data analysis approaches in high throughput screening

... AccessDiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data Chadi Saad1,2* , Laurent Noé1, Hugues Richard3, Julie Leclerc2, Marie-Pierre Buisine2, Hélène Touzet1 and Martin ... We shown that DiNAMO software can serve as a tool to search for degenerate motifs in an exact manner using IUPAC models DiNAMO can be used in scanning mode with sliding windows or in fixed position ... from sequencing errors However, high-coverage sequencing does not eliminate all errors, especially the systematic sequencing errors, which are a major issue in high-throughput sequencing platforms

Ngày tải lên: 25/11/2020, 13:57

... Morgridge Institute for Research No funding body played any role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Availability of data ... Competing interests The authors declare that they have no competing interests. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional ... to estimate k breakpoints, b k g,1, b k g,2, , b k g ,k, occurring between t1and t T We also estimate k +2β’s: β k 0 indicates the intercept and the remaining k + 1β’s indicate slopes for the

Ngày tải lên: 25/11/2020, 14:44

... AccessCorrecting nucleotide-specific biases in high-throughput sequencing data Abstract Background: High-throughput sequence (HTS) data exhibit position-specific nucleotide biases that obscure the intended ... binding characterized by local dips in digestion within larger DNase peaks [12] These methods focus on cor-recting only bias introduced by the nucleotide-specific preferences in DNase I binding ... protocols for detecting genomic features, including open chromatin regions and transcription-factor binding footprints Methods Sequence reads from a variety of HTS assays, includ-ing DNase-seq, ChIP-seq,

Ngày tải lên: 25/11/2020, 17:13

... crystal structure The docking result of the low-affinity linear-chain inhibitor MGBG (PDB ID: 1I7C) was not as good as the others, suggesting that forming ring-ring stacking interactions with Phe7 ... its potential in inhibitor screening by coupling to in silico HTP screening Previously, Brooks et al.13 reported a virtual screening study of hAdoMetDC They found NSC 354961 could inhibit hAdoMetDC ... HTP screening of hAdoMetDC inhibitors Altogether, this paper describes a novel HTP pipeline for screening hAdoMetDC inhibitors in silico and in vitro, as well as the discovery of an hAdoMetDC inhibitor

Ngày tải lên: 24/11/2022, 17:50

... to integrate the microRNA library and tissue profiling data This analysis revealed that miR-9 is the microRNA that has the highest ability to in-duce HCC invasiveness, it is highly expressed in ... through binding to its 3′UTR and indir-ectly by controlling PPARA expression PPARA inhibition resulted in suppression of CDH1 mRNA levels, while CDH1 inhibition, by using an siRNA against CDH1, ... HCC Conclusions Integration of high throughput microRNA library screening and microRNA profiling in HCC tissues revealed that miR-9 has both functional and clinical significance in HCC Fur-thermore,

Ngày tải lên: 28/09/2020, 10:19

... resulting T > C conversion can be read out by high-throughput sequencing Identifying nucleotide conversions in high-throughput sequencing data comes with two major challenges: First, depending ... events in high-throughput sequencing datasets demands specialized bioinformatics approaches Results: Here, we present Digital Unmasking of Nucleotide conversions in K-mers (DUNK), a data analysis ... robust against variation in coverage and base compos-ition in genomic intervals e.g 3′ intervals Here we introduce Digital Unmasking of Nucleotide-conversions in k-mers (DUNK), a data analysis

Ngày tải lên: 25/11/2020, 12:22

... for screening lignin-degrading enzymes that can convert lignin to vanillin Keywords: Directed evolution, Fluorescence-activated cell sorting, RNA sequencing, Lignin, Vanillin, Enzyme engineering, ... selecting engineered enzymes using genuine lignin substrates This is partially due to unavailability of high-throughput screening tools to detect lignin degradation and also because lignins have ... programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries Barindra Sana1, Kuan Hui Burton Chia2, Sarada S Raghavan1, Balamurugan Ramalingam3, Niranjan

Ngày tải lên: 24/11/2022, 17:55

... string Crystal structure in the VASP-specific poscar format kpoints string k-points in the VASP-specific kpoints format incar string simulation parameters definition file in the VASP-specific incar ... better performing electronics as well as miniaturization Furthermore, with the increasing use of electronics and electric motors in engineering applications, dielectric materials are starting to play ... our publicly available data In addition, we integrate our dataset with the Materials Project allowing users easy access to material properties Finally, we explain how our dataset and calculation

Ngày tải lên: 04/12/2022, 10:37

... These findings suggest the potential roles of miRNAs in sex determination and reproductive developmental processes in asparagus Keywords: Asparagus officinalis, miRNAs, High-throughput sequencing, ... of miRNAs and their targets through high-throughput sequencing and degradome analysis in male and female Asparagus officinalis Jingli Chen1†, Yi Zheng2†, Li Qin1†, Yan Wang1, Lifei Chen1, Yanjun ... (5′ RLM-RACE) [9] With recent advances on se-quencing technologies, degradome analysis combined with high-throughput sequencing and bioinformatics analysis has been proved to be an efficient approach

Ngày tải lên: 22/05/2020, 04:15

... To obtain more insight into the function of miRNAs in cold stress tolerance, Illumina sequencing of C sinensis sRNA was conducted Result: Solexa sequencing technology was used for high-throughput ... in Arabidopsis thaliana Most of these conserved target genes were protein-coding genes, including zinc finger family pro-tein (C2H2 and C3HC4 type), late embryogenesis abun-dant family protein ... simi-lar to Arabidopsis proteins coded by plant calmodulin-binding protein-related, FS954022.1 coded for a protein highly homologous to rubredoxin-like superfamily protein, GD254786.1 coded for a

