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Breeze: an integrated quality control and data analysis application for high-throughput drug screening

2020 Bioinformatics  
Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data.  ...  High throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents.  ...  Acknowledgements We would like to thank all FIMM Breeze application users for valuable input and beta testing.  ... 
doi:10.1093/bioinformatics/btaa138 pmid:32119072 pmcid:PMC7267830 fatcat:kqstvjud3jcafgfafs33vnntly


2005 Science  
Glyco-Stain detects both glycosylated and non-glycosylated proteins. G-Biosciences/Genotech For information 314-911-6034  ...  technique, it offers nanogram levels of sensitivity, with greater than twofold increase in glycoprotein and proteoglycan detection.  ...  Automated Sample Processing With a footprint of just 2 m by 1.2 m, the BioCel 1200 is a compact system capable of automating a wide range of applications, from compound plate replication and high-throughput  ... 
doi:10.1126/science.310.5750.1035 fatcat:fnkdynnav5e7bjs6ar65fwrwf4

Abstracts of papers presented at the 2002 Pittsburgh Conference

2002 Journal of automated methods & management in chemistry (Print)  
For example, consolidation of synthetic compounds that pass quality control or positive hits from biological screening are applications.  ...  Improving throughput for stability analysis, quality control assays and dissolution testing are all key motivations for improvement in separation speed in the pharmaceutical industry.  ... 
doi:10.1155/s1463924602000196 pmid:18924747 pmcid:PMC2562979 fatcat:5j4eagxgc5bj5h2qnxcpxw2ama

Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: Matching high information content with high throughput

Geoff A. Holdgate, Malcolm Anderson, Fredrik Edfeldt, Stefan Geschwindner
2010 Journal of Structural Biology  
This paper discusses some of the theoretical and experimental aspects of the most common affinity-based methods, what type of information can be gained from each one of those approaches, and what requirements  ...  Affinity-based technologies have become impactful tools to detect, monitor and characterize molecular interactions using recombinant target proteins.  ...  We would like to thank Tomas Lundqvist and Alex Breeze for critical feedback on the content and form of this manuscript and all the researchers whose work has been well documented and published so we could  ... 
doi:10.1016/j.jsb.2010.06.024 pmid:20609391 fatcat:2mwy6pr72ra5lglvwyg7wj3iuy

Highlights from the 11th ISCB Student Council Symposium 2015

Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman, Griet Laenen, Sander Willems (+37 others)
2016 BMC Bioinformatics  
Student presentations The student presentations were begun by Griet Laenen, who shared a new method for identifying drug targets [8].  ...  Nagarajan Raju reported the identification of different modes of protein-RNA interaction in different organisms, based on structural analysis and molecular dynamics simulation [9].  ...  We are very grateful to all the volunteer reviewers for their work on ensuring the quality of the scientific program, and to the program and travel fellowship committees for coordinating the reviewing  ... 
doi:10.1186/s12859-016-0901-4 pmid:26986007 pmcid:PMC4895264 fatcat:vxzbcsulqfdctoylhyoebrbzpm

Association of tamoxifen resistance and lipid reprogramming in breast cancer

Susanne Hultsch, Matti Kankainen, Lassi Paavolainen, Ruusu-Maaria Kovanen, Elina Ikonen, Sara Kangaspeska, Vilja Pietiäinen, Olli Kallioniemi
2018 BMC Cancer  
Conclusion: Altogether, our findings highlight a major role of LMP prevention in tamoxifen resistance, and suggest novel drug vulnerabilities associated with this phenotype.  ...  In the tamoxifen-resistant T-47D cell variants we observed a striking increase of neutral lipids in lipid droplets as well as an accumulation of free cholesterol in the lysosomes.  ...  High Throughput Biomedicine (HTB) unit (Laura Turunen, Maria Nurmi and Swapnil Podar), Sequencing unit (Pirkko Mattila), and High Content Imaging and Analysis (HCA) unit at the Institute for Molecular  ... 
doi:10.1186/s12885-018-4757-z pmid:30143015 pmcid:PMC6109356 fatcat:cnzktuwumbhanhwaf5m66q35dy

Novel pharmacological actions of Trequinsin Hydrochloride improve human sperm cell motility and function

R.C. McBrinn, J. Fraser, A.G. Hope, D.W. Gray, C.L.R. Barratt, S.J. Martins da Silva, S.G. Brown
2019 British Journal of Pharmacology  
We have demonstrated that a high-throughput screening (HTS) strategy and established in vitro tests can identify and characterise compounds that improve sperm motility.  ...  A validated HTS fluorometric [Ca2+ ]i assay was used to screen an in-house library of compounds.  ...  All assay plates in the screen were subject to quality control analysis.  ... 
doi:10.1111/bph.14814 pmid:31368510 pmcid:PMC6932944 fatcat:eg3xybn4zzawpoemtumxkcgclu

Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer

Liye He, Daria Bulanova, Jaana Oikkonen, Antti Häkkinen, Kaiyang Zhang, Shuyu Zheng, Wenyu Wang, Erdogan Pekcan Erkan, Olli Carpén, Titta Joutsiniemi, Sakari Hietanen, Johanna Hynninen (+6 others)
2021 Briefings in Bioinformatics  
In this case study, we show how the platform enables prediction of cancer-selective drug combinations for patients with high-grade serous ovarian cancer using single-cell imaging cytometry drug response  ...  RNA-sequencing data to deconvolute cell population-specific transcriptome profiles from bulk RNA-seq data, (iii) and whether multi-patient or patient-specific predictive models lead to better predictive  ...  High-throughput drug screening (HTS) of the phenotypic effects of drug combinations in preclinical cancer models is often used for unbiased exploration of candidate drug combinations.  ... 
doi:10.1093/bib/bbab272 pmid:34343245 pmcid:PMC8574973 fatcat:nejdkbbqp5bwhjrahqnzb3tgf4

