LIVIVO - Search results -

Search results

Result 1 - 10 of total 42

Search options

Article ; Online: Novel TCF4:TCF12 heterodimer inhibits glioblastoma growth.

Mikheeva, Svetlana A / Funk, Cory C / Horner, Philip J / Rostomily, Robert C / Mikheev, Andrei M

2023 Volume 18, Issue 3, Page(s) 517–527

Abstract: TWIST1 (TW) is a pro-oncogenic basic helix-loop-helix (bHLH) transcription factor and promotes the hallmark features of malignancy (e.g., cell invasion, cancer cell stemness, and treatment resistance), which contribute to poor prognoses of glioblastoma ( ... ...

Abstract	TWIST1 (TW) is a pro-oncogenic basic helix-loop-helix (bHLH) transcription factor and promotes the hallmark features of malignancy (e.g., cell invasion, cancer cell stemness, and treatment resistance), which contribute to poor prognoses of glioblastoma (GBM). We previously reported that specific TW dimerization motifs regulate unique cellular phenotypes in GBM. For example, the TW:E12 heterodimer increases periostin (POSTN) expression and promotes cell invasion. TW dimer-specific transcriptional regulation requires binding to the regulatory E-box consensus sequences, but alternative bHLH dimers that balance TW dimer activity in regulating pro-oncogenic TW target genes are unknown. We leveraged the ENCODE DNase I hypersensitivity data to identify E-box sites and tethered TW:E12 and TW:TW proteins to validate dimer binding to E-boxes in vitro. Subsequently, TW knockdown revealed a novel TCF4:TCF12 bHLH dimer occupying the same TW E-box site that, when expressed as a tethered TCF4:TCF12 dimer, markedly repressed POSTN expression and extended animal survival. These observations support TCF4:TCF12 as a novel dimer with tumor-suppressor activity in GBM that functions in part through displacement of and/or competitive inhibition of pro-oncogenic TW dimers at E-box sites.
MeSH term(s)	Animals ; Glioblastoma/genetics ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; Gene Expression Regulation ; Dimerization
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors
Language	English
Publishing date	2023-08-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2415106-3
ISSN	1878-0261 ; 1574-7891
ISSN (online)	1878-0261
ISSN	1574-7891
DOI	10.1002/1878-0261.13496
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6637: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: iREAD: a tool for intron retention detection from RNA-seq data.

Li, Hong-Dong / Funk, Cory C / Price, Nathan D

BMC genomics

2020 Volume 21, Issue 1, Page(s) 128

Abstract: Background: Intron retention (IR) has been traditionally overlooked as 'noise' and received negligible attention in the field of gene expression analysis. In recent years, IR has become an emerging field for interrogating transcriptomes because it has ... ...

Abstract	Background: Intron retention (IR) has been traditionally overlooked as 'noise' and received negligible attention in the field of gene expression analysis. In recent years, IR has become an emerging field for interrogating transcriptomes because it has been recognized to carry out important biological functions such as gene expression regulation and it has been found to be associated with complex diseases such as cancers. However, methods for detecting IR today are limited. Thus, there is a need to develop novel methods to improve IR detection. Results: Here we present iREAD (intron REtention Analysis and Detector), a tool to detect IR events genome-wide from high-throughput RNA-seq data. The command line interface for iREAD is implemented in Python. iREAD takes as input a BAM file, representing the transcriptome, and a text file containing the intron coordinates of a genome. It then 1) counts all reads that overlap intron regions, 2) detects IR events by analyzing the features of reads such as depth and distribution patterns, and 3) outputs a list of retained introns into a tab-delimited text file. iREAD provides significant added value in detecting IR compared with output from IRFinder with a higher AUC on all datasets tested. Both methods showed low false positive rates and high false negative rates in different regimes, indicating that use together is generally beneficial. The output from iREAD can be directly used for further exploratory analysis such as differential intron expression and functional enrichment. The software is freely available at https://github.com/genemine/iread. Conclusion: Being complementary to existing tools, iREAD provides a new and generic tool to interrogate poly-A enriched transcriptomic data of intron regions. Intron retention analysis provides a complementary approach for understanding transcriptome.
MeSH term(s)	Algorithms ; Animals ; Humans ; Introns ; Mice ; RNA-Seq ; Software
Language	English
Publishing date	2020-02-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-020-6541-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Systems modeling of metabolic dysregulation in neurodegenerative diseases.

