LIVIVO - Search results -

Search results

Result 1 - 10 of total 39

Search options

Article ; Online: Challenges and best practices in omics benchmarking.

Brooks, Thomas G / Lahens, Nicholas F / Mrčela, Antonijo / Grant, Gregory R

2024 Volume 25, Issue 5, Page(s) 326–339

Abstract: Technological advances enabling massively parallel measurement of biological features - such as microarrays, high-throughput sequencing and mass spectrometry - have ushered in the omics era, now in its third decade. The resulting complex landscape of ... ...

Abstract	Technological advances enabling massively parallel measurement of biological features - such as microarrays, high-throughput sequencing and mass spectrometry - have ushered in the omics era, now in its third decade. The resulting complex landscape of analytical methods has naturally fostered the growth of an omics benchmarking industry. Benchmarking refers to the process of objectively comparing and evaluating the performance of different computational or analytical techniques when processing and analysing large-scale biological data sets, such as transcriptomics, proteomics and metabolomics. With thousands of omics benchmarking studies published over the past 25 years, the field has matured to the point where the foundations of benchmarking have been established and well described. However, generating meaningful benchmarking data and properly evaluating performance in this complex domain remains challenging. In this Review, we highlight some common oversights and pitfalls in omics benchmarking. We also establish a methodology to bring the issues that can be addressed into focus and to be transparent about those that cannot: this takes the form of a spreadsheet template of guidelines for comprehensive reporting, intended to accompany publications. In addition, a survey of recent developments in benchmarking is provided as well as specific guidance for commonly encountered difficulties.
MeSH term(s)	Benchmarking ; Proteomics/methods ; Metabolomics/methods ; Gene Expression Profiling ; Mass Spectrometry
Language	English
Publishing date	2024-01-12
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2035157-4
ISSN	1471-0064 ; 1471-0056
ISSN (online)	1471-0064
ISSN	1471-0056
DOI	10.1038/s41576-023-00679-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5474: 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)
Zs.MG 40: Show issues

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: BEERS2: RNA-Seq simulation through high fidelity in silico modeling.

Brooks, Thomas G / Lahens, Nicholas F / Mrčela, Antonijo / Sarantopoulou, Dimitra / Nayak, Soumyashant / Naik, Amruta / Sengupta, Shaon / Choi, Peter S / Grant, Gregory R

Briefings in bioinformatics

2024 Volume 25, Issue 3

Abstract: Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, ... ...

Abstract	Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
MeSH term(s)	RNA-Seq ; Sequence Analysis, RNA ; Computer Simulation ; RNA/genetics ; Genome ; High-Throughput Nucleotide Sequencing
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2024-04-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbae164
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6262: 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

Details ▾
- See ZB MED holdings
- Order with fees

Article: Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms.

Schwarz, Jessica E / Mrčela, Antonijo / Lahens, Nicholas F / Li, Yongjun / Hsu, Cynthia T / Grant, Gregory / Skarke, Carsten / Zhang, Shirley L / Sehgal, Amita

bioRxiv : the preprint server for biology

2023

Abstract: Aging is associated with a number of physiologic changes including perturbed circadian rhythms; however, mechanisms by which rhythms are altered remain unknown. To test the idea that circulating factors mediate age-dependent changes in peripheral rhythms, ...

Abstract	Aging is associated with a number of physiologic changes including perturbed circadian rhythms; however, mechanisms by which rhythms are altered remain unknown. To test the idea that circulating factors mediate age-dependent changes in peripheral rhythms, we compared the ability of human serum from young and old individuals to synchronize circadian rhythms in culture. We collected blood from apparently healthy young (age 25-30) and old (age 70-76) individuals and used the serum to synchronize cultured fibroblasts. We found that young and old sera are equally competent at driving robust ~24h oscillations of a luciferase reporter driven by clock gene promoter. However, cyclic gene expression is affected, such that young and old sera drive cycling of different genes. While genes involved in the cell cycle and transcription/translation remain rhythmic in both conditions, genes identified by STRING and IPA analyses as associated with oxidative phosphorylation and Alzheimer's Disease lose rhythmicity in the aged condition. Also, the expression of cycling genes associated with cholesterol biosynthesis increases in the cells entrained with old serum. We did not observe a global difference in the distribution of phase between groups, but find that peak expression of several clock controlled genes (
Language	English
Publishing date	2023-04-20
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.04.19.537477
Database	MEDical Literature Analysis and Retrieval System OnLINE

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.

Details ▾

Article ; Online: Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank.

Brooks, Thomas G / Lahens, Nicholas F / Grant, Gregory R / Sheline, Yvette I / FitzGerald, Garret A / Skarke, Carsten

Nature communications

2023 Volume 14, Issue 1, Page(s) 5172

Abstract: Many chronic disease symptomatologies involve desynchronized sleep-wake cycles, indicative of disrupted biorhythms. This can be interrogated using body temperature rhythms, which have circadian as well as sleep-wake behavior/environmental evoked ... ...