State-of-the-art of 3D cultures (organs-on-a-chip) in safety testing and pathophysiology

Natalie Alépée
2014 ALTEX: Alternatives to Animal Experimentation  
Moreover, they refer to the application in disease modeling, drug discovery and safety assessment.  ...  Integrated approaches using different in vitro methods in combination with bioinformatics can (i) increase the success rate and speed of drug development; (ii) improve the accuracy of toxicological risk  ...  Acknowledgement We are grateful to many participants of the CAAt-europe workshop and information day on 3D models for sharing their ideas and for giving input. the valuable help of many members of the  ... 
doi:10.14573/altex.1406111 pmid:25027500 pmcid:PMC4783151 fatcat:6i4pxhi2a5fuhjmqqw3lk7fe54

Molecular networks in Network Medicine: Development and applications

Edwin K Silverman, Harald H H W Schmidt, Eleni Anastasiadou, Lucia Altucci, Marco Angelini, Lina Badimon, Jean-Luc Balligand, Giuditta Benincasa, Giovambattista Capasso, Federica Conte, Antonella Di Costanzo, Lorenzo Farina (+14 others)
2020 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Successful applications of molecular network analysis have been reported in pulmonary arterial hypertension, coronary heart disease, diabetes mellitus, chronic lung diseases, and drug development.  ...  Network Medicine applies these integrated approaches to Omics Big Data (including genetics, epigenetics, transcriptomics, metabolomics, and proteomics) using computational biology tools and, thereby, has  ...  Gerasch et al. (2014) proposed a system for visually analyzing high-throughput Omics data in the context of networks; in particular, for differential analysis between groups of subjects and the analysis  ... 
doi:10.1002/wsbm.1489 pmid:32307915 fatcat:ps5v2yzn3ncidcf7avay6f5xli

State-of-the-art of 3D cultures (organs-on-a-chip) in safety testing and pathophysiology

Natalie Alépée
2014 ALTEX: Alternatives to Animal Experimentation  
Moreover, they refer to the application in disease modeling, drug discovery and safety assessment.  ...  Finally, consensus recommendations indicate a roadmap for the successful implementation of 3D models in routine screening.  ...  Acknowledgement We are grateful to many participants of the CAAt-europe workshop and information day on 3D models for sharing their ideas and for giving input. the valuable help of many members of the  ... 
doi:10.14573/altex1406111 fatcat:h2373gjoirg6hj2qv556jlliya

The Promises and Challenges of Toxico-Epigenomics: Environmental Chemicals and Their Impacts on the Epigenome

Felicia Fei-Lei Chung, Zdenko Herceg
2020 Environmental Health Perspectives  
Until recently, efforts to apply epigenomic data in toxicology and risk assessment were restricted by an incomplete understanding of epigenomic variability across tissue types and populations.  ...  We present an overview of epigenetic regulation and a summary of reported evidence of environmental toxicants as epigenetic disruptors.  ...  The authors certify that their freedom to design, conduct, interpret, and publish research was not compromised by any controlling sponsor.  ... 
doi:10.1289/ehp6104 pmid:31950866 pmcid:PMC7015548 fatcat:6gfmg755xveunn4rmhtpzhmafa

Activated Surfaces for Laser Desorption Mass Spectrometry: Application for Peptide and Protein Analysis

C. Afonso, N. Budimir, F. Fournier, J- Tabet
2005 Current pharmaceutical design  
This review will discuss the various surface modifications used in combination with laser desorption mass spectrometry and their application for the analysis of peptides and proteins.  ...  In an other hand chemical and biochemical modified surfaces developed to isolate species with more or less specific interactions can be used for onslide sample clean-up before MALDI-MS analysis.  ...  The MALDI process can be miniaturised and fully automated for high throughput analysis.  ... 
doi:10.2174/1381612054546888 pmid:16101459 fatcat:fyafo7ncwjan5gmnrq26w2jmsi

Programme Booklet Of The 11Th Iscb Student Council Symposium, Dublin, 2015 [article]

Mehedi Hassan, R Gonzalo Parra
2015 Zenodo  
To understand cross-talk we developed pipelines and methods for the analysis of high throughput data to survey the direct and indirect association of several families of repetitive elements with known  ...  In particular we show strategic analysis of high throughput data for ERVs which reveals the differential cross regulation of subsets of HERVs by host factors and vice-versa in vivo and in vitro stem cells  ...  Manuel Corpas gave an excellent keynote talk along with 7 student presentations. The chairs for this meeting were Yassine Souilmi and Chinmay Kumar Dwibedi.  ... 
doi:10.5281/zenodo.1253018 fatcat:b75h2xdwmralzfqdhs6jd6k4vm

Tuesday posters

2010 Journal of the American Society for Mass Spectrometry  
Analysis of Compounds for Early Drug Discovery: Quantitative and Qualitative Screening in One Pass; Xiaojie C.  ...  , CT TP 498 Evaluation of Accurate Mass TOF-MS for Use in High Throughput PAMPA Screening; Michelle Romm; Nikunj Parikh; Vaughn Miller; William A.  ... 
doi:10.1016/j.jasms.2010.03.020 fatcat:vkjwc7lrgzebvf467q7sh2ny74
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