Baloni, Priyanka / Funk, Cory C / Readhead, Ben / Price, Nathan D

Current opinion in pharmacology

2021 Volume 60, Page(s) 59–65

Abstract: Neurodegenerative diseases (NDDs) encompass a wide range of conditions that arise owing to progressive degeneration and the ultimate loss of nerve cells in the brain and peripheral nervous system. NDDs such as Alzheimer's, Parkinson's, and Huntington's ... ...

Abstract	Neurodegenerative diseases (NDDs) encompass a wide range of conditions that arise owing to progressive degeneration and the ultimate loss of nerve cells in the brain and peripheral nervous system. NDDs such as Alzheimer's, Parkinson's, and Huntington's diseases negatively impact both length and quality of life, due to lack of effective disease-modifying treatments. Herein, we review the use of genome-scale metabolic models, network-based approaches, and integration with multiomics data to identify key biological processes that characterize NDDs. We describe powerful systems biology approaches for modeling NDD pathophysiology by leveraging in silico models that are informed by patient-derived multiomics data. These approaches can enable mechanistic insights into NDD-specific metabolic dysregulations that can be leveraged to identify potential metabolic markers of disease and predisease states.
MeSH term(s)	Brain ; Humans ; Huntington Disease ; Neurodegenerative Diseases ; Quality of Life ; Systems Biology
Language	English
Publishing date	2021-08-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2037057-X
ISSN	1471-4973 ; 1471-4892
ISSN (online)	1471-4973
ISSN	1471-4892
DOI	10.1016/j.coph.2021.06.012
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5608: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Dense data enables 21st century clinical trials.

Roach, Jared C / Hodes, John F / Funk, Cory C / Shankle, William R / Merrill, David A / Hood, Leroy / Bramen, Jennifer

Alzheimer's & dementia (New York, N. Y.)

2022 Volume 8, Issue 1, Page(s) e12297

Language	English
Publishing date	2022-06-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2832891-7
ISSN	2352-8737 ; 2352-8737
ISSN (online)	2352-8737
ISSN	2352-8737
DOI	10.1002/trc2.12297
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Details ▾
- Full text online
- Order with fees

Article ; Online: The viral hypothesis: how herpesviruses may contribute to Alzheimer's disease.

Wainberg, Michael / Luquez, Tain / Koelle, David M / Readhead, Ben / Johnston, Christine / Darvas, Martin / Funk, Cory C

Molecular psychiatry

2021 Volume 26, Issue 10, Page(s) 5476–5480

Abstract: The hypothesis that infectious agents, particularly herpesviruses, contribute to Alzheimer's disease (AD) pathogenesis has been investigated for decades but has long engendered controversy. In the past 3 years, several studies in mouse models, human ... ...

Abstract	The hypothesis that infectious agents, particularly herpesviruses, contribute to Alzheimer's disease (AD) pathogenesis has been investigated for decades but has long engendered controversy. In the past 3 years, several studies in mouse models, human tissue models, and population cohorts have reignited interest in this hypothesis. Collectively, these studies suggest that many of the hallmarks of AD, like amyloid beta production and neuroinflammation, can arise as a protective response to acute infection that becomes maladaptive in the case of chronic infection. We place this work in its historical context and explore its etiological implications.
MeSH term(s)	Alzheimer Disease/genetics ; Amyloid beta-Peptides ; Animals ; Disease Models, Animal ; Herpesviridae ; Mice
Chemical Substances	Amyloid beta-Peptides
Language	English
Publishing date	2021-05-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/s41380-021-01138-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 4812: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article: SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis.

