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14 results

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RNAi screening in Drosophila cells and in vivo.
Mohr SE. Mohr SE. Methods. 2014 Jun 15;68(1):82-8. doi: 10.1016/j.ymeth.2014.02.018. Epub 2014 Feb 24. Methods. 2014. PMID: 24576618 Free PMC article. Review.
Specifically, I discuss the types of high-throughput assays that can be done in Drosophila cells and in vivo, RNAi reagent design and available reagent collections, automated screen pipelines, analysis of screen results, and approaches to RNAi results verification....
Specifically, I discuss the types of high-throughput assays that can be done in Drosophila cells and in vivo, RNAi reagent design and availa …
Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq.
Biancon G, Busarello E, Joshi P, Lesch BJ, Halene S, Tebaldi T. Biancon G, et al. STAR Protoc. 2022 Dec 16;3(4):101823. doi: 10.1016/j.xpro.2022.101823. Epub 2022 Nov 16. STAR Protoc. 2022. PMID: 36595959 Free PMC article.
Thousands of RNA-binding proteins orchestrate RNA processing and altered protein-RNA interactions frequently lead to disease. Here, we present experimental and computational analysis pipelines of fractionated eCLIP-seq (freCLIP-seq), a modification of enhanced UV-crosslink …
Thousands of RNA-binding proteins orchestrate RNA processing and altered protein-RNA interactions frequently lead to disease. Here, we prese …
CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data.
Tippani M, Pattie EA, Davis BA, Nguyen CV, Wang Y, Sripathy SR, Maher BJ, Martinowich K, Jaffe AE, Page SC. Tippani M, et al. BMC Neurosci. 2022 Nov 30;23(1):71. doi: 10.1186/s12868-022-00751-7. BMC Neurosci. 2022. PMID: 36451089 Free PMC article.
RESULTS: To address this need we developed CaPTure, a scalable, automated Ca(2+) imaging analysis pipeline ( https://github.com/LieberInstitute/CaPTure ). CaPTuredetects neurons, classifies and quantifies spontaneous activity, quantifies synchrony metrics, and generates ce …
RESULTS: To address this need we developed CaPTure, a scalable, automated Ca(2+) imaging analysis pipeline ( https://github.com/Liebe …
Discovery of clinically relevant fusions in pediatric cancer.
LaHaye S, Fitch JR, Voytovich KJ, Herman AC, Kelly BJ, Lammi GE, Arbesfeld JA, Wijeratne S, Franklin SJ, Schieffer KM, Bir N, McGrath SD, Miller AR, Wetzel A, Miller KE, Bedrosian TA, Leraas K, Varga EA, Lee K, Gupta A, Setty B, Boué DR, Leonard JR, Finlay JL, Abdelbaki MS, Osorio DS, Koo SC, Koboldt DC, Wagner AH, Eisfeld AK, Mrózek K, Magrini V, Cottrell CE, Mardis ER, Wilson RK, White P. LaHaye S, et al. BMC Genomics. 2021 Dec 4;22(1):872. doi: 10.1186/s12864-021-08094-z. BMC Genomics. 2021. PMID: 34863095 Free PMC article.
RESULTS: Our Ensemble Fusion (EnFusion) approach utilizes seven fusion calling algorithms: Arriba, CICERO, FusionMap, FusionCatcher, JAFFA, MapSplice, and STAR-Fusion, which are packaged as a fully automated pipeline using Docker and Amazon Web Services (AWS) serverless te …
RESULTS: Our Ensemble Fusion (EnFusion) approach utilizes seven fusion calling algorithms: Arriba, CICERO, FusionMap, FusionCatcher, JAFFA, …
Spatio-temporal mixture process estimation to detect dynamical changes in population.
Pruilh S, Jannot AS, Allassonnière S. Pruilh S, et al. Artif Intell Med. 2022 Apr;126:102258. doi: 10.1016/j.artmed.2022.102258. Epub 2022 Feb 23. Artif Intell Med. 2022. PMID: 35346441 Free PMC article.
