Genetics: Recent submissions
Now showing items 1-20 of 146
-
Transcript cleavage and polyadenylation in plants
Eukaryotic gene expression is finely regulated at the post-transcriptional level by the untranslated regions of mRNA. The coding sequence (CDS) of mRNA is flanked by 5’- and 3’-untranslated regions (UTRs). The end boundary ... -
Single-cell Analysis Reveals the Molecular Roadmap of Mouse Embryogenesis
Mammalian embryogenesis is a rapid and complex process that involves the proliferation and diversification of cells. Within a few weeks, a single-cell zygote gives rise to hundreds of millions of cells that express a wide ... -
Inferring whole-genome 3D chromatin structures from diploid Hi-C data
The three-dimensional organization of the genome plays an important part in regulating numerous basic cellular functions, including gene regulation, differentiation, the cell cycle, DNA replication, and DNA repair. Assays ... -
Feature Detection for the Hidden Proteome
Proteomics primarily focuses on identifying and quantifying peptides using database searches. However, there are instances where certain features of interest, such as unexpected byproducts, abnormal cleavages, unknown ... -
CRISPR-based functional genomics to study gene regulatory architecture and consequences of genetic variation
If we divide the human genome into its noncoding and coding parts, the noncoding portion takes up ~98-99% of the genome, and the coding portion takes up ~1-2% (ENCODE Project Consortium, 2012). The coding portion of the ... -
Systematic Data Acquisition and Analysis Strategies for Quantitative Proteomics
Mass spectrometry-based proteomics has emerged as a powerful tool to gain insight into biological systems. As biological studies get more complex, there is a pressing need to increase throughput without sacrificing quality ... -
Expanding cancer therapy options through genome-scale identification of synthetic lethal paralogs
Synthetic lethal therapies have the potential to expand cancer treatment options. Synthetic lethality is a form of context-dependent gene essentiality in which dual inactivation of a gene pair leads to cell death but ... -
Evolutionary and spatial dynamics underlying intra-tumor heterogeneity
Intra-tumor heterogeneity (ITH) is a pervasive feature of solid tumors that complicates clinical prognosis and management. Yet, the evolutionary processes that explain ITH remain largely unresolved. Here, we demonstrate ... -
Building multiplexed genomic tools for editing and interpreting human variation
Advances in DNA sequencing over the past twenty years have led to an unprecedented expansion in our ability to read DNA sequences and find genetic variation in individuals. However, our ability to manipulate and interpret ... -
Understanding recursive splicing in the human genome
Recursive splicing is a non-canonical splicing mechanism that results in an intron being removed in two or more segments. Identifying recursive splicing presents technical challenges due to the lack of evidence in mRNA and ... -
High-throughput functional characterization of cancer specific alternative polyadenylation
RNA dysregulation is a ubiquitous feature of human cancers and misexpression of even a single RNA isoform is sufficient to drive cancer. Among types of RNA processing, alternative cleavage and polyadenylation (APA), a ... -
Investigating the duplication and evolution of essential fertilization proteins
Duplication processes such as whole gene duplication and tandem domain expansion are important for the evolution and functional diversification of essential protein families. While whole gene duplications are well established ... -
Quantifying progeny production from individual influenza virus-infected cells
The distribution of progeny virions produced by virus-infected cells is extremely heterogeneous. This trend has been observed in diverse viruses, including bacteriaphage and pathogenic human viruses. To date, it has been ... -
Ultra-large-scale genomics approaches to improve cancer therapeutic response
The advent of low-cost, high-throughput sequencing technologies has elucidated targetable cancer-specific genomic alterations and allowed the development of precision therapies and their deployment into clinical use. ... -
Development and application of combinatorial single cell methods to tissue physiology and disease
Advances in single-cell sequencing technologies present an opportunity to study the cellular and molecular basis of complex tissue physiology at global scale with unprecedented throughput. In this work, methods for application ... -
Immune consequences and therapeutic targeting of disrupted RNA splicing in cancer
Immunotherapies, such as checkpoint blockade, CAR-T cells, and vaccines, have proven to be a valuable tool to treat various types of cancer. This class of therapy capitalizes on the immune system’s natural ability to ... -
Identifying Neural Pathways of Stress and Fear with Retrograde Viral Tracing and Single Cell RNA Sequencing
The brain is made up of millions of neurons, often making thousands of connections each. Interrogating individual neurons activated by stressors is the equivalent of finding a needle in a haystack. Here we describe ... -
Quantitative cross-linking mass spectrometry for protein structural stability studies
Mass spectrometry-based methods for protein-ligand identification have expanded classical techniques for the bioanalytical characterization of small molecule target engagement and their modes of action. In the last decade, ... -
Species-scale high-throughput functional analysis of natural variants in yeast
The impact of natural genetic variation on phenotype is difficult to measure because we only partially understand how polymorphisms present in a population affect gene function. Understanding the relationship between genetic ... -
Oncogene-driven post-transcriptional regulation in lung cancer
Lung cancer is often caused by genetic mutations which alter the activity of proteins in the RAS family, with somatic mutation of the KRAS gene occurring in ~30% of lung adenocarcinoma tumors. A gene of the same family, ...