Abstract	Many chronic disease symptomatologies involve desynchronized sleep-wake cycles, indicative of disrupted biorhythms. This can be interrogated using body temperature rhythms, which have circadian as well as sleep-wake behavior/environmental evoked components. Here, we investigated the association of wrist temperature amplitudes with a future onset of disease in the UK Biobank one year after actigraphy. Among 425 disease conditions (range n = 200-6728) compared to controls (range n = 62,107-91,134), a total of 73 (17%) disease phenotypes were significantly associated with decreased amplitudes of wrist temperature (Benjamini-Hochberg FDR q < 0.05) and 26 (6.1%) PheCODEs passed a more stringent significance level (Bonferroni-correction α < 0.05). A two-standard deviation (1.8° Celsius) lower wrist temperature amplitude corresponded to hazard ratios of 1.91 (1.58-2.31 95% CI) for NAFLD, 1.69 (1.53-1.88) for type 2 diabetes, 1.25 (1.14-1.37) for renal failure, 1.23 (1.17-1.3) for hypertension, and 1.22 (1.11-1.33) for pneumonia (phenome-wide atlas available at http://bioinf.itmat.upenn.edu/biorhythm_atlas/ ). This work suggests peripheral thermoregulation as a digital biomarker.
MeSH term(s)	Humans ; Biological Specimen Banks ; Diabetes Mellitus, Type 2/epidemiology ; Temperature ; Wrist ; Circadian Rhythm ; United Kingdom/epidemiology
Language	English
Publishing date	2023-08-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-40977-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: BEERS2: RNA-Seq simulation through high fidelity

Brooks, Thomas G / Lahens, Nicholas F / Mrčela, Antonijo / Sarantopoulou, Dimitra / Nayak, Soumyashant / Naik, Amruta / Sengupta, Shaon / Choi, Peter S / Grant, Gregory R

bioRxiv : the preprint server for biology

2023

Abstract: Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, ... ...

Abstract	Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
Language	English
Publishing date	2023-04-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.04.21.537847
Database	MEDical Literature Analysis and Retrieval System OnLINE

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.

Details ▾

Article ; Online: Comparative evaluation of full-length isoform quantification from RNA-Seq.

Sarantopoulou, Dimitra / Brooks, Thomas G / Nayak, Soumyashant / Mrčela, Antonijo / Lahens, Nicholas F / Grant, Gregory R

BMC bioinformatics

2021 Volume 22, Issue 1, Page(s) 266

Abstract: Background: Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA- ...

Abstract	Background: Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short. Results: Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control. Conclusions: Salmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively.
MeSH term(s)	Gene Expression Profiling ; Protein Isoforms/genetics ; RNA-Seq ; Sequence Analysis, RNA ; Transcriptome
Chemical Substances	Protein Isoforms
Language	English
Publishing date	2021-05-25
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-021-04198-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: RNA splicing analysis using heterogeneous and large RNA-seq datasets.

Vaquero-Garcia, Jorge / Aicher, Joseph K / Jewell, San / Gazzara, Matthew R / Radens, Caleb M / Jha, Anupama / Norton, Scott S / Lahens, Nicholas F / Grant, Gregory R / Barash, Yoseph

Nature communications

2023 Volume 14, Issue 1, Page(s) 1230

Abstract: The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across ... ...

Abstract	The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across dozens of experimental conditions, exhibit increased variability compared to biological replicates, and involve thousands of unannotated splice variants resulting in increased transcriptome complexity. We describe here a suite of algorithms and tools implemented in the MAJIQ v2 package to address challenges in detection, quantification, and visualization of splicing variations from such datasets. Using both large scale synthetic data and GTEx v8 as benchmark datasets, we assess the advantages of MAJIQ v2 compared to existing methods. We then apply MAJIQ v2 package to analyze differential splicing across 2,335 samples from 13 brain subregions, demonstrating its ability to offer insights into brain subregion-specific splicing regulation.
MeSH term(s)	RNA-Seq ; RNA Splicing ; Algorithms ; Benchmarking ; Brain
Language	English
Publishing date	2023-03-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36585-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Nitecap: An Exploratory Circadian Analysis Web Application.

Brooks, Thomas G / Mrčela, Antonijo / Lahens, Nicholas F / Paschos, Georgios K / Grosser, Tilo / Skarke, Carsten / FitzGerald, Garret A / Grant, Gregory R

Journal of biological rhythms

2021 Volume 37, Issue 1, Page(s) 43–52

Abstract: Circadian omics analyses present investigators with large amounts of data to consider and many choices for methods of analysis. Visualization is crucial as rhythmicity can take many forms ... ...

Abstract	Circadian omics analyses present investigators with large amounts of data to consider and many choices for methods of analysis. Visualization is crucial as rhythmicity can take many forms and
MeSH term(s)	ARNTL Transcription Factors/genetics ; ARNTL Transcription Factors/metabolism ; CLOCK Proteins/genetics ; Circadian Clocks/genetics ; Circadian Rhythm/genetics ; Liver/metabolism ; Software
Chemical Substances	ARNTL Transcription Factors ; CLOCK Proteins (EC 2.3.1.48)
Language	English
Publishing date	2021-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	896387-3
ISSN	1552-4531 ; 0748-7304
ISSN (online)	1552-4531
ISSN	0748-7304
DOI	10.1177/07487304211054408
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2872: 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: A circadian clock regulates efflux by the blood-brain barrier in mice and human cells.