Magis, Andrew T / Funk, Cory C / Price, Nathan D

IEEE life sciences letters

2015 Volume 1, Issue 2, Page(s) 22–25

Abstract: The process of converting raw RNA sequencing data to interpretable results can be circuitous and time consuming, requiring multiple steps. We present an RNA-seq mapping algorithm that streamlines this process. Our algorithm utilizes a hash table approach ...

Abstract	The process of converting raw RNA sequencing data to interpretable results can be circuitous and time consuming, requiring multiple steps. We present an RNA-seq mapping algorithm that streamlines this process. Our algorithm utilizes a hash table approach to leverage the availability and power of high memory machines. SNAPR, which can be run on a single library or thousands of libraries, can take compressed or uncompressed FASTQ and BAM files as inputs, and can output a sorted BAM file, individual read counts, gene fusions and identify exogenous RNA species in a single step. SNAPR also does native Phred score filtering of reads. SNAPR is also well suited for future sequencing platforms that generate longer reads. Using SNAPR, we show how we can analyze data from hundreds of TCGA samples in a matter of hours, while identifying gene fusions and viral events at the same time. With the references genome and transcriptome undergoing periodic updates, and the need for uniform parameters when integrating multiple data sets, there is great need for a streamlined process for RNA-seq analysis. We demonstrate how SNAPR does this efficiently and accurately, with the high-throughput capacity needed to do high-volume analyses.
Language	English
Publishing date	2015-08-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833666-5
ISSN	2332-7685
ISSN	2332-7685
DOI	10.1109/LLS.2015.2465870
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Risk factors for severe COVID-19 differ by age for hospitalized adults.

Molani, Sevda / Hernandez, Patricia V / Roper, Ryan T / Duvvuri, Venkata R / Baumgartner, Andrew M / Goldman, Jason D / Ertekin-Taner, Nilüfer / Funk, Cory C / Price, Nathan D / Rappaport, Noa / Hadlock, Jennifer J

Scientific reports

2022 Volume 12, Issue 1, Page(s) 6568

Abstract: Risk stratification for hospitalized adults with COVID-19 is essential to inform decisions about individual patients and allocation of resources. So far, risk models for severe COVID outcomes have included age but have not been optimized to best serve ... ...

Abstract	Risk stratification for hospitalized adults with COVID-19 is essential to inform decisions about individual patients and allocation of resources. So far, risk models for severe COVID outcomes have included age but have not been optimized to best serve the needs of either older or younger adults. Models also need to be updated to reflect improvements in COVID-19 treatments. This retrospective study analyzed data from 6906 hospitalized adults with COVID-19 from a community health system across five states in the western United States. Risk models were developed to predict mechanical ventilation illness or death across one to 56 days of hospitalization, using clinical data available within the first hour after either admission with COVID-19 or a first positive SARS-CoV-2 test. For the seven-day interval, models for age ≥ 18 and < 50 years reached AUROC 0.81 (95% CI 0.71-0.91) and models for age ≥ 50 years reached AUROC 0.82 (95% CI 0.77-0.86). Models revealed differences in the statistical significance and relative predictive value of risk factors between older and younger patients including age, BMI, vital signs, and laboratory results. In addition, for hospitalized patients, sex and chronic comorbidities had lower predictive value than vital signs and laboratory results.
MeSH term(s)	Adult ; COVID-19/epidemiology ; Hospitalization ; Humans ; Middle Aged ; Retrospective Studies ; Risk Factors ; SARS-CoV-2 ; United States
Language	English
Publishing date	2022-04-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-10344-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Fostering synergy between cell biology and systems biology.

Eddy, James A / Funk, Cory C / Price, Nathan D

Trends in cell biology

2015 Volume 25, Issue 8, Page(s) 440–445

Abstract: In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative ... ...

Abstract	In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship.
MeSH term(s)	Animals ; Cell Biology/trends ; Genome ; Humans ; Models, Biological ; Systems Biology/methods ; Systems Biology/trends
Language	English
Publishing date	2015-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	30122-x
ISSN	1879-3088 ; 0962-8924
ISSN (online)	1879-3088
ISSN	0962-8924
DOI	10.1016/j.tcb.2015.04.005
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Full text

In stock of ZB MED Cologne/Königswinter

Zs.MG 25: Show issues
Zs.MO 113: Show issues
Zs.A 3410: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article: Case Study: A Precision Medicine Approach to Multifactorial Dementia and Alzheimer's Disease.

