Use Of Sequence Analysis Research Articles

Understanding the temporal dynamics of problem anger using sequence analysis.

Problem anger is a common, and potentially destructive mental health issue in trauma-affected populations, affecting up to 30% of veteran and military populations. Problem anger is associated with a range of psychosocial and functional difficulties and elevated risk of harm to self and others. Increasingly, ecological momentary assessment (EMA) is being used to understand the microlevel dynamics of emotions, and this information is valuable to inform treatment approaches. Using a data-driven approach, we used sequence analysis to determine whether heterogeneity exists amongst veterans with problem anger using EMA-recorded experiences of anger intensity. Veterans with problem anger (N = 60; Mage = 40.28) completed 10 days of EMA with four prompts per day. We identified four subtypes of veterans within the data, whose anger intensity dynamics differed significantly, and the subtypes mapped onto macrolevel indicators of anger and well-being. Taken together, these results highlight the importance of microlevel investigations of mood states in clinical populations, and in some instances, the novel use of sequence analysis may be appropriate. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Interacting Proteins, Polymorphisms and the Susceptibility of Animals to SARS-CoV-2.

Simple SummaryCOVID-19 is the disease caused by a coronavirus: SARS-CoV-2. The disease was declared by WHO in March 2020 as a pandemic and is still affecting countries around the world. Although considered a human disease, it is thought to have its origins in bats, and transmitted to humans potentially through an intermediate animal. What is not fully understood is the likelihood of the virus transmitting back to animal populations, either to companion or wild animals. For the virus to enter host cells, it needs to interact with particular proteins on the cell surface. Here we review the susceptibility of animals to the SARS-CoV-2 virus through the comparison of proteins between animals and humans. The most studied is the angiotensin-converting enzyme 2 receptor (ACE2), which has been used to rank the viral susceptibility of a range of vertebrates. Here, we also assess three other proteins. Of these, TMPRSS2 may be helpful in determining susceptibility, whereas the other two would appear to be of limited use. We propose that future work should examine changes seen in these proteins which alter the ease by which the virus can enter cells. This type of analysis may contribute limited evidence in predicting if animals are safe from such viruses and may help to guide future welfare concerns.COVID-19, caused by SARS-CoV-2, is a world-wide problem for the human population. It is known that some animal species, such as mink, can become infected and transmit the virus. However, the susceptibility of most animals is not known. Here, we review the use of sequence analysis of the proteins which are known to interact with SARS-CoV-2 as a way to estimate an animal’s susceptibility. Although most such work concentrates on the angiotensin-converting enzyme 2 receptor (ACE2), here TMPRSS2 (Transmembrane Serine Protease 2), neuropilin-1 and furin are also considered. Polymorphisms, especially ones which are known to alter viral/host interactions are also discussed. Analysis of ACE2 and TMPRSS2 protein sequences across species suggests this approach may be of some utility in predicting susceptibility; however, this analysis fails to highlight some susceptible animals such as mink. However, combined with observational data which emerges over time about which animals actually become infected, this may, in the future, be a useful tool to assist the management of risks associated with human/animal contact and support conservation and animal welfare measures.

Associations between self-reported spontaneous thought and temporal sequences of EEG microstates

Thought dynamically evolves from one moment to the next even in the absence of external stimulation. The extent to which patterns of spontaneous thought covary with time-varying fluctuations in intrinsic brain activity is of great interest but remains unknown. We conducted novel analyses of data originally reported by Portnova et al. (2019) to examine associations between the intrinsic dynamics of EEG microstates and self-reported thought measured using the Amsterdam Resting-State Questionnaire (ARSQ). Accordingly, the millisecond fluctuations of microstates were associated with specific dimensions of thought. We evaluated the reliability of these findings by combining our results with those of another study using meta-analysis. Importantly, we extended this investigation using multivariate methods to evaluate multidimensional thought profiles of individuals and their links to sequences of successive microstates. Thought profiles were identified based on hierarchical clustering of ARSQ ratings and were distinguished in terms of the temporal ordering of successive microstates based on sequence analytic methods. These findings demonstrate the relevance of assessing spontaneous thought for understanding intrinsic brain activity and the novel use of sequence analysis for characterizing microstate dynamics. Integrating the phenomenological view from within remains crucial for understanding the functional significance of intrinsic large-scale neurodynamics.

