Search publications

40 results for “functional genomics”

Clear

  1. Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism.

    Nucleic acids research · 2017 · 45(21): 12509-12528

    To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, …

    PMID 29069457 DOI ↗

  2. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer.

    Cancer discovery · 2017 · 7(4): 410-423

    Recent studies have characterized the extensive somatic alterations that arise during cancer. However, the somatic evolution of a tumor may be significantly affected by inherited polymorphisms carried in the germline. Here, we analyze genomic data for 5,954 tumors to reveal …

    PMID 28188128 DOI ↗

  3. iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.

    Stem cell reports · 2017 · 8(4): 1086-1100

    Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 …

    PMID 28410642 DOI ↗

  4. Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing.

    Nature genetics · 2017 · 49(3): 457-464

    Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg<sup>2+</sup>-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) …

    PMID 28092684 DOI ↗

  5. Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins.

    Advances in experimental medicine and biology · 2016 · 907: 61-88

    Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, …

    PMID 27256382 DOI ↗

  6. Rbfox2 function in RNA metabolism is impaired in hypoplastic left heart syndrome patient hearts.

    Scientific reports · 2016 · 6: 30896

    Hypoplastic left heart syndrome (HLHS) is a fatal congenital heart disease in which the left side of the heart is underdeveloped, impairing the systemic circulation. Underdeveloped left ventricle exerts biomechanical stress on the right ventricle that can progress into heart …

    PMID 27485310 DOI ↗

  7. Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects.

    PLoS genetics · 2015 · 11(4): e1005123

    Endogenous retroviruses and retrotransposons contribute functional genetic variation in animal genomes. In mice, Intracisternal A Particles (IAPs) are a frequent source of both new mutations and polymorphism across laboratory strains. Intronic IAPs can induce alternative RNA processing choices, including alternative …

    PMID 25835743 DOI ↗

  8. RNA-binding proteins in neurodegeneration: Seq and you shall receive.

    Trends in neurosciences · 2015 · 38(4): 226-36

    As critical players in gene regulation, RNA binding proteins (RBPs) are taking center stage in our understanding of cellular function and disease. In our era of bench-top sequencers and unprecedented computational power, biological questions can be addressed in a systematic, …

    PMID 25765321 DOI ↗

  9. A novel splice-site mutation in ALS2 establishes the diagnosis of juvenile amyotrophic lateral sclerosis in a family with early onset anarthria and generalized dystonias.

    PloS one · 2014 · 9(12): e113258

    The diagnosis of childhood neurological disorders remains challenging given the overlapping clinical presentation across subgroups and heterogeneous presentation within subgroups. To determine the underlying genetic cause of a severe neurological disorder in a large consanguineous Pakistani family presenting with severe …

    PMID 25474699 DOI ↗

  10. Human cytomegalovirus infection of human embryonic stem cell-derived primitive neural stem cells is restricted at several steps but leads to the persistence of viral DNA.

    Journal of virology · 2014 · 88(8): 4021-39

    Congenital human cytomegalovirus (HCMV) infection is a major cause of central nervous system structural anomalies and sensory impairments. It is likely that the stage of fetal development, as well as the state of differentiation of susceptible cells at the time …

    PMID 24453373 DOI ↗

  11. Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans.

    PLoS genetics · 2013 · 9(3): e1003353

    The let-7 microRNA (miRNA) regulates cellular differentiation across many animal species. Loss of let-7 activity causes abnormal development in Caenorhabditis elegans and unchecked cellular proliferation in human cells, which contributes to tumorigenesis. These defects are due to improper expression of …

    PMID 23516374 DOI ↗

  12. Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.

    The Journal of biological chemistry · 2013 · 288(49): 35372-86

    Diabetic cardiomyopathy is one of the complications of diabetes that eventually leads to heart failure and death. Aberrant activation of PKC signaling contributes to diabetic cardiomyopathy by mechanisms that are poorly understood. Previous reports indicate that PKC is implicated in …

    PMID 24151077 DOI ↗

  13. Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases.

    Frontiers in neuroscience · 2012 · 6: 144

    Translational control of messenger RNAs (mRNAs) is a key aspect of neurobiology, defects of which can lead to neurological diseases. In response to stimuli, local translation of mRNAs is activated at synapses to facilitate long-lasting forms of synaptic plasticity, the …

    PMID 23060744 DOI ↗

  14. The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians.

    RNA (New York, N.Y.) · 2008 · 14(6): 1174-86

    PIWI proteins are expressed in germ cells in a wide variety of metazoans, where they participate in the synthesis and function of a novel class of small RNAs called PIWI associated RNAs (piRNAs). One function of piRNAs is to preserve …

    PMID 18456843 DOI ↗

  15. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.

    PLoS genetics · 2007 · 3(5): e85

    Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs). Our …

    PMID 17530930 DOI ↗

Datasets 2

GSE17536 GSE · GEO

Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)

Homo sapiens · GPL570

GSE83687 GSE · GEO

A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease

Homo sapiens · GPL16791

Analyses 1

GSE83687 Processing Pipeline

GSE83687 · 4 steps · RNA-Seq · code_examples

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)