Synergistic interaction between hypergastrinemia and Helicobacter infection in a mouse model of gastric cancer
…, D Chen, JR Goldenring, T Koh, R Raychowdhury… - Gastroenterology, 2000 - Elsevier
Background & Aims: Hypergastrinemia occurs frequently in association with acid suppression
and Helicobacter infection, but its role in the progression to gastric atrophy and gastric …
and Helicobacter infection, but its role in the progression to gastric atrophy and gastric …
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
…, JZ Levin, L Fan, X Adiconis, R Raychowdhury… - Nature …, 2011 - nature.com
Cellular RNA levels are determined by the interplay of RNA production, processing and
degradation. However, because most studies of RNA regulation do not distinguish the separate …
degradation. However, because most studies of RNA regulation do not distinguish the separate …
[PDF][PDF] A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks
Finding the components of cellular circuits and determining their functions systematically
remains a major challenge in mammalian cells. Here, we introduced genome-wide pooled …
remains a major challenge in mammalian cells. Here, we introduced genome-wide pooled …
Dynamic profiling of the protein life cycle in response to pathogens
…, AP Fields, S Schwartz, R Raychowdhury… - Science, 2015 - science.org
INTRODUCTION Mammalian gene expression is tightly controlled through the interplay
between the RNA and protein life cycles. Although studies of individual genes have shown that …
between the RNA and protein life cycles. Although studies of individual genes have shown that …