Use of sequence analysis for classifying individual antidepressant trajectories to monitor population mental health

BackgroundOver the past decade, antidepressant prescriptions have increased in European countries and the United States, partly due to an increase in the number of new cases of mental illness. This paper demonstrates an innovative approach to the classification of population level change in mental health status, using administrative data for a large sample of the Scottish population. We aimed to identify groups of individuals with similar patterns of change in pattern of prescribing, validate these groups by comparison with other indicators of mental illness, and characterise the population most at risk of increasing mental ill health.MethodsNational Health Service (NHS) prescription data were linked to the Scottish Longitudinal Study (SLS), a 5.3% sample of the Scottish population (N = 151,418). Antidepressant prescription status over the previous 6 months was recorded for every month for which data were available (January 2009–December 2014), and sequence dissimilarity was computed by optimal matching. Hierarchical clustering was used to create groups of participants who had similar patterns of change, with multi-level logistic regression used to understand group membership.ResultsFive distinct prescription pattern groups were observed, indicating: no prescriptions (76%), occasional prescriptions (10%), continuation of prior use of prescriptions (8%), a new course of prescriptions started (4%) or ceased taking prescriptions (3%). Young, white, female participants, of low social grade, residing in socially deprived neighbourhoods, living alone, being separated/divorced or out of the labour force, were more likely to be in the group that started a new course of antidepressant prescriptions.ConclusionsThe use of sequence analysis for classifying individual antidepressant trajectories offers a novel approach for capturing population-level changes in mental health risk. By classifying individuals into groups based on their anti-depressant medication use we can better identify how over time, mental health is associated with individual risk factors and contextual factors at the local level and the macro political and economic scale.

Accumulation and conversion of capitals in professorial careers. The importance of scientific reputation, network relations, and internationality in economics and business studies

This paper studies the different biographic pathways to an economics and business studies professor position between 1957 and 2000 on the specific case of Switzerland. It focuses on the accumulation and conversion of capitals during academic trajectories, and their relation to three types of resources: scientific reputation, network relations, and internationality. Based on an original biographical database of 411 professors and an innovative use of sequence analysis and multinomial logistic regression, it shows that the three main principles of career structuration divide them between (1) academic and extra-academic trajectories, (2) “standard” positions and executive positions in influent academic organizations, and (3) according to the timing of the accession to a professor position (“early” vs. “slower” appointments). It also shows that careers are increasingly academic between 1957 and 2000. Academic only and long full professor trajectories are linked to reputation in the scientific field (through citations in “prestigious” journals) and internationality of the professors’ profile, while an earlier appointment as professor is associated to developed scientific collaboration networks. Relatively long careers in executive positions in influent academic organizations are linked to important connections to economic, political, and administrative “elite” members (through the supervision of their PhD) as well as scientific expertise for the state, while extra-academic careers only lead to subordinate (associate) professor positions and no detention of other resources within economics and business studies whatsoever.

Prosopography, Networks, Life Course Sequences, and so on. Quantifying with or beyond Bourdieu?

This article focuses on the importance of quantifying Bourdieu’s “research programme”, linked with the concepts of field, habitus, and capital. It presents possible ways of doing statistics within this framework and argues that continuous methodological development should be pursued. To support this argument, the article highlights the methodology and empirical results of a doctoral dissertation on the Swiss field of economic sciences. It stresses the relevance of using a prosopographical strategy and advocates further development of multiple correspondence analysis, and the use of sequence analysis and social network analysis. The main contributions of these methods concern the investigation of subgroup profiles in fields, the trajectories of accumulation and conversion of capitals and the structure of social capital. When asking whether or not we should think with or beyond Bourdieu when suggesting new methodological developments to his programme, this article argues that we ought to think beyond his strict written work, but still within his theoretical framework, which proves particularly relevant to the study of power relations among individuals.

Towards a Methodological Framework for Sequence Analysis in the Field of Self-Regulated Learning

In recent decades, conceptualizations and operationalizations of self-regulated learning (SRL) have shifted from SRL as an aptitude to SRL as an event. Alongside this shift, increased technological capability has introduced computer log files to the investigation of SRL, uncovering new research avenues. One such avenue investigates the time-related characteristics of SRL through learners’ behavioural sequences. Although sequence analysis is still relatively new in SRL research, other fields have fruitful traditions in its application and may serve as a basis for applications in the field of SRL. Ten years of investigating SRL through sequence analysis have produced a wide range of methodological approaches. While this variety of methods illustrates the diversity of opportunities, it also indicates the lack of consensus regarding the most appropriate approach. Since the introduction of sequences analysis in the field of SRL, researchers have emphasized the need for a methodological framework to guide its application. Yet, to date, no such framework has been proposed, hindering our progress through (1) transparent methods and (2) comparative studies to (3) empirical and ecological applications. To help overcome this issue, this manuscript aims to foster discussions of a methodological framework for the use of sequence analysis in SRL research. We first make a case for why such a framework is necessary; secondly, we propose a set of considerations which could serve as a starting point for the construction of a framework.