Ross, Mary Kay / Raji, Cyrus / Lokken, Kristine L / Bredesen, Dale E / Roach, Jared C / Funk, Cory C / Price, Nathan / Rappaport, Noa / Hood, Leroy / Heath, James R

Journal of Alzheimer's disease & Parkinsonism

2021 Volume 11, Issue Suppl 5

Abstract: We report a case of a patient with mixed dementia successfully treated with a personalized multimodal therapy. Monotherapeutics are inadequate for the treatment of Alzheimer's disease (AD) and mixed dementia; therefore, we approach treatment through an ... ...

Abstract	We report a case of a patient with mixed dementia successfully treated with a personalized multimodal therapy. Monotherapeutics are inadequate for the treatment of Alzheimer's disease (AD) and mixed dementia; therefore, we approach treatment through an adaptive personalized multimodal program. Many multimodal programs are pre-determined, and thus may not address the underlying contributors to cognitive decline in each particular individual. The combination of a targeted, personalized, precision medicine approach using a multimodal program promises advantages over monotherapies and untargeted multimodal therapies for multifactorial dementia. In this case study, we describe successful treatment for a patient diagnosed with AD, using a multimodal, programmatic, precision medicine intervention encompassing therapies targeting multiple dementia diastheses. We describe specific interventions used in this case that are derived from a comprehensive protocol for AD precision medicine. After treatment, our patient demonstrated improvements in quantitative neuropsychological testing, volumetric neuroimaging, PET scans, and serum chemistries, accompanied by symptomatic improvement over a 3.5-year period. This case outcome supports the need for rigorous trials of comprehensive, targeted combination therapies to stabilize, restore, and prevent cognitive decline in individuals with potentially many underlying causes of such decline and dementia. Our multimodal therapy included personalized treatments to address each potential perturbation to neuroplasticity. In particular, neuroinflammation and metabolic subsystems influence cognitive function and hippocampal volume. In this patient with a primary biliary cholangitis (PBC) multimorbidity component, we introduced a personalized diet that helped reduce liver inflammation. Together, all these components of multimodal therapy showed a sustained functional and cognitive benefit. Multimodal therapies may have systemwide benefits on all dementias, particularly in the context of multimorbidity. Furthermore, these therapies provide generalized health benefits, as many of the factors - such as inflammation - that impact cognitive function also impact other systems.
Language	English
Publishing date	2021-08-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2711981-6
ISSN	2161-0460
ISSN	2161-0460
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Author Correction: Partial inhibition of mitochondrial complex I ameliorates Alzheimer's disease pathology and cognition in APP/PS1 female mice.

Stojakovic, Andrea / Trushin, Sergey / Sheu, Anthony / Khalili, Layla / Chang, Su-Youne / Li, Xing / Christensen, Trace / Salisbury, Jeffrey L / Geroux, Rachel E / Gateno, Benjamin / Flannery, Padraig J / Dehankar, Mrunal / Funk, Cory C / Wilkins, Jordan / Stepanova, Anna / O'Hagan, Tara / Galkin, Alexander / Nesbitt, Jarred / Zhu, Xiujuan /

Tripathi, Utkarsh / Macura, Slobodan / Tchkonia, Tamar / Pirtskhalava, Tamar / Kirkland, James L / Kudgus, Rachel A / Schoon, Renee A / Reid, Joel M / Yamazaki, Yu / Kanekiyo, Takahisa / Zhang, Song / Nemutlu, Emirhan / Dzeja, Petras / Jaspersen, Adam / Kwon, Ye In Christopher / Lee, Michael K / Trushina, Eugenia

Communications biology

2024 Volume 7, Issue 1, Page(s) 234

Language	English
Publishing date	2024-02-26
Publishing country	England
Document type	Published Erratum
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-05810-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED