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2010
2010 IEEE International Conference on BioInformatics and BioEngineering
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Phased Small RNA Cycle Counting Algorithms ........................................................................................130 Forrest Sheng Bao, Zhixin Xie, and Yuanlin Zhang ...
Sequencing by Hybridization ......................................................................................................................................................124 Yang Chen and Jinglu Hu Fast ...
doi:10.1109/bibe.2010.4
fatcat:yvd5gkaegrbdfjr6vpdf6oy2vq
Computational challenges of cell cycle analysis using single cell transcriptomics
[article]
2022
arXiv
pre-print
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Here we review the main computational tasks in such analysis: 1) identification of cell cycle phases, 2) pseudotime inference, 3) identification and profiling of cell cycle-related genes, 4) removing cell ...
Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle transcriptome dynamics in an unprecedented range of conditions (cell types and perturbations), with thousands of publicly ...
A simple and fast heuristic algorithm for labeling cells for their cell cycle phases based on the analysis of single cell transcriptomic profiles is implemented in Seurat (R-based) and Scanpy (Python) ...
arXiv:2208.05229v1
fatcat:nzz3c6jhzvabzpwoygpwknyi5a
High count rate first-pass radionuclide angiography using a digital gamma camera
1986
Journal of Nuclear Medicine
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Total counts/sec in the whole field-of-view in the right ventricular phase were 150,352 +/- 26,006. ...
Background uncorrected counts in the representative cycle were 7,651 +/- 2,527 at end-diastolie and 4,904 +/- 2,314 at end-systolie. ...
Herskovicci (Elscint, Inc.) in providing the necessary algorithms and software modifications, and the assistance of Ms. Jean Ciske in manuscript preparation. ...
pmid:3519892
fatcat:tbtx23uxkbed5auhphony4ucwe
Transcriptome analysis using next-generation sequencing
2013
Current Opinion in Biotechnology
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Up to date research in biology, biotechnology, and medicine requires fast genome and transcriptome analysis technologies for the investigation of cellular state, physiology, and activity. ...
Since microarray technology is limited towards the amount of RNA, the quantification of transcript levels and the sequence information, RNA-Seq provides nearly unlimited possibilities in modern bioanalysis ...
Non-conding RNAs, including transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear and small nucleolar RNA, micro RNA (miRNA), and small interfering RNA (siRNA), are not translated into proteins. ...
doi:10.1016/j.copbio.2012.09.004
pmid:23020966
fatcat:an2cvnzatrev3faba33cc2tdze
Control of tissue development and cell diversity by cell cycle-dependent transcriptional filtering
2021
eLife
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Cell cycle duration changes dramatically during development, starting out fast to generate cells quickly and slowing down over time as the organism matures. ...
Our predictions are supported by comparison to single-cell RNA-seq data captured over embryonic development. ...
Typically, the complete cell cycle is divided into four phases: first gap phase (G1), synthesis phase (S), second gap phase (G2), and mitotic phase (M). ...
doi:10.7554/elife.64951
pmid:34212855
pmcid:PMC8279763
fatcat:2akolmee4vai7pnt6tzjjydkzy
Genome architecture and transcription data reveal allelic bias during the cell cycle
[article]
2020
bioRxiv
pre-print
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By integrating allele specific RNA-seq, Bru-seq, and Hi-C data through three phases of the cell cycle, along with publicly available protein binding data, we provide a more comprehensive understanding ...
We collected and analyzed haplotype-resolved genome-wide data from B-Lymphocytes (NA12878) in G1, S, and G2/M, using RNA sequencing (RNA-seq), bromouridine sequencing (Bru-seq), and genome wide chromosome ...
Acknowledgements We thank the University of Michigan Sequencing Core members for producing high quality Bru-seq, RNA-seq, and Hi-C data. ...
doi:10.1101/2020.03.15.992164
fatcat:scpkhngpczcpzn5brzfje5zzdq
Bioinformatics Tools for RNA-seq Gene and Isoform Quantification
2016
Journal of Next Generation Sequencing & Applications
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Recently, a number of tools have been developed for RNA-seq isoform quantification. ...
In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression. 'Union-exon' and transcript based approaches are widely used in gene quantification. ...
One is that Salmon implements a dual-phase inference algorithm, consisting of both an online and offline phase, while Sailfish uses only an offline algorithm. ...
doi:10.4172/2469-9853.1000140
fatcat:5ov3cuwjrngfnjicxofzlw6rd4
A population-based human enCYCLOPedia for circadian medicine
[article]
2018
bioRxiv
pre-print
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Here, we have applied CYCLOPS, an algorithm designed to reconstruct sample order in the absence of time-of-day information, to the GTEx collection of 632 human donors contributing 4,292 RNA-seq samples ...
While the vast majority of cycling genes are protein-coding, a small share in each tissue are noncoding elements, including antisense RNAs, miRNAs, and lincRNAs ( fig. S2B , Data file S1). ...
Cycling gene counts by statistical thresholds and noncoding element type. fig. S3. Phase set enrichment in human and mouse counterpart tissues. fig. S4. ...
doi:10.1101/301580
fatcat:ofecjz5jfzgizizzr6sw65nyj4
Left ventricular volume calculation using a count-based ratio method applied to multigated radionuclide angiography
1990
Journal of Nuclear Medicine
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An equation is developed that relates total chamber volume, Vt, to the area of a pixel (M) and the ratio (R) of total counts within the chamber to the counts within the hottest pixel in the chamber such ...
The value of M is a constant for the particular scintillation camera-collimator system and R is obtained from observed count rates. ...
constant of eccentricity count method algorithm de scribedin detailin the Addendum.The total counts ofthe entire LV phase were summed into one frame. ...
pmid:2324820
fatcat:bjr5hn3kvfhyffolgypbyzbscy
Maximizing power efficiency with asymmetric multicore systems
2009
Communications of the ACM
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A typical AMP consists of several fast and powerful cores (high clock frequency, complex out-of-order pipeline, and high power consumption) and a large number of slower low-power cores (low clock frequency ...
Applications with small sequential phases (wupwise, for example) experience no speedup from the PA policy, because they do not stand to benefit from acceleration of sequential phases on fast cores. ...
RNA is a bioinformatics application performing RNA sequence matching. The figure shows a variety of speedup values. ...
doi:10.1145/1610252.1610270
fatcat:gxciol6x3jdcbhtee2rxqdrlpu
Synchronizing asynchronous bounded delay networks
1990
IEEE Transactions on Communications
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Two types of synchronlzaiioo algorithms are presented. Both types require an initializing phase that costs IEl messages (where IEl is the number of links). ...
Distributed algorithms that operate in phases or cycles fit naturally into this model. ...
However. this small difference in initial synchronization causes the algorithm to operate incorrectly. ...
doi:10.1109/26.47845
fatcat:jb3jqumbqzfzxecfrkalpvalam
Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
2018
Scientific Reports
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NcRNAs from a few to 200 nucleotides (nt) are defined small non-coding RNAs (sncRNAs), whereas those longer than 200 nt and up to several kilobases are called long non-coding RNAs (lncRNAs) 8 . ...
Nevertheless, only 1-2% of the human genome codes for proteins, grouping all RNAs in two cluster: 1) RNAs with coding potential and 2) RNAs without coding potential, defined non-coding RNAs (ncRNAs) 2 ...
Small RNA Analysis and piRNA filtering. Using CLC Genomics Workbench software, small RNAs were extracted from whole RNA-Seq data and counted. ...
doi:10.1038/s41598-018-35086-z
pmid:30413775
pmcid:PMC6226517
fatcat:5ynsizfj5bfixite3f5klckaji
Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression
2016
BMC Genomics
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Methods: Following an optimized FACS, a complex initiative of high throughput platforms (microarray, Taqman Low Density Array, small RNA sequencing) were performed to study gene and miRNA expression profiles ...
DNA content-based fluorescence activated cell sorting (FACS) is able to sort the different cell cycle phases without perturbing the cell cycle. ...
Small RNA sequencing was performed at BGI using Illumina Small RNA Sequencing Platform. For library preparation TruSeq Small RNA library preparation kit (Illumina, San Diego, California) was used. ...
doi:10.1186/s12864-016-2747-6
pmid:27234232
pmcid:PMC4884355
fatcat:v27saulpxrey5camwmbvicr6ou
Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms
2021
Science Advances
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Small interfering RNA transfection Cells were plated in standard medium. ...
In setting the sleep-wake cycle, the SCN evokes the feeding-fasting cycle, a major zeitgeber (synchronizer) for the periphery (15) (16) (17) (18) . ...
Data and materials availability: The RNA-seq, ATAC-seq, and ChIP-seq data have been deposited in the GEO with accession numbers GSE158600, GSE171432, and GSE171184 (RNA-seq); GSE154902 (ATAC-seq); and ...
doi:10.1126/sciadv.abi7828
pmid:34550736
pmcid:PMC8457671
fatcat:7irwkfm5nnccjbbedtimyih7k4
Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle
2009
BMC Systems Biology
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In particular, the ribosome biogenesis clusters expressed in G2 phase reveal new, highly conserved RNA motifs. ...
Finally, using an enhanced Bayesian algorithm to co-cluster the expression data, we obtained 31 clusters of co-regulated genes 1) which constitute regulatory modules from different phases of the cell cycle ...
The same count increased to more than 2,100 genes when the experiment in which a gene deviated most from its median phase was excluded [57] . ...
doi:10.1186/1752-0509-3-93
pmid:19758441
pmcid:PMC2758837
fatcat:jole4stxj5c2veebmvjvpbm6na
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