Identification of aquatic mycobacteria based on sequence analysis of the 16S-23S rRNA internal transcribed spacer region.

Mycobacteria are common causative agents of bacterial infections in many species of freshwater and marine fish. Identification of mycobacteria to the species level based on phenotypic tests is inappropriate and time consuming. Molecular methods such as partial or entire gene sequence determination in mycobacteria have been employed to resolve these problems. The objective of this study was to assess the use of sequence analysis of the mycobacterial 16S-23S internal transcribed spacer (ITS) region for the identification of different aquatic mycobacteria species. Using published primers, the ITS sequences of 64 field and reference strains were determined.Results/Key findings. The identity of all isolates previously identified as Mycobacterium marinum by RFLP was confirmed as M. marinum by sequence analysis. With the exception of five rapidly growing mycobacteria isolates, all other mycobacteria were easily identified by sequencing of the ITS region. Using this spacer region, it was possible to differentiate between slowly growing and rapidly growing mycobacteria, even before sequence analysis, by the size of the PCR product, although species identification could not be made by size alone. Overall, direct sequencing of this genetic element following PCR has been shown to be useful in the identification of aquatic mycobacteria species. With regard to the variability of the ITS region for different mycobacteria isolates, this may be a useful tool in epidemiological studies.

How we can and why we have to reconstruct teaching

PurposeThe purpose of this paper is to arrest an ongoing didactisation of teaching leading to the disappearance of the original content of knowledge.Design/methodology/approachTeaching can only be understood within its inner logic by exploring the individual expression of pedagogical practice in three dimensions: education, formation (Bildung), and didactics.FindingsThe use of sequence analysis is an effective method for the pedagogically based formation of teachers as professionals.Originality/valueThis research exposes evident contradictions between teaching and learning. It advances the view that Lesson Study be seen as the reconstruction of teaching for learning through sequence analysis of lessons.

Party animals, career changers and other pathways into parliament

Research on parliamentary careers has paid little attention to variations in pre-parliamentary career patterns and their value in explaining legislators’ parliamentary success. Using sequence and cluster analysis, this article identifies typical career tracks taken by Party Animals, Local Heroes, Late Bloomers, Land Legislators, High-Flyers and Career Changers based on a comprehensive dataset of German parliamentarians’ biographies (1998–2014). The analysis confirms the role of the party as the primary career facilitator before and within parliament. Nonetheless both Career Changers and High-Flyers climb the greasy pole all the way to the national parliament without much service to the party. The former type, however, suffers from a lack of networks and experience, which is reflected in the limited career success within parliament. This article demonstrates that the use of sequence analysis on career paths offers a promising approach in distinguishing and explaining the opportunities, choices and obstacles MPs face in parliament.

Norovirus GII.Pe Genotype: Tracking a Foodborne Outbreak on a Cruise Ship Through Molecular Epidemiology, Brazil, 2014.

Norovirus (NoV) is recognized as the most common cause of foodborne outbreaks. In 2014, an outbreak of acute gastroenteritis occurred on a cruise ship in Brazil, and NoV became the suspected etiology. Here we present the molecular identification of the NoV strains and the use of sequence analysis to determine modes of virus transmission. Food (cream cheese, tuna salad, grilled fish, orange mousse, and vegetables soup) and clinical samples were analyzed by ELISA, conventional RT-PCR, qRT-PCR, and sequencing. Genogroup GII NoV was identified by ELISA and conventional RT-PCR in fecal samples from 5 of 12 patients tested (41.7%), and in the orange mousse food sample by conventional RT-PCR and qRT-PCR. Two fecal GII NoV samples and the orange mousse GII NoV sample were successfully genotyped as GII.Pe (ORF 1), revealed 98.0-98.8% identities among them, and shared phylogenetically distinct cluster. Establishing the source of a NoV outbreak can be a challenging task. In this report, the molecular analysis of the partial RdRp NoV gene provided a powerful tool for genotyping (GII.Pe) and tracking of outbreak-related samples. In addition, the same fast and simple extraction methods applied to clinical samples could be successfully used for complex food matrices, and have the potential to be introduced in routine laboratories for screening foods for presence of NoV.