Zhang, Shirley L / Lahens, Nicholas F / Yue, Zhifeng / Arnold, Denice M / Pakstis, Peter P / Schwarz, Jessica E / Sehgal, Amita

Nature communications

2021 Volume 12, Issue 1, Page(s) 617

Abstract: The blood-brain barrier (BBB) is critical for neural function. We report here circadian regulation of the BBB in mammals. Efflux of xenobiotics by the BBB oscillates in mice, with highest levels during the active phase and lowest during the resting phase. ...

Abstract	The blood-brain barrier (BBB) is critical for neural function. We report here circadian regulation of the BBB in mammals. Efflux of xenobiotics by the BBB oscillates in mice, with highest levels during the active phase and lowest during the resting phase. This oscillation is abrogated in circadian clock mutants. To elucidate mechanisms of circadian regulation, we profiled the transcriptome of brain endothelial cells; interestingly, we detected limited circadian regulation of transcription, with no evident oscillations in efflux transporters. We recapitulated the cycling of xenobiotic efflux using a human microvascular endothelial cell line to find that the molecular clock drives cycling of intracellular magnesium through transcriptional regulation of TRPM7, which appears to contribute to the rhythm in efflux. Our findings suggest that considering circadian regulation may be important when therapeutically targeting efflux transporter substrates to the CNS.
MeSH term(s)	ARNTL Transcription Factors/metabolism ; ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism ; Animals ; Biological Transport ; Blood-Brain Barrier/metabolism ; Cell Line ; Circadian Clocks ; Endothelial Cells/metabolism ; Gene Expression Regulation ; Humans ; Magnesium/metabolism ; Mice, Inbred C57BL ; Models, Biological ; Permeability ; Protein Serine-Threonine Kinases/genetics ; Protein Serine-Threonine Kinases/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Substrate Specificity ; TRPM Cation Channels/genetics ; TRPM Cation Channels/metabolism ; Xenobiotics/metabolism ; Mice
Chemical Substances	ARNTL Transcription Factors ; ATP Binding Cassette Transporter, Subfamily B, Member 1 ; RNA, Messenger ; TRPM Cation Channels ; Xenobiotics ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; TRPM7 protein, human (EC 2.7.11.1) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2021-01-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-20795-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: G1/S cell cycle regulators mediate effects of circadian dysregulation on tumor growth and provide targets for timed anticancer treatment.

Lee, Yool / Lahens, Nicholas F / Zhang, Shirley / Bedont, Joseph / Field, Jeffrey M / Sehgal, Amita

PLoS biology

2019 Volume 17, Issue 4, Page(s) e3000228

Abstract: Circadian disruption has multiple pathological consequences, but the underlying mechanisms are largely unknown. To address such mechanisms, we subjected transformed cultured cells to chronic circadian desynchrony (CCD), mimicking a chronic jet-lag scheme, ...

Abstract	Circadian disruption has multiple pathological consequences, but the underlying mechanisms are largely unknown. To address such mechanisms, we subjected transformed cultured cells to chronic circadian desynchrony (CCD), mimicking a chronic jet-lag scheme, and assayed a range of cellular functions. The results indicated a specific circadian clock-dependent increase in cell proliferation. Transcriptome analysis revealed up-regulation of G1/S phase transition genes (myelocytomatosis oncogene cellular homolog [Myc], cyclin D1/3, chromatin licensing and DNA replication factor 1 [Cdt1]), concomitant with increased phosphorylation of the retinoblastoma (RB) protein by cyclin-dependent kinase (CDK) 4/6 and increased G1-S progression. Phospho-RB (Ser807/811) was found to oscillate in a circadian fashion and exhibit phase-shifted rhythms in circadian desynchronized cells. Consistent with circadian regulation, a CDK4/6 inhibitor approved for cancer treatment reduced growth of cultured cells and mouse tumors in a time-of-day-specific manner. Our study identifies a mechanism that underlies effects of circadian disruption on tumor growth and underscores the use of treatment timed to endogenous circadian rhythms.
MeSH term(s)	Animals ; Cell Cycle/physiology ; Cell Division/physiology ; Cell Line ; Chronobiology Disorders/metabolism ; Circadian Rhythm/physiology ; Cyclin-Dependent Kinase 4 ; Cyclin-Dependent Kinase 6 ; Cyclin-Dependent Kinases/metabolism ; G1 Phase/physiology ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Neoplasms/metabolism ; Phosphorylation ; Proto-Oncogene Proteins/genetics ; Retinoblastoma Protein ; S Phase/physiology
Chemical Substances	Proto-Oncogene Proteins ; Retinoblastoma Protein ; CDK4 protein, human (EC 2.7.11.22) ; CDK6 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 4 (EC 2.7.11.22) ; Cyclin-Dependent Kinase 6 (EC 2.7.11.22) ; Cyclin-Dependent Kinases (EC 2.7.11.22)
Language	English
Publishing date	2019-04-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3000228
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6193: 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

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

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