Finally, we validate STMPs on a real data set of positive diagnosed patients to coronavirus disease 2019. We show that our pipeline correctly models evolving real data and detects epidemic changes....
Finally, we validate STMPs on a real data set of positive diagnosed patients to coronavirus disease 2019. We show that our pipeline c …
The Potential For Bias In Machine Learning And Opportunities For Health Insurers To Address It.
Gervasi SS, Chen IY, Smith-McLallen A, Sontag D, Obermeyer Z, Vennera M, Chawla R. Gervasi SS, et al. Health Aff (Millwood). 2022 Feb;41(2):212-218. doi: 10.1377/hlthaff.2021.01287. Health Aff (Millwood). 2022. PMID: 35130064
We present a guide to the data ecosystem used by health insurers to highlight where bias can arise along machine learning pipelines. We suggest mechanisms for identifying and dealing with bias and discuss challenges and opportunities to increase fairness through analytics …
We present a guide to the data ecosystem used by health insurers to highlight where bias can arise along machine learning pipelines. …
Prenatal opioid exposure is associated with smaller brain volumes in multiple regions.
Merhar SL, Kline JE, Braimah A, Kline-Fath BM, Tkach JA, Altaye M, He L, Parikh NA. Merhar SL, et al. Pediatr Res. 2021 Aug;90(2):397-402. doi: 10.1038/s41390-020-01265-w. Epub 2020 Nov 11. Pediatr Res. 2021. PMID: 33177677 Free PMC article.
T2-weighted images were processed using the Developing Human Connectome Project structural pipeline. We compared 63 relative regional brain volumes between groups. ...
T2-weighted images were processed using the Developing Human Connectome Project structural pipeline. We compared 63 relative regional …
Going beyond bibliometrics: A system to track the progress and impact of biomedical research funded by Susan G. Komen.
Dworkin AM, Reffey S, Wojtanik K. Dworkin AM, et al. Clin Transl Sci. 2022 Sep;15(9):2127-2134. doi: 10.1111/cts.13346. Epub 2022 Jun 29. Clin Transl Sci. 2022. PMID: 35709242 Free PMC article.
Komen has developed a research product tracking system to monitor the progress of Komen-funded research products along the research pipeline and to measure the potential impact on patients more directly. ...Progress through the research pipeline is updated each year …
Komen has developed a research product tracking system to monitor the progress of Komen-funded research products along the research pipel …
Epigenetic machine learning: utilizing DNA methylation patterns to predict spastic cerebral palsy.
Crowgey EL, Marsh AG, Robinson KG, Yeager SK, Akins RE. Crowgey EL, et al. BMC Bioinformatics. 2018 Jun 21;19(1):225. doi: 10.1186/s12859-018-2224-0. BMC Bioinformatics. 2018. PMID: 29925314 Free PMC article.
The aim of this study was to evaluate epigenetic profiles as biomarkers for spastic CP. A novel analysis pipeline was employed to assess DNA methylation patterns between peripheral blood cells of adolescent subjects (14.9 0.3 years old) with spastic CP and controls at sing …
The aim of this study was to evaluate epigenetic profiles as biomarkers for spastic CP. A novel analysis pipeline was employed to ass …
Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.
Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, Allen-Vercoe E, von Bergen M. Starke R, et al. J Proteomics. 2020 Jun 30;222:103791. doi: 10.1016/j.jprot.2020.103791. Epub 2020 Apr 23. J Proteomics. 2020. PMID: 32335296
The significance of our research is in providing a freely available pipeline to analyze the incorporation of deuterium and 18-oxygen into proteins together with the validation of the applicability of tracing heavy water as a proxy for activity. ...
The significance of our research is in providing a freely available pipeline to analyze the incorporation of deuterium and 18-oxygen …
14 results