Use of sequence analysis of the P2 domain for characterization of norovirus strains causing a large multistate outbreak of norovirus gastroenteritis in Germany 2012

Human norovirus is the main cause of non-bacterial gastroenteritis worldwide. It is transmitted from person to person, by fecally contaminated food or water or through virus containing aerosols originating during vomiting of infected persons.In September and October 2012, the largest foodborne norovirus outbreak in Germany so far spread over 5 Federal States (Berlin, Brandenburg, Saxony, Saxony-Anhalt, and Thuringia) affecting nearly 11,000 people mainly in schools and child care facilities. Epidemiological and trace-back investigations supported the assumption that a batch of frozen strawberries imported from China was the likely source of the outbreak.Sequence analysis of the capsid region encoding the P2 domain was used successfully for identification of transmission routes and epidemiologic relationship but was hampered by a lack of universal primers for all known genotypes so far.In the present study, a molecular approach was designed to track outbreak-related samples from the affected states of the large foodborne outbreak in Germany. Therefore, sequence analysis within the highly variable P2 domain of the capsid gene using newly developed universal P2 primers for genogroup I and genogroup II strains in combination with sequencing of the polymerase gene (region A) and the orf1/orf2 junction (region c) was used.The sequence analysis of 138 norovirus positive stool samples suspected to be outbreak-related revealed a considerable genomic diversity. At least 3 strains of genogroup I (I.3, I.4, and I.9) and 5 strains of genogroup II (II.6, II.7, II. 8, and recombinants II.P7_II.6, and II.P16_II.13) as well as 19 samples containing mixtures of these strains were detected. Six samples were considered as not linked to the outbreak. The most prevalent genotype was GI.4 (48/132; 36%). Genotype I.9 and the recombinant strain II.P16_II.13 were detected for the first time in Germany. Notably, the genotype II.P16_II.13 could also be determined in one of the samples of the frozen strawberry lot suspected as infection source. Especially, due to the good concordance of the P2 sequences from infected patients of 5 Federal States the outbreak-relation of the strains could be demonstrated. The high diversity of virus strains and the occurrence of sub-clusters within genotypes I.3, II.8, II.P16_II.13, and II.7 revealed the complex mixture of the outbreak source suggesting a possible waterborne fecal contamination of the strawberries.The typing system described here is in general useful for analysis of outbreaks caused by mixed infection sources. Extensive sequence analysis of different gene regions including the highly variable P2 domain in a sufficient number of cases is required to confirm the epidemiological relation of samples from outbreaks with high diversity of strains spreading over several geographic locations.

Potential risk of misclassification HCV 2k/1b strains as HCV 2a/2c using VERSANT HCV Genotype 2.0 assay

The performance of a hepatitis C virus (HCV) NS5B sequencing method described by Murphy et al. (Use of sequence analysis of the NS5B region for routine genotyping of hepatitis C virus with reference to C/E1 and 5′ untranslated region sequences. J Clin Microbiol 2007;45(4):1102–12.) was compared with the VERSANT HCV Genotype 2.0 assay. The sequencing strategy led to detection of HCV recombinant genotype 2k/1b, previously identified as genotype 2a/2c, which reveals the importance of exact HCV genotyping and subtyping.

Separate paths, same direction? De-standardization of male employment biographies in East and West Germany

Until the mid-1980s, labour markets in Germany were characterized by a high level of employment stability. Employment biographies of men were dominated by full-time employment in both East and West Germany and were hence quite similar in this respect, despite the two regions’ enormously different institutional settings. Since that time however, important changes have occurred. Labour markets have become more flexible, as have employment biographies. However, the process towards de-standardization and increased discontinuity in employment biographies began in East Germany later than it did in the West. East German change started namely in 1990, when the German Democratic Republic was incorporated into the Federal Republic of Germany. This study uses the German Socio-Economic Panel (SOEP) to analyse how men’s employment patterns in Germany have changed over three different birth cohorts. Through the use of sequence analysis the authors not only observe an increase of non-standard episodes in such biographies, such as unemployment and part-time work, but also investigate whether employment biographies have on the whole become more discontinuous in nature. In addition, the authors analyse the main differences in trends observed in East as opposed to West Germany as a result of differing societal and economic changes. The results of this analysis show evidence of de-standardization in employment in both regions. However, this trend follows a separate path in each region, with the process being faster in East Germany than in the West.