Ngày tải lên: 27/05/2020, 00:08

... salt stress in broccoli, using high-throughput sequencing and bioinformatics analysis Yunhong Tian1,2, Yunming Tian3,4, Xiaojun Luo1, Tao Zhou2, Zuoping Huang2, Ying Liu2, Yihan Qiu2, Bing Hou2, ... used in the criteria for filtering out low quality reads The sequence tags from the HiSeq sequencing were processed via a data-cleaning pipeline developed by Beijing Genome Institute (BGI, Beijing, ... used according to the manufacturer’s protocol sRNA analysis The very basic figure from sequencing was converted into sequence data by the base calling step Such sequence data called raw data or

Ngày tải lên: 27/05/2020, 01:09

... the MN scoring platforms following 4-h treatment (Fig 2c) In contrast, conflicting results were seen follow-ing 30-h continuous treatment with OTA (Fig 2d) In this instance, no increase in the MN ... any significant increase in the MN induction follow-ing 4-h treatment In contrast, a significant increase in MN frequency was detected at 5 μg/ml MMS when scoring was carried out using the MicroFlow ... 0.05) increase in MN frequency at 5 μg/ml MMS concentration In contrast, no significant increase in MN induction was seen when the scoring was carried out using the Metafer™ platform Surprisingly,

Ngày tải lên: 24/11/2022, 17:56

... involved in floral development, such as auxin response factors (ARFs), SQUAMOSA promoter binding protein box (SBP-box), MYB, basic region-leucine zipper (bZIP), APETALA2 (AP2) and transport inhibitor ... non-conding RNA types, including rRNA (~1 %), tRNA (~0.1 %), snoRNA (~0.02 %) and snRNA (~0.04 %) The detailed data for each library are shown in Table 1 The remaining sequences were examined to ... nucleus, suggesting that DREB is a nuclear protein (Fig 9b) Discussion Identification of miRNAs and their targets by high throughput sequencing The development of high throughput sequencing technol-ogy

Ngày tải lên: 04/12/2022, 10:38

... resorting and matching of all involved data-sets: the number of features and the original sorting order in each dataset should be the same The corresponding R script (match_2tables_byID.R) is included ... typical workflows of data processing and integrative analysis with NucTools reveal information on the interplay of nucleosome positioning with other features such as for example binding of a transcription ... observed transcription factor binding occupancies [81], as e.g in the case of the interplay of CTCF binding and nucleosome positioning in our previous work [71] In such cases the script extract_rows_occup.pl

Ngày tải lên: 04/12/2022, 15:57

... done by searching for the local maximum point around each data point Assume there is a data set of N data points to be clustered The local maximum of a data pointi is the data point whose magnitude ... Keywords and phrases: data cluster, clustering method, microarray, gene expression, classification, model data sets. 1 INTRODUCTION Data analysis is a key step in obtaining information from large-scale ... the data points within a certain distance from the data pointi A peak has the maximum magnitude in its lo-cal area, therefore, its lolo-cal maximum is itself By identify-ing all data points

Ngày tải lên: 23/06/2014, 01:20

... computations pertaining to parameters involved in the random coefficient factors from those pertaining to the time processes and errors The procedures are illustrated with Pothoff and Roy’s data example ... mixtes / r´ egression al´ eatoire / donn´ ees longitudinales 1 INTRODUCTION There has been a great deal of interest in longitudinal data analysis among biometricians over the last decade: see ... These data shown in Table I contain facial growth measurements made on 11 girls and 16 boys at four ages (8, 10, 12 and 14 years) with the nine deleted values at age 10 defined in Little and Rubin

Ngày tải lên: 09/08/2014, 18:21

... from high-throughput sequencing data The comprehensive identification of the full repertoire of miRNAs in a given organism is of general interest Early bioinformatics approaches used machine learning ... reduced dataset In addition, miRTRAP also predicted 44 false positive loci These rates are comparable to the results obtained with the original dataset containing eight-fold more information In addition, ... scaffold 20 in C intestinalis are not conserved in C savignyi, suggesting these clusters may have arisen in C intestinalis through recent tandem duplications Prevalence of antisense miRs in Ciona

Ngày tải lên: 09/08/2014, 20:21

... enrichment in some of the examined marks The combinatorial patterns of resulting repeat enrich-ment estimates are shown in Figure 5b As in the analy-sis of the mouse data, we find that repeats belonging ... may be hard to distinguish based on the reads available in the dataset Combining similar repeat types into a single group typically allows utilization of additional reads, providing more precise ... the H3K36me3 mark is main-tained at most SINE repeat types from set 4 in MEF cells but is lost in NP cells NP cells, however, do main-tain significant H3K4me3 enrichment in many tRNA repeats (set

Ngày tải lên: 09/08/2014, 20:22

... hairpins in a single screening pool, then performed a short-term screen (long enough for viral integration, but minimising hairpin viability effects) and examined the difference in hairpin representation ... typically used in multiwell plate-based screening, shRNAs are commonly used for pooled competitive screening approaches, often called barcode screening Barcode screening offers improvements in speed ... negatives in the 50% and 75% depleted hairpin groups were in hairpins with low starting representation Filtering of the data to remove hairpins with low representation in the reference set resulted in

Ngày tải lên: 09/08/2014, 23:20

... High Throughput Screening Assays 1 Design and Implementation of High Throughput Screening Assays Ricardo Macarrón and Robert P Hertzberg Introduction In most pharmaceutical ... supply-chain model similar to that used in industrial factories Successful HTS implementation is multidisciplinary and requires close alignment of personnel maintaining and distributing screening collections, ... potent inhibitors Certain subsets of protein-protein interaction targets have been successful from an HTS point of view For example, chemokines receptors are technically a protein-protein interaction...

Ngày tải lên: 11/04/2014, 09:46