Molecular characterization of muscle-parasitizing didymozoid from a chub mackerel, Scomber japonicus.

Didymozoids found in the muscles of marine fish are almost always damaged because they are usually found after being sliced. Therefore, identifying muscle-parasitizing didymozoids is difficult because of the difficulty in collecting non-damaged worms and observing their organs as key points for morphological identification. Moreover, muscle-parasitizing didymozoids are not easily found because they parasitize at the trunk muscles. Therefore, muscle-parasitizing didymozoid classification has not progressed because there are few opportunities to detect them. Our recent report was the first to describe the usefulness of sequencing analysis for discrimination among muscle-parasitizing didymozoids. Recently, we found a didymozoid in the trunk muscle of a chub mackerel Scomber japonicus. The present study genetically compares the present isolate with other muscle-parasitizing didymozoids. The present isolate differs markedly from the previously unidentified didymozoid from an Atlantic mackerel S. scombrus by phylogenetic analysis of 18S rDNA. It also differs from other muscle-parasitizing didymozoids from other host species based on phylogenetic analyses of 18S, 28S rDNAs, and coxI loci. These results suggest that sequencing analysis is useful for the discrimination of muscle-parasitizing didymozoids. Combining the present data with earlier data for sequencing analysis, muscle-parasitizing didymozoids from seven marine fish species were classified as seven species. We proposed appellations for six distinct muscle-parasitizing didymozoids for future analysis: sweetlips fish type from Diagramma pictum and Plectorhinchus cinctus, red sea bream type from Pagrus major, flying fish type from Cypselurus heterurus, Atlantic mackerel type from Scomber scombrus, chub mackerel type from S. japonicus, and purple rockcod type from Epinephelus cyanopodus.

Burden of potentially novel species of non tuberculosis mycobacteria in Iranian tuberculosis laboratories

Aims and objectivesNontuberculous mycobacterium (NTM) infections are caused by mycobacteria that are found in water and soil. The chances of missing NTM species are higher in tuberculosis endemic countries like Iran, which are poorly equipped and overburdened with other diseases. The aim of this study is to access the diversity of rare, unusual and frequent species in Iranian tuberculosis laboratories. MethodsFrom 2012–2014 a total of 243 different clinical isolates of NTM were recovered from Mycobacteriology Reference Laboratories across Iran (Ahvaz, Esfahan, Tehran, Gorgan, Kermanshah). The isolates identified by rpoB gene sequencing are useful markers in mycobacterium identification. ResultsBased on rpoB gene sequencing, 20 groups do not belong to any of the officially recognized mycobacteria. A total of 210 isolates of NTM were identified to species level, including M. fortuitum (66), M. kansasii (20), M. simiae (20), M. conceptionense (10), M. peregrinum (9), M. thermoresistibile (9), M gordonae (8), M. lentiflavum (8), M. phlei (6), M. intracellulare (6), M. abscessus subsp. abscessus (5), M. chelonae (5), M. abscessus subsp. bolletii (4), M. avium (4), M. flavescents (4), M. nonchromogenicum (4), M. terrae (4), M. branderi (3), M. iranicum (3), M. mucogenicum (3), M. scrofulaceum (3), M. smegmatis (3) and M. triplex (2).Among all isolates, M. fortuitum was identified as the most frequent encounter (27%) of NTM, and M. kansasii and M. simiae were the second most dominant species (8.2%) among the isolates. A total of 33 isolates (13%) were unidentifiable to species level. M. fortutium was the most frequent species in Ahvaz, Esfahan, Tehran and Gorgan, but M. simiae was the most frequent species in Kermanshah. Thirty-three isolates (20 groups) presented unique genetic features. Further molecular tests should be carried out to reliable identification of these isolates to species level. ConclusionsThe present study provides evidence for the importance of NTM identification in the clinical setting and the presence of diverse species in clinical samples as a causative agent of disease.The presence of diverse species of NTM and unidentifiable strains in a clinical setting in Iran emphasizes the use of sequence analysis of genes for reliable identification.

To Develop Strain Specific Molecular Marker for Easy and Proper Identification of Fungal Species Based on Molecular Characters: A Review

The sequencing of fungal genomes is advancing at breakneck-speed, producing voluminous amounts of data. Within the next five years, it is possible that over a couple thousand genomes, representing every major fungal family will be completed and available to the scientific community. In order for this data to have a truly transformative effect on mycological and other research, however, several factors need to be addressed. These include; (1) the establishment of user friendly platforms for examining, sorting, and sifting through the genomes, (2) integration, or at least cross-communication, between the various databases that house the genomic data, and (3) investment in community resources that can act as repositories for and provide materials to researchers, i.e. strains, clones, plasmids, etc. The frameworks for some these needs, e.g. the materials available from the Fungal Genetics Stock Center (FGSC, University of Missouri), are already established and should be reinforced, whereas for others, e.g. data accessibility, the sooner that a plan can be implemented the better. The Fungal Kingdom is considered to contribute greater than 15% of the species richness found in the major groups of organisms .This study is a reflection of the usefulness of sequence analysis of the 28S ribosomal RNA gene in identifying fungal as well as determining fungal diversity. Various techniques that are based on utilizing the 28S rRNA have been discussed. Of critical importance is the manner in which massively parallel sequencing was exploited to correct the under representation of fungal species in compilations of fungal hat were drawn using traditional methods of surveying fungal species from ecosystems.

English

This study reflects the usefulness of sequence analysis of the 16S ribosomal RNA gene in identifying bacteria and determining bacterial diversity. Various techniques that are based on utilizing the 16S rRNA gene are discussed. Of critical importance is the use of massively parallel sequencing to study bacterial diversity. Through massively parallel sequencing which is replacing traditional methods of bacterial identification; various bacterial habitats are surveyed to compile their species compositions.    Key words: Bacterial identification, 16S ribosomal RNA gene, DNA.

Mining History of Gamification Towards Finding Expertise in Question and Answering Communities: Experience and Practice with Stack Exchange

Recently, an online Q&A tool has become an essential part of individual communities and organizations of experts on specific topics. Using the answers to questions about specific topics will help such communities work more efficiently in their fields. Currently, Q&A online communities are adopting gamification to engage users by granting awards to successful users. In this paper, we investigate how to mine award achievement histories to find expertise. We propose the use of sequence analysis and clustering techniques. Specifically, we study the history of Stack Exchange, a large Q&A community that employs gamification. To the best of our knowledge, this is the first study of using award achievement history to find expertise in Q&A communities.

Abstract 4033: Gene expression of EdU proliferating cells made possible with improved click chemistry.

Abstract Gene expression profiling of cancer cells has become increasingly common over the past five years. Especially important is identifying changes in gene expression caused by drug treatment leading to side populations with altered pathways. These populations can escape drug treatment and lead to recurrence. Characterizing gene expression of proliferating cells requires a method of identifying proliferation while simultaneously maintaining high quality RNA. Typically, cells are screened in a drug panel in the presence of tritiated thymidine or BrdU to identify the drug resistance in the proliferating population. Proliferation detection with these methods is neither rapid nor does it yield high quality RNA for profiling. A new proliferation method based on click chemistry using an alkyne modified thymidine analog (EdU), which can be used to rapidly identify replicating cells appears ideally suited for this application; however, copper used for the catalysis of the click reaction causes undesired degradation of RNA. Recent improvements to the copper based click reaction are presented here whereby the copper is tightly controlled, resulting in higher quality RNA useful for sequencing. In this study we demonstrate gene expression changes in the proliferating population of a drug resistant cancer cell line compared to the parental cell lines. Proliferating cells were identified using an improved click reaction comprising of a copper(I) ligand combined with a picolyl modified dye azide detection reagent. Total RNA from these cells was isolated and gene expression was assessed by targeted RNA sequencing using an RNA Apoptosis panel and an RNA Cancer panel using proton based sequencing technology. Use of an improved copper “safe” click reaction for detection of nascent DNA, allows for detection of incorporated click analog for measuring proliferation and subsequent isolation of high quality RNA for use in sequence analysis. Citation Format: Scott T. Clarke, Angie Cheng, Aleksey Rukavishnikov, Michelle Yan, Upinder Singh, Kyle Gee, Susan Magdaleno. Gene expression of EdU proliferating cells made possible with improved click chemistry. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4033. doi:10.1158/1538-7445.AM2013-4033